1
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Hall ET, Dillard ME, Cleverdon ER, Zhang Y, Daly CA, Ansari SS, Wakefield R, Stewart DP, Pruett-Miller SM, Lavado A, Carisey AF, Johnson A, Wang YD, Selner E, Tanes M, Ryu YS, Robinson CG, Steinberg J, Ogden SK. Cytoneme signaling provides essential contributions to mammalian tissue patterning. Cell 2024; 187:276-293.e23. [PMID: 38171360 PMCID: PMC10842732 DOI: 10.1016/j.cell.2023.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/06/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024]
Abstract
During development, morphogens pattern tissues by instructing cell fate across long distances. Directly visualizing morphogen transport in situ has been inaccessible, so the molecular mechanisms ensuring successful morphogen delivery remain unclear. To tackle this longstanding problem, we developed a mouse model for compromised sonic hedgehog (SHH) morphogen delivery and discovered that endocytic recycling promotes SHH loading into signaling filopodia called cytonemes. We optimized methods to preserve in vivo cytonemes for advanced microscopy and show endogenous SHH localized to cytonemes in developing mouse neural tubes. Depletion of SHH from neural tube cytonemes alters neuronal cell fates and compromises neurodevelopment. Mutation of the filopodial motor myosin 10 (MYO10) reduces cytoneme length and density, which corrupts neuronal signaling activity of both SHH and WNT. Combined, these results demonstrate that cytoneme-based signal transport provides essential contributions to morphogen dispersion during mammalian tissue development and suggest MYO10 is a key regulator of cytoneme function.
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Affiliation(s)
- Eric T Hall
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Miriam E Dillard
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Elizabeth R Cleverdon
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yan Zhang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Christina A Daly
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shariq S Ansari
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Randall Wakefield
- Cellular Imaging Shared Resource, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Daniel P Stewart
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Alfonso Lavado
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Center for Pediatric Neurological Disease Research, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Alex F Carisey
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Amanda Johnson
- Cellular Imaging Shared Resource, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yong-Dong Wang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Emma Selner
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michael Tanes
- Center for In Vivo Imaging and Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Young Sang Ryu
- Center for In Vivo Imaging and Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Camenzind G Robinson
- Cellular Imaging Shared Resource, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jeffrey Steinberg
- Center for In Vivo Imaging and Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stacey K Ogden
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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2
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Li L, Li J, Yuan L. A direct interaction between CENTLEIN and RABIN8 is required for primary cilium formation. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1434-1444. [PMID: 37475549 PMCID: PMC10520482 DOI: 10.3724/abbs.2023064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/23/2023] [Indexed: 04/05/2023] Open
Abstract
Primary cilia are formed in nearly all growth-arrested cells and are essential for mammalian development and tissue homeostasis. Defects in primary cilia result in a range of disorders in humans, named ciliopathies. The spatiotemporal localization of RABIN8 on the pericentrosome is an early step in ciliogenesis. Here, we show that CENTLEIN depletion causes the persistent accumulation of RABIN8 on the pericentrosome and primary cilium loss in hTERT-immortalized retinal pigment epithelial cells and murine embryonic fibroblasts. CENTLEIN interacts with RABIN8 directly. A stretch of a 31-amino acid sequence located in the 200‒230 region of the RABIN8 GEF domain is responsible for its physical interaction with CENTLEIN, while expression of the full-length but not the internal deletion lacking the RABIN8-binding site of CENTLEIN largely rescues the ciliogenesis defect provoked by CENTLEIN depletion. Expression of activated RAB8A partially reverses cilium loss in CENTLEIN-null RPE1 cells, so the functional importance of the CENTLEIN-RABIN8 interaction is defined.
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Affiliation(s)
- Liansheng Li
- />Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijing101408China
| | - Junlin Li
- />Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijing101408China
| | - Li Yuan
- />Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijing101408China
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3
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Petriman NA, Loureiro-López M, Taschner M, Zacharia NK, Georgieva MM, Boegholm N, Wang J, Mourão A, Russell RB, Andersen JS, Lorentzen E. Biochemically validated structural model of the 15-subunit intraflagellar transport complex IFT-B. EMBO J 2022; 41:e112440. [PMID: 36354106 PMCID: PMC9753473 DOI: 10.15252/embj.2022112440] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022] Open
Abstract
Cilia are ubiquitous eukaryotic organelles impotant for cellular motility, signaling, and sensory reception. Cilium formation requires intraflagellar transport of structural and signaling components and involves 22 different proteins organized into intraflagellar transport (IFT) complexes IFT-A and IFT-B that are transported by molecular motors. The IFT-B complex constitutes the backbone of polymeric IFT trains carrying cargo between the cilium and the cell body. Currently, high-resolution structures are only available for smaller IFT-B subcomplexes leaving > 50% structurally uncharacterized. Here, we used Alphafold to structurally model the 15-subunit IFT-B complex. The model was validated using cross-linking/mass-spectrometry data on reconstituted IFT-B complexes, X-ray scattering in solution, diffraction from crystals as well as site-directed mutagenesis and protein-binding assays. The IFT-B structure reveals an elongated and highly flexible complex consistent with cryo-electron tomographic reconstructions of IFT trains. The IFT-B complex organizes into IFT-B1 and IFT-B2 parts with binding sites for ciliary cargo and the inactive IFT dynein motor, respectively. Interestingly, our results are consistent with two different binding sites for IFT81/74 on IFT88/70/52/46 suggesting the possibility of different structural architectures for the IFT-B1 complex. Our data present a structural framework to understand IFT-B complex assembly, function, and ciliopathy variants.
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Affiliation(s)
- Narcis A Petriman
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Marta Loureiro-López
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Michael Taschner
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Nevin K Zacharia
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | | | - Niels Boegholm
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Jiaolong Wang
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - André Mourão
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | | | - Jens S Andersen
- Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Esben Lorentzen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
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4
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Hooshmand K, Halliday GM, Pineda SS, Sutherland GT, Guennewig B. Overlap between Central and Peripheral Transcriptomes in Parkinson’s Disease but Not Alzheimer’s Disease. Int J Mol Sci 2022; 23:ijms23095200. [PMID: 35563596 PMCID: PMC9104085 DOI: 10.3390/ijms23095200] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 12/20/2022] Open
Abstract
Most neurodegenerative disorders take decades to develop, and their early detection is challenged by confounding non-pathological ageing processes. Therefore, the discovery of genes and molecular pathways in both peripheral and brain tissues that are highly predictive of disease evolution is necessary. To find genes that influence Alzheimer’s disease (AD) and Parkinson’s disease (PD) pathogenesis, human RNA-Seq transcriptomic data from Brodmann Area 9 (BA9) of the dorsolateral prefrontal cortex (DLPFC), whole blood (WB), and peripheral blood mononuclear cells (PBMC) were analysed using a combination of differential gene expression and a random forest-based machine learning algorithm. The results suggest that there is little overlap between PD and AD, and the AD brain signature is unique mainly compared to blood-based samples. Moreover, the AD-BA9 was characterised by changes in ‘nervous system development’ with Myocyte-specific enhancer factor 2C (Mef2C), encoding a transcription factor that induces microglia activation, a prominent feature. The peripheral AD transcriptome was associated with alterations in ‘viral process’, and FYN, which has been previously shown to link amyloid-beta and tau, was the prominent feature. However, in the absence of any overlap with the central transcriptome, it is unclear whether peripheral FYN levels reflect AD severity or progression. In PD, central and peripheral signatures are characterised by anomalies in ‘exocytosis’ and specific genes related to the SNARE complex, including Vesicle-associated membrane protein 2 (VAMP2), Syntaxin 1A (STX1A), and p21-activated kinase 1 (PAK1). This is consistent with our current understanding of the physiological role of alpha-synuclein and how alpha-synuclein oligomers compromise vesicle docking and neurotransmission. Overall, the results describe distinct disease-specific pathomechanisms, both within the brain and peripherally, for the two most common neurodegenerative disorders.
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Affiliation(s)
- Kosar Hooshmand
- Brain and Mind Centre, Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW 2050, Australia; (K.H.); (G.M.H.); (S.S.P.)
| | - Glenda M. Halliday
- Brain and Mind Centre, Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW 2050, Australia; (K.H.); (G.M.H.); (S.S.P.)
| | - Sandy S. Pineda
- Brain and Mind Centre, Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW 2050, Australia; (K.H.); (G.M.H.); (S.S.P.)
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Greg T. Sutherland
- Charles Perkins Centre, Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW 2050, Australia;
| | - Boris Guennewig
- Brain and Mind Centre, Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW 2050, Australia; (K.H.); (G.M.H.); (S.S.P.)
- Correspondence:
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5
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Hop Mice Display Synchronous Hindlimb Locomotion and a Ventrally Fused Lumbar Spinal Cord Caused by a Point Mutation in Ttc26. eNeuro 2022; 9:ENEURO.0518-21.2022. [PMID: 35210288 PMCID: PMC8925726 DOI: 10.1523/eneuro.0518-21.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/01/2022] [Accepted: 02/05/2022] [Indexed: 11/28/2022] Open
Abstract
Identifying the spinal circuits controlling locomotion is critical for unravelling the mechanisms controlling the production of gaits. Development of the circuits governing left-right coordination relies on axon guidance molecules such as ephrins and netrins. To date, no other class of proteins have been shown to play a role during this process. Here, we have analyzed hop mice, which walk with a characteristic hopping gait using their hindlimbs in synchrony. Fictive locomotion experiments suggest that a local defect in the ventral spinal cord contributes to the aberrant locomotor phenotype. Hop mutant spinal cords had severe morphologic defects, including the absence of the ventral midline and a poorly defined border between white and gray matter. The hop mice represent the first model where, exclusively found in the lumbar domain, the left and right components of the central pattern generators (CPGs) are fused with a synchronous hindlimb gait as a functional consequence. These defects were associated with abnormal developmental processes, including a misplaced notochord and reduced induction of ventral progenitor domains. Whereas the underlying mutation in hop mice has been suggested to lie within the Ttc26 gene, other genes in close vicinity have been associated with gait defects. Mouse embryos carrying a CRISPR replicated point mutation within Ttc26 displayed an identical morphologic phenotype. Thus, our data suggest that the assembly of the lumbar CPG network is dependent on fully functional TTC26 protein.
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6
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McKnight I, Hart C, Park IH, Shim JW. Genes causing congenital hydrocephalus: Their chromosomal characteristics of telomere proximity and DNA compositions. Exp Neurol 2021; 335:113523. [PMID: 33157092 PMCID: PMC7750280 DOI: 10.1016/j.expneurol.2020.113523] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/10/2020] [Accepted: 10/30/2020] [Indexed: 01/06/2023]
Abstract
Congenital hydrocephalus (CH) is caused by genetic mutations, but whether factors impacting human genetic mutations are disease-specific remains elusive. Given two factors associated with high mutation rates, we reviewed how many disease-susceptible genes match with (i) proximity to telomeres or (ii) high adenine and thymine (A + T) content in human CH as compared to other disorders of the central nervous system (CNS). We extracted genomic information using a genome data viewer. Importantly, 98 of 108 genes causing CH satisfied (i) or (ii), resulting in >90% matching rate. However, such a high accordance no longer sustained as we checked two factors in Alzheimer's disease (AD) and/or familial Parkinson's disease (fPD), resulting in 84% and 59% matching, respectively. A disease-specific matching of telomere proximity or high A + T content predicts causative genes of CH much better than neurodegenerative diseases and other CNS conditions, likely due to sufficient number of known causative genes (n = 108) and precise determination and classification of the genotype and phenotype. Our analysis suggests a need for identifying genetic basis of both factors before human clinical studies, to prioritize putative genes found in preclinical models into the likely (meeting at least one) and more likely candidate (meeting both), which predisposes human genes to mutations.
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Affiliation(s)
- Ian McKnight
- Department of Biomedical Engineering, Marshall University, Huntington, WV 25755, USA
| | - Christoph Hart
- Department of Biomedical Engineering, Marshall University, Huntington, WV 25755, USA
| | - In-Hyun Park
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Joon W Shim
- Department of Biomedical Engineering, Marshall University, Huntington, WV 25755, USA.
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7
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Abstract
Pituitary stalk interruption syndrome (PSIS) is a distinct developmental defect of the pituitary gland identified by magnetic resonance imaging and characterized by a thin, interrupted, attenuated or absent pituitary stalk, hypoplasia or aplasia of the adenohypophysis, and an ectopic posterior pituitary. The precise etiology of PSIS still remains elusive or incompletely confirmed in most cases. Adverse perinatal events, including breech delivery and hypoxia, were initially proposed as the underlying mechanism affecting the hypothalamic-pituitary axis. Nevertheless, recent findings have uncovered a wide variety of PSIS-associated molecular defects in genes involved in pituitary development, holoprosencephaly (HPE), neural development, and other important cellular processes such as cilia function. The application of whole exome sequencing (WES) in relatively large cohorts has identified an expanded pool of potential candidate genes, mostly related to the Wnt, Notch, and sonic hedgehog signaling pathways that regulate pituitary growth and development during embryogenesis. Importantly, WES has revealed coexisting pathogenic variants in a significant number of patients; therefore, pointing to a multigenic origin and inheritance pattern of PSIS. The disorder is characterized by inter- and intrafamilial variability and incomplete or variable penetrance. Overall, PSIS is currently viewed as a mild form of an expanded HPE spectrum. The wide and complex clinical manifestations include evolving pituitary hormone deficiencies (with variable timing of onset and progression) and extrapituitary malformations. Severe and life-threatening symptomatology is observed in a subset of patients with complete pituitary hormone deficiency during the neonatal period. Nevertheless, most patients are referred later in childhood for growth retardation. Prompt and appropriate hormone substitution therapy constitutes the cornerstone of treatment. Further studies are needed to uncover the etiopathogenesis of PSIS.
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Affiliation(s)
- Antonis Voutetakis
- Department of Pediatrics, School of Medicine, Democritus University of Thrace, Alexandroupolis, Thrace, Greece.
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8
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Pleuger C, Lehti MS, Dunleavy JE, Fietz D, O'Bryan MK. Haploid male germ cells-the Grand Central Station of protein transport. Hum Reprod Update 2020; 26:474-500. [PMID: 32318721 DOI: 10.1093/humupd/dmaa004] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/15/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The precise movement of proteins and vesicles is an essential ability for all eukaryotic cells. Nowhere is this more evident than during the remarkable transformation that occurs in spermiogenesis-the transformation of haploid round spermatids into sperm. These transformations are critically dependent upon both the microtubule and the actin cytoskeleton, and defects in these processes are thought to underpin a significant percentage of human male infertility. OBJECTIVE AND RATIONALE This review is aimed at summarising and synthesising the current state of knowledge around protein/vesicle transport during haploid male germ cell development and identifying knowledge gaps and challenges for future research. To achieve this, we summarise the key discoveries related to protein transport using the mouse as a model system. Where relevant, we anchored these insights to knowledge in the field of human spermiogenesis and the causality of human male infertility. SEARCH METHODS Relevant studies published in English were identified using PubMed using a range of search terms related to the core focus of the review-protein/vesicle transport, intra-flagellar transport, intra-manchette transport, Golgi, acrosome, manchette, axoneme, outer dense fibres and fibrous sheath. Searches were not restricted to a particular time frame or species although the emphasis within the review is on mammalian spermiogenesis. OUTCOMES Spermiogenesis is the final phase of sperm development. It results in the transformation of a round cell into a highly polarised sperm with the capacity for fertility. It is critically dependent on the cytoskeleton and its ability to transport protein complexes and vesicles over long distances and often between distinct cytoplasmic compartments. The development of the acrosome covering the sperm head, the sperm tail within the ciliary lobe, the manchette and its role in sperm head shaping and protein transport into the tail, and the assembly of mitochondria into the mid-piece of sperm, may all be viewed as a series of overlapping and interconnected train tracks. Defects in this redistribution network lead to male infertility characterised by abnormal sperm morphology (teratozoospermia) and/or abnormal sperm motility (asthenozoospermia) and are likely to be causal of, or contribute to, a significant percentage of human male infertility. WIDER IMPLICATIONS A greater understanding of the mechanisms of protein transport in spermiogenesis offers the potential to precisely diagnose cases of male infertility and to forecast implications for children conceived using gametes containing these mutations. The manipulation of these processes will offer opportunities for male-based contraceptive development. Further, as increasingly evidenced in the literature, we believe that the continuous and spatiotemporally restrained nature of spermiogenesis provides an outstanding model system to identify, and de-code, cytoskeletal elements and transport mechanisms of relevance to multiple tissues.
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Affiliation(s)
- Christiane Pleuger
- School of Biological Sciences, Monash University, Clayton 3800, Australia.,Institute for Veterinary Anatomy, Histology and Embryology, Justus-Liebig University Giessen, Giessen 35392, Germany.,Hessian Centre of Reproductive Medicine, Justus Liebig University Giessen, Giessen 35392, Germany
| | - Mari S Lehti
- School of Biological Sciences, Monash University, Clayton 3800, Australia.,Institute of Biomedicine, University of Turku, Turku 20520, Finland
| | | | - Daniela Fietz
- Institute for Veterinary Anatomy, Histology and Embryology, Justus-Liebig University Giessen, Giessen 35392, Germany.,Hessian Centre of Reproductive Medicine, Justus Liebig University Giessen, Giessen 35392, Germany
| | - Moira K O'Bryan
- School of Biological Sciences, Monash University, Clayton 3800, Australia
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9
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Nakano Y, Wiechert S, Fritzsch B, Bánfi B. Inhibition of a transcriptional repressor rescues hearing in a splicing factor-deficient mouse. Life Sci Alliance 2020; 3:3/12/e202000841. [PMID: 33087486 PMCID: PMC7652395 DOI: 10.26508/lsa.202000841] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 11/26/2022] Open
Abstract
The vital role of the splicing factor SRRM4 in vestibular and inner hair cells of the ear is inactivation of the gene repressor REST; however, in outer hair cells, SRRM4 is dispensable for REST inactivation, which SRRM3 accomplishes independently. In mechanosensory hair cells (HCs) of the ear, the transcriptional repressor REST is continuously inactivated by alternative splicing of its pre-mRNA. This mechanism of REST inactivation is crucial for hearing in humans and mice. Rest is one of many pre-mRNAs whose alternative splicing is regulated by the splicing factor SRRM4; Srrm4 loss-of-function mutation in mice (Srrm4bv/bv) causes deafness, balance defects, and degeneration of all HC types other than the outer HCs (OHCs). The specific splicing alterations that drive HC degeneration in Srrm4bv/bv mice are unknown, and the mechanism underlying SRRM4-independent survival of OHCs is undefined. Here, we show that transgenic expression of a dominant-negative REST fragment in Srrm4bv/bv mice is sufficient for long-term rescue of hearing, balancing, HCs, alternative splicing of Rest, and expression of REST target genes including the Srrm4 paralog Srrm3. We also show that in HCs, SRRM3 regulates many of the same exons as SRRM4; OHCs are unique among HCs in that they transiently down-regulate Rest transcription as they mature to express Srrm3 independently of SRRM4; and simultaneous SRRM4–SRRM3 deficiency causes complete HC loss by preventing inactivation of REST in all HCs. Thus, our data reveal that REST inactivation is the primary and essential role of SRRM4 in the ear, and that OHCs differ from other HCs in the SRRM4-independent expression of the functionally SRRM4-like splicing factor SRRM3.
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Affiliation(s)
- Yoko Nakano
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Inflammation Program, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Susan Wiechert
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Inflammation Program, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Bernd Fritzsch
- Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, IA, USA
| | - Botond Bánfi
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA .,Inflammation Program, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Department of Otolaryngology-Head and Neck Surgery, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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10
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Shaheen R, Alsahli S, Ewida N, Alzahrani F, Shamseldin HE, Patel N, Al Qahtani A, Alhebbi H, Alhashem A, Al-Sheddi T, Alomar R, Alobeid E, Abouelhoda M, Monies D, Al-Hussaini A, Alzouman MA, Shagrani M, Faqeih E, Alkuraya FS. Biallelic Mutations in Tetratricopeptide Repeat Domain 26 (Intraflagellar Transport 56) Cause Severe Biliary Ciliopathy in Humans. Hepatology 2020; 71:2067-2079. [PMID: 31595528 DOI: 10.1002/hep.30982] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 09/27/2019] [Indexed: 01/05/2023]
Abstract
BACKGROUND AND AIMS The clinical consequences of defective primary cilium (ciliopathies) are characterized by marked phenotypic and genetic heterogeneity. Although fibrocystic liver disease is an established ciliopathy phenotype, severe neonatal cholestasis is rarely recognized as such. APPROACH AND RESULTS We describe seven individuals from seven families with syndromic ciliopathy clinical features, including severe neonatal cholestasis (lethal in one and necessitating liver transplant in two). Positional mapping revealed a single critical locus on chromosome 7. Whole-exome sequencing revealed three different homozygous variants in Tetratricopeptide Repeat Domain 26 (TTC26) that fully segregated with the phenotype. TTC26 (intraflagellar transport [IFT] 56/DYF13) is an atypical component of IFT-B complex, and deficiency of its highly conserved orthologs has been consistently shown to cause defective ciliary function in several model organisms. We show that cilia in TTC26-mutated patient cells display variable length and impaired function, as indicated by dysregulated sonic hedgehog signaling, abnormal staining for IFT-B components, and transcriptomic clustering with cells derived from individuals with closely related ciliopathies. We also demonstrate a strong expression of Ttc26 in the embryonic mouse liver in a pattern consistent with its proposed role in the normal development of the intrahepatic biliary system. CONCLUSIONS In addition to establishing a TTC26-related ciliopathy phenotype in humans, our results highlight the importance of considering ciliopathies in the differential diagnosis of severe neonatal cholestasis even in the absence of more typical features.
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Affiliation(s)
- Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Saud Alsahli
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nour Ewida
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fatema Alzahrani
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Awad Al Qahtani
- Department of Pediatric Gastroenterology & Hepatologist, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Homoud Alhebbi
- Department of Pediatric Gastroenterology & Hepatologist, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Department of Pediatric, Prince Sultan Medical Military City, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Tarfa Al-Sheddi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rana Alomar
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eman Alobeid
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohamed Abouelhoda
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Dorota Monies
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Abdulrahman Al-Hussaini
- Department of Pediatric Subspecialties, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,Prince Abdullah Bin Khaled Celiac Disease Research Chair, Department of Pediatrics, Faculty of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Muneerah A Alzouman
- Histopathology Division, Central Military Laboratory and Blood Bank, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Mohammad Shagrani
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,King Faisal Specialist Hospital and Research Center, Organ Transplant Centre, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Department of Pediatric Subspecialties, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
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11
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Collin GB, Gogna N, Chang B, Damkham N, Pinkney J, Hyde LF, Stone L, Naggert JK, Nishina PM, Krebs MP. Mouse Models of Inherited Retinal Degeneration with Photoreceptor Cell Loss. Cells 2020; 9:cells9040931. [PMID: 32290105 PMCID: PMC7227028 DOI: 10.3390/cells9040931] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 12/12/2022] Open
Abstract
Inherited retinal degeneration (RD) leads to the impairment or loss of vision in millions of individuals worldwide, most frequently due to the loss of photoreceptor (PR) cells. Animal models, particularly the laboratory mouse, have been used to understand the pathogenic mechanisms that underlie PR cell loss and to explore therapies that may prevent, delay, or reverse RD. Here, we reviewed entries in the Mouse Genome Informatics and PubMed databases to compile a comprehensive list of monogenic mouse models in which PR cell loss is demonstrated. The progression of PR cell loss with postnatal age was documented in mutant alleles of genes grouped by biological function. As anticipated, a wide range in the onset and rate of cell loss was observed among the reported models. The analysis underscored relationships between RD genes and ciliary function, transcription-coupled DNA damage repair, and cellular chloride homeostasis. Comparing the mouse gene list to human RD genes identified in the RetNet database revealed that mouse models are available for 40% of the known human diseases, suggesting opportunities for future research. This work may provide insight into the molecular players and pathways through which PR degenerative disease occurs and may be useful for planning translational studies.
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Affiliation(s)
- Gayle B. Collin
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Navdeep Gogna
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Bo Chang
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Nattaya Damkham
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Jai Pinkney
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Lillian F. Hyde
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Lisa Stone
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Jürgen K. Naggert
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Patsy M. Nishina
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
- Correspondence: (P.M.N.); (M.P.K.); Tel.: +1-207-2886-383 (P.M.N.); +1-207-2886-000 (M.P.K.)
| | - Mark P. Krebs
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
- Correspondence: (P.M.N.); (M.P.K.); Tel.: +1-207-2886-383 (P.M.N.); +1-207-2886-000 (M.P.K.)
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12
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Pazour GJ, Quarmby L, Smith AO, Desai PB, Schmidts M. Cilia in cystic kidney and other diseases. Cell Signal 2019; 69:109519. [PMID: 31881326 DOI: 10.1016/j.cellsig.2019.109519] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 12/21/2019] [Accepted: 12/21/2019] [Indexed: 12/23/2022]
Abstract
Epithelial cells lining the ducts and tubules of the kidney nephron and collecting duct have a single non-motile cilium projecting from their surface into the lumen of the tubule. These organelles were long considered vestigial remnants left as a result of evolution from a ciliated ancestor, but we now recognize them as critical sensory antennae. In the kidney, the polycystins and fibrocystin, products of the major human polycystic kidney disease genes, localize to this organelle. The polycystins and fibrocystin, through an unknown mechanism, monitor the diameter of the kidney tubules and regulate the proliferation and differentiation of the cells lining the tubule. When the polycystins, fibrocystin or cilia themselves are defective, the cell perceives this as a pro-proliferative signal, which leads to tubule dilation and cystic disease. In addition to critical roles in preventing cyst formation in the kidney, cilia are also important in cystic and fibrotic diseases of the liver and pancreas, and ciliary defects lead to a variety of developmental abnormalities that cause structural birth defects in most organs.
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Affiliation(s)
- Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech II, Suite 213, 373 Plantation Street, Worcester, MA 01605, United States of America.
| | - Lynne Quarmby
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
| | - Abigail O Smith
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech II, Suite 213, 373 Plantation Street, Worcester, MA 01605, United States of America
| | - Paurav B Desai
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech II, Suite 213, 373 Plantation Street, Worcester, MA 01605, United States of America
| | - Miriam Schmidts
- Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, Mathildenstrasse 1, 79112 Freiburg, Germany.
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13
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Gable DL, Gaysinskaya V, Atik CC, Talbot CC, Kang B, Stanley SE, Pugh EW, Amat-Codina N, Schenk KM, Arcasoy MO, Brayton C, Florea L, Armanios M. ZCCHC8, the nuclear exosome targeting component, is mutated in familial pulmonary fibrosis and is required for telomerase RNA maturation. Genes Dev 2019; 33:1381-1396. [PMID: 31488579 PMCID: PMC6771387 DOI: 10.1101/gad.326785.119] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/15/2019] [Indexed: 11/25/2022]
Abstract
In this study, Gable et al. follow a family with early onset pulmonary fibrosis and report the discovery of a new genetic cause of pulmonary fibrosis. They use multidimensional analysis methods, involving molecular studies, mouse model, and transcriptome-wide studies to show that heterozygous loss-of-function of the exosomal targeting protein ZCCHC8 to identify a novel cause of telomerase insufficiency in human disease. Short telomere syndromes manifest as familial idiopathic pulmonary fibrosis; they are the most common premature aging disorders. We used genome-wide linkage to identify heterozygous loss of function of ZCCHC8, a zinc-knuckle containing protein, as a cause of autosomal dominant pulmonary fibrosis. ZCCHC8 associated with TR and was required for telomerase function. In ZCCHC8 knockout cells and in mutation carriers, genomically extended telomerase RNA (TR) accumulated at the expense of mature TR, consistent with a role for ZCCHC8 in mediating TR 3′ end targeting to the nuclear RNA exosome. We generated Zcchc8-null mice and found that heterozygotes, similar to human mutation carriers, had TR insufficiency but an otherwise preserved transcriptome. In contrast, Zcchc8−/− mice developed progressive and fatal neurodevelopmental pathology with features of a ciliopathy. The Zcchc8−/− brain transcriptome was highly dysregulated, showing accumulation and 3′ end misprocessing of other low-abundance RNAs, including those encoding cilia components as well as the intronless replication-dependent histones. Our data identify a novel cause of human short telomere syndromes-familial pulmonary fibrosis and uncover nuclear exosome targeting as an essential 3′ end maturation mechanism that vertebrate TR shares with replication-dependent histones.
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Affiliation(s)
- Dustin L Gable
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Telomere Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Valeriya Gaysinskaya
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Telomere Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Christine C Atik
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Telomere Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - C Conover Talbot
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Byunghak Kang
- Department of Comparative and Molecular Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Susan E Stanley
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Telomere Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Elizabeth W Pugh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Nuria Amat-Codina
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Telomere Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Kara M Schenk
- Osler Medical Housestaff Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Murat O Arcasoy
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina 27708, USA
| | - Cory Brayton
- Department of Comparative and Molecular Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Liliana Florea
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Mary Armanios
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Telomere Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
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14
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Nakayama K, Katoh Y. Ciliary protein trafficking mediated by IFT and BBSome complexes with the aid of kinesin-2 and dynein-2 motors. J Biochem 2017; 163:155-164. [DOI: 10.1093/jb/mvx087] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 06/20/2017] [Indexed: 12/21/2022] Open
Affiliation(s)
- Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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15
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Dong B, Wu S, Wang J, Liu YX, Peng Z, Meng DM, Huang K, Wu M, Fan ZC. Chlamydomonas IFT25 is dispensable for flagellar assembly but required to export the BBSome from flagella. Biol Open 2017; 6:1680-1691. [PMID: 28838966 PMCID: PMC5703605 DOI: 10.1242/bio.026278] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Intraflagellar transport (IFT) particles are composed of polyprotein complexes IFT-A and IFT-B as well as cargo adaptors such as the BBSome. Two IFT-B subunits, IFT25 and IFT27 were found to form a heterodimer, which is essential in exporting the BBSome out of the cilium but not involved in flagellar assembly and cytokinesis in vertebrates. Controversial results were, however, recorded to show that defects in IFT, flagellar assembly and even cytokinesis were caused by IFT27 knockdown in Chlamydomonas reinhardtii. Using C. reinhardtii as a model organism, we report that depletion of IFT25 has no effect on flagellar assembly and does not affect the entry of the BBSome into the flagellum, but IFT25 depletion did impair BBSome movement out of the flagellum, clarifying the evolutionally conserved role of IFT25 in regulating the exit of the BBSome from the flagellum cross species. Interestingly, depletion of IFT25 causes dramatic reduction of IFT27 as expected, which does not cause defects in flagellar assembly and cytokinesis in C. reinhardtii. Our data thus support that Chlamydomonas IFT27, like its vertebrate homologues, is not involved in flagellar assembly and cytokinesis. Summary: Chlamydomonas IFT25 is not involved in flagellar assembly, but is required for export of the BBSome from the flagellum.
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Affiliation(s)
- Bin Dong
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Institute of Health Biotechnology, International Collaborative Research Center for Health Biotechnology, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Song Wu
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Institute of Health Biotechnology, International Collaborative Research Center for Health Biotechnology, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Jing Wang
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Institute of Health Biotechnology, International Collaborative Research Center for Health Biotechnology, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Yan-Xia Liu
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Institute of Health Biotechnology, International Collaborative Research Center for Health Biotechnology, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Zhao Peng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
| | - De-Mei Meng
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Institute of Health Biotechnology, International Collaborative Research Center for Health Biotechnology, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China
| | - Kaiyao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
| | - Mingfu Wu
- Cardiovascular Science Center, Albany Medical College, Albany, New York 12208, USA
| | - Zhen-Chuan Fan
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Institute of Health Biotechnology, International Collaborative Research Center for Health Biotechnology, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, People's Republic of China .,Obesita & Algaegen LLC, College Station, Texas 77845, USA
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16
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Bangs F, Anderson KV. Primary Cilia and Mammalian Hedgehog Signaling. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a028175. [PMID: 27881449 DOI: 10.1101/cshperspect.a028175] [Citation(s) in RCA: 395] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
It has been a decade since it was discovered that primary cilia have an essential role in Hedgehog (Hh) signaling in mammals. This discovery came from screens in the mouse that identified a set of genes that are required for both normal Hh signaling and for the formation of primary cilia. Since then, dozens of mouse mutations have been identified that disrupt cilia in a variety of ways and have complex effects on Hedgehog signaling. Here, we summarize the genetic and developmental studies used to deduce how Hedgehog signal transduction is linked to cilia and the complex effects that perturbation of cilia structure can have on Hh signaling. We conclude by describing the current status of our understanding of the cell-type-specific regulation of ciliogenesis and how that determines the ability of cells to respond to Hedgehog ligands.
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Affiliation(s)
- Fiona Bangs
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Kathryn V Anderson
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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17
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Xin D, Christopher KJ, Zeng L, Kong Y, Weatherbee SD. IFT56 regulates vertebrate developmental patterning by maintaining IFTB complex integrity and ciliary microtubule architecture. Development 2017; 144:1544-1553. [PMID: 28264835 DOI: 10.1242/dev.143255] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 02/27/2017] [Indexed: 12/19/2022]
Abstract
Cilia are key regulators of animal development and depend on intraflagellar transport (IFT) proteins for their formation and function, yet the roles of individual IFT proteins remain unclear. We examined the Ift56hop mouse mutant and reveal novel insight into the function of IFT56, a poorly understood IFTB protein. Ift56hop mice have normal cilia distribution but display defective cilia structure, including abnormal positioning and number of ciliary microtubule doublets. We show that Ift56hop cilia are unable to accumulate Gli proteins efficiently, resulting in developmental patterning defects in Shh signaling-dependent tissues such as the limb and neural tube. Strikingly, core IFTB proteins are unable to accumulate normally within Ift56hop cilia, including IFT88, IFT81 and IFT27, which are crucial for key processes such as tubulin transport and Shh signaling. IFT56 is required specifically for the IFTB complex, as IFTA components and proteins that rely on IFTA function are unaffected in Ift56hop cilia. These studies define a distinct and novel role for IFT56 in IFTB complex integrity that is crucial for cilia structure and function and, ultimately, animal development.
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Affiliation(s)
- Daisy Xin
- Department of Genetics, Yale University, New Haven, CT 06520, USA
| | | | - Lewie Zeng
- Department of Genetics, Yale University, New Haven, CT 06520, USA
| | - Yong Kong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.,W.M. Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT 06520, USA
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18
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Funabashi T, Katoh Y, Michisaka S, Terada M, Sugawa M, Nakayama K. Ciliary entry of KIF17 is dependent on its binding to the IFT-B complex via IFT46-IFT56 as well as on its nuclear localization signal. Mol Biol Cell 2017; 28:624-633. [PMID: 28077622 PMCID: PMC5328621 DOI: 10.1091/mbc.e16-09-0648] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 12/27/2016] [Accepted: 01/03/2017] [Indexed: 12/21/2022] Open
Abstract
Cilia function as cellular antennae to sense and transduce extracellular signals. A number of proteins are specifically localized in cilia. Anterograde and retrograde ciliary protein trafficking are mediated by the IFT-B and IFT-A complexes in concert with kinesin-2 and dynein-2 motors, respectively. However, the role of KIF17, a homodimeric kinesin-2 protein, in protein trafficking has not been fully understood in vertebrate cilia. In this study, we demonstrated, by using the visible immunoprecipitation assay, that KIF17 interacts with the IFT46-IFT56 dimer in the IFT-B complex through its C-terminal sequence located immediately upstream of the nuclear localization signal (NLS). We then showed that KIF17 reaches the ciliary tip independently of its motor domain and requires IFT-B binding for its entry into cilia rather than for its intraciliary trafficking. We further showed that KIF17 ciliary entry depends not only on its binding to IFT-B but also on its NLS, to which importin α proteins bind. Taking the results together, we conclude that in mammalian cells, KIF17 is dispensable for ciliogenesis and IFT-B trafficking but requires IFT-B, as well as its NLS, for its ciliary entry across the permeability barrier located at the ciliary base.
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Affiliation(s)
- Teruki Funabashi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Saki Michisaka
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Masaya Terada
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Maho Sugawa
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
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19
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Nozaki S, Katoh Y, Terada M, Michisaka S, Funabashi T, Takahashi S, Kontani K, Nakayama K. Regulation of ciliary retrograde protein trafficking by the Joubert syndrome proteins ARL13B and INPP5E. J Cell Sci 2017; 130:563-576. [PMID: 27927754 DOI: 10.1242/jcs.197004] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/29/2016] [Indexed: 12/17/2022] Open
Abstract
ARL13B (a small GTPase) and INPP5E (a phosphoinositide 5-phosphatase) are ciliary proteins encoded by causative genes of Joubert syndrome. We here showed, by taking advantage of a visible immunoprecipitation assay, that ARL13B interacts with the IFT46 -: IFT56 (IFT56 is also known as TTC26) dimer of the intraflagellar transport (IFT)-B complex, which mediates anterograde ciliary protein trafficking. However, the ciliary localization of ARL13B was found to be independent of its interaction with IFT-B, but dependent on the ciliary-targeting sequence RVEP in its C-terminal region. ARL13B-knockout cells had shorter cilia than control cells and exhibited aberrant localization of ciliary proteins, including INPP5E. In particular, in ARL13B-knockout cells, the IFT-A and IFT-B complexes accumulated at ciliary tips, and GPR161 (a negative regulator of Hedgehog signaling) could not exit cilia in response to stimulation with Smoothened agonist. This abnormal phenotype was rescued by the exogenous expression of wild-type ARL13B, as well as by its mutant defective in the interaction with IFT-B, but not by its mutants defective in INPP5E binding or in ciliary localization. Thus, ARL13B regulates IFT-A-mediated retrograde protein trafficking within cilia through its interaction with INPP5E.
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Affiliation(s)
- Shohei Nozaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masaya Terada
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Saki Michisaka
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Teruki Funabashi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Senye Takahashi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kenji Kontani
- Department of Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588, Japan
| | - Kazuhisa Nakayama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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20
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Taschner M, Lorentzen E. The Intraflagellar Transport Machinery. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a028092. [PMID: 27352625 DOI: 10.1101/cshperspect.a028092] [Citation(s) in RCA: 237] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Eukaryotic cilia and flagella are evolutionarily conserved organelles that protrude from the cell surface. The unique location and properties of cilia allow them to function in vital processes such as motility and signaling. Ciliary assembly and maintenance rely on intraflagellar transport (IFT), the bidirectional movement of a multicomponent transport system between the ciliary base and tip. Since its initial discovery more than two decades ago, considerable effort has been invested in dissecting the molecular mechanisms of IFT in a variety of model organisms. Importantly, IFT was shown to be essential for mammalian development, and defects in this process cause a number of human pathologies known as ciliopathies. Here, we review current knowledge of IFT with a particular emphasis on the IFT machinery and specific mechanisms of ciliary cargo recognition and transport.
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Affiliation(s)
- Michael Taschner
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Esben Lorentzen
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried, Germany
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21
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Katoh Y, Terada M, Nishijima Y, Takei R, Nozaki S, Hamada H, Nakayama K. Overall Architecture of the Intraflagellar Transport (IFT)-B Complex Containing Cluap1/IFT38 as an Essential Component of the IFT-B Peripheral Subcomplex. J Biol Chem 2016; 291:10962-75. [PMID: 26980730 PMCID: PMC4900248 DOI: 10.1074/jbc.m116.713883] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/14/2016] [Indexed: 01/22/2023] Open
Abstract
Intraflagellar transport (IFT) is essential for assembly and maintenance of cilia and flagella as well as ciliary motility and signaling. IFT is mediated by multisubunit complexes, including IFT-A, IFT-B, and the BBSome, in concert with kinesin and dynein motors. Under high salt conditions, purified IFT-B complex dissociates into a core subcomplex composed of at least nine subunits and at least five peripherally associated proteins. Using the visible immunoprecipitation assay, which we recently developed as a convenient protein-protein interaction assay, we determined the overall architecture of the IFT-B complex, which can be divided into core and peripheral subcomplexes composed of 10 and 6 subunits, respectively. In particular, we identified TTC26/IFT56 and Cluap1/IFT38, neither of which was included with certainty in previous models of the IFT-B complex, as integral components of the core and peripheral subcomplexes, respectively. Consistent with this, a ciliogenesis defect of Cluap1-deficient mouse embryonic fibroblasts was rescued by exogenous expression of wild-type Cluap1 but not by mutant Cluap1 lacking the binding ability to other IFT-B components. The detailed interaction map as well as comparison of subcellular localization of IFT-B components between wild-type and Cluap1-deficient cells provides insights into the functional relevance of the architecture of the IFT-B complex.
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Affiliation(s)
- Yohei Katoh
- From the Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masaya Terada
- From the Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuya Nishijima
- From the Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Ryota Takei
- From the Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shohei Nozaki
- From the Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroshi Hamada
- the Developmental Genetics Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan, and the Center for Developmental Biology, RIKEN, Chuou-ku, Kobe 650-0047, Japan
| | - Kazuhisa Nakayama
- From the Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan,
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Taschner M, Weber K, Mourão A, Vetter M, Awasthi M, Stiegler M, Bhogaraju S, Lorentzen E. Intraflagellar transport proteins 172, 80, 57, 54, 38, and 20 form a stable tubulin-binding IFT-B2 complex. EMBO J 2016; 35:773-90. [PMID: 26912722 PMCID: PMC4818760 DOI: 10.15252/embj.201593164] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 01/21/2016] [Indexed: 12/31/2022] Open
Abstract
Intraflagellar transport (IFT) relies on the IFT complex and is required for ciliogenesis. The IFT‐B complex consists of 9–10 stably associated core subunits and six “peripheral” subunits that were shown to dissociate from the core structure at moderate salt concentration. We purified the six “peripheral” IFT‐B subunits of Chlamydomonas reinhardtii as recombinant proteins and show that they form a stable complex independently of the IFT‐B core. We suggest a nomenclature of IFT‐B1 (core) and IFT‐B2 (peripheral) for the two IFT‐B subcomplexes. We demonstrate that IFT88, together with the N‐terminal domain of IFT52, is necessary to bridge the interaction between IFT‐B1 and B2. The crystal structure of IFT52N reveals highly conserved residues critical for IFT‐B1/IFT‐B2 complex formation. Furthermore, we show that of the three IFT‐B2 subunits containing a calponin homology (CH) domain (IFT38, 54, and 57), only IFT54 binds αβ‐tubulin as a potential IFT cargo, whereas the CH domains of IFT38 and IFT57 mediate the interaction with IFT80 and IFT172, respectively. Crystal structures of IFT54 CH domains reveal that tubulin binding is mediated by basic surface‐exposed residues.
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Affiliation(s)
- Michael Taschner
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Kristina Weber
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - André Mourão
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Melanie Vetter
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Mayanka Awasthi
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Marc Stiegler
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Sagar Bhogaraju
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Esben Lorentzen
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany
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