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Ewerling A, May-Simera HL. Evolutionary trajectory for nuclear functions of ciliary transport complex proteins. Microbiol Mol Biol Rev 2024:e0000624. [PMID: 38995044 DOI: 10.1128/mmbr.00006-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024] Open
Abstract
SUMMARYCilia and the nucleus were two defining features of the last eukaryotic common ancestor. In early eukaryotic evolution, these structures evolved through the diversification of a common membrane-coating ancestor, the protocoatomer. While in cilia, the descendants of this protein complex evolved into parts of the intraflagellar transport complexes and BBSome, the nucleus gained its selectivity by recruiting protocoatomer-like proteins to the nuclear envelope to form the selective nuclear pore complexes. Recent studies show a growing number of proteins shared between the proteomes of the respective organelles, and it is currently unknown how ciliary transport proteins could acquire nuclear functions and vice versa. The nuclear functions of ciliary proteins are still observable today and remain relevant for the understanding of the disease mechanisms behind ciliopathies. In this work, we review the evolutionary history of cilia and nucleus and their respective defining proteins and integrate current knowledge into theories for early eukaryotic evolution. We postulate a scenario where both compartments co-evolved and that fits current models of eukaryotic evolution, explaining how ciliary proteins and nucleoporins acquired their dual functions.
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Affiliation(s)
- Alexander Ewerling
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
| | - Helen Louise May-Simera
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
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2
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Chen Y, Zhang Y, Zhou X. Non-classical functions of nuclear pore proteins in ciliopathy. Front Mol Biosci 2023; 10:1278976. [PMID: 37908226 PMCID: PMC10614291 DOI: 10.3389/fmolb.2023.1278976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023] Open
Abstract
Nucleoporins (NUPs) constitute integral nuclear pore protein (NPC) elements. Although traditional NUP functions have been extensively researched, evidence of additional vital non-NPC roles, referred to herein as non-classical NUP functions, is also emerging. Several NUPs localise at the ciliary base. Indeed, Nup188, Nup93 or Nup205 knockdown results in cilia loss, impacting cardiac left-right patterning in models and cell lines. Genetic variants of Nup205 and Nup188 have been identified in patients with congenital heart disease and situs inversus totalis or heterotaxy, a prevalent human ciliopathy. These findings link non-classical NUP functions to human diseases. This mini-review summarises pivotal NUP interactions with NIMA-related kinases or nephronophthisis proteins that regulate ciliary function and explores other NUPs potentially implicated in cilia-related disorders. Overall, elucidating the non-classical roles of NUPs will enhance comprehension of ciliopathy aetiology.
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Affiliation(s)
- Yan Chen
- Obstetrics and Gynecology Hospital of Fudan University, Fudan University Shanghai Medical College, Shanghai, China
| | - Yuan Zhang
- Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiangyu Zhou
- Obstetrics and Gynecology Hospital of Fudan University, Fudan University Shanghai Medical College, Shanghai, China
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3
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DeMars KM, Ross MR, Starr A, McIntyre JC. Neuronal primary cilia integrate peripheral signals with metabolic drives. Front Physiol 2023; 14:1150232. [PMID: 37064917 PMCID: PMC10090425 DOI: 10.3389/fphys.2023.1150232] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
Neuronal primary cilia have recently emerged as important contributors to the central regulation of energy homeostasis. As non-motile, microtubule-based organelles, primary cilia serve as signaling antennae for metabolic status. The impairment of ciliary structure or function can produce ciliopathies for which obesity is a hallmark phenotype and global ablation of cilia induces non-syndromic adiposity in mouse models. This organelle is not only a hub for metabolic signaling, but also for catecholamine neuromodulation that shapes neuronal circuitry in response to sensory input. The objective of this review is to highlight current research investigating the mechanisms of primary cilium-regulated metabolic drives for maintaining energy homeostasis.
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Affiliation(s)
- Kelly M. DeMars
- Department of Neuroscience, University of Florida, Gainesville, FL, United States
| | - Madeleine R. Ross
- Department of Neuroscience, University of Florida, Gainesville, FL, United States
- Summer Neuroscience Internship Program, University of Florida, Gainesville, FL, United States
| | - Alana Starr
- Department of Neuroscience, University of Florida, Gainesville, FL, United States
| | - Jeremy C. McIntyre
- Department of Neuroscience, University of Florida, Gainesville, FL, United States
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4
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Damizia M, Altieri L, Lavia P. Non-transport roles of nuclear import receptors: In need of the right balance. Front Cell Dev Biol 2022; 10:1041938. [PMID: 36438555 PMCID: PMC9686011 DOI: 10.3389/fcell.2022.1041938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 10/21/2022] [Indexed: 11/12/2023] Open
Abstract
Nuclear import receptors ensure the recognition and transport of proteins across the nuclear envelope into the nucleus. In addition, as diverse processes as mitosis, post-translational modifications at mitotic exit, ciliogenesis, and phase separation, all share a common need for regulation by nuclear import receptors - particularly importin beta-1 and importin beta-2/transportin - independent on nuclear import. In particular, 1) nuclear import receptors regulate the mitotic spindle after nuclear envelope breakdown, 2) they shield cargoes from unscheduled ubiquitination, regulating their timely proteolysis; 3) they regulate ciliary factors, crucial to cell communications and tissue architecture during development; and 4) they prevent phase separation of toxic proteins aggregates in neurons. The balance of nuclear import receptors to cargoes is critical in all these processes, albeit in opposite directions: overexpression of import receptors, as often found in cancer, inhibits cargoes and impairs downstream processes, motivating the therapeutic design of specific inhibitors. On the contrary, elevated expression is beneficial in neuronal contexts, where nuclear import receptors are regarded as potential therapeutic tools in counteracting the formation of aggregates that may cause neurodegeneration. This paradox demonstrates the amplitude of nuclear import receptors-dependent functions in different contexts and adds complexity in considering their therapeutic implications.
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Affiliation(s)
- Michela Damizia
- Department of Cellular, Computational and Integrated Biology (CIBIO), University of Trento, Trento, Italy
| | - Ludovica Altieri
- Institute of Molecular Biology and Pathology (IBPM), CNR National Research Council of Italy, Sapienza University of Rome, Rome, Italy
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | - Patrizia Lavia
- Institute of Molecular Biology and Pathology (IBPM), CNR National Research Council of Italy, Sapienza University of Rome, Rome, Italy
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Rome, Italy
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5
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Gupta N, D'Acierno M, Zona E, Capasso G, Zacchia M. Bardet-Biedl syndrome: The pleiotropic role of the chaperonin-like BBS6, 10, and 12 proteins. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:9-19. [PMID: 35373910 PMCID: PMC9325507 DOI: 10.1002/ajmg.c.31970] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/08/2022] [Accepted: 03/27/2022] [Indexed: 12/11/2022]
Abstract
Bardet–Biedl syndrome (BBS) is a rare pleiotropic disorder known as a ciliopathy. Despite significant genetic heterogeneity, BBS1 and BBS10 are responsible for major diagnosis in western countries. It is well established that eight BBS proteins, namely BBS1, 2, 4, 5, 7, 8, 9, and 18, form the BBSome, a multiprotein complex serving as a regulator of ciliary membrane protein composition. Less information is available for BBS6, BBS10, and BBS12, three proteins showing sequence homology with the CCT/TRiC family of group II chaperonins. Even though their chaperonin function is debated, scientific evidence demonstrated that they are required for initial BBSome assembly in vitro. Recent studies suggest that genotype may partially predict clinical outcomes. Indeed, patients carrying truncating mutations in any gene show the most severe phenotype; moreover, mutations in chaperonin‐like BBS proteins correlated with severe kidney impairment. This study is a critical review of the literature on genetics, expression level, cellular localization and function of BBS proteins, focusing primarily on the chaperonin‐like BBS proteins, and aiming to provide some clues to understand the pathomechanisms of disease in this setting.
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Affiliation(s)
- Neha Gupta
- Unit of Nephrology, Department of Translational Medical Sciences, University of Campania L. Vanvitelli, Naples, Italy.,BioGem S.C.A.R.L., Benevento, Benevento Province, Italy
| | - Mariavittoria D'Acierno
- Unit of Nephrology, Department of Translational Medical Sciences, University of Campania L. Vanvitelli, Naples, Italy.,BioGem S.C.A.R.L., Benevento, Benevento Province, Italy
| | - Enrica Zona
- Unit of Nephrology, Department of Translational Medical Sciences, University of Campania L. Vanvitelli, Naples, Italy
| | | | - Miriam Zacchia
- Unit of Nephrology, Department of Translational Medical Sciences, University of Campania L. Vanvitelli, Naples, Italy
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6
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McMahon DB, Kuek LE, Johnson ME, Johnson PO, Horn RL, Carey RM, Adappa ND, Palmer JN, Lee RJ. The bitter end: T2R bitter receptor agonists elevate nuclear calcium and induce apoptosis in non-ciliated airway epithelial cells. Cell Calcium 2022; 101:102499. [PMID: 34839223 PMCID: PMC8752513 DOI: 10.1016/j.ceca.2021.102499] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/21/2021] [Accepted: 10/31/2021] [Indexed: 01/03/2023]
Abstract
Bitter taste receptors (T2Rs) localize to airway motile cilia and initiate innate immune responses in retaliation to bacterial quorum sensing molecules. Activation of cilia T2Rs leads to calcium-driven NO production that increases cilia beating and directly kills bacteria. Several diseases, including chronic rhinosinusitis, COPD, and cystic fibrosis, are characterized by loss of motile cilia and/or squamous metaplasia. To understand T2R function within the altered landscape of airway disease, we studied T2Rs in non-ciliated airway cell lines and primary cells. Several T2Rs localize to the nucleus in de-differentiated cells that typically localize to cilia in differentiated cells. As cilia and nuclear import utilize shared proteins, some T2Rs may target to the nucleus in the absence of motile cilia. T2R agonists selectively elevated nuclear and mitochondrial calcium through a G-protein-coupled receptor phospholipase C mechanism. Additionally, T2R agonists decreased nuclear cAMP, increased nitric oxide, and increased cGMP, consistent with T2R signaling. Furthermore, exposure to T2R agonists led to nuclear calcium-induced mitochondrial depolarization and caspase activation. T2R agonists induced apoptosis in primary bronchial and nasal cells differentiated at air-liquid interface but then induced to a squamous phenotype by apical submersion. Air-exposed well-differentiated cells did not die. This may be a last-resort defense against bacterial infection. However, it may also increase susceptibility of de-differentiated or remodeled epithelia to damage by bacterial metabolites. Moreover, the T2R-activated apoptosis pathway occurs in airway cancer cells. T2Rs may thus contribute to microbiome-tumor cell crosstalk in airway cancers. Targeting T2Rs may be useful for activating cancer cell apoptosis while sparing surrounding tissue.
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Affiliation(s)
- Derek B. McMahon
- Department of Otorhinolaryngology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA,Correspondence: Derek B. McMahon, PhD or Robert J. Lee, PhD, Department of Otorhinolaryngology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA, 215-573-9766, (D.B.M.) or (R.J.L)
| | - Li Eon Kuek
- Department of Otorhinolaryngology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Madeline E. Johnson
- Department of Otorhinolaryngology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Paige O. Johnson
- Department of Otorhinolaryngology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Rachel L.J. Horn
- Department of Otorhinolaryngology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ryan M. Carey
- Department of Otorhinolaryngology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Nithin D. Adappa
- Department of Otorhinolaryngology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - James N. Palmer
- Department of Otorhinolaryngology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Robert J. Lee
- Department of Otorhinolaryngology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA,Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA,Correspondence: Derek B. McMahon, PhD or Robert J. Lee, PhD, Department of Otorhinolaryngology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA, 215-573-9766, (D.B.M.) or (R.J.L)
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7
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Markiewicz Ł, Uśpieński T, Baran B, Niedziółka SM, Niewiadomski P. Xpo7 negatively regulates Hedgehog signaling by exporting Gli2 from the nucleus. Cell Signal 2021; 80:109907. [PMID: 33383157 DOI: 10.1016/j.cellsig.2020.109907] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/22/2020] [Accepted: 12/27/2020] [Indexed: 01/01/2023]
Abstract
Dynamic bidirectional transport between the nucleus and the cytoplasm is critical for the regulation of many transcription factors, whose levels inside the nucleus must be tightly controlled. Efficient shuttling across the nuclear membrane is especially crucial with regard to the Hedgehog (Hh) pathway, where the transcriptional signal depends on the fine balance between the amounts of Gli protein activator and repressor forms in the nucleus. The nuclear export machinery prevents the unchecked nuclear accumulation of Gli proteins, but the mechanistic insight into this process is limited. We show that the atypical exportin Xpo7 functions as a major nuclear export receptor that actively excludes Gli2 from the nucleus and controls the outcome of Hh signaling. We show that Xpo7 interacts with several domains of Gli2 and that this interaction is modulated by SuFu, a key negative regulator of Hh signaling. Our data pave the way for a more complete understanding of the nuclear shuttling of Gli proteins and the regulation of their transcriptional activity.
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Affiliation(s)
- Łukasz Markiewicz
- Laboratory of Molecular and Cellular Signaling, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Tomasz Uśpieński
- Laboratory of Molecular and Cellular Signaling, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Brygida Baran
- Laboratory of Molecular and Cellular Signaling, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Sylwia M Niedziółka
- Laboratory of Molecular and Cellular Signaling, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Paweł Niewiadomski
- Laboratory of Molecular and Cellular Signaling, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.
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8
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Baluška F, Lyons S. Archaeal Origins of Eukaryotic Cell and Nucleus. Biosystems 2021; 203:104375. [PMID: 33549602 DOI: 10.1016/j.biosystems.2021.104375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/29/2021] [Accepted: 01/29/2021] [Indexed: 01/12/2023]
Abstract
Symbiosis is a major evolutionary force, especially at the cellular level. Here we discuss several older and new discoveries suggesting that besides mitochondria and plastids, eukaryotic nuclei also have symbiotic origins. We propose an archaea-archaea scenario for the evolutionary origin of the eukaryotic cells. We suggest that two ancient archaea-like cells, one based on the actin cytoskeleton and another one based on the tubulin-centrin cytoskeleton, merged together to form the first nucleated eukaryotic cell. This archaeal endosymbiotic origin of eukaryotic cells and their nuclei explains several features of eukaryotic cells which are incompatible with the currently preferred autogenous scenarios of eukaryogenesis.
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Affiliation(s)
| | - Sherrie Lyons
- Union College, 130 N. College, St. - Schenectady, NY, 12305, USA.
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9
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Craft Van De Weghe J, Harris JA, Kubo T, Witman GB, Lechtreck KF. Diffusion rather than intraflagellar transport likely provides most of the tubulin required for axonemal assembly in Chlamydomonas. J Cell Sci 2020; 133:jcs.249805. [PMID: 32801124 DOI: 10.1242/jcs.249805] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/31/2020] [Indexed: 12/18/2022] Open
Abstract
Tubulin enters the cilium by diffusion and motor-based intraflagellar transport (IFT). However, the respective contribution of each route in providing tubulin for axonemal assembly remains unknown. Using Chlamydomonas, we attenuated IFT-based tubulin transport of GFP-β-tubulin by altering the IFT74N-IFT81N tubulin-binding module and the C-terminal E-hook of tubulin. E-hook-deficient GFP-β-tubulin was incorporated into the axonemal microtubules, but its transport frequency by IFT was reduced by ∼90% in control cells and essentially abolished when the tubulin-binding site of IFT81 was incapacitated. Despite the strong reduction in IFT, the proportion of E-hook-deficient GFP-β-tubulin in the axoneme was only moderately reduced. In vivo imaging showed more GFP-β-tubulin particles entering cilia by diffusion than by IFT. Extrapolated to endogenous tubulin, the data indicate that diffusion provides most of the tubulin required for axonemal assembly. We propose that IFT of tubulin is nevertheless needed for ciliogenesis, because it augments the tubulin pool supplied to the ciliary tip by diffusion, thus ensuring that free tubulin there is maintained at the critical concentration for plus-end microtubule assembly during rapid ciliary growth.
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Affiliation(s)
| | - J Aaron Harris
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Tomohiro Kubo
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - George B Witman
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Karl F Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
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10
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Candelori A, Yamamoto TG, Iwamoto M, Montani M, Amici A, Vallesi A. Subcellular Targeting of the Euplotes raikovi Kinase Er-MAPK1, as Revealed by Expression in Different Cell Systems. Front Cell Dev Biol 2019; 7:244. [PMID: 31681773 PMCID: PMC6811501 DOI: 10.3389/fcell.2019.00244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/04/2019] [Indexed: 11/13/2022] Open
Abstract
In the ciliate Euplotes raikovi, a 631-amino acid Er-MAPK1 protein kinase was found to localize in nucleoli of the transcriptionally active nucleus (macronucleus) and act as a key component of an autocrine, cell-growth promoting self-signaling mechanism. While its 283-amino acid N-terminal domain includes all the structural specificities of the mitogen-activated protein kinases required for a catalytic function, the 348-amino acid C-terminal domain is structurally unique with undetermined functions. By expressing the two Er-MAPK1 domains tagged with the green fluorescent protein in mammalian fibroblasts, the yeast Schizosaccharomyces pombe and the ciliate Tetrahymena thermophila, evidence was obtained that the C-terminal domain contains all the sequence information responsible for the Er-MAPK1 subcellular localization. However, in fibroblasts and S. pombe this information determined a nucleolar localization of the GFP-tagged C-terminal domain, and a ciliary localization in T. thermophila. In the light of these findings, the Er-MAPK1 localization in E. raikovi was re-examined via immunoreactions and shown to be ciliary besides that nuclear, as is the case for the mammalian intestinal cell kinase with which the Er-MAPK1 N-terminal domain shares a strong sequence identity and a catalytic function.
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Affiliation(s)
- Annalisa Candelori
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Takaharu G Yamamoto
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Japan
| | - Masaaki Iwamoto
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Japan
| | - Maura Montani
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Augusto Amici
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Adriana Vallesi
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
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11
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The Nuclear Arsenal of Cilia. Dev Cell 2019; 49:161-170. [DOI: 10.1016/j.devcel.2019.03.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/07/2018] [Accepted: 03/08/2019] [Indexed: 12/31/2022]
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12
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Hoff S, Epting D, Falk N, Schroda S, Braun DA, Halbritter J, Hildebrandt F, Kramer-Zucker A, Bergmann C, Walz G, Lienkamp SS. The nucleoside-diphosphate kinase NME3 associates with nephronophthisis proteins and is required for ciliary function during renal development. J Biol Chem 2018; 293:15243-15255. [PMID: 30111592 PMCID: PMC6166740 DOI: 10.1074/jbc.ra117.000847] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 08/07/2018] [Indexed: 01/12/2023] Open
Abstract
Nephronophthisis (NPH) is an autosomal recessive renal disease leading to kidney failure in children and young adults. The protein products of the corresponding genes (NPHPs) are localized in primary cilia or their appendages. Only about 70% of affected individuals have a mutation in one of 100 renal ciliopathy genes, and no unifying pathogenic mechanism has been identified. Recently, some NPHPs, including NIMA-related kinase 8 (NEK8) and centrosomal protein 164 (CEP164), have been found to act in the DNA-damage response pathway and to contribute to genome stability. Here, we show that NME/NM23 nucleoside-diphosphate kinase 3 (NME3) that has recently been found to facilitate DNA-repair mechanisms binds to several NPHPs, including NEK8, CEP164, and ankyrin repeat and sterile α motif domain-containing 6 (ANKS6). Depletion of nme3 in zebrafish and Xenopus resulted in typical ciliopathy-associated phenotypes, such as renal malformations and left-right asymmetry defects. We further found that endogenous NME3 localizes to the basal body and that it associates also with centrosomal proteins, such as NEK6, which regulates cell cycle arrest after DNA damage. The ciliopathy-typical manifestations of NME3 depletion in two vertebrate in vivo models, the biochemical association of NME3 with validated NPHPs, and its localization to the basal body reveal a role for NME3 in ciliary function. We conclude that mutations in the NME3 gene may aggravate the ciliopathy phenotypes observed in humans.
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Affiliation(s)
- Sylvia Hoff
- From the Department of Medicine, Renal Division, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Daniel Epting
- From the Department of Medicine, Renal Division, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Nathalie Falk
- From the Department of Medicine, Renal Division, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Sophie Schroda
- From the Department of Medicine, Renal Division, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Daniela A Braun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Jan Halbritter
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Albrecht Kramer-Zucker
- From the Department of Medicine, Renal Division, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Carsten Bergmann
- From the Department of Medicine, Renal Division, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Center for Human Genetics, Bioscientia, 55218 Ingelheim, Germany, and
| | - Gerd Walz
- From the Department of Medicine, Renal Division, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Center for Biological Signaling Studies (BIOSS), 79104 Freiburg, Germany
| | - Soeren S Lienkamp
- From the Department of Medicine, Renal Division, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany,
- Center for Biological Signaling Studies (BIOSS), 79104 Freiburg, Germany
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13
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Gilder AL, Chapin HC, Padovano V, Hueschen CL, Rajendran V, Caplan MJ. Newly synthesized polycystin-1 takes different trafficking pathways to the apical and ciliary membranes. Traffic 2018; 19:933-945. [PMID: 30125442 PMCID: PMC6237641 DOI: 10.1111/tra.12612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 08/15/2018] [Accepted: 08/15/2018] [Indexed: 12/26/2022]
Abstract
Mutations in the genes encoding polycystin-1 (PC1) and polycystin 2 (PC2) cause autosomal dominant polycystic kidney disease. These transmembrane proteins colocalize in the primary cilia of renal epithelial cells, where they may participate in sensory processes. PC1 is also found in the apical membrane when expressed in cultured epithelial cells. PC1 undergoes autocatalytic cleavage, producing an extracellular N-terminal fragment that remains noncovalently attached to the transmembrane C-terminus. Exposing cells to alkaline solutions elutes the N-terminal fragment while the C-terminal fragment is retained in the cell membrane. Utilizing this observation, we developed a "strip-recovery" synchronization protocol to study PC1 trafficking in polarized LLC-PK1 renal epithelial cells. Following alkaline strip, a new cohort of PC1 repopulates the cilia within 30 minutes, while apical delivery of PC1 was not detectable until 3 hours. Brefeldin A (BFA) blocked apical PC1 delivery, while ciliary delivery of PC1 was BFA insensitive. Incubating cells at 20°C to block trafficking out of the trans-Golgi network also inhibits apical but not ciliary delivery. These results suggest that newly synthesized PC1 takes distinct pathways to the ciliary and apical membranes. Ciliary PC1 appears to by-pass BFA sensitive Golgi compartments, while apical delivery of PC1 traverses these compartments.
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Affiliation(s)
- Allison L Gilder
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut
| | - Hannah C Chapin
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut
| | - Valeria Padovano
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut
| | - Christina L Hueschen
- Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut
| | - Vanathy Rajendran
- Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut
| | - Michael J Caplan
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut.,Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut
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14
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Scott CA, Marsden AN, Rebagliati MR, Zhang Q, Chamling X, Searby CC, Baye LM, Sheffield VC, Slusarski DC. Nuclear/cytoplasmic transport defects in BBS6 underlie congenital heart disease through perturbation of a chromatin remodeling protein. PLoS Genet 2017; 13:e1006936. [PMID: 28753627 PMCID: PMC5550010 DOI: 10.1371/journal.pgen.1006936] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 08/09/2017] [Accepted: 07/20/2017] [Indexed: 01/31/2023] Open
Abstract
Mutations in BBS6 cause two clinically distinct syndromes, Bardet-Biedl syndrome (BBS), a syndrome caused by defects in cilia transport and function, as well as McKusick-Kaufman syndrome, a genetic disorder characterized by congenital heart defects. Congenital heart defects are rare in BBS, and McKusick-Kaufman syndrome patients do not develop retinitis pigmentosa. Therefore, the McKusick-Kaufman syndrome allele may highlight cellular functions of BBS6 distinct from the presently understood functions in the cilia. In support, we find that the McKusick-Kaufman syndrome disease-associated allele, BBS6H84Y; A242S, maintains cilia function. We demonstrate that BBS6 is actively transported between the cytoplasm and nucleus, and that BBS6H84Y; A242S, is defective in this transport. We developed a transgenic zebrafish with inducible bbs6 to identify novel binding partners of BBS6, and we find interaction with the SWI/SNF chromatin remodeling protein Smarcc1a (SMARCC1 in humans). We demonstrate that through this interaction, BBS6 modulates the sub-cellular localization of SMARCC1 and find, by transcriptional profiling, similar transcriptional changes following smarcc1a and bbs6 manipulation. Our work identifies a new function for BBS6 in nuclear-cytoplasmic transport, and provides insight into the disease mechanism underlying the congenital heart defects in McKusick-Kaufman syndrome patients. To understand how mutations in one gene can cause two distinct human syndromes (McKusick-Kaufman syndrome and Bardet-Bield syndrome), we investigated the cellular functions of the implicated gene BBS6. We found that BBS6 is actively transported between the cytoplasm and nucleus, and this interaction is disrupted in McKusick-Kaufman syndrome, but not Bardet-Biedl syndrome. We find that by manipulating BBS6, we can affect another protein, SMARCC1, which has a direct role in regulating gene expression. When we profiled these changes in gene expression, we find that many genes, which can be directly linked to the symptoms of McKusick-Kaufman syndrome, are affected. Therefore, our data support that the nuclear-cytoplasmic transport defect of BBS6, through disruption of proteins controlling gene expression, cause the symptoms observed in McKusick-Kaufman syndrome patients.
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Affiliation(s)
- Charles Anthony Scott
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Autumn N. Marsden
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
| | - Michael R. Rebagliati
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Qihong Zhang
- Department of Pediatrics and Ophthalmology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Xitiz Chamling
- Department of Pediatrics and Ophthalmology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Charles C. Searby
- Department of Pediatrics and Ophthalmology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Lisa M. Baye
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Val C. Sheffield
- Department of Pediatrics and Ophthalmology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Wynn Institute for Vision Research University of Iowa, Iowa City, Iowa, United States of America
| | - Diane C. Slusarski
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
- Wynn Institute for Vision Research University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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15
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Rout MP, Field MC. The Evolution of Organellar Coat Complexes and Organization of the Eukaryotic Cell. Annu Rev Biochem 2017; 86:637-657. [DOI: 10.1146/annurev-biochem-061516-044643] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Mark C. Field
- Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
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16
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Lechtreck KF, Van De Weghe JC, Harris JA, Liu P. Protein transport in growing and steady-state cilia. Traffic 2017; 18:277-286. [PMID: 28248449 DOI: 10.1111/tra.12474] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 02/22/2017] [Accepted: 02/22/2017] [Indexed: 12/18/2022]
Abstract
Cilia and eukaryotic flagella are threadlike cell extensions with motile and sensory functions. Their assembly requires intraflagellar transport (IFT), a bidirectional motor-driven transport of protein carriers along the axonemal microtubules. IFT moves ample amounts of structural proteins including tubulin into growing cilia likely explaining its critical role for assembly. IFT continues in non-growing cilia contributing to a variety of processes ranging from axonemal maintenance and the export of non-ciliary proteins to cell locomotion and ciliary signaling. Here, we discuss recent data on cues regulating the type, amount and timing of cargo transported by IFT. A regulation of IFT-cargo interactions is critical to establish, maintain and adjust ciliary length, protein composition and function.
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Affiliation(s)
- Karl F Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, Georgia
| | | | | | - Peiwei Liu
- Department of Cellular Biology, University of Georgia, Athens, Georgia
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17
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Abstract
This is a history of cilia research before and after the discovery of intraflagellar transport (IFT) and the link between primary cilia ciliogenesis and polycystic kidney disease (PKD). Before IFT, ca. the beginning of the new millennium, although sensory and primary cilia were well described, research was largely focused on motile cilia, their structure, movement, and biogenesis. After IFT and the link to PKD, although work on motile cilia has continued to progress, research on primary cilia has exploded, leading to new insights into the role of cilia in cell signaling and development. Genomics, proteomics, and new imaging techniques have unified the field and pointed out the critical role of cilia as a restricted cell organellar compartment, functionally integrated with other cell organelles including the autophagosome and the nucleus.
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Affiliation(s)
- Peter Satir
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY USA
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18
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Tilston-Lünel AM, Haley KE, Schlecht NF, Wang Y, Chatterton ALD, Moleirinho S, Watson A, Hundal HS, Prystowsky MB, Gunn-Moore FJ, Reynolds PA. Crumbs 3b promotes tight junctions in an ezrin-dependent manner in mammalian cells. J Mol Cell Biol 2016; 8:439-455. [PMID: 27190314 PMCID: PMC5055084 DOI: 10.1093/jmcb/mjw020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/19/2016] [Accepted: 01/25/2016] [Indexed: 01/30/2023] Open
Abstract
Crumbs 3 (CRB3) is a component of epithelial junctions, which has been implicated in apical-basal polarity, apical identity, apical stability, cell adhesion, and cell growth. CRB3 undergoes alternative splicing to yield two variants: CRB3a and CRB3b. Here, we describe novel data demonstrating that, as with previous studies on CRB3a, CRB3b also promotes the formation of tight junctions (TJs). However, significantly we demonstrate that the 4.1-ezrin-radixin-moesin-binding motif of CRB3b is required for CRB3b functionality and that ezrin binds to the FBM of CRB3b. Furthermore, we show that ezrin contributes to CRB3b functionality and the correct distribution of TJ proteins. We demonstrate that both CRB3 isoforms are required for the production of functionally mature TJs and also the localization of ezrin to the plasma membrane. Finally, we demonstrate that reduced CRB3b expression in head and neck squamous cell carcinoma (HNSCC) correlates with cytoplasmic ezrin, a biomarker for aggressive disease, and shows evidence that while CRB3a expression has no effect, low CRB3b and high cytoplasmic ezrin expression combined may be prognostic for HNSCC.
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Affiliation(s)
- Andrew M Tilston-Lünel
- Medical and Biological Sciences Building, School of Biology, University of St Andrews, St Andrews, KY16 9TF, UK
| | - Kathryn E Haley
- Medical and Biological Sciences Building, School of Medicine, University of St Andrews, St Andrews, KY16 9TF, UK
| | - Nicolas F Schlecht
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Yanhua Wang
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Abigail L D Chatterton
- Medical and Biological Sciences Building, School of Medicine, University of St Andrews, St Andrews, KY16 9TF, UK
| | - Susana Moleirinho
- Medical and Biological Sciences Building, School of Biology, University of St Andrews, St Andrews, KY16 9TF, UK.,Medical and Biological Sciences Building, School of Medicine, University of St Andrews, St Andrews, KY16 9TF, UK.,Present address: Scripps Research Institute, Jupiter, FL, USA
| | - Ailsa Watson
- Department of Pathology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Harinder S Hundal
- Department of Pathology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | | | - Frank J Gunn-Moore
- Medical and Biological Sciences Building, School of Biology, University of St Andrews, St Andrews, KY16 9TF, UK
| | - Paul A Reynolds
- Medical and Biological Sciences Building, School of Medicine, University of St Andrews, St Andrews, KY16 9TF, UK
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19
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Del Viso F, Huang F, Myers J, Chalfant M, Zhang Y, Reza N, Bewersdorf J, Lusk CP, Khokha MK. Congenital Heart Disease Genetics Uncovers Context-Dependent Organization and Function of Nucleoporins at Cilia. Dev Cell 2016; 38:478-92. [PMID: 27593162 PMCID: PMC5021619 DOI: 10.1016/j.devcel.2016.08.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 07/07/2016] [Accepted: 08/08/2016] [Indexed: 01/21/2023]
Abstract
Human genomics is identifying candidate genes for congenital heart disease (CHD), but discovering the underlying mechanisms remains challenging. In a patient with CHD and heterotaxy (Htx), a disorder of left-right patterning, we previously identified a duplication in Nup188. However, a mechanism to explain how a component of the nuclear pore complex (NPC) could cause Htx/CHD was undefined. Here, we show that knockdown of Nup188 or its binding partner Nup93 leads to a loss of cilia during embryonic development while leaving NPC function largely intact. Many data, including the localization of endogenous Nup188/93 at cilia bases, support their direct role at cilia. Super-resolution imaging of Nup188 shows two barrel-like structures with dimensions and organization incompatible with an NPC-like ring, arguing against a proposed "ciliary pore complex." We suggest that the nanoscale organization and function of nucleoporins are context dependent in a way that is required for the structure of the heart.
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Affiliation(s)
- Florencia Del Viso
- Program in Vertebrate Developmental Biology, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Fang Huang
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Weldon School of Biomedical Engineering, College of Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Jordan Myers
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Madeleine Chalfant
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Yongdeng Zhang
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Nooreen Reza
- Program in Vertebrate Developmental Biology, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - C Patrick Lusk
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
| | - Mustafa K Khokha
- Program in Vertebrate Developmental Biology, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
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20
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Torrado B, Graña M, Badano JL, Irigoín F. Ciliary Entry of the Hedgehog Transcriptional Activator Gli2 Is Mediated by the Nuclear Import Machinery but Differs from Nuclear Transport in Being Imp-α/β1-Independent. PLoS One 2016; 11:e0162033. [PMID: 27579771 PMCID: PMC5007031 DOI: 10.1371/journal.pone.0162033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 08/16/2016] [Indexed: 01/20/2023] Open
Abstract
Gli2 is the primary transcriptional activator of Hedgehog signalling in mammals. Upon stimulation of the pathway, Gli2 moves into the cilium before reaching the nucleus. However, the mechanisms underlying its entry into the cilium are not completely understood. Since several similarities have been reported between nuclear and ciliary import, we investigated if the nuclear import machinery participates in Gli2 ciliary entry. Here we show that while two conserved classical nuclear localization signals mediate Gli2 nuclear localization via importin (Imp)-α/β1, these sequences are not required for Gli2 ciliary import. However, blocking Imp-mediated transport through overexpression of GTP-locked Ran reduced the percentage of Gli2 positive cilia, an effect that was not explained by increased CRM1-dependent export of Gli2 from the cilium. We explored the participation of Imp-β2 in Gli2 ciliary traffic and observed that this transporter is involved in moving Gli2 into the cilium, as has been described for other ciliary proteins. In addition, our data indicate that Imp-β2 might also collaborate in Gli2 nuclear entry. How does Imp-β2 determine the final destination of a protein that can localize to two distinct subcellular compartments remains an open question. Therefore, our data shows that the nuclear-cytoplasmic shuttling machinery plays a critical role mediating the subcellular distribution of Gli2 and the activation of the pathway, but distinct importins likely play a differential role mediating its ciliary and nuclear translocation.
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Affiliation(s)
- Belén Torrado
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP11400, Uruguay
| | - Martín Graña
- Bioinformatics Unit, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP11400, Uruguay
| | - José L. Badano
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP11400, Uruguay
| | - Florencia Irigoín
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP11400, Uruguay
- Departamento de Histología y Embriología, Facultad de Medicina, Universidad de la República, Gral. Flores 2125, Montevideo CP11800, Uruguay
- * E-mail:
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21
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Verhey KJ, Yang W. Permeability barriers for generating a unique ciliary protein and lipid composition. Curr Opin Cell Biol 2016; 41:109-16. [PMID: 27232950 DOI: 10.1016/j.ceb.2016.05.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 05/04/2016] [Accepted: 05/10/2016] [Indexed: 01/08/2023]
Abstract
Cilia (and flagella) are microtubule-based protrusions that are found in single or multiple copies on the surface of most eukaryotic cells. Defects in cilia formation and/or function have now been correlated with an expanding spectrum of human genetic diseases termed ciliopathies. Recent work indicates that cilia are indeed a bona fide organelle with a unique protein and lipid content that enables specific cellular functions. Despite the physiological and clinical relevance of cilia, our understanding of how a unique protein and lipid composition is generated for this organelle remains poor. Here we review recent work on the mechanisms that determine the protein and lipid content, and thus the functional outputs, of this unique organelle.
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Affiliation(s)
- Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
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22
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Promponas VJ, Katsani KR, Blencowe BJ, Ouzounis CA. Sequence evidence for common ancestry of eukaryotic endomembrane coatomers. Sci Rep 2016; 6:22311. [PMID: 26931514 PMCID: PMC4773986 DOI: 10.1038/srep22311] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/12/2016] [Indexed: 12/27/2022] Open
Abstract
Eukaryotic cells are defined by compartments through which the trafficking of macromolecules is mediated by large complexes, such as the nuclear pore, transport vesicles and intraflagellar transport. The assembly and maintenance of these complexes is facilitated by endomembrane coatomers, long suspected to be divergently related on the basis of structural and more recently phylogenomic analysis. By performing supervised walks in sequence space across coatomer superfamilies, we uncover subtle sequence patterns that have remained elusive to date, ultimately unifying eukaryotic coatomers by divergent evolution. The conserved residues shared by 3,502 endomembrane coatomer components are mapped onto the solenoid superhelix of nucleoporin and COPII protein structures, thus determining the invariant elements of coatomer architecture. This ancient structural motif can be considered as a universal signature connecting eukaryotic coatomers involved in multiple cellular processes across cell physiology and human disease.
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Affiliation(s)
- Vasilis J. Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, New Campus, University of Cyprus, PO Box 20537, CY-1678 Nicosia, Cyprus
| | - Katerina R. Katsani
- Department of Molecular Biology & Genetics, Democritus University of Thrace, GR-68100 Alexandroupolis, Greece
| | - Benjamin J. Blencowe
- Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Christos A. Ouzounis
- Bioinformatics Research Laboratory, Department of Biological Sciences, New Campus, University of Cyprus, PO Box 20537, CY-1678 Nicosia, Cyprus
- Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Biological Computation & Process Laboratory (BCPL), Chemical Process Research Institute (CPERI), Centre for Research & Technology (CERTH), PO Box 361, GR-57001 Thessalonica, Greece
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23
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TOPORS, a Dual E3 Ubiquitin and Sumo1 Ligase, Interacts with 26 S Protease Regulatory Subunit 4, Encoded by the PSMC1 Gene. PLoS One 2016; 11:e0148678. [PMID: 26872363 PMCID: PMC4752349 DOI: 10.1371/journal.pone.0148678] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 01/20/2016] [Indexed: 11/19/2022] Open
Abstract
The significance of the ubiquitin-proteasome system (UPS) for protein degradation has been highlighted in the context of neurodegenerative diseases, including retinal dystrophies. TOPORS, a dual E3 ubiquitin and SUMO1 ligase, forms a component of the UPS and selected substrates for its enzymatic activities, such as DJ-1/PARK7 and APOBEC2, are important for neuronal as well as retinal homeostasis, respectively. TOPORS is ubiquitously expressed, yet its mutations are only known to result in autosomal dominant retinitis pigmentosa. We performed a yeast two-hybrid (Y2H) screen of a human retinal cDNA library in order to identify interacting protein partners of TOPORS from the retina, and thus begin delineating the putative disease mechanism(s) associated with the retina-specific phenotype resulting from mutations in TOPORS. The screen led to isolation of the 26 S protease regulatory subunit 4 (P26s4/ PSMC1), an ATPase indispensable for correct functioning of UPS-mediated proteostasis. The interaction between endogenous TOPORS and P26s4 proteins was validated by co-immuno-precipitation from mammalian cell extracts and further characterised by immunofluorescent co-localisation studies in cell lines and retinal sections. Findings from hTERT-RPE1 and 661W cells demonstrated that TOPORS and P26s4 co-localise at the centrosome in cultured cells. Immunofluorescent staining of mouse retinae revealed a strong P26s4 reactivity at the interface between retinal pigmented epithelium (RPE) layer and the photoreceptors outer segments (OS). This finding leads us to speculate that P26s4, along with TOPORS, may have a role(s) in RPE phagocytosis, in addition to contributing to the overall photoreceptor and retinal homeostasis via the UPS.
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24
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Takao D, Verhey KJ. Gated entry into the ciliary compartment. Cell Mol Life Sci 2016; 73:119-27. [PMID: 26472341 PMCID: PMC4959937 DOI: 10.1007/s00018-015-2058-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 11/26/2022]
Abstract
Cilia and flagella play important roles in cell motility and cell signaling. These functions require that the cilium establishes and maintains a unique lipid and protein composition. Recent work indicates that a specialized region at the base of the cilium, the transition zone, serves as both a barrier to entry and a gate for passage of select components. For at least some cytosolic proteins, the barrier and gate functions are provided by a ciliary pore complex (CPC) that shares molecular and mechanistic properties with nuclear gating. Specifically, nucleoporins of the CPC limit the diffusional entry of cytosolic proteins in a size-dependent manner and enable the active transport of large molecules and complexes via targeting signals, importins, and the small G protein Ran. For membrane proteins, the septin protein SEPT2 is part of the barrier to entry whereas the gating function is carried out and/or regulated by proteins associated with ciliary diseases (ciliopathies) such as nephronophthisis, Meckel–Gruber syndrome and Joubert syndrome. Here, we discuss the evidence behind these models of ciliary gating as well as the similarities to and differences from nuclear gating.
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Affiliation(s)
- Daisuke Takao
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Pl, Ann Arbor, MI 48109 USA
| | - Kristen J. Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Pl, Ann Arbor, MI 48109 USA
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25
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Abstract
Cilia and flagella are microtubule-based organelles that play important roles in human health by contributing to cellular motility as well as sensing and responding to environmental cues. Defects in cilia formation and function cause a broad class of human genetic diseases called ciliopathies. To carry out their specialized functions, cilia contain a unique complement of proteins that must be imported into the ciliary compartment. In this chapter, we describe methods to measure the permeability barrier of the ciliary gate by microinjection of fluorescent proteins and dextrans of different sizes into ciliated cells. We also describe a fluorescence recovery after photobleaching (FRAP) assay to measure the entry of ciliary proteins into the ciliary compartment. These assays can be used to determine the molecular mechanisms that regulate the formation and function of cilia in mammalian cells.
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Affiliation(s)
- Daisuke Takao
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI, 48109, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI, 48109, USA.
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26
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Dona M, Bachmann-Gagescu R, Texier Y, Toedt G, Hetterschijt L, Tonnaer EL, Peters TA, van Beersum SEC, Bergboer JGM, Horn N, de Vrieze E, Slijkerman RWN, van Reeuwijk J, Flik G, Keunen JE, Ueffing M, Gibson TJ, Roepman R, Boldt K, Kremer H, van Wijk E. NINL and DZANK1 Co-function in Vesicle Transport and Are Essential for Photoreceptor Development in Zebrafish. PLoS Genet 2015; 11:e1005574. [PMID: 26485514 PMCID: PMC4617706 DOI: 10.1371/journal.pgen.1005574] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 09/16/2015] [Indexed: 12/04/2022] Open
Abstract
Ciliopathies are Mendelian disorders caused by dysfunction of cilia, ubiquitous organelles involved in fluid propulsion (motile cilia) or signal transduction (primary cilia). Retinal dystrophy is a common phenotypic characteristic of ciliopathies since photoreceptor outer segments are specialized primary cilia. These ciliary structures heavily rely on intracellular minus-end directed transport of cargo, mediated at least in part by the cytoplasmic dynein 1 motor complex, for their formation, maintenance and function. Ninein-like protein (NINL) is known to associate with this motor complex and is an important interaction partner of the ciliopathy-associated proteins lebercilin, USH2A and CC2D2A. Here, we scrutinize the function of NINL with combined proteomic and zebrafish in vivo approaches. We identify Double Zinc Ribbon and Ankyrin Repeat domains 1 (DZANK1) as a novel interaction partner of NINL and show that loss of Ninl, Dzank1 or both synergistically leads to dysmorphic photoreceptor outer segments, accumulation of trans-Golgi-derived vesicles and mislocalization of Rhodopsin and Ush2a in zebrafish. In addition, retrograde melanosome transport is severely impaired in zebrafish lacking Ninl or Dzank1. We further demonstrate that NINL and DZANK1 are essential for intracellular dynein-based transport by associating with complementary subunits of the cytoplasmic dynein 1 motor complex, thus shedding light on the structure and stoichiometry of this important motor complex. Altogether, our results support a model in which the NINL-DZANK1 protein module is involved in the proper assembly and folding of the cytoplasmic dynein 1 motor complex in photoreceptor cells, a process essential for outer segment formation and function. The cytoplasmic dynein 1 motor complex is known to be essential for photoreceptor outer segment formation and function. NINL, an important interaction partner of three ciliopathy-associated proteins (lebercilin, USH2A and CC2D2A), was previously shown to associate with this motor complex. In this work, we scrutinize the role of NINL using a combination of affinity proteomics and zebrafish studies, in order to gain insight into the pathogenic mechanisms underlying these three associated hereditary disorders. We identify DZANK1 as an important interaction partner of NINL and show that loss of Ninl, Dzank1, or a combination of both synergistically results in impaired transport of trans Golgi-derived vesicles and, as a consequence, defective photoreceptor outer segment formation. Using affinity proteomics, we demonstrate that NINL and DZANK1 associate with complementary subunits of the cytoplasmic dynein 1 complex. Our results support a model in which the NINL-DZANK1 protein module is essential for the proper assembly and folding of the cytoplasmic dynein 1 motor complex, shedding light on the structure and stoichiometry of this important motor complex.
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Affiliation(s)
- Margo Dona
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Ruxandra Bachmann-Gagescu
- Institute of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
- Institute of Medical Genetics, University of Zurich, Zürich, Switzerland
| | - Yves Texier
- Division of Experimental Ophthalmology, and Medical Proteome Center, Centre for Ophthalmology, Eberhard Karls University Tuebingen, Tübingen, Germany
| | - Grischa Toedt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Lisette Hetterschijt
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Edith L. Tonnaer
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Theo A. Peters
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Sylvia E. C. van Beersum
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Judith G. M. Bergboer
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Nicola Horn
- Division of Experimental Ophthalmology, and Medical Proteome Center, Centre for Ophthalmology, Eberhard Karls University Tuebingen, Tübingen, Germany
| | - Erik de Vrieze
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Ralph W. N. Slijkerman
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Jeroen van Reeuwijk
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Gert Flik
- Department of Organismal Animal Physiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Jan E. Keunen
- Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Marius Ueffing
- Division of Experimental Ophthalmology, and Medical Proteome Center, Centre for Ophthalmology, Eberhard Karls University Tuebingen, Tübingen, Germany
| | - Toby J. Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ronald Roepman
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Karsten Boldt
- Division of Experimental Ophthalmology, and Medical Proteome Center, Centre for Ophthalmology, Eberhard Karls University Tuebingen, Tübingen, Germany
| | - Hannie Kremer
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
- * E-mail:
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Photoreceptor Sensory Cilium: Traversing the Ciliary Gate. Cells 2015; 4:674-86. [PMID: 26501325 PMCID: PMC4695852 DOI: 10.3390/cells4040674] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 10/07/2015] [Accepted: 10/09/2015] [Indexed: 01/13/2023] Open
Abstract
Cilia are antenna-like extensions of the plasma membrane found in nearly all cell types. In the retina of the eye, photoreceptors develop unique sensory cilia. Not much was known about the mechanisms underlying the formation and function of photoreceptor cilia, largely because of technical limitations and the specific structural and functional modifications that cannot be modeled in vitro. With recent advances in microscopy techniques and molecular and biochemical approaches, we are now beginning to understand the molecular basis of photoreceptor ciliary architecture, ciliary function and its involvement in human diseases. Here, I will discuss the studies that have revealed new knowledge of how photoreceptor cilia regulate their identity and function while coping with high metabolic and trafficking demands associated with processing light signal.
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Bauer NC, Doetsch PW, Corbett AH. Mechanisms Regulating Protein Localization. Traffic 2015; 16:1039-61. [PMID: 26172624 DOI: 10.1111/tra.12310] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Revised: 07/08/2015] [Accepted: 07/08/2015] [Indexed: 12/23/2022]
Abstract
Cellular functions are dictated by protein content and activity. There are numerous strategies to regulate proteins varying from modulating gene expression to post-translational modifications. One commonly used mode of regulation in eukaryotes is targeted localization. By specifically redirecting the localization of a pool of existing protein, cells can achieve rapid changes in local protein function. Eukaryotic cells have evolved elegant targeting pathways to direct proteins to the appropriate cellular location or locations. Here, we provide a general overview of these localization pathways, with a focus on nuclear and mitochondrial transport, and present a survey of the evolutionarily conserved regulatory strategies identified thus far. We end with a description of several specific examples of proteins that exploit localization as an important mode of regulation.
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Affiliation(s)
- Nicholas C Bauer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University School of Medicine, Atlanta, GA 30322, USA.,Current address: Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Paul W Doetsch
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
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29
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Schou KB, Pedersen LB, Christensen ST. Ins and outs of GPCR signaling in primary cilia. EMBO Rep 2015; 16:1099-113. [PMID: 26297609 DOI: 10.15252/embr.201540530] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/01/2015] [Indexed: 12/17/2022] Open
Abstract
Primary cilia are specialized microtubule-based signaling organelles that convey extracellular signals into a cellular response in most vertebrate cell types. The physiological significance of primary cilia is underscored by the fact that defects in assembly or function of these organelles lead to a range of severe diseases and developmental disorders. In most cell types of the human body, signaling by primary cilia involves different G protein-coupled receptors (GPCRs), which transmit specific signals to the cell through G proteins to regulate diverse cellular and physiological events. Here, we provide an overview of GPCR signaling in primary cilia, with main focus on the rhodopsin-like (class A) and the smoothened/frizzled (class F) GPCRs. We describe how such receptors dynamically traffic into and out of the ciliary compartment and how they interact with other classes of ciliary GPCRs, such as class B receptors, to control ciliary function and various physiological and behavioral processes. Finally, we discuss future avenues for developing GPCR-targeted drug strategies for the treatment of ciliopathies.
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30
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Ramachandran H, Herfurth K, Grosschedl R, Schäfer T, Walz G. SUMOylation Blocks the Ubiquitin-Mediated Degradation of the Nephronophthisis Gene Product Glis2/NPHP7. PLoS One 2015; 10:e0130275. [PMID: 26083374 PMCID: PMC4471195 DOI: 10.1371/journal.pone.0130275] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 05/19/2015] [Indexed: 11/19/2022] Open
Abstract
Glis2/NPHP7 is a transcriptional regulator mutated in type 7 nephronophthisis, an autosomal recessive ciliopathy associated with cystic and fibrotic kidney disease as well as characteristic extrarenal manifestations. While most ciliopathy-associated molecules are found in the cilium, Glis2/NPHP7 presumably localizes to the nucleus. However, the detection of endogenous Glis2/NPHP7 has remained unsuccessful, potentially due to its ubiquitylation-dependent rapid degradation. We report now that Glis2/NPHP7 is also SUMOylated, preferentially by PIAS4, which conjugates Glis2/NPHP7 to SUMO3. SUMOylation interferes with ubiquitylation and degradation of Glis2/NPHP7, suggesting that Glis2/NPHP7 protein levels are regulated by competing ubiquitylation/ SUMOylation. SUMOylation also alters the transcriptional activity of Glis2/NPHP7. While Glis2/NPHP7 activates the mouse insulin-2-promotor (mIns2), SUMOylated Glis2/NPHP7 lacks this property, and seems to act as a repressor. Taken together, our data reveal that Glis2/NPHP7 is extensively modified by post-translational modifications, suggesting that a tight control of this transcriptional regulator is required for normal development and tissue homeostasis.
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Affiliation(s)
- Haribaskar Ramachandran
- Department of Medicine, Renal Division, University of Freiburg Medical Center, 79106 Freiburg, Germany
| | - Konstantin Herfurth
- Department of Medicine, Renal Division, University of Freiburg Medical Center, 79106 Freiburg, Germany
| | - Rudolf Grosschedl
- Max-Planck-Institute of Immunobiology and Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
| | - Tobias Schäfer
- Department of Medicine, Renal Division, University of Freiburg Medical Center, 79106 Freiburg, Germany
| | - Gerd Walz
- Department of Medicine, Renal Division, University of Freiburg Medical Center, 79106 Freiburg, Germany
- BIOSS Center for Biological Signaling Studies, 79108 Freiburg, Germany
- * E-mail:
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31
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Slaats GG, Giles RH. Are renal ciliopathies (replication) stressed out? Trends Cell Biol 2015; 25:317-9. [DOI: 10.1016/j.tcb.2015.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/24/2015] [Accepted: 03/31/2015] [Indexed: 12/22/2022]
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32
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Zhang L, Li W, Ni J, Wu J, Liu J, Zhang Z, Zhang Y, Li H, Shi Y, Teves ME, Song S, Strauss JF, Zhang Z. RC/BTB2 is essential for formation of primary cilia in mammalian cells. Cytoskeleton (Hoboken) 2015; 72:171-81. [PMID: 25762510 DOI: 10.1002/cm.21214] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 03/02/2015] [Accepted: 03/04/2015] [Indexed: 01/19/2023]
Abstract
RC/BTB2 is a binding partner of sperm associated antigen 16S (SPAG16S), which is a regulator of spermiogenesis in mice, a process during which sperm flagella are formed. The expression of Rc/btb2 is also regulated by multicilin, a protein that controls ciliogenesis. Given that mouse Rc/btb2 mRNA is not only expressed in tissues bearing motile cilia, but also in tissues without motile cilia, we investigated whether RC/BTB2 plays a role in the general process of ciliogenesis by studying two cell lines that have primary cilia, NIH3T3, and IMCD3. We discovered that the subcellular localization of RC/BTB2 in the NIH3T3 and IMCD3 cells encompasses the pathway for ciliogenesis. RC/BTB2 was found in the Golgi bodies and centrosomes, two key structures essential for normal ciliogenesis. Knockdown of Rc/btb2 gene expression in these cell lines disrupted ciliogenesis. The percentage of cells with primary cilia was significantly reduced in stable cell lines transduced with specific Rc/btb2 shRNA viruses as compared to the control cells. When cilia were formed in the knockdown cells, they were significantly shorter than those in the control cells. Knockdown of Rc/btb2 expression did not affect cell proliferation and the cell cycle. Exogenous expression of RC/BTB2 in these stable knockdown cells restored ciliogenesis. These findings suggest that RC/BTB2 is a necessary component of the process of formation of primary cilia in somatic cells, perhaps through the transportation of cargos from Golgi bodies to centrosomes for cilia assembling.
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Affiliation(s)
- Ling Zhang
- School of Public Health, Wuhan University of Science and Technology, Wuhan, Hubei, China
- Department of Obstetrics & Gynecology, Virginia Commonwealth University, Richmond, Virginia
| | - Wei Li
- Department of Obstetrics & Gynecology, Virginia Commonwealth University, Richmond, Virginia
| | - Jin Ni
- Department of Radiation Medicine, Second Military Medical University, Shanghai, China
| | - Jinghua Wu
- Department of Obstetrics & Gynecology, Virginia Commonwealth University, Richmond, Virginia
| | - Junping Liu
- School of Public Health, Wuhan University of Science and Technology, Wuhan, Hubei, China
- Department of Obstetrics & Gynecology, Virginia Commonwealth University, Richmond, Virginia
| | - Zhengang Zhang
- Department of Infectious Diseases, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yong Zhang
- Department of Obstetrics & Gynecology, Virginia Commonwealth University, Richmond, Virginia
- Department of Dermatology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hongfei Li
- Department of Obstetrics & Gynecology, Virginia Commonwealth University, Richmond, Virginia
| | - Yuqin Shi
- School of Public Health, Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Maria E Teves
- Department of Obstetrics & Gynecology, Virginia Commonwealth University, Richmond, Virginia
| | - Shizheng Song
- School of Public Health, Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Jerome F Strauss
- Department of Obstetrics & Gynecology, Virginia Commonwealth University, Richmond, Virginia
| | - Zhibing Zhang
- School of Public Health, Wuhan University of Science and Technology, Wuhan, Hubei, China
- Department of Obstetrics & Gynecology, Virginia Commonwealth University, Richmond, Virginia
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33
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McIntyre JC, Joiner AM, Zhang L, Iñiguez-Lluhí J, Martens JR. SUMOylation regulates ciliary localization of olfactory signaling proteins. J Cell Sci 2015; 128:1934-45. [PMID: 25908845 PMCID: PMC4457158 DOI: 10.1242/jcs.164673] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 03/24/2015] [Indexed: 11/20/2022] Open
Abstract
Cilia are evolutionarily conserved organelles found on many mammalian cell types, including neuronal populations. Although neuronal cilia, including those on olfactory sensory neurons (OSNs), are often delineated by localization of adenylyl cyclase 3 (AC3, also known as ADCY3), the mechanisms responsible for targeting integral membrane proteins are largely unknown. Post-translational modification by small ubiquitin-like modifier (SUMO) proteins plays an important role in protein localization processes such as nuclear-cytosolic transport. Here, we identified through bioinformatic analysis that adenylyl cyclases harbor conserved SUMOylation motifs, and show that AC3 is a substrate for SUMO modification. Functionally, overexpression of the SUMO protease SENP2 prevented ciliary localization of AC3, without affecting ciliation or cilia maintenance. Furthermore, AC3-SUMO mutants did not localize to cilia. To test whether SUMOylation is sufficient for cilia entry, we compared localization of ANO2, which possesses a SUMO motif, and ANO1, which lacks SUMOylation sites and does not localize to cilia. Introduction of SUMOylation sites into ANO1 was not sufficient for ciliary entry. These data suggest that SUMOylation is necessary but not sufficient for ciliary trafficking of select constituents, further establishing the link between ciliary and nuclear import.
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Affiliation(s)
- Jeremy C McIntyre
- Department of Pharmacology and Therapeutics, University of Florida, PO Box 100267, Gainesville, FL 32610, USA
| | - Ariell M Joiner
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lian Zhang
- Department of Pharmacology and Therapeutics, University of Florida, PO Box 100267, Gainesville, FL 32610, USA
| | - Jorge Iñiguez-Lluhí
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeffrey R Martens
- Department of Pharmacology and Therapeutics, University of Florida, PO Box 100267, Gainesville, FL 32610, USA
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34
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Schlacht A, Dacks JB. Unexpected ancient paralogs and an evolutionary model for the COPII coat complex. Genome Biol Evol 2015; 7:1098-109. [PMID: 25747251 PMCID: PMC4419792 DOI: 10.1093/gbe/evv045] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The coat protein complex II (COPII) is responsible for the transport of protein cargoes from the Endoplasmic Reticulum (ER) to the Golgi apparatus. COPII has been functionally characterized extensively in vivo in humans and yeast. This complex shares components with the nuclear pore complex and the Seh1-Associated (SEA) complex, inextricably linking its evolution with that of the nuclear pore and other protocoatomer domain-containing complexes. Importantly, this is one of the last coat complexes to be examined from a comparative genomic and phylogenetic perspective. We use homology searching of eight components across 74 eukaryotic genomes, followed by phylogenetic analyses, to assess both the distribution of the COPII components across eukaryote diversity and to assess its evolutionary history. We report that Sec12, but not Sed4 was present in the Last Eukaryotic Common Ancestor along with Sec16, Sar1, Sec13, Sec31, Sec23, and Sec24. We identify a previously undetected paralog of Sec23 that, at least, predates the archaeplastid clade. We also describe three Sec24 paralogs likely present in the Last Eukaryotic Common Ancestor, including one newly detected that was anciently present but lost from both opisthokonts and excavates. Altogether, we report previously undescribed complexity of the COPII coat in the ancient eukaryotic ancestor and speculate on models for the evolution, not only of the complex, but its relationship to other protocoatomer-derived complexes.
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Affiliation(s)
- Alexander Schlacht
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Joel B Dacks
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
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35
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Craft JM, Harris JA, Hyman S, Kner P, Lechtreck KF. Tubulin transport by IFT is upregulated during ciliary growth by a cilium-autonomous mechanism. ACTA ACUST UNITED AC 2015; 208:223-37. [PMID: 25583998 PMCID: PMC4298693 DOI: 10.1083/jcb.201409036] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In Chlamydomonas cilia, IFT concentrates soluble tubulin by regulating IFT train occupancy and thereby promotes elongation of axonemal microtubules. The assembly of the axoneme, the structural scaffold of cilia and flagella, requires translocation of a vast quantity of tubulin into the growing cilium, but the mechanisms that regulate the targeting, quantity, and timing of tubulin transport are largely unknown. In Chlamydomonas, GFP-tagged α-tubulin enters cilia as an intraflagellar transport (IFT) cargo and by diffusion. IFT-based transport of GFP-tubulin is elevated in growing cilia and IFT trains carry more tubulin. Cells possessing both nongrowing and growing cilia selectively target GFP-tubulin into the latter. The preferential delivery of tubulin boosts the concentration of soluble tubulin in the matrix of growing versus steady-state cilia. Cilia length mutants show abnormal kinetics of tubulin transport. We propose that cells regulate the extent of occupancy of IFT trains by tubulin cargoes. During ciliary growth, IFT concentrates soluble tubulin in cilia and thereby promotes elongation of the axonemal microtubules.
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Affiliation(s)
- Julie M Craft
- Department of Cellular Biology and College of Engineering, University of Georgia, Athens, GA 30602
| | - J Aaron Harris
- Department of Cellular Biology and College of Engineering, University of Georgia, Athens, GA 30602
| | - Sebastian Hyman
- Department of Cellular Biology and College of Engineering, University of Georgia, Athens, GA 30602
| | - Peter Kner
- Department of Cellular Biology and College of Engineering, University of Georgia, Athens, GA 30602
| | - Karl F Lechtreck
- Department of Cellular Biology and College of Engineering, University of Georgia, Athens, GA 30602
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36
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Diener DR, Lupetti P, Rosenbaum JL. Proteomic analysis of isolated ciliary transition zones reveals the presence of ESCRT proteins. Curr Biol 2015; 25:379-384. [PMID: 25578910 DOI: 10.1016/j.cub.2014.11.066] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/13/2014] [Accepted: 11/20/2014] [Indexed: 10/24/2022]
Abstract
The transition zone (TZ) is a specialized region of the cilium characterized by Y-shaped connectors between the microtubules of the ciliary axoneme and the ciliary membrane [1]. Located near the base of the cilium, the TZ is in the prime location to act as a gate for proteins into and out of the ciliary compartment, a role supported by experimental evidence [2-6]. The importance of the TZ has been underscored by studies showing that mutations affecting proteins located in the TZ result in cilia-related diseases, or ciliopathies, presenting symptoms including renal cysts, retinal degeneration, and situs inversus [7-9]. Some TZ proteins have been identified and shown to interact with each other through coprecipitation studies in vertebrate cells [4, 10, 11] and genetics studies in C. elegans [3]. As a distinct approach to identify TZ proteins, we have taken advantage of the biology of Chlamydomonas to isolate TZs. Proteomic analysis identified 115 proteins, ten of which were known TZ proteins related to ciliopathies, indicating that the preparation was highly enriched for TZs. Interestingly, six proteins of the endosomal sorting complexes required for transport (ESCRT) were also associated with the TZs. Identification of these and other proteins in the TZ will provide new insights into functions of the TZ, as well as candidate ciliopathy genes.
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Affiliation(s)
- Dennis R Diener
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA.
| | - Pietro Lupetti
- Department of Life Sciences, University of Siena, Siena 53100, Italy
| | - Joel L Rosenbaum
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA.
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37
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Pedersen LB. Editorial. Cilia 2014; 3:8. [PMID: 25136442 PMCID: PMC4136402 DOI: 10.1186/2046-2530-3-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 07/25/2014] [Indexed: 11/10/2022] Open
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38
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Abstract
The primary cilium compartmentalizes a tiny fraction of the cell surface and volume, yet many proteins are highly enriched in this area and so efficient mechanisms are necessary to concentrate them in the ciliary compartment. Here we review mechanisms that are thought to deliver protein cargo to the base of cilia and are likely to interact with ciliary gating mechanisms. Given the immense variety of ciliary cytosolic and transmembrane proteins, it is almost certain that multiple, albeit frequently interconnected, pathways mediate this process. It is also clear that none of these pathways is fully understood at the present time. Mechanisms that are discussed below facilitate ciliary localization of structural and signaling molecules, which include receptors, G-proteins, ion channels, and enzymes. These mechanisms form a basis for every aspect of cilia function in early embryonic patterning, organ morphogenesis, sensory perception and elsewhere.
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Affiliation(s)
- Jarema Malicki
- MRC Centre for Developmental and Biomedical Genetics; Department of Biomedical Science; The University of Sheffield; Sheffield, UK
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39
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Picariello T, Valentine MS, Yano J, Van Houten J. Reduction of meckelin leads to general loss of cilia, ciliary microtubule misalignment and distorted cell surface organization. Cilia 2014; 3:2. [PMID: 24484742 PMCID: PMC4124839 DOI: 10.1186/2046-2530-3-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 01/07/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Meckelin (MKS3), a conserved protein linked to Meckel Syndrome, assists in the migration of centrioles to the cell surface for ciliogenesis. We explored for additional functions of MKS3p using RNA interference (RNAi) and expression of FLAG epitope tagged protein in the ciliated protozoan Paramecium tetraurelia. This cell has a highly organized cell surface with thousands of cilia and basal bodies that are grouped into one or two basal body units delineated by ridges. The highly systematized nature of the P. tetraurelia cell surface provides a research model of MKS and other ciliopathies where changes in ciliary structure, subcellular organization and overall arrangement of the cell surface can be easily observed. We used cells reduced in IFT88 for comparison, as the involvement of this gene's product with cilia maintenance and growth is well understood. RESULTS FLAG-MKS3p was found above the plane of the distal basal body in the transition zone. Approximately 95% of those basal bodies observed had staining for FLAG-MKS3. The RNAi phenotype for MKS3 depleted cells included global shortening and loss of cilia. Basal body structure appeared unaffected. On the dorsal surface, the basal bodies and their associated rootlets appeared rotated out of alignment from the normal anterior-posterior rows. Likewise, cortical units were abnormal in shape and out of alignment from normal rows. A GST pull down using the MKS3 coiled-coil domain suggests previously unidentified interacting partners. CONCLUSIONS Reduction of MKS3p shows that this protein affects development and maintenance of cilia over the entire cell surface. Reduction of MKS3p is most visible on the dorsal surface. The anterior basal body is attached to and moves along the striated rootlet of the posterior basal body in preparation for duplication. We propose that with reduced MKS3p, this attachment and guidance of the basal body is lost. The basal body veers off course, causing basal body rows to be misaligned and units to be misshapen. Rootlets form normally on these misaligned basal bodies but are rotated out of their correct orientation. Our hypothesis is further supported by the identification of novel interacting partners of MKS3p including a kinetodesmal fiber protein, KdB2.
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Affiliation(s)
- Tyler Picariello
- Department of Biology, University of Vermont, 120A Marsh Life Science Bldg, Burlington, VT 05405, USA
| | - Megan Smith Valentine
- Department of Biology, University of Vermont, 120A Marsh Life Science Bldg, Burlington, VT 05405, USA
| | - Junji Yano
- Department of Biology, University of Vermont, 120A Marsh Life Science Bldg, Burlington, VT 05405, USA
| | - Judith Van Houten
- Department of Biology, University of Vermont, 120A Marsh Life Science Bldg, Burlington, VT 05405, USA
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40
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Vézina A, Vaillancourt-Jean E, Albarao S, Annabi B. Mesenchymal stromal cell ciliogenesis is abrogated in response to tumor necrosis factor-α and requires NF-κB signaling. Cancer Lett 2013; 345:100-5. [PMID: 24333718 DOI: 10.1016/j.canlet.2013.11.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 11/04/2013] [Accepted: 11/27/2013] [Indexed: 12/15/2022]
Abstract
The primary cilium is a cell surface-anchored sensory organelle which expression is lost in hypoxic cancer cells and during mesenchymal stromal cells (MSC) adaptation to low oxygen levels. Since pro-inflammatory cues are among the early events which promote tumor angiogenesis, we tested the inflammatory cytokine tumor necrosis factor (TNF)-α and found that it triggered a dose-dependent loss of the primary cilia in MSC. This loss was independent of IFT88 expression, was abrogated by progranulin, an antagonist of the TNF receptor and required the NF-κB signaling intermediates IκB kinase α, β, and γ, as well as NF-κB p65. These findings strengthen the concept that the primary cilium may serve as a biomarker reflecting the tumor-supporting potential of MSC and their capacity to adapt to hypoxic and pro-inflammatory cues.
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Affiliation(s)
- Amélie Vézina
- Laboratoire d'Oncologie Moléculaire, Département de Chimie, Centre de Recherche BioMED, Université du Québec à Montréal, Quebec, Canada
| | - Eric Vaillancourt-Jean
- Laboratoire d'Oncologie Moléculaire, Département de Chimie, Centre de Recherche BioMED, Université du Québec à Montréal, Quebec, Canada
| | - Stéphanie Albarao
- Laboratoire d'Oncologie Moléculaire, Département de Chimie, Centre de Recherche BioMED, Université du Québec à Montréal, Quebec, Canada
| | - Borhane Annabi
- Laboratoire d'Oncologie Moléculaire, Département de Chimie, Centre de Recherche BioMED, Université du Québec à Montréal, Quebec, Canada.
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