1
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Quirion L, Robert A, Boulais J, Huang S, Bernal Astrain G, Strakhova R, Jo CH, Kherdjemil Y, Faubert D, Thibault MP, Kmita M, Baskin JM, Gingras AC, Smith MJ, Côté JF. Mapping the global interactome of the ARF family reveals spatial organization in cellular signaling pathways. J Cell Sci 2024; 137:jcs262140. [PMID: 38606629 PMCID: PMC11166204 DOI: 10.1242/jcs.262140] [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: 03/23/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024] Open
Abstract
The ADP-ribosylation factors (ARFs) and ARF-like (ARL) GTPases serve as essential molecular switches governing a wide array of cellular processes. In this study, we used proximity-dependent biotin identification (BioID) to comprehensively map the interactome of 28 out of 29 ARF and ARL proteins in two cellular models. Through this approach, we identified ∼3000 high-confidence proximal interactors, enabling us to assign subcellular localizations to the family members. Notably, we uncovered previously undefined localizations for ARL4D and ARL10. Clustering analyses further exposed the distinctiveness of the interactors identified with these two GTPases. We also reveal that the expression of the understudied member ARL14 is confined to the stomach and intestines. We identified phospholipase D1 (PLD1) and the ESCPE-1 complex, more precisely, SNX1, as proximity interactors. Functional assays demonstrated that ARL14 can activate PLD1 in cellulo and is involved in cargo trafficking via the ESCPE-1 complex. Overall, the BioID data generated in this study provide a valuable resource for dissecting the complexities of ARF and ARL spatial organization and signaling.
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Affiliation(s)
- Laura Quirion
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Amélie Robert
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | - Jonathan Boulais
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | - Shiying Huang
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Gabriela Bernal Astrain
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Regina Strakhova
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Chang Hwa Jo
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Yacine Kherdjemil
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | - Denis Faubert
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | | | - Marie Kmita
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Department of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Department of Experimental Medicine, McGill University, Montréal, QC H3G 2M1, Canada
| | - Jeremy M. Baskin
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Matthew J. Smith
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Jean-François Côté
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Department of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC H3A 0C7, Canada
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2
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Quirion L, Robert A, Boulais J, Huang S, Bernal Astrain G, Strakhova R, Jo CH, Kherdjemil Y, Thibault MP, Faubert D, Kmita M, Baskin JM, Gingras AC, Smith MJ, Cote JF. Mapping the global interactome of the ARF family reveals spatial organization in cellular signaling pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.01.530598. [PMID: 36909472 PMCID: PMC10002736 DOI: 10.1101/2023.03.01.530598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
The ADP-ribosylation factors (ARFs) and ARF-like (ARLs) GTPases serve as essential molecular switches governing a wide array of cellular processes. In this study, we utilized proximity-dependent biotin identification (BioID) to comprehensively map the interactome of 28 out of 29 ARF and ARL proteins in two cellular models. Through this approach, we identified ~3000 high-confidence proximal interactors, enabling us to assign subcellular localizations to the family members. Notably, we uncovered previously undefined localizations for ARL4D and ARL10. Clustering analyses further exposed the distinctiveness of the interactors identified with these two GTPases. We also reveal that the expression of the understudied member ARL14 is confined to the stomach and intestines. We identified phospholipase D1 (PLD1) and the ESCPE-1 complex, more precisely SNX1, as proximity interactors. Functional assays demonstrated that ARL14 can activate PLD1 in cellulo and is involved in cargo trafficking via the ESCPE-1 complex. Overall, the BioID data generated in this study provide a valuable resource for dissecting the complexities of ARF and ARL spatial organization and signaling.
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3
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Tran MV, Khuntsariya D, Fetter RD, Ferguson JW, Wang JT, Long AF, Cote LE, Wellard SR, Vázquez-Martínez N, Sallee MD, Genova M, Magiera MM, Eskinazi S, Lee JD, Peel N, Janke C, Stearns T, Shen K, Lansky Z, Magescas J, Feldman JL. MAP9/MAPH-9 supports axonemal microtubule doublets and modulates motor movement. Dev Cell 2024; 59:199-210.e11. [PMID: 38159567 DOI: 10.1016/j.devcel.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/15/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
Microtubule doublets (MTDs) comprise an incomplete microtubule (B-tubule) attached to the side of a complete cylindrical microtubule. These compound microtubules are conserved in cilia across the tree of life; however, the mechanisms by which MTDs form and are maintained in vivo remain poorly understood. Here, we identify microtubule-associated protein 9 (MAP9) as an MTD-associated protein. We demonstrate that C. elegans MAPH-9, a MAP9 homolog, is present during MTD assembly and localizes exclusively to MTDs, a preference that is in part mediated by tubulin polyglutamylation. We find that loss of MAPH-9 causes ultrastructural MTD defects, including shortened and/or squashed B-tubules with reduced numbers of protofilaments, dysregulated axonemal motor velocity, and perturbed cilia function. Because we find that the mammalian ortholog MAP9 localizes to axonemes in cultured mammalian cells and mouse tissues, we propose that MAP9/MAPH-9 plays a conserved role in regulating ciliary motors and supporting the structure of axonemal MTDs.
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Affiliation(s)
- Michael V Tran
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Daria Khuntsariya
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, 25250 Vestec, Prague West, Czech Republic
| | - Richard D Fetter
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - James W Ferguson
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jennifer T Wang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Alexandra F Long
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Lauren E Cote
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | | | - Maria D Sallee
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Mariya Genova
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France; Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Maria M Magiera
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France; Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Sani Eskinazi
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Nina Peel
- The College of New Jersey, Ewing, NJ 08628, USA
| | - Carsten Janke
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France; Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Tim Stearns
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kang Shen
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Zdenek Lansky
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, 25250 Vestec, Prague West, Czech Republic
| | - Jérémy Magescas
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| | - Jessica L Feldman
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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Li FL, Guan KL. The Arf family GTPases: Regulation of vesicle biogenesis and beyond. Bioessays 2023; 45:e2200214. [PMID: 36998106 PMCID: PMC10282109 DOI: 10.1002/bies.202200214] [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: 11/05/2022] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 04/01/2023]
Abstract
The Arf family proteins are best known for their roles in the vesicle biogenesis. However, they also play fundamental roles in a wide range of cellular regulation besides vesicular trafficking, such as modulation of lipid metabolic enzymes, cytoskeleton remodeling, ciliogenesis, lysosomal, and mitochondrial morphology and functions. Growing studies continue to expand the downstream effector landscape of Arf proteins, especially for the less-studied members, revealing new biological functions, such as amino acid sensing. Experiments with cutting-edge technologies and in vivo functional studies in the last decade help to provide a more comprehensive view of Arf family functions. In this review, we summarize the cellular functions that are regulated by at least two different Arf members with an emphasis on those beyond vesicle biogenesis.
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Affiliation(s)
- Fu-Long Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Kun-Liang Guan
- Department of Pharmacology and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
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Chen L, Xie X, Wang T, Xu L, Zhai Z, Wu H, Deng L, Lu Q, Chen Z, Yang X, Lu H, Chen YG, Luo S. ARL13B promotes angiogenesis and glioma growth by activating VEGFA-VEGFR2 signaling. Neuro Oncol 2023; 25:871-885. [PMID: 36322624 PMCID: PMC10158193 DOI: 10.1093/neuonc/noac245] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Tumor angiogenesis is essential for solid tumor progression, invasion and metastasis. The aim of this study was to identify potential signaling pathways involved in tumor angiogenesis. METHODS Genetically engineered mouse models were used to investigate the effects of endothelial ARL13B(ADP-ribosylation factor-like GTPase 13B) over-expression and deficiency on retinal and cerebral vasculature. An intracranially transplanted glioma model and a subcutaneously implanted melanoma model were employed to examine the effects of ARL13B on tumor growth and angiogenesis. Immunohistochemistry was used to measure ARL13B in glioma tissues, and scRNA-seq was used to analyze glioma and endothelial ARL13B expression. GST-fusion protein-protein interaction and co-immunoprecipitation assays were used to determine the ARL13B-VEGFR2 interaction. Immunobloting, qPCR, dual-luciferase reporter assay and functional experiments were performed to evaluate the effects of ARL13B on VEGFR2 activation. RESULTS Endothelial ARL13B regulated vascular development of both the retina and brain in mice. Also, ARL13B in endothelial cells regulated the growth of intracranially transplanted glioma cells and subcutaneously implanted melanoma cells by controlling tumor angiogenesis. Interestingly, this effect was attributed to ARL13B interaction with VEGFR2, through which ARL13B regulated the membrane and ciliary localization of VEGFR2 and consequently activated its downstream signaling in endothelial cells. Consistent with its oncogenic role, ARL13B was highly expressed in human gliomas, which was well correlated with the poor prognosis of glioma patients. Remarkably, ARL13B, transcriptionally regulated by ZEB1, enhanced the expression of VEGFA by activating Hedgehog signaling in glioma cells. CONCLUSIONS ARL13B promotes angiogenesis and tumor growth by activating VEGFA-VEGFR2 signaling. Thus, targeting ARL13B might serve as a potential approach for developing an anti-glioma or anti-melanoma therapy.
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Affiliation(s)
- Limin Chen
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xinsheng Xie
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Tiantian Wang
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Linlin Xu
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhenyu Zhai
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Haibin Wu
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Libin Deng
- Department of Epidemiology and Biostatistics, School of Public Health, Nanchang University, Nanchang, China
| | - Quqin Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanchang University, Nanchang, China
| | - Zhengjun Chen
- Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xiao Yang
- Genetic Laboratory of Development and Disease, Institute of Lifeomics, National Center for Protein Sciences, Beijing, China
| | - Hua Lu
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, USA
| | - Ye-Guang Chen
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Shiwen Luo
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
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Zhao H, Khan Z, Westlake CJ. Ciliogenesis membrane dynamics and organization. Semin Cell Dev Biol 2023; 133:20-31. [PMID: 35351373 PMCID: PMC9510604 DOI: 10.1016/j.semcdb.2022.03.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 12/28/2022]
Abstract
Ciliogenesis is a complex multistep process used to describe assembly of cilia and flagella. These organelles play essential roles in motility and signaling on the surface of cells. Cilia are built at the distal ends of centrioles through the formation of an axoneme that is surrounded by the ciliary membrane. As is the case in the biogenesis of other cellular organelles, regulators of membrane trafficking play essential roles in ciliogenesis, albeit with a unique feature that membranes are organized around microtubule-based structures. Membrane association with the distal end of the centriole is a critical initiating step for ciliogenesis. Studies of this process in different cell types suggests that a singular mechanism may not be utilized to initiate cilium assembly. In this review, we focus on recent insights into cilium biogenesis and the roles membrane trafficking regulators play in described ciliogenesis mechanisms with relevance to human disease.
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Affiliation(s)
- Huijie Zhao
- Center for Cancer Research, NCI Frederick, Laboratory of Cellular and Developmental, Signaling, Frederick, MD 21702, USA
| | - Ziam Khan
- Center for Cancer Research, NCI Frederick, Laboratory of Cellular and Developmental, Signaling, Frederick, MD 21702, USA
| | - Christopher J Westlake
- Center for Cancer Research, NCI Frederick, Laboratory of Cellular and Developmental, Signaling, Frederick, MD 21702, USA.
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7
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Liu YX, Sun WY, Xue B, Zhang RK, Li WJ, Xie X, Fan ZC. ARL3 mediates BBSome ciliary turnover by promoting its outward movement across the transition zone. J Cell Biol 2022; 221:213491. [PMID: 36129685 PMCID: PMC9499826 DOI: 10.1083/jcb.202111076] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/13/2022] [Accepted: 07/11/2022] [Indexed: 01/16/2023] Open
Abstract
Ciliary receptors and their certain downstream signaling components undergo intraflagellar transport (IFT) as BBSome cargoes to maintain their ciliary dynamics for sensing and transducing extracellular stimuli inside the cell. Cargo-laden BBSomes pass the transition zone (TZ) for ciliary retrieval, but how this passage is controlled remains elusive. Here, we show that phospholipase D (PLD)-laden BBSomes shed from retrograde IFT trains at the proximal ciliary region right above the TZ to act as Arf-like 3 (ARL3) GTPase-specific effectors in Chlamydomonas cilia. Under physiological condition, ARL3GDP binds to the membrane for diffusing into cilia. Following nucleotide exchange, ARL3GTP detaches from the ciliary membrane, binds to retrograde IFT train-shed and PLD-laden BBSomes at the proximal ciliary region right above the TZ, and recruits them to pass the TZ for ciliary retrieval likely via diffusion. ARL3 mediates the ciliary dynamics of certain signaling molecules through facilitating BBSome ciliary retrieval, providing a mechanistic understanding behind why ARL3-related Joubert syndrome shares overlapping phenotypes with Bardet-Biedl syndrome.
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Affiliation(s)
- Yan-Xia Liu
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Wei-Yue Sun
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Bin Xue
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Rui-Kai Zhang
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Wen-Juan Li
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xixian Xie
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhen-Chuan Fan
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Correspondence to Zhen-Chuan Fan:
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8
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Dai J, Zhang G, Alkhofash RA, Mekonnen B, Saravanan S, Xue B, Fan ZC, Betleja E, Cole DG, Liu P, Lechtreck K. Loss of ARL13 impedes BBSome-dependent cargo export from Chlamydomonas cilia. J Cell Biol 2022; 221:213429. [PMID: 36040375 PMCID: PMC9436004 DOI: 10.1083/jcb.202201050] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/12/2022] [Accepted: 07/11/2022] [Indexed: 12/25/2022] Open
Abstract
The GTPase Arl13b participates in ciliary protein transport, but its contribution to intraflagellar transport (IFT), the main motor-based protein shuttle of cilia, remains largely unknown. Chlamydomonas arl13 mutant cilia were characterized by both abnormal reduction and accumulation of select membrane-associated proteins. With respect to the latter, a similar set of proteins including phospholipase D (PLD) also accumulated in BBSome-deficient cilia. IFT and BBSome traffic were apparently normal in arl13. However, transport of PLD, which in control cells moves by BBSome-dependent IFT, was impaired in arl13, causing PLD to accumulate in cilia. ARL13 only rarely and transiently traveled by IFT, indicating that it is not a co-migrating adapter securing PLD to IFT trains. In conclusion, the loss of Chlamydomonas ARL13 impedes BBSome-dependent protein transport, resulting in overlapping biochemical defects in arl13 and bbs mutant cilia.
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Affiliation(s)
- Jin Dai
- Cellular Biology, University of Georgia, Athens, GA
| | - Gui Zhang
- Cellular Biology, University of Georgia, Athens, GA
| | | | | | | | - Bin Xue
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhen-Chuan Fan
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | | | | | - Peiwei Liu
- College of Life Science, Shandong Normal University, Jinan, Shandong, China
| | - Karl Lechtreck
- Cellular Biology, University of Georgia, Athens, GA,Correspondence to Karl F. Lechtreck:
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9
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Umer N, Phadke S, Shakeri F, Arévalo L, Lohanadan K, Kirfel G, Sylvester M, Buness A, Schorle H. PFN4 is required for manchette development and acrosome biogenesis during mouse spermiogenesis. Development 2022; 149:276289. [PMID: 35950913 PMCID: PMC9481974 DOI: 10.1242/dev.200499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 07/14/2022] [Indexed: 11/26/2022]
Abstract
Profilin 4 (Pfn4) is expressed during spermiogenesis and localizes to the acrosome-acroplaxome-manchette complex. Here, we generated PFN4-deficient mice, with sperm displaying severe impairment in manchette formation. Interestingly, HOOK1 staining suggests that the perinuclear ring is established; however, ARL3 staining is disrupted, suggesting that lack of PFN4 does not interfere with the formation of the perinuclear ring and initial localization of HOOK1, but impedes microtubular organization of the manchette. Furthermore, amorphous head shape and flagellar defects were detected, resulting in reduced sperm motility. Disrupted cis- and trans-Golgi networks and aberrant production of proacrosomal vesicles caused impaired acrosome biogenesis. Proteomic analysis showed that the proteins ARF3, SPECC1L and FKBP1, which are involved in Golgi membrane trafficking and PI3K/AKT pathway, are more abundant in Pfn4−/− testes. Levels of PI3K, AKT and mTOR were elevated, whereas AMPK level was reduced, consistent with inhibition of autophagy. This seems to result in blockage of autophagic flux, which could explain the failure in acrosome formation. In vitro fertilization demonstrated that PFN4-deficient sperm is capable of fertilizing zona-free oocytes, suggesting a potential treatment for PFN4-related human infertility. Summary: PFN4-deficient male mice exhibit impaired acrosome formation and malformation of the manchette, leading to amorphous sperm head shape, flagellar abnormalities and sterility.
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Affiliation(s)
- Naila Umer
- Institute of Pathology, University Hospital Bonn 1 Department of Developmental Pathology , , 53127 Bonn , Germany
| | - Sharang Phadke
- Institute of Pathology, University Hospital Bonn 1 Department of Developmental Pathology , , 53127 Bonn , Germany
| | - Farhad Shakeri
- Institute for Medical Biometry, Informatics and Epidemiology 2 , Medical Faculty , , 53127 Bonn , Germany
- University of Bonn 2 , Medical Faculty , , 53127 Bonn , Germany
- Institute for Genomic Statistics and Bioinformatics 3 , Medical Faculty , , 53127 Bonn , Germany
- University of Bonn 3 , Medical Faculty , , 53127 Bonn , Germany
| | - Lena Arévalo
- Institute of Pathology, University Hospital Bonn 1 Department of Developmental Pathology , , 53127 Bonn , Germany
| | | | - Gregor Kirfel
- Institute for Cell Biology, University of Bonn 4 , 53121 Bonn , Germany
| | - Marc Sylvester
- Institute of Biochemistry and Molecular Biology 5 Core Facility Mass Spectrometry , , Medical Faculty , , 53115 Bonn , Germany
- University of Bonn 5 Core Facility Mass Spectrometry , , Medical Faculty , , 53115 Bonn , Germany
| | - Andreas Buness
- Institute for Medical Biometry, Informatics and Epidemiology 2 , Medical Faculty , , 53127 Bonn , Germany
- University of Bonn 2 , Medical Faculty , , 53127 Bonn , Germany
- Institute for Genomic Statistics and Bioinformatics 3 , Medical Faculty , , 53127 Bonn , Germany
- University of Bonn 3 , Medical Faculty , , 53127 Bonn , Germany
| | - Hubert Schorle
- Institute of Pathology, University Hospital Bonn 1 Department of Developmental Pathology , , 53127 Bonn , Germany
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10
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Thirugnanam K, Prabhudesai S, Van Why E, Pan A, Gupta A, Foreman K, Zennadi R, Rarick KR, Nauli SM, Palecek SP, Ramchandran R. Ciliogenesis mechanisms mediated by PAK2-ARL13B signaling in brain endothelial cells is responsible for vascular stability. Biochem Pharmacol 2022; 202:115143. [PMID: 35700757 PMCID: PMC11274820 DOI: 10.1016/j.bcp.2022.115143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/02/2022]
Abstract
In the developing vasculature, cilia, microtubule-based organelles that project from the apical surface of endothelial cells (ECs), have been identified to function cell autonomously to promote vascular integrity and prevent hemorrhage. To date, the underlying mechanisms of endothelial cilia formation (ciliogenesis) are not fully understood. Understanding these mechanisms is likely to open new avenues for targeting EC-cilia to promote vascular stability. Here, we hypothesized that brain ECs ciliogenesis and the underlying mechanisms that control this process are critical for brain vascular stability. To investigate this hypothesis, we utilized multiple approaches including developmental zebrafish model system and primary cell culture systems. In the p21 activated kinase 2 (pak2a) zebrafish vascular stability mutant [redhead (rhd)] that shows cerebral hemorrhage, we observed significant decrease in cilia-inducing protein ADP Ribosylation Factor Like GTPase 13B (Arl13b), and a 4-fold decrease in cilia numbers. Overexpressing ARL13B-GFP fusion mRNA rescues the cilia numbers (1-2-fold) in brain vessels, and the cerebral hemorrhage phenotype. Further, this phenotypic rescue occurs at a critical time in development (24 h post fertilization), prior to initiation of blood flow to the brain vessels. Extensive biochemical mechanistic studies in primary human brain microvascular ECs implicate ligands platelet-derived growth factor-BB (PDGF-BB), and vascular endothelial growth factor-A (VEGF-A) trigger PAK2-ARL13B ciliogenesis and signal through cell surface VEGFR-2 receptor. Thus, collectively, we have implicated a critical brain ECs ciliogenesis signal that converges on PAK2-ARL13B proteins to promote vascular stability.
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Affiliation(s)
- Karthikeyan Thirugnanam
- Department of Pediatrics, Division of Neonatology, Developmental Vascular Biology Program, Medical College of Wisconsin, Children's Research Institute (CRI), Milwaukee, WI, United States
| | - Shubhangi Prabhudesai
- Department of Pediatrics, Division of Neonatology, Developmental Vascular Biology Program, Medical College of Wisconsin, Children's Research Institute (CRI), Milwaukee, WI, United States
| | - Emma Van Why
- Department of Pediatrics, Division of Neonatology, Developmental Vascular Biology Program, Medical College of Wisconsin, Children's Research Institute (CRI), Milwaukee, WI, United States
| | - Amy Pan
- Department of Pediatrics, Division of Quantitative Health Sciences, Medical College of Wisconsin, CRI, Milwaukee, WI, United States
| | - Ankan Gupta
- Department of Pediatrics, Division of Neonatology, Developmental Vascular Biology Program, Medical College of Wisconsin, Children's Research Institute (CRI), Milwaukee, WI, United States
| | - Koji Foreman
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Rahima Zennadi
- Department of Medicine, Duke University, Durham, NC, United States
| | - Kevin R Rarick
- Department of Pediatrics, Division of Critical Care, Medical College of Wisconsin, CRI, Milwaukee, WI, United States
| | - Surya M Nauli
- Department of Pharmaceutical Sciences, Chapman University, Irvine, CA, United States
| | - Sean P Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Ramani Ramchandran
- Department of Pediatrics, Division of Neonatology, Developmental Vascular Biology Program, Medical College of Wisconsin, Children's Research Institute (CRI), Milwaukee, WI, United States.
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11
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Zhang H, Huang Z, LV L, Xin Y, Wang Q, Li F, Dong L, Wu C, Ingham PW, Zhao Z. A transgenic zebrafish for in vivo visualization of cilia. Open Biol 2022; 12:220104. [PMID: 35946311 PMCID: PMC9364149 DOI: 10.1098/rsob.220104] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cilia are organelles for cellular signalling and motility. Mutations affecting ciliary function are also associated with cilia-related disorders (ciliopathies). The identification of cilia markers is critical for studying their function at the cellular level. Due to the lack of a conserved, short ciliary localization motif, the full-length ARL13b or 5HT6 proteins are normally used for cilia labelling. Overexpression of these genes, however, can affect the function of cilia, leading to artefacts in cilia studies. Here, we show that Nephrocystin-3 (Nphp3) is highly conserved among vertebrates and demonstrate that the N-terminal truncated peptide of zebrafish Nphp3 can be used as a gratuitous cilia-specific marker. To visualize the dynamics of cilia in vivo, we generated a stable transgenic zebrafish Tg (β-actin: nphp3N-mCherry)sx1001. The cilia in multiple cell types are efficiently labelled by the encoded fusion protein from embryonic stages to adulthood, without any developmental and physiological defects. We show that the line allows live imaging of ciliary dynamics and trafficking of cilia proteins, such as Kif7 and Smo, key regulators of the Hedgehog signalling pathway. Thus, we have generated an effective new tool for in vivo cilia studies that will help shed further light on the roles of these important organelles.
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Affiliation(s)
- Hongyu Zhang
- Institute of Biomedical Sciences, 1331 Local Bio-Resources and Health Industry Collaborative Innovation Center of Shanxi Province, Key Laboratory of Biomedical Shanxi Province, Shanxi University, Taiyuan 030006, People's Republic of China,School of Life Science, Shanxi University, Taiyuan 030006, People's Republic of China
| | - Zhuoya Huang
- Institute of Biomedical Sciences, 1331 Local Bio-Resources and Health Industry Collaborative Innovation Center of Shanxi Province, Key Laboratory of Biomedical Shanxi Province, Shanxi University, Taiyuan 030006, People's Republic of China,Chemical Biology and Molecular Engineering Key Laboratory of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, People's Republic of China
| | - Liuliu LV
- Institute of Biomedical Sciences, 1331 Local Bio-Resources and Health Industry Collaborative Innovation Center of Shanxi Province, Key Laboratory of Biomedical Shanxi Province, Shanxi University, Taiyuan 030006, People's Republic of China,School of Life Science, Shanxi University, Taiyuan 030006, People's Republic of China
| | - Yuye Xin
- Institute of Biomedical Sciences, 1331 Local Bio-Resources and Health Industry Collaborative Innovation Center of Shanxi Province, Key Laboratory of Biomedical Shanxi Province, Shanxi University, Taiyuan 030006, People's Republic of China,Chemical Biology and Molecular Engineering Key Laboratory of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, People's Republic of China
| | - Qian Wang
- Institute of Biomedical Sciences, 1331 Local Bio-Resources and Health Industry Collaborative Innovation Center of Shanxi Province, Key Laboratory of Biomedical Shanxi Province, Shanxi University, Taiyuan 030006, People's Republic of China,School of Life Science, Shanxi University, Taiyuan 030006, People's Republic of China
| | - Feng Li
- Department of Molecular Biology, Shanxi Cancer Hospital, Affiliated Cancer Hospital of Shanxi Medical University, Taiyuan 030013, People's Republic of China
| | - Lina Dong
- Central Laboratory, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan 030012, People's Republic of China
| | - Changxin Wu
- Institute of Biomedical Sciences, 1331 Local Bio-Resources and Health Industry Collaborative Innovation Center of Shanxi Province, Key Laboratory of Biomedical Shanxi Province, Shanxi University, Taiyuan 030006, People's Republic of China,School of Life Science, Shanxi University, Taiyuan 030006, People's Republic of China
| | - Philip W. Ingham
- LKC Medicine School, Nanyang Technological University, 639798, Singapore
| | - Zhonghua Zhao
- Institute of Biomedical Sciences, 1331 Local Bio-Resources and Health Industry Collaborative Innovation Center of Shanxi Province, Key Laboratory of Biomedical Shanxi Province, Shanxi University, Taiyuan 030006, People's Republic of China,School of Life Science, Shanxi University, Taiyuan 030006, People's Republic of China
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12
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Yang Y, Shuai P, Li X, Sun K, Jiang X, Liu W, Le W, Jiang H, Liu Y, Zhu X. Mettl14-mediated m6A modification is essential for visual function and retinal photoreceptor survival. BMC Biol 2022; 20:140. [PMID: 35698136 PMCID: PMC9195452 DOI: 10.1186/s12915-022-01335-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/18/2022] [Indexed: 12/13/2022] Open
Abstract
Background As the most abundant epigenetic modification of eukaryotic mRNA, N6-methyladenosine (m6A) modification has been shown to play a role in mammalian nervous system development and function by regulating mRNA synthesis and degeneration. However, the role of m6A modification in retinal photoreceptors remains unknown. Results We generated the first retina-specific Mettl14-knockout mouse models using the Rho-Cre and HRGP-Cre lines and investigated the functions of Mettl14 in retinal rod and cone photoreceptors. Our data showed that loss of Mettl14 in rod cells causes a weakened scotopic photoresponse and rod degeneration. Further study revealed the ectopic accumulation of multiple outer segment (OS) proteins in the inner segment (IS). Deficiency of Mettl14 in cone cells led to the mislocalization of cone opsin proteins and the progressive death of cone cells. Moreover, Mettl14 depletion resulted in drastic decreases in METTL3/WTAP levels and reduced m6A methylation levels. Mechanistically, transcriptomic analyses in combination with MeRIP-seq illustrated that m6A depletion via inactivation of Mettl14 resulted in reduced expression levels of multiple phototransduction- and cilium-associated genes, which subsequently led to compromised ciliogenesis and impaired synthesis and transport of OS-residing proteins in rod cells. Conclusions Our data demonstrate that Mettl14 plays an important role in regulating phototransduction and ciliogenesis events and is essential for photoreceptor function and survival, highlighting the importance of m6A modification in visual function. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01335-x.
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Affiliation(s)
- Yeming Yang
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 61007, Sichuan, China.,The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, China.,Key Laboratory of Tibetan Medicine Research, Chinese Academy of Sciences and Qinghai Provincial Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, 810008, Qinghai, China
| | - Ping Shuai
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 61007, Sichuan, China.,The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, China
| | - Xiao Li
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 61007, Sichuan, China.,The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, China
| | - Kuanxiang Sun
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 61007, Sichuan, China
| | - Xiaoyan Jiang
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 61007, Sichuan, China
| | - Wenjing Liu
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 61007, Sichuan, China
| | - Weidong Le
- Institute of Neurology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, China.,Department of Neurology, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Haisong Jiang
- Institute of Neurology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, China. .,Department of Neurology, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China.
| | - Yuping Liu
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 61007, Sichuan, China.
| | - Xianjun Zhu
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 61007, Sichuan, China. .,The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, China. .,Key Laboratory of Tibetan Medicine Research, Chinese Academy of Sciences and Qinghai Provincial Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, 810008, Qinghai, China. .,Research Unit for Blindness Prevention of the Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, 610072, Sichuan, China. .,Henan Eye Institute, Henan Eye Hospital, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, 450003, Henan, China.
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13
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Dutta P, Ray K. Ciliary membrane, localised lipid modification and cilia function. J Cell Physiol 2022; 237:2613-2631. [PMID: 35661356 DOI: 10.1002/jcp.30787] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 11/08/2022]
Abstract
Cilium, a tiny microtubule-based cellular appendage critical for cell signalling and physiology, displays a large variety of receptors. The composition and turnover of ciliary lipids and receptors determine cell behaviour. Due to the exclusion of ribosomal machinery and limited membrane area, a cilium needs adaptive logistics to actively reconstitute the lipid and receptor compositions during development and differentiation. How is this dynamicity generated? Here, we examine whether, along with the Intraflagellar-Transport, targeted changes in sector-wise lipid composition could control the receptor localisation and functions in the cilia. We discuss how an interplay between ciliary lipid composition, localised lipid modification, and receptor function could contribute to cilia growth and signalling. We argue that lipid modification at the cell-cilium interface could generate an added thrust for a selective exchange of membrane lipids and the transmembrane and membrane-associated proteins.
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Affiliation(s)
- Priya Dutta
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Krishanu Ray
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
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14
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Masyuk AI, Masyuk TV, Trussoni CE, Pirius NE, LaRusso NF. Autophagy promotes hepatic cystogenesis in polycystic liver disease by depletion of cholangiocyte ciliogenic proteins. Hepatology 2022; 75:1110-1122. [PMID: 34942041 PMCID: PMC9035076 DOI: 10.1002/hep.32298] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/13/2021] [Accepted: 12/16/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUNDS AND AIMS Polycystic liver disease (PLD) is characterized by defective cholangiocyte cilia that regulate progressive growth of hepatic cysts. Because formation of primary cilia is influenced by autophagy through degradation of proteins involved in ciliogenesis, we hypothesized that ciliary defects in PLD cholangiocytes (PLDCs) originate from autophagy-mediated depletion of ciliogenic proteins ADP-ribosylation factor-like protein 3 (ARL3) and ADP-ribosylation factor-like protein 13B (ARL13B) and ARL-dependent mislocation of a ciliary-localized bile acid receptor, Takeda G-protein-coupled receptor 5 (TGR5), the activation of which enhances hepatic cystogenesis (HCG). The aims here were to determine whether: (1) ciliogenesis is impaired in PLDC, is associated with increased autophagy, and involves autophagy-mediated depletion of ARL3 and ARL13B; (2) depletion of ARL3 and ARL13B in PLDC cilia impacts ciliary localization of TGR5; and (3) pharmacological inhibition of autophagy re-establishes cholangiocyte cilia and ciliary localization of ARL3, ARL3B, and TGR5 and reduces HCG. APPROACH AND RESULTS By using liver tissue from healthy persons and patients with PLD, in vitro and in vivo models of PLD, and in vitro models of ciliogenesis, we demonstrated that, in PLDCs: ciliogenesis is impaired; autophagy is enhanced; ARL3 and ARL13B are ubiquitinated by HDAC6, depleted in cilia, and present in autophagosomes; depletion of ARL3 and ARL13B impacts ciliary localization of TGR5; and pharmacological inhibition of autophagy with mefloquine and verteporfin re-establishes cholangiocyte cilia and ciliary localization of ARL3, ARL13B, and TGR5 and reduces HCG. CONCLUSIONS The intersection between autophagy, defective cholangiocyte cilia, and enhanced HCG contributes to PLD progression and can be considered a target for therapeutic interventions.
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Affiliation(s)
- Anatoliy I. Masyuk
- Mayo Clinic College of Medicine and Science, 200 First Street, SW Rochester, Minnesota 55905, USA
| | - Tatyana V. Masyuk
- Mayo Clinic College of Medicine and Science, 200 First Street, SW Rochester, Minnesota 55905, USA
| | - Christy E. Trussoni
- Mayo Clinic College of Medicine and Science, 200 First Street, SW Rochester, Minnesota 55905, USA
| | - Nicholas E. Pirius
- Mayo Clinic College of Medicine and Science, 200 First Street, SW Rochester, Minnesota 55905, USA
| | - Nicholas F. LaRusso
- Mayo Clinic College of Medicine and Science, 200 First Street, SW Rochester, Minnesota 55905, USA
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15
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Quidwai T, Wang J, Hall EA, Petriman NA, Leng W, Kiesel P, Wells JN, Murphy LC, Keighren MA, Marsh JA, Lorentzen E, Pigino G, Mill P. A WDR35-dependent coat protein complex transports ciliary membrane cargo vesicles to cilia. eLife 2021; 10:e69786. [PMID: 34734804 PMCID: PMC8754431 DOI: 10.7554/elife.69786] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 11/04/2021] [Indexed: 11/13/2022] Open
Abstract
Intraflagellar transport (IFT) is a highly conserved mechanism for motor-driven transport of cargo within cilia, but how this cargo is selectively transported to cilia is unclear. WDR35/IFT121 is a component of the IFT-A complex best known for its role in ciliary retrograde transport. In the absence of WDR35, small mutant cilia form but fail to enrich in diverse classes of ciliary membrane proteins. In Wdr35 mouse mutants, the non-core IFT-A components are degraded and core components accumulate at the ciliary base. We reveal deep sequence homology of WDR35 and other IFT-A subunits to α and ß' COPI coatomer subunits and demonstrate an accumulation of 'coat-less' vesicles that fail to fuse with Wdr35 mutant cilia. We determine that recombinant non-core IFT-As can bind directly to lipids and provide the first in situ evidence of a novel coat function for WDR35, likely with other IFT-A proteins, in delivering ciliary membrane cargo necessary for cilia elongation.
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Affiliation(s)
- Tooba Quidwai
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Jiaolong Wang
- Department of Molecular Biology and Genetics, Aarhus UniversityAarhusDenmark
| | - Emma A Hall
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Narcis A Petriman
- Department of Molecular Biology and Genetics, Aarhus UniversityAarhusDenmark
| | - Weihua Leng
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Petra Kiesel
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Jonathan N Wells
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Laura C Murphy
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Margaret A Keighren
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Esben Lorentzen
- Department of Molecular Biology and Genetics, Aarhus UniversityAarhusDenmark
| | - Gaia Pigino
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Human TechnopoleMilanItaly
| | - Pleasantine Mill
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
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16
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Primary Ciliogenesis by 2-Isopropylmalic Acid Prevents PM2.5-Induced Inflammatory Response and MMP-1 Activation in Human Dermal Fibroblasts and a 3-D-Skin Model. Int J Mol Sci 2021; 22:ijms222010941. [PMID: 34681602 PMCID: PMC8535518 DOI: 10.3390/ijms222010941] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 11/23/2022] Open
Abstract
Particulate matters (PMs) increase oxidative stress and inflammatory response in different tissues. PMs disrupt the formation of primary cilia in various skin cells, including keratinocytes and melanocytes. In this study, we found that 2-isopropylmalic acid (2-IPMA) promoted primary ciliogenesis and restored the PM2.5-induced dysgenesis of primary cilia in dermal fibroblasts. Moreover, 2-IPMA inhibited the generation of excessive reactive oxygen species and the activation of stress kinase in PM2.5-treated dermal fibroblasts. Further, 2-IPMA inhibited the production of pro-inflammatory cytokines, including IL-6 and TNF-α, which were upregulated by PM2.5. However, the inhibition of primary ciliogenesis by IFT88 depletion reversed the downregulated cytokines by 2-IPMA. Moreover, we found that PM2.5 treatment increased the MMP-1 expression in dermal fibroblasts and a human 3-D-skin model. The reduced MMP-1 expression by 2-IPMA was further reversed by IFT88 depletion in PM2.5-treated dermal fibroblasts. These findings suggest that 2-IPMA ameliorates PM2.5-induced inflammation by promoting primary ciliogenesis in dermal fibroblasts.
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17
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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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18
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Suciu SK, Long AB, Caspary T. Smoothened and ARL13B are critical in mouse for superior cerebellar peduncle targeting. Genetics 2021; 218:6300527. [PMID: 34132778 PMCID: PMC8864748 DOI: 10.1093/genetics/iyab084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/15/2021] [Indexed: 01/07/2023] Open
Abstract
Patients with the ciliopathy Joubert syndrome present with physical anomalies, intellectual disability, and a hindbrain malformation described as the "molar tooth sign" due to its appearance on an MRI. This radiological abnormality results from a combination of hypoplasia of the cerebellar vermis and inappropriate targeting of the white matter tracts of the superior cerebellar peduncles. ARL13B is a cilia-enriched regulatory GTPase established to regulate cell fate, cell proliferation, and axon guidance through vertebrate Hedgehog signaling. In patients, mutations in ARL13B cause Joubert syndrome. To understand the etiology of the molar tooth sign, we used mouse models to investigate the role of ARL13B during cerebellar development. We found that ARL13B regulates superior cerebellar peduncle targeting and these fiber tracts require Hedgehog signaling for proper guidance. However, in mouse, the Joubert-causing R79Q mutation in ARL13B does not disrupt Hedgehog signaling nor does it impact tract targeting. We found a small cerebellar vermis in mice lacking ARL13B function but no cerebellar vermis hypoplasia in mice expressing the Joubert-causing R79Q mutation. In addition, mice expressing a cilia-excluded variant of ARL13B that transduces Hedgehog normally showed normal tract targeting and vermis width. Taken together, our data indicate that ARL13B is critical for the control of cerebellar vermis width as well as superior cerebellar peduncle axon guidance, likely via Hedgehog signaling. Thus, our work highlights the complexity of ARL13B in molar tooth sign etiology.
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Affiliation(s)
- Sarah K Suciu
- Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA 30322, USA,Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Alyssa B Long
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Tamara Caspary
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA,Corresponding author: Department of Human Genetics, 615 Michael Street, Suite 301, Atlanta, GA 30322.
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19
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Cevik S, Kaplan OI. The Joubert syndrome protein CEP41 is excluded from the distal segment of cilia in C. elegans. MICROPUBLICATION BIOLOGY 2021; 2021:10.17912/micropub.biology.000406. [PMID: 34113804 PMCID: PMC8185565 DOI: 10.17912/micropub.biology.000406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/21/2021] [Accepted: 06/02/2021] [Indexed: 11/16/2022]
Abstract
Rare diseases are a fundamental issue in today's world, affecting more than 300 million individuals worldwide. According to data from Orphanet and OMIM, about 50-60 new conditions are added to the list of over 6,000 clinically distinct diseases each year, rendering disease diagnosis and treatment even more challenging. Ciliopathies comprise a heterogeneous category of rare diseases made up of over 35 distinct diseases, including Joubert syndrome (JBTS; OMIM 213300), that are caused by functional and structural defects in cilia. JBTS is an autosomal recessive condition characterized by a range of symptoms, including cerebellar vermis hypoplasia and poor muscle tone. There are now a total of 38 genes that cause JBTS, almost all of which encode protein products that are found in cilia and cilia-associated compartments, such as the basal body and transition zone. CEP41 is a JBTS-associated protein that is found in cilia and the basal body of mammals, but its localization in other ciliary organisms remains elusive. C. elegans is an excellent model organism for studying the molecular mechanisms of rare diseases like JBTS. We, therefore, decided to use C. elegans to identify the localization of CEP41. Our microscopy analysis revealed that CEPH-41(CEntrosomal Protein Homolog 41) not only localizes to cilia but is excluded from the distal segment of the amphid and phasmid cilia in C. elegans. Furthermore, we discovered a putative X-box motif located in the promoter of ceph-41 and the expression of ceph-41 is regulated by DAF-19, a sole Regulatory Factor X (RFX) transcription factor.
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Affiliation(s)
- Sebiha Cevik
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| | - Oktay I. Kaplan
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
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20
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Lauri A, Fasano G, Venditti M, Dallapiccola B, Tartaglia M. In vivo Functional Genomics for Undiagnosed Patients: The Impact of Small GTPases Signaling Dysregulation at Pan-Embryo Developmental Scale. Front Cell Dev Biol 2021; 9:642235. [PMID: 34124035 PMCID: PMC8194860 DOI: 10.3389/fcell.2021.642235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/12/2021] [Indexed: 12/24/2022] Open
Abstract
While individually rare, disorders affecting development collectively represent a substantial clinical, psychological, and socioeconomic burden to patients, families, and society. Insights into the molecular mechanisms underlying these disorders are required to speed up diagnosis, improve counseling, and optimize management toward targeted therapies. Genome sequencing is now unveiling previously unexplored genetic variations in undiagnosed patients, which require functional validation and mechanistic understanding, particularly when dealing with novel nosologic entities. Functional perturbations of key regulators acting on signals' intersections of evolutionarily conserved pathways in these pathological conditions hinder the fine balance between various developmental inputs governing morphogenesis and homeostasis. However, the distinct mechanisms by which these hubs orchestrate pathways to ensure the developmental coordinates are poorly understood. Integrative functional genomics implementing quantitative in vivo models of embryogenesis with subcellular precision in whole organisms contribute to answering these questions. Here, we review the current knowledge on genes and mechanisms critically involved in developmental syndromes and pediatric cancers, revealed by genomic sequencing and in vivo models such as insects, worms and fish. We focus on the monomeric GTPases of the RAS superfamily and their influence on crucial developmental signals and processes. We next discuss the effectiveness of exponentially growing functional assays employing tractable models to identify regulatory crossroads. Unprecedented sophistications are now possible in zebrafish, i.e., genome editing with single-nucleotide precision, nanoimaging, highly resolved recording of multiple small molecules activity, and simultaneous monitoring of brain circuits and complex behavioral response. These assets permit accurate real-time reporting of dynamic small GTPases-controlled processes in entire organisms, owning the potential to tackle rare disease mechanisms.
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Affiliation(s)
- Antonella Lauri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | | | | | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
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21
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Akella JS, Barr MM. The tubulin code specializes neuronal cilia for extracellular vesicle release. Dev Neurobiol 2021; 81:231-252. [PMID: 33068333 PMCID: PMC8052387 DOI: 10.1002/dneu.22787] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 09/07/2020] [Accepted: 09/23/2020] [Indexed: 12/17/2022]
Abstract
Cilia are microtubule-based organelles that display diversity in morphology, ultrastructure, protein composition, and function. The ciliary microtubules of C. elegans sensory neurons exemplify this diversity and provide a paradigm to understand mechanisms driving ciliary specialization. Only a subset of ciliated neurons in C. elegans are specialized to make and release bioactive extracellular vesicles (EVs) into the environment. The cilia of extracellular vesicle releasing neurons have distinct axonemal features and specialized intraflagellar transport that are important for releasing EVs. In this review, we discuss the role of the tubulin code in the specialization of microtubules in cilia of EV releasing neurons.
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Affiliation(s)
- Jyothi S Akella
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Maureen M Barr
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
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22
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Bernatik O, Paclikova P, Kotrbova A, Bryja V, Cajanek L. Primary Cilia Formation Does Not Rely on WNT/β-Catenin Signaling. Front Cell Dev Biol 2021; 9:623753. [PMID: 33718363 PMCID: PMC7952446 DOI: 10.3389/fcell.2021.623753] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/04/2021] [Indexed: 11/13/2022] Open
Abstract
Primary cilia act as crucial regulators of embryo development and tissue homeostasis. They are instrumental for modulation of several signaling pathways, including Hedgehog, WNT, and TGF-β. However, gaps exist in our understanding of how cilia formation and function is regulated. Recent work has implicated WNT/β-catenin signaling pathway in the regulation of ciliogenesis, yet the results are conflicting. One model suggests that WNT/β-catenin signaling negatively regulates cilia formation, possibly via effects on cell cycle. In contrast, second model proposes a positive role of WNT/β-catenin signaling on cilia formation, mediated by the re-arrangement of centriolar satellites in response to phosphorylation of the key component of WNT/β-catenin pathway, β-catenin. To clarify these discrepancies, we investigated possible regulation of primary cilia by the WNT/β-catenin pathway in cell lines (RPE-1, NIH3T3, and HEK293) commonly used to study ciliogenesis. We used WNT3a to activate or LGK974 to block the pathway, and examined initiation of ciliogenesis, cilium length, and percentage of ciliated cells. We show that the treatment by WNT3a has no- or lesser inhibitory effect on cilia formation. Importantly, the inhibition of secretion of endogenous WNT ligands using LGK974 blocks WNT signaling but does not affect ciliogenesis. Finally, using knock-out cells for key WNT pathway components, namely DVL1/2/3, LRP5/6, or AXIN1/2 we show that neither activation nor deactivation of the WNT/β-catenin pathway affects the process of ciliogenesis. These results suggest that WNT/β-catenin-mediated signaling is not generally required for efficient cilia formation. In fact, activation of the WNT/β-catenin pathway in some systems seems to moderately suppress ciliogenesis.
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Affiliation(s)
- Ondrej Bernatik
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Petra Paclikova
- Section of Animal Physiology and Immunology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Anna Kotrbova
- Section of Animal Physiology and Immunology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Vitezslav Bryja
- Section of Animal Physiology and Immunology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Lukas Cajanek
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czechia
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23
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Nechipurenko I, Lavrentyeva S, Sengupta P. GRDN-1/Girdin regulates dendrite morphogenesis and cilium position in two specialized sensory neuron types in C. elegans. Dev Biol 2021; 472:38-51. [PMID: 33460640 DOI: 10.1016/j.ydbio.2020.12.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/18/2020] [Accepted: 12/22/2020] [Indexed: 10/22/2022]
Abstract
Primary cilia are located at the dendritic tips of sensory neurons and house the molecular machinery necessary for detection and transduction of sensory stimuli. The mechanisms that coordinate dendrite extension with cilium position during sensory neuron development are not well understood. Here, we show that GRDN-1, the Caenorhabditis elegans ortholog of the highly conserved scaffold and signaling protein Girdin/GIV, regulates both cilium position and dendrite extension in the postembryonic AQR and PQR gas-sensing neurons. Mutations in grdn-1 disrupt dendrite outgrowth and mislocalize cilia to the soma or proximal axonal segments in AQR, and to a lesser extent, in PQR. GRDN-1 is localized to the basal body and regulates localization of HMR-1/Cadherin to the distal AQR dendrite. However, knockdown of HMR-1 and/or loss of SAX-7/LICAM, molecules previously implicated in sensory dendrite development in C. elegans, do not alter AQR dendrite morphology or cilium position. We find that GRDN-1 localization in AQR is regulated by UNC-116/Kinesin-1, and that correspondingly, unc-116 mutants exhibit severe AQR dendrite outgrowth and cilium positioning defects. In contrast, GRDN-1 and cilium localization in PQR is modulated by LIN-44/Wnt signaling. Together, these findings identify upstream regulators of GRDN-1, and describe new cell-specific roles for this multifunctional protein in sensory neuron development.
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Affiliation(s)
- Inna Nechipurenko
- Department of Biology, Brandeis University, Waltham, MA, USA; Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, USA.
| | | | - Piali Sengupta
- Department of Biology, Brandeis University, Waltham, MA, USA.
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24
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Powell L, Barroso-Gil M, Clowry GJ, Devlin LA, Molinari E, Ramsbottom SA, Miles CG, Sayer JA. Expression patterns of ciliopathy genes ARL3 and CEP120 reveal roles in multisystem development. BMC DEVELOPMENTAL BIOLOGY 2020; 20:26. [PMID: 33297941 PMCID: PMC7727171 DOI: 10.1186/s12861-020-00231-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/11/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND Joubert syndrome and related disorders (JSRD) and Jeune syndrome are multisystem ciliopathy disorders with overlapping phenotypes. There are a growing number of genetic causes for these rare syndromes, including the recently described genes ARL3 and CEP120. METHODS We sought to explore the developmental expression patterns of ARL3 and CEP120 in humans to gain additional understanding of these genetic conditions. We used an RNA in situ detection technique called RNAscope to characterise ARL3 and CEP120 expression patterns in human embryos and foetuses in collaboration with the MRC-Wellcome Trust Human Developmental Biology Resource. RESULTS Both ARL3 and CEP120 are expressed in early human brain development, including the cerebellum and in the developing retina and kidney, consistent with the clinical phenotypes seen with pathogenic variants in these genes. CONCLUSIONS This study provides insights into the potential pathogenesis of JSRD by uncovering the spatial expression of two JSRD-causative genes during normal human development.
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Affiliation(s)
- L Powell
- Translational and Clinical Research Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - M Barroso-Gil
- Translational and Clinical Research Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - G J Clowry
- Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - L A Devlin
- Translational and Clinical Research Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - E Molinari
- Translational and Clinical Research Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - S A Ramsbottom
- Translational and Clinical Research Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - C G Miles
- Translational and Clinical Research Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - J A Sayer
- Translational and Clinical Research Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK.
- The Newcastle Hospitals NHS Foundation Trust, Freeman Road, Newcastle upon Tyne, NE7 7DN, UK.
- National Institute for Health Research Newcastle Biomedical Research Centre, Newcastle upon Tyne, NE4 5PL, UK.
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25
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Kazatskaya A, Yuan L, Amin-Wetzel N, Philbrook A, de Bono M, Sengupta P. The URX oxygen-sensing neurons in C. elegans are ciliated. MICROPUBLICATION BIOLOGY 2020; 2020:10.17912/micropub.biology.000303. [PMID: 33005885 PMCID: PMC7520127 DOI: 10.17912/micropub.biology.000303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/08/2020] [Accepted: 09/09/2020] [Indexed: 12/21/2022]
Affiliation(s)
| | - Lisa Yuan
- Brandeis University, Waltham, MA 02454
| | - Niko Amin-Wetzel
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | | | - Mario de Bono
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
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26
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Pandey M, Huang Y, Lim TK, Lin Q, He CY. Flagellar targeting of an arginine kinase requires a conserved lipidated protein intraflagellar transport (LIFT) pathway in Trypanosoma brucei. J Biol Chem 2020; 295:11326-11336. [PMID: 32587088 DOI: 10.1074/jbc.ra120.014287] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/18/2020] [Indexed: 12/31/2022] Open
Abstract
Both intraflagellar transport (IFT) and lipidated protein intraflagellar transport (LIFT) pathways are essential for cilia/flagella biogenesis, motility, and sensory functions. In the LIFT pathway, lipidated cargoes are transported into the cilia through the coordinated actions of cargo carrier proteins such as Unc119 or PDE6δ, as well as small GTPases Arl13b and Arl3 in the cilium. Our previous studies have revealed a single Arl13b ortholog in the evolutionarily divergent Trypanosoma brucei, the causative agent of African sleeping sickness. TbArl13 catalyzes two TbArl3 homologs, TbArl3A and TbArl3C, suggesting the presence of a conserved LIFT pathway in these protozoan parasites. Only a single homolog to the cargo carrier protein Unc119 has been identified in T. brucei genome, but its function in lipidated protein transport has not been characterized. In this study, we exploited the proximity-based biotinylation approach to identify binding partners of TbUnc119. We showed that TbUnc119 binds to a flagellar arginine kinase TbAK3 in a myristoylation-dependent manner and is responsible for its targeting to and enrichment in the flagellum. Interestingly, only TbArl3A, but not TbArl3C interacted with TbUnc119 in a GTP-dependent manner, suggesting functional specialization of Arl3-GTPases in T. brucei These results establish the function of TbUnc119 as a myristoylated cargo carrier and support the presence of a conserved LIFT pathway in T. brucei.
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Affiliation(s)
- Maneesha Pandey
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Yameng Huang
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Teck Kwang Lim
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Cynthia Y He
- Department of Biological Sciences, National University of Singapore, Singapore
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27
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Fisher S, Kuna D, Caspary T, Kahn RA, Sztul E. ARF family GTPases with links to cilia. Am J Physiol Cell Physiol 2020; 319:C404-C418. [PMID: 32520609 PMCID: PMC7500214 DOI: 10.1152/ajpcell.00188.2020] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The ADP-ribosylation factor (ARF) superfamily of regulatory GTPases, including both the ARF and ARF-like (ARL) proteins, control a multitude of cellular functions, including aspects of vesicular traffic, lipid metabolism, mitochondrial architecture, the assembly and dynamics of the microtubule and actin cytoskeletons, and other pathways in cell biology. Considering their general utility, it is perhaps not surprising that increasingly ARF/ARLs have been found in connection to primary cilia. Here, we critically evaluate the current knowledge of the roles four ARF/ARLs (ARF4, ARL3, ARL6, ARL13B) play in cilia and highlight key missing information that would help move our understanding forward. Importantly, these GTPases are themselves regulated by guanine nucleotide exchange factors (GEFs) that activate them and by GTPase-activating proteins (GAPs) that act as both effectors and terminators of signaling. We believe that the identification of the GEFs and GAPs and better models of the actions of these GTPases and their regulators will provide a much deeper understanding and appreciation of the mechanisms that underly ciliary functions and the causes of a number of human ciliopathies.
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Affiliation(s)
- Skylar Fisher
- 1Department of Biochemistry, Emory University
School of Medicine, Atlanta,
Georgia
| | - Damian Kuna
- 2Department of Cell, Developmental and Integrative
Biology, University of Alabama at Birmingham,
Birmingham, Alabama
| | - Tamara Caspary
- 3Department of Human Genetics, Emory
University School of Medicine, Atlanta,
Georgia
| | - Richard A. Kahn
- 1Department of Biochemistry, Emory University
School of Medicine, Atlanta,
Georgia
| | - Elizabeth Sztul
- 2Department of Cell, Developmental and Integrative
Biology, University of Alabama at Birmingham,
Birmingham, Alabama
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28
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Jászai J, Thamm K, Karbanová J, Janich P, Fargeas CA, Huttner WB, Corbeil D. Prominins control ciliary length throughout the animal kingdom: New lessons from human prominin-1 and zebrafish prominin-3. J Biol Chem 2020; 295:6007-6022. [PMID: 32201384 DOI: 10.1074/jbc.ra119.011253] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 03/18/2020] [Indexed: 01/18/2023] Open
Abstract
Prominins (proms) are transmembrane glycoproteins conserved throughout the animal kingdom. They are associated with plasma membrane protrusions, such as primary cilia, as well as extracellular vesicles derived thereof. Primary cilia host numerous signaling pathways affected in diseases known as ciliopathies. Human PROM1 (CD133) is detected in both somatic and cancer stem cells and is also expressed in terminally differentiated epithelial and photoreceptor cells. Genetic mutations in the PROM1 gene result in retinal degeneration by impairing the proper formation of the outer segment of photoreceptors, a modified cilium. Here, we investigated the impact of proms on two distinct examples of ciliogenesis. First, we demonstrate that the overexpression of a dominant-negative mutant variant of human PROM1 (i.e. mutation Y819F/Y828F) significantly decreases ciliary length in Madin-Darby canine kidney cells. These results contrast strongly to the previously observed enhancing effect of WT PROM1 on ciliary length. Mechanistically, the mutation impeded the interaction of PROM1 with ADP-ribosylation factor-like protein 13B, a key regulator of ciliary length. Second, we observed that in vivo knockdown of prom3 in zebrafish alters the number and length of monocilia in the Kupffer's vesicle, resulting in molecular and anatomical defects in the left-right asymmetry. These distinct loss-of-function approaches in two biological systems reveal that prom proteins are critical for the integrity and function of cilia. Our data provide new insights into ciliogenesis and might be of particular interest for investigations of the etiologies of ciliopathies.
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Affiliation(s)
- József Jászai
- Tissue Engineering Laboratories, Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-49, 01307 Dresden, Germany; Institute of Anatomy, Medizinische Fakultät der Technischen Universität Dresden, Fiedlerstrasse 42, 01307 Dresden, Germany.
| | - Kristina Thamm
- Tissue Engineering Laboratories, Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-49, 01307 Dresden, Germany
| | - Jana Karbanová
- Tissue Engineering Laboratories, Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-49, 01307 Dresden, Germany
| | - Peggy Janich
- Tissue Engineering Laboratories, Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-49, 01307 Dresden, Germany
| | - Christine A Fargeas
- Tissue Engineering Laboratories, Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-49, 01307 Dresden, Germany
| | - Wieland B Huttner
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Denis Corbeil
- Tissue Engineering Laboratories, Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-49, 01307 Dresden, Germany.
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29
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Establishing and regulating the composition of cilia for signal transduction. Nat Rev Mol Cell Biol 2020; 20:389-405. [PMID: 30948801 DOI: 10.1038/s41580-019-0116-4] [Citation(s) in RCA: 244] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The primary cilium is a hair-like surface-exposed organelle of the eukaryotic cell that decodes a variety of signals - such as odorants, light and Hedgehog morphogens - by altering the local concentrations and activities of signalling proteins. Signalling within the cilium is conveyed through a diverse array of second messengers, including conventional signalling molecules (such as cAMP) and some unusual intermediates (such as sterols). Diffusion barriers at the ciliary base establish the unique composition of this signalling compartment, and cilia adapt their proteome to signalling demands through regulated protein trafficking. Much progress has been made on the molecular understanding of regulated ciliary trafficking, which encompasses not only exchanges between the cilium and the rest of the cell but also the shedding of signalling factors into extracellular vesicles.
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30
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Gigante ED, Taylor MR, Ivanova AA, Kahn RA, Caspary T. ARL13B regulates Sonic hedgehog signaling from outside primary cilia. eLife 2020; 9:50434. [PMID: 32129762 PMCID: PMC7075693 DOI: 10.7554/elife.50434] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/25/2020] [Indexed: 01/13/2023] Open
Abstract
ARL13B is a regulatory GTPase highly enriched in cilia. Complete loss of Arl13b disrupts cilia architecture, protein trafficking and Sonic hedgehog signaling. To determine whether ARL13B is required within cilia, we knocked in a cilia-excluded variant of ARL13B (V358A) and showed it retains all known biochemical function. We found that ARL13BV358A protein was expressed but could not be detected in cilia, even when retrograde ciliary transport was blocked. We showed Arl13bV358A/V358A mice are viable and fertile with normal Shh signal transduction. However, in contrast to wild type cilia, Arl13bV358A/V358A cells displayed short cilia and lacked ciliary ARL3 and INPP5E. These data indicate that ARL13B's role within cilia can be uncoupled from its function outside of cilia. Furthermore, these data imply that the cilia defects upon complete absence of ARL13B do not underlie the alterations in Shh transduction, which is unexpected given the requirement of cilia for Shh transduction.
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Affiliation(s)
- Eduardo D Gigante
- Neuroscience Graduate Program, Emory University School of MedicineAtlantaUnited States,Department of Human Genetics, Emory University School of MedicineAtlantaUnited States
| | - Megan R Taylor
- Emory College of Arts and Sciences, Emory University School of MedicineAtlantaUnited States
| | - Anna A Ivanova
- Department of Biochemistry, Emory University School of MedicineAtlantaUnited States
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of MedicineAtlantaUnited States
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of MedicineAtlantaUnited States
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31
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ERICH3 in Primary Cilia Regulates Cilium Formation and the Localisations of Ciliary Transport and Sonic Hedgehog Signaling Proteins. Sci Rep 2019; 9:16519. [PMID: 31712586 PMCID: PMC6848114 DOI: 10.1038/s41598-019-52830-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/23/2019] [Indexed: 01/05/2023] Open
Abstract
Intraflagellar transport (IFT) is essential for the formation and function of the microtubule-based primary cilium, which acts as a sensory and signalling device at the cell surface. Consisting of IFT-A/B and BBSome cargo adaptors that associate with molecular motors, IFT transports protein into (anterograde IFT) and out of (retrograde IFT) the cilium. In this study, we identify the mostly uncharacterised ERICH3 protein as a component of the mammalian primary cilium. Loss of ERICH3 causes abnormally short cilia and results in the accumulation of IFT-A/B proteins at the ciliary tip, together with reduced ciliary levels of retrograde transport regulators, ARL13B, INPP5E and BBS5. We also show that ERICH3 ciliary localisations require ARL13B and BBSome components. Finally, ERICH3 loss causes positive (Smoothened) and negative (GPR161) regulators of sonic hedgehog signaling (Shh) to accumulate at abnormally high levels in the cilia of pathway-stimulated cells. Together, these findings identify ERICH3 as a novel component of the primary cilium that regulates cilium length and the ciliary levels of Shh signaling molecules. We propose that ERICH3 functions within retrograde IFT-associated pathways to remove signaling proteins from cilia.
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32
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Kuhns S, Seixas C, Pestana S, Tavares B, Nogueira R, Jacinto R, Ramalho JS, Simpson JC, Andersen JS, Echard A, Lopes SS, Barral DC, Blacque OE. Rab35 controls cilium length, function and membrane composition. EMBO Rep 2019; 20:e47625. [PMID: 31432619 PMCID: PMC6776896 DOI: 10.15252/embr.201847625] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 07/23/2019] [Accepted: 07/31/2019] [Indexed: 12/12/2022] Open
Abstract
Rab and Arl guanine nucleotide-binding (G) proteins regulate trafficking pathways essential for the formation, function and composition of primary cilia, which are sensory devices associated with Sonic hedgehog (Shh) signalling and ciliopathies. Here, using mammalian cells and zebrafish, we uncover ciliary functions for Rab35, a multitasking G protein with endocytic recycling, actin remodelling and cytokinesis roles. Rab35 loss via siRNAs, morpholinos or knockout reduces cilium length in mammalian cells and the zebrafish left-right organiser (Kupffer's vesicle) and causes motile cilia-associated left-right asymmetry defects. Consistent with these observations, GFP-Rab35 localises to cilia, as do GEF (DENND1B) and GAP (TBC1D10A) Rab35 regulators, which also regulate ciliary length and Rab35 ciliary localisation. Mammalian Rab35 also controls the ciliary membrane levels of Shh signalling regulators, promoting ciliary targeting of Smoothened, limiting ciliary accumulation of Arl13b and the inositol polyphosphate 5-phosphatase (INPP5E). Rab35 additionally regulates ciliary PI(4,5)P2 levels and interacts with Arl13b. Together, our findings demonstrate roles for Rab35 in regulating cilium length, function and membrane composition and implicate Rab35 in pathways controlling the ciliary levels of Shh signal regulators.
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Affiliation(s)
- Stefanie Kuhns
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublin 4Ireland
- Department of Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Cecília Seixas
- CEDOCNOVA Medical School|Faculdade de Ciências MédicasUniversidade NOVA de LisboaLisboaPortugal
| | - Sara Pestana
- CEDOCNOVA Medical School|Faculdade de Ciências MédicasUniversidade NOVA de LisboaLisboaPortugal
| | - Bárbara Tavares
- CEDOCNOVA Medical School|Faculdade de Ciências MédicasUniversidade NOVA de LisboaLisboaPortugal
| | - Renata Nogueira
- CEDOCNOVA Medical School|Faculdade de Ciências MédicasUniversidade NOVA de LisboaLisboaPortugal
| | - Raquel Jacinto
- CEDOCNOVA Medical School|Faculdade de Ciências MédicasUniversidade NOVA de LisboaLisboaPortugal
| | - José S Ramalho
- CEDOCNOVA Medical School|Faculdade de Ciências MédicasUniversidade NOVA de LisboaLisboaPortugal
| | - Jeremy C Simpson
- School of Biology and Environmental ScienceUniversity College DublinDublin 4Ireland
| | - Jens S Andersen
- Department of Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | | | - Susana S Lopes
- CEDOCNOVA Medical School|Faculdade de Ciências MédicasUniversidade NOVA de LisboaLisboaPortugal
| | - Duarte C Barral
- CEDOCNOVA Medical School|Faculdade de Ciências MédicasUniversidade NOVA de LisboaLisboaPortugal
| | - Oliver E Blacque
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublin 4Ireland
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33
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DiTirro D, Philbrook A, Rubino K, Sengupta P. The Caenorhabditis elegans Tubby homolog dynamically modulates olfactory cilia membrane morphogenesis and phospholipid composition. eLife 2019; 8:48789. [PMID: 31259686 PMCID: PMC6624019 DOI: 10.7554/elife.48789] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 06/21/2019] [Indexed: 12/13/2022] Open
Abstract
Plasticity in sensory signaling is partly mediated via regulated trafficking of signaling molecules to and from primary cilia. Tubby-related proteins regulate ciliary protein transport; however, their roles in remodeling cilia properties are not fully understood. We find that the C. elegans TUB-1 Tubby homolog regulates membrane morphogenesis and signaling protein transport in specialized sensory cilia. In particular, TUB-1 is essential for sensory signaling-dependent reshaping of olfactory cilia morphology. We show that compromised sensory signaling alters cilia membrane phosphoinositide composition via TUB-1-dependent trafficking of a PIP5 kinase. TUB-1 regulates localization of this lipid kinase at the cilia base in part via localization of the AP-2 adaptor complex subunit DPY-23. Our results describe new functions for Tubby proteins in the dynamic regulation of cilia membrane lipid composition, morphology, and signaling protein content, and suggest that this conserved family of proteins plays a critical role in mediating cilia structural and functional plasticity.
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Affiliation(s)
- Danielle DiTirro
- Department of Biology, Brandeis University, Waltham, United States
| | - Alison Philbrook
- Department of Biology, Brandeis University, Waltham, United States
| | - Kendrick Rubino
- Department of Biology, Brandeis University, Waltham, United States
| | - Piali Sengupta
- Department of Biology, Brandeis University, Waltham, United States
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Hor CH, Goh EL. Small GTPases in hedgehog signalling: emerging insights into the disease mechanisms of Rab23-mediated and Arl13b-mediated ciliopathies. Curr Opin Genet Dev 2019; 56:61-68. [PMID: 31465935 DOI: 10.1016/j.gde.2019.07.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 01/31/2023]
Abstract
Small GTPases are known to have pivotal roles in intracellular trafficking, and several members of the small GTPases superfamily such as Rab10 [1,2•], Rab11 [3-5], Rab34 [6•,7], Rab8 [3,8], Rab23 [9-12], RSG1 [13-15], Arl13b [16-22], and Arl6 [22,23] were recently reported to mediate primary cilia function and/or Hh signalling. Although these functions are implicated in diseases such as ciliopathies, the molecular basis underlying how these small GTPases mediate primary cilia-dependent Hh signalling and pathogenesis of ciliopathies warrants further investigations. Notably, Rab23 and Arl13b have been implicated in ciliopathy-associated human diseases and could regulate Hh signalling cascade in multifaceted manners. This review thus specifically discuss the roles of Rab23 and Arl13b in primary cilia of mammalian systems, their cilia-dependent and cilia-independent modulation of hedgehog signalling pathways and their implications in Carpenter Syndrome and Joubert Syndrome respectively.
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Affiliation(s)
- Catherine Hh Hor
- Neuroscience Academic Clinical Programme, Duke-NUS Medical School, Singapore 169857, Singapore; Department of Chemistry, Research Cluster on Health and Drug Discovery, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong
| | - Eyleen Lk Goh
- Neuroscience Academic Clinical Programme, Duke-NUS Medical School, Singapore 169857, Singapore; Department of Research, National Neuroscience Institute, Singapore 308433, Singapore; Neuroscience and Mental Health Faculty, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore; KK Research Center, KK Women's and Children's Hospital, Singapore 229899, Singapore.
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35
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Zhang P, Kiseleva AA, Korobeynikov V, Liu H, Einarson MB, Golemis EA. Microscopy-Based Automated Live Cell Screening for Small Molecules That Affect Ciliation. Front Genet 2019; 10:75. [PMID: 30809247 PMCID: PMC6379280 DOI: 10.3389/fgene.2019.00075] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 01/28/2019] [Indexed: 12/19/2022] Open
Abstract
The primary monocilium, or cilium, is a single antenna-like organelle that protrudes from the surface of most mammalian cell types, and serves as a signaling hub. Mutations of cilia-associated genes result in severe genetic disorders termed ciliopathies. Among these, the most common is autosomal dominant polycystic kidney disease (ADPKD); less common genetic diseases include Bardet–Biedl syndrome, Joubert syndrome, nephronophthisis, and others. Important signaling cascades with receptor systems localized exclusively or in part at cilia include Sonic Hedgehog (SHH), platelet derived growth factor alpha (PDGFRα), WNTs, polycystins, and others. Changes in ciliation during development or in pathological conditions such as cancer impacts signaling by these proteins. Notably, ciliation status of cells is coupled closely to the cell cycle, with cilia protruding in quiescent (G0) or early G1 cells, declining in S/G2, and absent in M phase, and has been proposed to contribute to cell cycle regulation. Because of this complex biology, the elaborate machinery regulating ciliary assembly and disassembly receives input from many cellular proteins relevant to cell cycle control, development, and oncogenic transformation, making study of genetic factors and drugs influencing ciliation of high interest. One of the most effective tools to investigate the dynamics of the cilia under different conditions is the imaging of live cells. However, developing assays to observe the primary cilium in real time can be challenging, and requires a consideration of multiple details related to the cilia biology. With the dual goals of identifying small molecules that may have beneficial activity through action on human diseases, and of identifying ciliary activities of existing agents that are in common use or development, we here describe creation and evaluation of three autofluorescent cell lines derived from the immortalized retinal pigmented epithelium parental cell line hTERT-RPE1. These cell lines stably express the ciliary-targeted fluorescent proteins L13-Arl13bGFP, pEGFP-mSmo, and tdTomato-MCHR1-N-10. We then describe methods for use of these cell lines in high throughput screening of libraries of small molecule compounds to identify positive and negative regulators of ciliary disassembly.
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Affiliation(s)
- Peishan Zhang
- School of Pharmacy, Jiangsu University, Zhenjiang, China.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Anna A Kiseleva
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, United States.,Department of Biochemistry and Biotechnology, Kazan Federal University, Kazan, Russia
| | - Vladislav Korobeynikov
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, United States.,Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
| | - Hanqing Liu
- School of Pharmacy, Jiangsu University, Zhenjiang, China
| | - Margret B Einarson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Erica A Golemis
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, United States
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Picariello T, Brown JM, Hou Y, Swank G, Cochran DA, King OD, Lechtreck K, Pazour GJ, Witman GB. A global analysis of IFT-A function reveals specialization for transport of membrane-associated proteins into cilia. J Cell Sci 2019; 132:jcs220749. [PMID: 30659111 PMCID: PMC6382014 DOI: 10.1242/jcs.220749] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 01/02/2019] [Indexed: 12/28/2022] Open
Abstract
Intraflagellar transport (IFT), which is essential for the formation and function of cilia in most organisms, is the trafficking of IFT trains (i.e. assemblies of IFT particles) that carry cargo within the cilium. Defects in IFT cause several human diseases. IFT trains contain the complexes IFT-A and IFT-B. To dissect the functions of these complexes, we studied a Chlamydomonas mutant that is null for the IFT-A protein IFT140. The mutation had no effect on IFT-B but destabilized IFT-A, preventing flagella assembly. Therefore, IFT-A assembly requires IFT140. Truncated IFT140, which lacks the N-terminal WD repeats of the protein, partially rescued IFT and supported formation of half-length flagella that contained normal levels of IFT-B but greatly reduced amounts of IFT-A. The axonemes of these flagella had normal ultrastructure and, as investigated by SDS-PAGE, normal composition. However, composition of the flagellar 'membrane+matrix' was abnormal. Analysis of the latter fraction by mass spectrometry revealed decreases in small GTPases, lipid-anchored proteins and cell signaling proteins. Thus, IFT-A is specialized for the import of membrane-associated proteins. Abnormal levels of the latter are likely to account for the multiple phenotypes of patients with defects in IFT140.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Tyler Picariello
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Jason M Brown
- Department of Biology, Salem State University, Salem, MA 01970, USA
| | - Yuqing Hou
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Gregory Swank
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Deborah A Cochran
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Oliver D King
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Karl Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - George B Witman
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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Baehr W, Hanke-Gogokhia C, Sharif A, Reed M, Dahl T, Frederick JM, Ying G. Insights into photoreceptor ciliogenesis revealed by animal models. Prog Retin Eye Res 2018; 71:26-56. [PMID: 30590118 DOI: 10.1016/j.preteyeres.2018.12.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 12/10/2018] [Accepted: 12/18/2018] [Indexed: 12/11/2022]
Abstract
Photoreceptors are polarized neurons, with very specific subcellular compartmentalization and unique requirements for protein expression and trafficking. Each photoreceptor contains an outer segment, the site of photon capture that initiates vision, an inner segment that houses the biosynthetic machinery and a synaptic terminal for signal transmission to downstream neurons. Outer segments and inner segments are connected by a connecting cilium (CC), the equivalent of a transition zone (TZ) of primary cilia. The connecting cilium is part of the basal body/axoneme backbone that stabilizes the outer segment. This report will update the reader on late developments in photoreceptor ciliogenesis and transition zone formation, specifically in mouse photoreceptors, focusing on early events in photoreceptor ciliogenesis. The connecting cilium, an elongated and narrow structure through which all outer segment proteins and membrane components must traffic, functions as a gate that controls access to the outer segment. Here we will review genes and their protein products essential for basal body maturation and for CC/TZ genesis, sorted by phenotype. Emphasis is given to naturally occurring mouse mutants and gene knockouts that interfere with CC/TZ formation and ciliogenesis.
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Affiliation(s)
- Wolfgang Baehr
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA.
| | - Christin Hanke-Gogokhia
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA
| | - Ali Sharif
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA
| | - Michelle Reed
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA
| | - Tiffanie Dahl
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA
| | - Jeanne M Frederick
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA
| | - Guoxin Ying
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA
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38
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ARL3 subcellular localization and its suspected role in autophagy. Biochimie 2018; 154:187-193. [DOI: 10.1016/j.biochi.2018.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/13/2018] [Indexed: 11/23/2022]
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39
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Zhang Y, Huang Y, Srivathsan A, Lim TK, Lin Q, He CY. The unusual flagellar-targeting mechanism and functions of the trypanosome ortholog of the ciliary GTPase Arl13b. J Cell Sci 2018; 131:jcs.219071. [PMID: 30097558 PMCID: PMC6140319 DOI: 10.1242/jcs.219071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/28/2018] [Indexed: 12/11/2022] Open
Abstract
The small GTPase Arl13b is one of the most conserved and ancient ciliary proteins. In human and animals, Arl13b is primarily associated with the ciliary membrane, where it acts as a guanine-nucleotide-exchange factor (GEF) for Arl3 and is implicated in a variety of ciliary and cellular functions. We have identified and characterized Trypanosoma brucei (Tb)Arl13, the sole Arl13b homolog in this evolutionarily divergent, protozoan parasite. TbArl13 has conserved flagellar functions and exhibits catalytic activity towards two different TbArl3 homologs. However, TbArl13 is distinctly associated with the axoneme through a dimerization/docking (D/D) domain. Replacing the D/D domain with a sequence encoding a flagellar membrane protein created a viable alternative to the wild-type TbArl13 in our RNA interference (RNAi)-based rescue assay. Therefore, flagellar enrichment is crucial for TbArl13, but mechanisms to achieve this could be flexible. Our findings thus extend the understanding of the roles of Arl13b and Arl13b–Arl3 pathway in a divergent flagellate of medical importance. This article has an associated First Person interview with the first author of the paper. Highlighted Article: All roads lead to cilia – how the essential flagellar enrichment of Arl13 is achieved in trypanosome cells using a fundamentally different strategy compared with that of animal cells.
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Affiliation(s)
- Yiliu Zhang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Yameng Huang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Amrita Srivathsan
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Teck Kwang Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Qingsong Lin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Cynthia Y He
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117543
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He K, Ma X, Xu T, Li Y, Hodge A, Zhang Q, Torline J, Huang Y, Zhao J, Ling K, Hu J. Axoneme polyglutamylation regulated by Joubert syndrome protein ARL13B controls ciliary targeting of signaling molecules. Nat Commun 2018; 9:3310. [PMID: 30120249 PMCID: PMC6098020 DOI: 10.1038/s41467-018-05867-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 07/02/2018] [Indexed: 12/12/2022] Open
Abstract
Tubulin polyglutamylation is a predominant axonemal post-translational modification. However, if and how axoneme polyglutamylation is essential for primary cilia and contribute to ciliopathies are unknown. Here, we report that Joubert syndrome protein ARL13B controls axoneme polyglutamylation, which is marginally required for cilia stability but essential for cilia signaling. ARL13B interacts with RAB11 effector FIP5 to promote cilia import of glutamylase TTLL5 and TTLL6. Hypoglutamylation caused by a deficient ARL13B-RAB11-FIP5 trafficking pathway shows no effect on ciliogenesis, but promotes cilia disassembly and, importantly, impairs cilia signaling by disrupting the proper anchoring of sensory receptors and trafficking of signaling molecules. Remarkably, depletion of deglutamylase CCP5, the predominant cilia deglutamylase, effectively restores hypoglutamylation-induced cilia defects. Our study reveals a paradigm that tubulin polyglutamylation is a major contributor for cilia signaling and suggests a potential therapeutic strategy by targeting polyglutamylation machinery to promote ciliary targeting of signaling machineries and correct signaling defects in ciliopathies.
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Affiliation(s)
- Kai He
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, 55905, USA
- Mayo Translational PKD Center, Mayo Clinic, Rochester, MN, 55905, USA
| | - Xiaoyu Ma
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, 55905, USA
- Mayo Translational PKD Center, Mayo Clinic, Rochester, MN, 55905, USA
| | - Tao Xu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, 55905, USA
- Mayo Translational PKD Center, Mayo Clinic, Rochester, MN, 55905, USA
| | - Yan Li
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, 55905, USA
- Mayo Translational PKD Center, Mayo Clinic, Rochester, MN, 55905, USA
| | - Allen Hodge
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Qing Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Julia Torline
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Yan Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jian Zhao
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jinghua Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA.
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, 55905, USA.
- Mayo Translational PKD Center, Mayo Clinic, Rochester, MN, 55905, USA.
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41
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Song P, Perkins BD. Developmental expression of the zebrafish Arf-like small GTPase paralogs arl13a and arl13b. Gene Expr Patterns 2018; 29:82-87. [PMID: 30009987 DOI: 10.1016/j.gep.2018.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 12/13/2022]
Abstract
Members of the Arf-like (Arl) family of small GTP-binding proteins regulate a number of cellular functions and play important roles in cilia structure and signaling. The small GTPase Arl13a is a close paralog to Arl13b, a small GTPase required for normal cilia formation that causes Joubert Syndrome when mutated. As mutation of arl13b causes a slow retinal degeneration in zebrafish (Song et al., 2016), we hypothesized that expression of arl13a may provide functional redundancy. We determined the expression domains of arl13a and arl13b during zebrafish development and examined subcellular localization by expression of fluorescence fusion proteins. Both genes are widely expressed during early cell division and gastrulation and Arl13a and Arl13b both localize to microtubules in ciliated and dividing cells of the early zebrafish embryo. Between 2 and 5 days post fertilization (dpf), arl13b is expressed in neural tissues while expression of arl13a is downregulated by 2 dpf and restricted to craniofacial structures. These results indicate that arl13a and arl13b have evolved different roles and that arl13a does not function in the zebrafish retina.
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Affiliation(s)
- Ping Song
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Brian D Perkins
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
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Abstract
Cilia are microtubule-based organelles extending from a basal body at the surface of eukaryotic cells. Cilia regulate cell and fluid motility, sensation and developmental signaling, and ciliary defects cause human diseases (ciliopathies) affecting the formation and function of many tissues and organs. Over the past decade, various Rab and Rab-like membrane trafficking proteins have been shown to regulate cilia-related processes such as basal body maturation, ciliary axoneme extension, intraflagellar transport and ciliary signaling. In this review, we provide a comprehensive overview of Rab protein ciliary associations, drawing on findings from multiple model systems, including mammalian cell culture, mice, zebrafish, C. elegans, trypanosomes, and green algae. We also discuss several emerging mechanistic themes related to ciliary Rab cascades and functional redundancy.
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Affiliation(s)
- Oliver E Blacque
- a School of Biomolecular and Biomedical Science , University College Dublin , Belfield, Dublin , Ireland
| | - Noemie Scheidel
- a School of Biomolecular and Biomedical Science , University College Dublin , Belfield, Dublin , Ireland
| | - Stefanie Kuhns
- a School of Biomolecular and Biomedical Science , University College Dublin , Belfield, Dublin , Ireland
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43
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Quantitative Comparison of Primary Cilia Marker Expression and Length in the Mouse Brain. J Mol Neurosci 2018; 64:397-409. [PMID: 29464516 DOI: 10.1007/s12031-018-1036-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 01/31/2018] [Indexed: 12/12/2022]
Abstract
Primary cilia are small, special cellular organelles that provide important sensory and signaling functions during the development of mammalian organs and coordination of postnatal cellular processes. Dysfunction of primary cilia are thought to be the main cause of ciliopathies, a group of genetic disorders characterized by overlapping developmental defects and prominent neurodevelopmental features. Although, disrupted cilia-linked signaling pathways have been implicated in the regulation of numerous neuronal functions, the precise role of primary cilia in the brain are still unknown. Importantly, studies of recent years have highlighted that different functions of primary cilia are reflected by their diverse morphology and unique signaling components localized in the ciliary membrane. In the present study, we conducted a comparative analysis of the expression pattern, distribution and length of adenylyl cyclase 3, somatostatin receptor 3, and ADP-ribosylation factor-like protein 13B expressing primary cilia in the mouse brain. We show that cilia of neurons and astrocytes display a well characterized distribution and ciliary marker arrangements. Moreover, quantitative comparison of their length, density and occurrence rate revealed that primary cilia exhibit region-specific alternations. In summary, our study provides a comprehensive overview of the cellular organization and morphological traits of primary cilia in regions of the physiological adult mouse brain.
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Functional interplay between cylindromatosis and histone deacetylase 6 in ciliary homeostasis revealed by phenotypic analysis of double knockout mice. Oncotarget 2018; 7:27527-37. [PMID: 27028867 PMCID: PMC5053669 DOI: 10.18632/oncotarget.8374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/16/2016] [Indexed: 01/04/2023] Open
Abstract
Cilia are present in most vertebrate tissues with a wide variety of functions, and abnormalities of cilia are linked to numerous human disorders. However, the molecular events underlying ciliary homeostasis are poorly understood. In this study, we generated double knockout (DKO) mice for the deubiquitinase cylindromatosis (CYLD) and histone deacetylase 6 (HDAC6), two critical ciliary regulators. The Cyld/Hdac6 DKO mice were phenotypically normal and showed no obvious variances in weight or behavior compared with their wild-type littermates. Strikingly, Cyld loss-induced ciliary defects in the testis, trachea, and kidney were abrogated in the Cyld/Hdac6 DKO mice. In addition, the diminished α-tubulin acetylation and impaired sonic hedgehog signaling caused by loss of Cyld were largely restored by simultaneous deletion of Hdac6. We further found by immunofluorescence microscopy a colocalization of CYLD and HDAC6 at the centrosome/basal body and, interestingly, loss of Cyld promoted the localization of HDAC6 at the centrosome/basal body. These findings provide physiological insight into the ciliary role of the CYLD/HDAC6 axis and suggest a functional interplay between these two proteins in ciliary homeostasis.
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45
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Fu W, Wang L, Kim S, Li J, Dynlacht BD. Role for the IFT-A Complex in Selective Transport to the Primary Cilium. Cell Rep 2017; 17:1505-1517. [PMID: 27806291 DOI: 10.1016/j.celrep.2016.10.018] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/05/2016] [Accepted: 10/05/2016] [Indexed: 11/27/2022] Open
Abstract
Intraflagellar transport sub-complex A (IFT-A) is known to regulate retrograde IFT in the cilium. To rigorously assess its other possible roles, we knocked out an IFT-A subunit, IFT121/WDR35, in mammalian cells and screened the localization of more than 50 proteins. We found that Wdr35 regulates cilium assembly by selectively regulating transport of distinct cargoes. Beyond its role in retrograde transport, we show that Wdr35 functions in fusion of Rab8 vesicles at the nascent cilium, protein exit from the cilium, and centriolar satellite organization. Furthermore, we show that Wdr35 is essential for entry of many membrane proteins into the cilium through robust interactions with cargoes and other IFT-A subunits, but the actin network functions to dampen this transport. Wdr35 is mutated in several ciliopathies, and we find that certain disease mutations impair interactions with cargo and other IFT-A subunits. Together, our data link defects in IFT-A mediated cargo transport with disease.
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Affiliation(s)
- Wenxiang Fu
- Department of Pathology and Perlmutter Cancer Center, NYU School of Medicine, Smilow Research Building, 522 First Avenue, New York, NY 10016, USA
| | - Lei Wang
- Department of Pathology and Perlmutter Cancer Center, NYU School of Medicine, Smilow Research Building, 522 First Avenue, New York, NY 10016, USA
| | - Sehyun Kim
- Department of Pathology and Perlmutter Cancer Center, NYU School of Medicine, Smilow Research Building, 522 First Avenue, New York, NY 10016, USA
| | - Ji Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Brian David Dynlacht
- Department of Pathology and Perlmutter Cancer Center, NYU School of Medicine, Smilow Research Building, 522 First Avenue, New York, NY 10016, USA.
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Schmitz F, Burtscher I, Stauber M, Gossler A, Lickert H. A novel Cre-inducible knock-in ARL13B-tRFP fusion cilium reporter. Genesis 2017; 55. [PMID: 28948682 DOI: 10.1002/dvg.23073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 09/14/2017] [Accepted: 09/20/2017] [Indexed: 12/29/2022]
Abstract
Cilia play a major role in the regulation of numerous signaling pathways and are essential for embryonic development. Mutations in genes affecting ciliary function can cause a variety of diseases in humans summarized as ciliopathies. To facilitate the detection and visualization of cilia in a temporal and spatial manner in mouse tissues, we generated a Cre-inducible cilium-specific reporter mouse line expressing an ARL13B-tRFP fusion protein driven by a CMV enhancer/chicken β actin promotor (pCAG) from the Hprt locus. We detected bright and specific ciliary signals by immunostainings of various mono- and multiciliated tissues and by time-lapse live-cell analysis of cultured embryos and organ explant cultures. Additionally, we monitored cilium assembly and disassembly in embryonic fibroblast cells using live-cell imaging. Thus, the ARL13B-tRFP reporter mouse strain is a valuable tool for the investigation of ciliary structure and function in a tissue-specific manner to understand processes, such as ciliary protein trafficking or cilium-dependent signaling in vitro and in vivo.
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Affiliation(s)
- Felizitas Schmitz
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Business Campus Garching, Parkring 11, Garching, D-85748, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, D-85764, Germany
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Business Campus Garching, Parkring 11, Garching, D-85748, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, D-85764, Germany
| | - Michael Stauber
- Institute of Molecular Biology OE5250, Medizinische Hochschule Hannover, Carl-Neuberg-Str.1, Hannover, 30625, Germany
| | - Achim Gossler
- Institute of Molecular Biology OE5250, Medizinische Hochschule Hannover, Carl-Neuberg-Str.1, Hannover, 30625, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Business Campus Garching, Parkring 11, Garching, D-85748, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, D-85764, Germany
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Hanke-Gogokhia C, Wu Z, Sharif A, Yazigi H, Frederick JM, Baehr W. The guanine nucleotide exchange factor Arf-like protein 13b is essential for assembly of the mouse photoreceptor transition zone and outer segment. J Biol Chem 2017; 292:21442-21456. [PMID: 29089384 DOI: 10.1074/jbc.ra117.000141] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 10/24/2017] [Indexed: 01/17/2023] Open
Abstract
Arf-like protein 13b (ARL13b) is a small GTPase that functions as a guanosine nucleotide exchange factor (GEF) for ARL3-GDP. ARL13b is located exclusively in photoreceptor outer segments (OS) presumably anchored to discs by palmitoylation, whereas ARL3 is an inner segment cytoplasmic protein. Hypomorphic mutations affecting the ARL13b G-domain inactivate GEF activity and lead to Joubert syndrome (JS) in humans. However, the molecular mechanisms in ARL13b mutation-induced Joubert syndrome, particularly the function of primary cilia, are still incompletely understood. Because Arl13b germline knockouts in mouse are lethal, we generated retina-specific deletions of ARL13b in which ARL3-GTP formation is impaired. In mouse retArl13b-/- central retina at postnatal day 6 (P6) and older, outer segments were absent, thereby preventing trafficking of outer segment proteins to their destination. Ultrastructure of postnatal day 10 (P10) central retArl13b-/- photoreceptors revealed docking of basal bodies to cell membranes, but mature transition zones and disc structures were absent. Deletion of ARL13b in adult mice via tamoxifen-induced Cre/loxP recombination indicated that axonemes gradually shorten and outer segments progressively degenerate. IFT88, essential for anterograde intraflagellar transport (IFT), was significantly reduced at tamArl13b-/- basal bodies, suggesting impairment of intraflagellar transport. AAV2/8 vector-mediated ARL13b expression in the retArl13b-/- retina rescued ciliogenesis.
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Affiliation(s)
- Christin Hanke-Gogokhia
- From the Department of Ophthalmology, John A. Moran Eye Center, University of Utah Health Science Center, Salt Lake City, Utah 84132
| | - Zhijian Wu
- NEI, National Institutes of Health, Bethesda, Maryland 20892
| | - Ali Sharif
- From the Department of Ophthalmology, John A. Moran Eye Center, University of Utah Health Science Center, Salt Lake City, Utah 84132
| | - Hussein Yazigi
- From the Department of Ophthalmology, John A. Moran Eye Center, University of Utah Health Science Center, Salt Lake City, Utah 84132
| | - Jeanne M Frederick
- From the Department of Ophthalmology, John A. Moran Eye Center, University of Utah Health Science Center, Salt Lake City, Utah 84132
| | - Wolfgang Baehr
- From the Department of Ophthalmology, John A. Moran Eye Center, University of Utah Health Science Center, Salt Lake City, Utah 84132, .,Department of Neurobiology and Anatomy, University of Utah Health Science Center, Salt Lake City, Utah 84132, and.,Department of Biology, University of Utah, Salt Lake City, Utah 84112
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48
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Roy K, Jerman S, Jozsef L, McNamara T, Onyekaba G, Sun Z, Marin EP. Palmitoylation of the ciliary GTPase ARL13b is necessary for its stability and its role in cilia formation. J Biol Chem 2017; 292:17703-17717. [PMID: 28848045 PMCID: PMC5663873 DOI: 10.1074/jbc.m117.792937] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 08/18/2017] [Indexed: 01/01/2023] Open
Abstract
Primary cilia are hairlike extensions of the plasma membrane of most mammalian cells that serve specialized signaling functions. To traffic properly to cilia, multiple cilia proteins rely on palmitoylation, the post-translational attachment of a saturated 16-carbon lipid. However, details regarding the mechanism of how palmitoylation affects cilia protein localization and function are unknown. Herein, we investigated the protein ADP-ribosylation factor-like GTPase 13b (ARL13b) as a model palmitoylated ciliary protein. Using biochemical, cellular, and in vivo studies, we found that ARL13b palmitoylation occurs in vivo in mouse kidneys and that it is required for trafficking to and function within cilia. Myristoylation, a 14-carbon lipid, is shown to largely substitute for palmitoylation with regard to cilia localization of ARL13b, but not with regard to its function within cilia. The functional importance of palmitoylation results in part from a dramatic increase in ARL13b stability, which is not observed with myristoylation. Additional results show that blockade of depalmitoylation slows the degradation of ARL13b that occurs during cilia resorption, raising the possibility that the sensitivity of ARL13b stability to palmitoylation may be exploited by the cell to accelerate degradation of ARL13b by depalmitoylating it. Together, the results show that palmitoylation plays a unique and critical role in controlling the localization, stability, abundance, and thus function of ARL13b. Pharmacological manipulation of protein palmitoylation may be a strategy to alter cilia function.
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Affiliation(s)
- Kasturi Roy
- From the Department of Internal Medicine, Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut 06520-8029 and
| | - Stephanie Jerman
- the Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520-8029
| | - Levente Jozsef
- From the Department of Internal Medicine, Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut 06520-8029 and
| | - Thomas McNamara
- From the Department of Internal Medicine, Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut 06520-8029 and
| | - Ginikanwa Onyekaba
- From the Department of Internal Medicine, Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut 06520-8029 and
| | - Zhaoxia Sun
- the Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520-8029
| | - Ethan P Marin
- From the Department of Internal Medicine, Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut 06520-8029 and
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49
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Abstract
Cilia are microtubule-based organelles extending from a basal body at the surface of eukaryotic cells. Cilia regulate cell and fluid motility, sensation and developmental signaling, and ciliary defects cause human diseases (ciliopathies) affecting the formation and function of many tissues and organs. Over the past decade, various Rab and Rab-like membrane trafficking proteins have been shown to regulate cilia-related processes such as basal body maturation, ciliary axoneme extension, intraflagellar transport and ciliary signaling. In this review, we provide a comprehensive overview of Rab protein ciliary associations, drawing on findings from multiple model systems, including mammalian cell culture, mice, zebrafish, C. elegans, trypanosomes, and green algae. We also discuss several emerging mechanistic themes related to ciliary Rab cascades and functional redundancy.
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Affiliation(s)
- Oliver E Blacque
- a School of Biomolecular and Biomedical Science , University College Dublin , Belfield, Dublin , Ireland
| | - Noemie Scheidel
- a School of Biomolecular and Biomedical Science , University College Dublin , Belfield, Dublin , Ireland
| | - Stefanie Kuhns
- a School of Biomolecular and Biomedical Science , University College Dublin , Belfield, Dublin , Ireland
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50
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Jean F, Pilgrim D. Coordinating the uncoordinated: UNC119 trafficking in cilia. Eur J Cell Biol 2017; 96:643-652. [PMID: 28935136 DOI: 10.1016/j.ejcb.2017.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/25/2017] [Accepted: 09/05/2017] [Indexed: 12/29/2022] Open
Abstract
Constructing the distinct subcellular environment of the cilium relies in a large part upon intraflagellar transport (IFT) proteins, which traffic cargo both to and within the cilium. However, evidence from the last 10 years suggests that IFT alone is not sufficient to generate the ciliary environment. One essential factor is UNC119, which interacts with known IFT molecular switches to transport ciliary cargos. Despite its apparent importance in ciliary trafficking though, human UNC119 mutations have only rarely been associated with diseases commonly linked with ciliopathies. This review will outline the trafficking pathways required for constructing the cilium by highlighting UNC119's role and the complexities involved in ciliary trafficking. Finally, despite important roles for UNC119 in cilia, UNC119 proteins also interact with non-ciliary proteins to affect other cellular processes.
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