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Mukhopadhyay AG, Toropova K, Daly L, Wells JN, Vuolo L, Mladenov M, Seda M, Jenkins D, Stephens DJ, Roberts AJ. Structure and tethering mechanism of dynein-2 intermediate chains in intraflagellar transport. EMBO J 2024; 43:1257-1272. [PMID: 38454149 PMCID: PMC10987677 DOI: 10.1038/s44318-024-00060-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 03/09/2024] Open
Abstract
Dynein-2 is a large multiprotein complex that powers retrograde intraflagellar transport (IFT) of cargoes within cilia/flagella, but the molecular mechanism underlying this function is still emerging. Distinctively, dynein-2 contains two identical force-generating heavy chains that interact with two different intermediate chains (WDR34 and WDR60). Here, we dissect regulation of dynein-2 function by WDR34 and WDR60 using an integrative approach including cryo-electron microscopy and CRISPR/Cas9-enabled cell biology. A 3.9 Å resolution structure shows how WDR34 and WDR60 use surprisingly different interactions to engage equivalent sites of the two heavy chains. We show that cilia can assemble in the absence of either WDR34 or WDR60 individually, but not both subunits. Dynein-2-dependent distribution of cargoes depends more strongly on WDR60, because the unique N-terminal extension of WDR60 facilitates dynein-2 targeting to cilia. Strikingly, this N-terminal extension can be transplanted onto WDR34 and retain function, suggesting it acts as a flexible tether to the IFT "trains" that assemble at the ciliary base. We discuss how use of unstructured tethers represents an emerging theme in IFT train interactions.
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Affiliation(s)
- Aakash G Mukhopadhyay
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK
| | - Katerina Toropova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK
| | - Lydia Daly
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK
- Randall Centre of Cell & Molecular Biophysics, King's College London, London, UK
| | - Jennifer N Wells
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK
- MRC London Institute of Medical Sciences (LMS), London, UK
| | - Laura Vuolo
- Cell Biology Laboratories, School of Biochemistry, University of Bristol, Bristol, UK
| | - Miroslav Mladenov
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute, London, UK
| | - Marian Seda
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Dagan Jenkins
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - David J Stephens
- Cell Biology Laboratories, School of Biochemistry, University of Bristol, Bristol, UK
| | - Anthony J Roberts
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK.
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2
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Brinzer RA, Winter AD, Page AP. The relationship between intraflagellar transport and upstream protein trafficking pathways and macrocyclic lactone resistance in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2024; 14:jkae009. [PMID: 38227795 PMCID: PMC10917524 DOI: 10.1093/g3journal/jkae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/08/2024] [Accepted: 01/08/2024] [Indexed: 01/18/2024]
Abstract
Parasitic nematodes are globally important and place a heavy disease burden on infected humans, crops, and livestock, while commonly administered anthelmintics used for treatment are being rendered ineffective by increasing levels of resistance. It has recently been shown in the model nematode Caenorhabditis elegans that the sensory cilia of the amphid neurons play an important role in resistance toward macrocyclic lactones such as ivermectin (an avermectin) and moxidectin (a milbemycin) either through reduced uptake or intertissue signaling pathways. This study interrogated the extent to which ciliary defects relate to macrocyclic lactone resistance and dye-filling defects using a combination of forward genetics and targeted resistance screening approaches and confirmed the importance of intraflagellar transport in this process. This approach also identified the protein trafficking pathways used by the downstream effectors and the components of the ciliary basal body that are required for effector entry into these nonmotile structures. In total, 24 novel C. elegans anthelmintic survival-associated genes were identified in this study. When combined with previously known resistance genes, there are now 46 resistance-associated genes that are directly involved in amphid, cilia, and intraflagellar transport function.
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Affiliation(s)
- Robert A Brinzer
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Scotland G61 1QH, UK
| | - Alan D Winter
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Scotland G61 1QH, UK
| | - Antony P Page
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Scotland G61 1QH, UK
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3
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Mao YQ, Seraphim TV, Wan Y, Wu R, Coyaud E, Bin Munim M, Mollica A, Laurent E, Babu M, Mennella V, Raught B, Houry WA. DPCD is a regulator of R2TP in ciliogenesis initiation through Akt signaling. Cell Rep 2024; 43:113713. [PMID: 38306274 DOI: 10.1016/j.celrep.2024.113713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/31/2023] [Accepted: 01/12/2024] [Indexed: 02/04/2024] Open
Abstract
R2TP is a chaperone complex consisting of the AAA+ ATPases RUVBL1 and RUVBL2, as well as RPAP3 and PIH1D1 proteins. R2TP is responsible for the assembly of macromolecular complexes mainly acting through different adaptors. Using proximity-labeling mass spectrometry, we identified deleted in primary ciliary dyskinesia (DPCD) as an adaptor of R2TP. Here, we demonstrate that R2TP-DPCD influences ciliogenesis initiation through a unique mechanism by interaction with Akt kinase to regulate its phosphorylation levels rather than its stability. We further show that DPCD is a heart-shaped monomeric protein with two domains. A highly conserved region in the cysteine- and histidine-rich domains-containing proteins and SGT1 (CS) domain of DPCD interacts with the RUVBL2 DII domain with high affinity to form a stable R2TP-DPCD complex both in cellulo and in vitro. Considering that DPCD is one among several CS-domain-containing proteins found to associate with RUVBL1/2, we propose that RUVBL1/2 are CS-domain-binding proteins that regulate complex assembly and downstream signaling.
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Affiliation(s)
- Yu-Qian Mao
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Thiago V Seraphim
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Yimei Wan
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Ruikai Wu
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Muhammad Bin Munim
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Antonio Mollica
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Estelle Laurent
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Vito Mennella
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; MRC Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge CB2 1QR, UK; Department of Pathology, School of Biological Sciences, University of Cambridge, Cambridge CB2 1QP, UK
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
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4
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Wang X, Yu J, Yue H, Li S, Yang A, Zhu Z, Guan Z, Wang J. Inpp5e Regulated the Cilium-Related Genes Contributing to the Neural Tube Defects Under 5-Fluorouracil Exposure. Mol Neurobiol 2024:10.1007/s12035-024-03946-7. [PMID: 38285286 DOI: 10.1007/s12035-024-03946-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/09/2024] [Indexed: 01/30/2024]
Abstract
Primary cilia are crucial for neurogenesis, and cilium-related genes are involved in the closure of neural tubes. Inositol polyphosphate-5-phosphatase (Inpp5e) was enriched in primary cilia and closely related to the occurrence of neural tube defects (NTDs). However, the role of Inpp5e in the development of NTDs is not well-known. To investigate whether Inpp5e gene is associated with the neural tube closure, we established a mouse model of NTDs by 5-fluorouracil (5-FU) exposure at gestational day 7.5 (GD7.5). The Inpp5e knockdown (Inpp5e-/-) mouse embryonic stem cells (mESCs) were produced by CRISPR/Cas9 system. The expressions of Inpp5e and other cilium-related genes including intraflagellar transport 80 (Ift80), McKusick-Kaufman syndrome (Mkks), and Kirsten rat sarcoma viral oncogene homolog (Kras) were determined, utilizing quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR), western blot, PCR array, and immunofluorescence staining. The result showed that the incidence of NTDs was 37.10% (23 NTDs/62 total embryos) and significantly higher than that in the control group (P < 0.001). The neuroepithelial cells of neural tubes were obviously disarranged in NTD embryos. The mRNA and protein levels of Inpp5e, Ift80, Mkks, and Kras were significantly decreased in NTD embryonic brain tissues, compared to the control (P < 0.05). Knockdown of the Inpp5e (Inpp5e-/-) reduced the expressions of Ift80, Mkks, and Kras in mESCs. Furthermore, the levels of α-tubulin were significantly reduced in NTD embryonic neural tissue and Inpp5e-/- mESCs. These results suggested that maternal 5-FU exposure inhibited the expression of Inpp5e, which resulted in the downregulation of cilium-related genes (Ift80, Mkks, and Kras), leading to the impairment of primary cilium development, and ultimately disrupted the neural tube closure.
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Affiliation(s)
- Xiuwei Wang
- Laboratory of Translational Medicine, Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Jialu Yu
- Laboratory of Translational Medicine, Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Huixuan Yue
- Department of Pediatrics, Beijing Chaoyang Hospital of Capital Medical University, Beijing, 100020, China
| | - Shen Li
- Laboratory of Translational Medicine, Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Aiyun Yang
- Laboratory of Translational Medicine, Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Zhiqiang Zhu
- Laboratory of Translational Medicine, Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Zhen Guan
- Laboratory of Translational Medicine, Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Jianhua Wang
- Laboratory of Translational Medicine, Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China.
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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5
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Freke GM, Martins T, Davies RJ, Beyer T, Seda M, Peskett E, Haq N, Prasai A, Otto G, Jeyabalan Srikaran J, Hernandez V, Diwan GD, Russell RB, Ueffing M, Huranova M, Boldt K, Beales PL, Jenkins D. De-Suppression of Mesenchymal Cell Identities and Variable Phenotypic Outcomes Associated with Knockout of Bbs1. Cells 2023; 12:2662. [PMID: 37998397 PMCID: PMC10670506 DOI: 10.3390/cells12222662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023] Open
Abstract
Bardet-Biedl syndrome (BBS) is an archetypal ciliopathy caused by dysfunction of primary cilia. BBS affects multiple tissues, including the kidney, eye and hypothalamic satiety response. Understanding pan-tissue mechanisms of pathogenesis versus those which are tissue-specific, as well as gauging their associated inter-individual variation owing to genetic background and stochastic processes, is of paramount importance in syndromology. The BBSome is a membrane-trafficking and intraflagellar transport (IFT) adaptor protein complex formed by eight BBS proteins, including BBS1, which is the most commonly mutated gene in BBS. To investigate disease pathogenesis, we generated a series of clonal renal collecting duct IMCD3 cell lines carrying defined biallelic nonsense or frameshift mutations in Bbs1, as well as a panel of matching wild-type CRISPR control clones. Using a phenotypic screen and an unbiased multi-omics approach, we note significant clonal variability for all assays, emphasising the importance of analysing panels of genetically defined clones. Our results suggest that BBS1 is required for the suppression of mesenchymal cell identities as the IMCD3 cell passage number increases. This was associated with a failure to express epithelial cell markers and tight junction formation, which was variable amongst clones. Transcriptomic analysis of hypothalamic preparations from BBS mutant mice, as well as BBS patient fibroblasts, suggested that dysregulation of epithelial-to-mesenchymal transition (EMT) genes is a general predisposing feature of BBS across tissues. Collectively, this work suggests that the dynamic stability of the BBSome is essential for the suppression of mesenchymal cell identities as epithelial cells differentiate.
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Affiliation(s)
- Grace Mercedes Freke
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Tiago Martins
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Rosalind Jane Davies
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Tina Beyer
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076 Tübingen, Germany; (T.B.); (M.U.); (K.B.)
| | - Marian Seda
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Emma Peskett
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Naila Haq
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Avishek Prasai
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic (M.H.)
| | - Georg Otto
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Jeshmi Jeyabalan Srikaran
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Victor Hernandez
- Life Sciences Department, CHMLS, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK;
| | - Gaurav D. Diwan
- BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; (G.D.D.); (R.B.R.)
- Biochemistry Center (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Robert B. Russell
- BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; (G.D.D.); (R.B.R.)
- Biochemistry Center (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Marius Ueffing
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076 Tübingen, Germany; (T.B.); (M.U.); (K.B.)
| | - Martina Huranova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic (M.H.)
| | - Karsten Boldt
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076 Tübingen, Germany; (T.B.); (M.U.); (K.B.)
| | - Philip L. Beales
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Dagan Jenkins
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
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6
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Clearman KR, Haycraft CJ, Croyle MJ, Collawn JF, Yoder BK. Functions of the primary cilium in the kidney and its connection with renal diseases. Curr Top Dev Biol 2023; 155:39-94. [PMID: 38043952 DOI: 10.1016/bs.ctdb.2023.07.001] [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] [Indexed: 12/05/2023]
Abstract
The nonmotile primary cilium is a sensory structure found on most mammalian cell types that integrates multiple signaling pathways involved in tissue development and postnatal function. As such, mutations disrupting cilia activities cause a group of disorders referred to as ciliopathies. These disorders exhibit a wide spectrum of phenotypes impacting nearly every tissue. In the kidney, primary cilia dysfunction caused by mutations in polycystin 1 (Pkd1), polycystin 2 (Pkd2), or polycystic kidney and hepatic disease 1 (Pkhd1), result in polycystic kidney disease (PKD), a progressive disorder causing renal functional decline and end-stage renal disease. PKD affects nearly 1 in 1000 individuals and as there is no cure for PKD, patients frequently require dialysis or renal transplantation. Pkd1, Pkd2, and Pkhd1 encode membrane proteins that all localize in the cilium. Pkd1 and Pkd2 function as a nonselective cation channel complex while Pkhd1 protein function remains uncertain. Data indicate that the cilium may act as a mechanosensor to detect fluid movement through renal tubules. Other functions proposed for the cilium and PKD proteins in cyst development involve regulation of cell cycle and oriented division, regulation of renal inflammation and repair processes, maintenance of epithelial cell differentiation, and regulation of mitochondrial structure and metabolism. However, how loss of cilia or cilia function leads to cyst development remains elusive. Studies directed at understanding the roles of Pkd1, Pkd2, and Pkhd1 in the cilium and other locations within the cell will be important for developing therapeutic strategies to slow cyst progression.
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Affiliation(s)
- Kelsey R Clearman
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Courtney J Haycraft
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Mandy J Croyle
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - James F Collawn
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Bradley K Yoder
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States.
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7
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Ishikawa T. Mass-Spec, Cryo-EM and AI join forces for a close look at the transporter complex in cilia. EMBO J 2023; 42:e113010. [PMID: 36519407 PMCID: PMC9841323 DOI: 10.15252/embj.2022113010] [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: 11/08/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
The intraflagellar transport (IFT) complex transports components between the cytoplasm and the ciliary tip. Two studies now report on the atomic structure of IFT-B, the core of IFT, using cutting-edge technology, such as cross-linking mass spectrometry (MS), cryo-electron tomography (cryo-ET) and Alphafold2-enabled AI-based folding prediction. The 3D structure of IFT-B reveals how the 15 component proteins are arranged to stabilize this gigantic complex and suggests a dynamic interplay between the proteins.
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Affiliation(s)
- Takashi Ishikawa
- Department of Biology and ChemistryPaul Scherrer InstituteVilligen PSISwitzerland
- Department of BiologyETH ZurichVilligen PSISwitzerland
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8
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Lacey SE, Foster HE, Pigino G. The molecular structure of IFT-A and IFT-B in anterograde intraflagellar transport trains. Nat Struct Mol Biol 2023; 30:584-593. [PMID: 36593313 DOI: 10.1038/s41594-022-00905-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/01/2022] [Indexed: 01/03/2023]
Abstract
Anterograde intraflagellar transport (IFT) trains are essential for cilia assembly and maintenance. These trains are formed of 22 IFT-A and IFT-B proteins that link structural and signaling cargos to microtubule motors for import into cilia. It remains unknown how the IFT-A/-B proteins are arranged into complexes and how these complexes polymerize into functional trains. Here we use in situ cryo-electron tomography of Chlamydomonas reinhardtii cilia and AlphaFold2 protein structure predictions to generate a molecular model of the entire anterograde train. We show how the conformations of both IFT-A and IFT-B are dependent on lateral interactions with neighboring repeats, suggesting that polymerization is required to cooperatively stabilize the complexes. Following three-dimensional classification, we reveal how IFT-B extends two flexible tethers to maintain a connection with IFT-A that can withstand the mechanical stresses present in actively beating cilia. Overall, our findings provide a framework for understanding the fundamental processes that govern cilia assembly.
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9
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Hesketh SJ, Mukhopadhyay AG, Nakamura D, Toropova K, Roberts AJ. IFT-A structure reveals carriages for membrane protein transport into cilia. Cell 2022; 185:4971-4985.e16. [PMID: 36462505 DOI: 10.1016/j.cell.2022.11.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/13/2022] [Accepted: 11/09/2022] [Indexed: 12/05/2022]
Abstract
Intraflagellar transport (IFT) trains are massive molecular machines that traffic proteins between cilia and the cell body. Each IFT train is a dynamic polymer of two large complexes (IFT-A and -B) and motor proteins, posing a formidable challenge to mechanistic understanding. Here, we reconstituted the complete human IFT-A complex and obtained its structure using cryo-EM. Combined with AlphaFold prediction and genome-editing studies, our results illuminate how IFT-A polymerizes, interacts with IFT-B, and uses an array of β-propeller and TPR domains to create "carriages" of the IFT train that engage TULP adaptor proteins. We show that IFT-A⋅TULP carriages are essential for cilia localization of diverse membrane proteins, as well as ICK-the key kinase regulating IFT train turnaround. These data establish a structural link between IFT-A's distinct functions, provide a blueprint for IFT-A in the train, and shed light on how IFT evolved from a proto-coatomer ancestor.
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Affiliation(s)
- Sophie J Hesketh
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck University of London, London, WC1E 7HX, UK
| | - Aakash G Mukhopadhyay
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck University of London, London, WC1E 7HX, UK
| | - Dai Nakamura
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck University of London, London, WC1E 7HX, UK
| | - Katerina Toropova
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck University of London, London, WC1E 7HX, UK.
| | - Anthony J Roberts
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck University of London, London, WC1E 7HX, UK.
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10
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Meleppattu S, Zhou H, Dai J, Gui M, Brown A. Mechanism of IFT-A polymerization into trains for ciliary transport. Cell 2022; 185:4986-4998.e12. [PMID: 36563665 PMCID: PMC9794116 DOI: 10.1016/j.cell.2022.11.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/14/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022]
Abstract
Intraflagellar transport (IFT) is the highly conserved process by which proteins are transported along ciliary microtubules by a train-like polymeric assembly of IFT-A and IFT-B complexes. IFT-A is sandwiched between IFT-B and the ciliary membrane, consistent with its putative role in transporting transmembrane and membrane-associated cargoes. Here, we have used single-particle analysis electron cryomicroscopy (cryo-EM) to determine structures of native IFT-A complexes. We show that subcomplex rearrangements enable IFT-A to polymerize laterally on anterograde IFT trains, revealing a cooperative assembly mechanism. Surprisingly, we discover that binding of IFT-A to IFT-B shields the preferred lipid-binding interface from the ciliary membrane but orients an interconnected network of β-propeller domains with the capacity to accommodate diverse cargoes toward the ciliary membrane. This work provides a mechanistic basis for understanding IFT-train assembly and cargo interactions.
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Affiliation(s)
- Shimi Meleppattu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Haixia Zhou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Jin Dai
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Miao Gui
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Alan Brown
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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11
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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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12
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Quidwai T, Wang J, Hall EA, Petriman NA, Leng W, Kiesel P, Wells JN, Murphy LC, Keighren MA, Marsh JA, Lorentzen E, Pigino G, Mill P. A WDR35-dependent coat protein complex transports ciliary membrane cargo vesicles to cilia. eLife 2021; 10:e69786. [PMID: 34734804 PMCID: PMC8754431 DOI: 10.7554/elife.69786] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 11/04/2021] [Indexed: 11/13/2022] Open
Abstract
Intraflagellar transport (IFT) is a highly conserved mechanism for motor-driven transport of cargo within cilia, but how this cargo is selectively transported to cilia is unclear. WDR35/IFT121 is a component of the IFT-A complex best known for its role in ciliary retrograde transport. In the absence of WDR35, small mutant cilia form but fail to enrich in diverse classes of ciliary membrane proteins. In Wdr35 mouse mutants, the non-core IFT-A components are degraded and core components accumulate at the ciliary base. We reveal deep sequence homology of WDR35 and other IFT-A subunits to α and ß' COPI coatomer subunits and demonstrate an accumulation of 'coat-less' vesicles that fail to fuse with Wdr35 mutant cilia. We determine that recombinant non-core IFT-As can bind directly to lipids and provide the first in situ evidence of a novel coat function for WDR35, likely with other IFT-A proteins, in delivering ciliary membrane cargo necessary for cilia elongation.
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Affiliation(s)
- Tooba Quidwai
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Jiaolong Wang
- Department of Molecular Biology and Genetics, Aarhus UniversityAarhusDenmark
| | - Emma A Hall
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Narcis A Petriman
- Department of Molecular Biology and Genetics, Aarhus UniversityAarhusDenmark
| | - Weihua Leng
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Petra Kiesel
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Jonathan N Wells
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Laura C Murphy
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Margaret A Keighren
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Esben Lorentzen
- Department of Molecular Biology and Genetics, Aarhus UniversityAarhusDenmark
| | - Gaia Pigino
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Human TechnopoleMilanItaly
| | - Pleasantine Mill
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
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13
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Abstract
The intraflagellar transport (IFT) system is a remarkable molecular machine used by cells to assemble and maintain the cilium, a long organelle extending from eukaryotic cells that gives rise to motility, sensing and signaling. IFT plays a critical role in building the cilium by shuttling structural components and signaling receptors between the ciliary base and tip. To provide effective transport, IFT-A and IFT-B adaptor protein complexes assemble into highly repetitive polymers, called IFT trains, that are powered by the motors kinesin-2 and IFT-dynein to move bidirectionally along the microtubules. This dynamic system must be precisely regulated to shuttle different cargo proteins between the ciliary tip and base. In this Cell Science at a Glance article and the accompanying poster, we discuss the current structural and mechanistic understanding of IFT trains and how they function as macromolecular machines to assemble the structure of the cilium.
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Affiliation(s)
- Mareike A Jordan
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Gaia Pigino
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Pfotenhauerstraße 108, 01307 Dresden, Germany.,Human Technopole, Via Cristina Belgioioso 171, 20157 Milan, Italy
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14
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Barnes CL, Malhotra H, Calvert PD. Compartmentalization of Photoreceptor Sensory Cilia. Front Cell Dev Biol 2021; 9:636737. [PMID: 33614665 PMCID: PMC7889997 DOI: 10.3389/fcell.2021.636737] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/07/2021] [Indexed: 12/12/2022] Open
Abstract
Functional compartmentalization of cells is a universal strategy for segregating processes that require specific components, undergo regulation by modulating concentrations of those components, or that would be detrimental to other processes. Primary cilia are hair-like organelles that project from the apical plasma membranes of epithelial cells where they serve as exclusive compartments for sensing physical and chemical signals in the environment. As such, molecules involved in signal transduction are enriched within cilia and regulating their ciliary concentrations allows adaptation to the environmental stimuli. The highly efficient organization of primary cilia has been co-opted by major sensory neurons, olfactory cells and the photoreceptor neurons that underlie vision. The mechanisms underlying compartmentalization of cilia are an area of intense current research. Recent findings have revealed similarities and differences in molecular mechanisms of ciliary protein enrichment and its regulation among primary cilia and sensory cilia. Here we discuss the physiological demands on photoreceptors that have driven their evolution into neurons that rely on a highly specialized cilium for signaling changes in light intensity. We explore what is known and what is not known about how that specialization appears to have driven unique mechanisms for photoreceptor protein and membrane compartmentalization.
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Affiliation(s)
| | | | - Peter D. Calvert
- Department of Ophthalmology and Visual Sciences, Center for Vision Research, SUNY Upstate Medical University, Syracuse, NY, United States
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15
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Webb S, Mukhopadhyay AG, Roberts AJ. Intraflagellar transport trains and motors: Insights from structure. Semin Cell Dev Biol 2020; 107:82-90. [PMID: 32684327 PMCID: PMC7561706 DOI: 10.1016/j.semcdb.2020.05.021] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/19/2020] [Accepted: 05/26/2020] [Indexed: 11/17/2022]
Abstract
Intraflagellar transport (IFT) sculpts the proteome of cilia and flagella; the antenna-like organelles found on the surface of virtually all human cell types. By delivering proteins to the growing ciliary tip, recycling turnover products, and selectively transporting signalling molecules, IFT has critical roles in cilia biogenesis, quality control, and signal transduction. IFT involves long polymeric arrays, termed IFT trains, which move to and from the ciliary tip under the power of the microtubule-based motor proteins kinesin-II and dynein-2. Recent top-down and bottom-up structural biology approaches are converging on the molecular architecture of the IFT train machinery. Here we review these studies, with a focus on how kinesin-II and dynein-2 assemble, attach to IFT trains, and undergo precise regulation to mediate bidirectional transport.
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Affiliation(s)
- Stephanie Webb
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London, United Kingdom
| | - Aakash G Mukhopadhyay
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London, United Kingdom
| | - Anthony J Roberts
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London, United Kingdom.
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16
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Vitre B, Guesdon A, Delaval B. Non-ciliary Roles of IFT Proteins in Cell Division and Polycystic Kidney Diseases. Front Cell Dev Biol 2020; 8:578239. [PMID: 33072760 PMCID: PMC7536321 DOI: 10.3389/fcell.2020.578239] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/26/2020] [Indexed: 12/30/2022] Open
Abstract
Cilia are small organelles present at the surface of most differentiated cells where they act as sensors for mechanical or biochemical stimuli. Cilia assembly and function require the Intraflagellar Transport (IFT) machinery, an intracellular transport system that functions in association with microtubules and motors. If IFT proteins have long been studied for their ciliary roles, recent evidences indicate that their functions are not restricted to the cilium. Indeed, IFT proteins are found outside the ciliary compartment where they are involved in a variety of cellular processes in association with non-ciliary motors. Recent works also provide evidence that non-ciliary roles of IFT proteins could be responsible for the development of ciliopathies related phenotypes including polycystic kidney diseases. In this review, we will discuss the interactions of IFT proteins with microtubules and motors as well as newly identified non-ciliary functions of IFT proteins, focusing on their roles in cell division. We will also discuss the potential contribution of non-ciliary IFT proteins functions to the etiology of kidney diseases.
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17
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Petriman NA, Lorentzen E. Structural insights into the architecture and assembly of eukaryotic flagella. MICROBIAL CELL (GRAZ, AUSTRIA) 2020; 7:289-299. [PMID: 33150161 PMCID: PMC7590530 DOI: 10.15698/mic2020.11.734] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/07/2020] [Accepted: 09/14/2020] [Indexed: 12/16/2022]
Abstract
Cilia and flagella are slender projections found on most eukaryotic cells including unicellular organisms such as Chlamydomonas, Trypanosoma and Tetrahymena, where they serve motility and signaling functions. The cilium is a large molecular machine consisting of hundreds of different proteins that are trafficked into the organelle to organize a repetitive microtubule-based axoneme. Several recent studies took advantage of improved cryo-EM methodology to unravel the high-resolution structures of ciliary complexes. These include the recently reported purification and structure determination of axonemal doublet microtubules from the green algae Chlamydomonas reinhardtii, which allows for the modeling of more than 30 associated protein factors to provide deep molecular insight into the architecture and repetitive nature of doublet microtubules. In addition, we will review several recent contributions that dissect the structure and function of ciliary trafficking complexes that ferry structural and signaling components between the cell body and the cilium organelle.
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Affiliation(s)
- Narcis-Adrian Petriman
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark
| | - Esben Lorentzen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark
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18
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Nakayama K, Katoh Y. Architecture of the IFT ciliary trafficking machinery and interplay between its components. Crit Rev Biochem Mol Biol 2020; 55:179-196. [PMID: 32456460 DOI: 10.1080/10409238.2020.1768206] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cilia and flagella serve as cellular antennae and propellers in various eukaryotic cells, and contain specific receptors and ion channels as well as components of axonemal microtubules and molecular motors to achieve their sensory and motile functions. Not only the bidirectional trafficking of specific proteins within cilia but also their selective entry and exit across the ciliary gate is mediated by the intraflagellar transport (IFT) machinery with the aid of motor proteins. The IFT-B complex, which is powered by the kinesin-2 motor, mediates anterograde protein trafficking from the base to the tip of cilia, whereas the IFT-A complex together with the dynein-2 complex mediates retrograde protein trafficking. The BBSome complex connects ciliary membrane proteins to the IFT machinery. Defects in any component of this trafficking machinery lead to abnormal ciliogenesis and ciliary functions, and results in a broad spectrum of disorders, collectively called the ciliopathies. In this review article, we provide an overview of the architectures of the components of the IFT machinery and their functional interplay in ciliary protein trafficking.
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Affiliation(s)
- Kazuhisa Nakayama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yohei Katoh
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
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19
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Shi L, Chi Y, Shen X, Lu G, Shen Y. Intraflagellar Transport 80 Is Required for Cilia Construction and Maintenance in Paramecium tetraurelia. J Eukaryot Microbiol 2020; 67:521-531. [PMID: 32369644 DOI: 10.1111/jeu.12799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 03/09/2020] [Accepted: 04/26/2020] [Indexed: 01/21/2023]
Abstract
Intraflagellar transport (IFT) represents a bidirectional dynamic process that carries cargo essential for cilia building and the maintenance of ciliary function, which is important for the locomotion of single cells, intracellular and intercellular signalling transduction. Accumulated evidence has revealed that defects in IFT cause several clinical disorders. Here, we determined the role of IFT80, an IFT-B protein that is mutated in Jeune asphyxiating thoracic dystrophy. Using the RNAi method in the ciliate Paramecium as model, we found that loss of IFT80 prevents cilia biogenesis and causes strong cell lethality. A specific antibody against IFT80 was also prepared in our study, which labelled IFT80 in cilia of Paramecium. GFP fusion experiments were performed to illustrate the dynamic movement of IFT-A and IFT-B proteins in cilia of Paramecium; then, we found that the depletion of IFT80 in cells prevents IFT-A and IFT-B proteins from entering the cilia. Our results showed the distribution change of other IFT proteins in cells that were depleted of IFT80, and we discuss the possible roles of IFT80 in Paramecium.
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Affiliation(s)
- Lei Shi
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, China
| | - Yuhao Chi
- School of Pharmacy, Xinxiang Medical University, Xinxiang, 453003, China
| | - Xiangyu Shen
- School of Pharmacy, Xinxiang Medical University, Xinxiang, 453003, China
| | - Guoliang Lu
- School of Pharmacy, Xinxiang Medical University, Xinxiang, 453003, China
| | - Yuan Shen
- School of Pharmacy, Xinxiang Medical University, Xinxiang, 453003, China.,Xinxiang Key Laboratory of Clinical Psychopharmacology, Xinxiang, 453003, China
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20
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LIU MIN, ALHARBI MOHAMMED, GRAVES DANA, YANG SHUYING. IFT80 Is Required for Fracture Healing Through Controlling the Regulation of TGF-β Signaling in Chondrocyte Differentiation and Function. J Bone Miner Res 2020; 35:571-582. [PMID: 31643106 PMCID: PMC7525768 DOI: 10.1002/jbmr.3902] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 10/10/2019] [Accepted: 10/17/2019] [Indexed: 12/14/2022]
Abstract
Primary cilia are essential cellular organelles that are anchored at the cell surface membrane to sense and transduce signaling. Intraflagellar transport (IFT) proteins are indispensable for cilia formation and function. Although major advances in understanding the roles of these proteins in bone development have been made, the mechanisms by which IFT proteins regulate bone repair have not been identified. We investigated the role of the IFT80 protein in chondrocytes during fracture healing by creating femoral fractures in mice with conditional deletion of IFT80 in chondrocytes utilizing tamoxifen inducible Col2α1-CreER mice. Col2α1cre IFT80f/f mice had smaller fracture calluses than IFT80f/f (control) mice. The max-width and max-callus area were 31% and 48% smaller than those of the control mice, respectively. Col2α1cre IFT80f/f mice formed low-density/porous woven bony tissue with significantly lower ratio of bone volume, Trabecular (Tb) number and Tb thickness, and greater Tb spacing compared to control mice. IFT80 deletion significantly downregulated the expression of angiogenesis markers-VEGF, PDGF and angiopoietin and inhibited fracture callus vascularization. Mechanistically, loss of IFT80 in chondrocytes resulted in a decrease in cilia formation and chondrocyte proliferation rate in fracture callus compared to the control mice. Meanwhile, IFT80 deletion downregulated the TGF-β signaling pathway by inhibiting the expression of TGF-βI, TGF-βR, and phosphorylation of Smad2/3 in the fracture callus. In primary chondrocyte cultures in vitro, IFT80 deletion dramatically reduced chondrocyte proliferation, cilia assembly, and chondrogenic gene expression and differentiation. Collectively, our findings demonstrate that IFT80 and primary cilia play an essential role in fracture healing, likely through controlling chondrocyte proliferation and differentiation, and the TGF-β signaling pathway. © 2019 American Society for Bone and Mineral Research.
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Affiliation(s)
- MIN LIU
- Dept. of Anatomy and Cell Biology, University of
Pennsylvania, Philadelphia, PA
| | - MOHAMMED ALHARBI
- Dept. of Endodontics, Faculty of Dentistry, King Abdulaziz
University, Saudi Arabia
| | - DANA GRAVES
- Dept. of Periodontics, School of Dental Medicine,
University of Pennsylvania, Philadelphia, PA
| | - SHUYING YANG
- Dept. of Anatomy and Cell Biology, University of
Pennsylvania, Philadelphia, PA
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21
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Perretta-Tejedor N, Freke G, Seda M, Long DA, Jenkins D. Generating Mutant Renal Cell Lines Using CRISPR Technologies. Methods Mol Biol 2020; 2067:323-340. [PMID: 31701460 PMCID: PMC9703199 DOI: 10.1007/978-1-4939-9841-8_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Gene editing using the CRISPR/Cas9 system is an extremely efficient approach for generating mutations within the genomic DNA of immortalized cell lines. This procedure begins with a straightforward cloning step to generate a single plasmid encoding the Cas9 enzyme as well as a synthetic guide RNA (sgRNA) which is selected to target specific sites within the genome. This plasmid is transfected into cells either alone, in order to generate random insertion-deletion alleles ("indels") at the desired locus via the nonhomologous end-joining pathway, or in conjunction with a homology-directed repair template oligonucleotide to generate a specific point mutation. Here we describe a procedure to perform gene editing in IMCD3 and HEK293 cells and to subsequently isolate clonal cell lines carrying mutations of interest.
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Affiliation(s)
- Nuria Perretta-Tejedor
- Developmental Biology and Cancer, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Grace Freke
- Genetics and Genomic Medicine Programmes, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Marian Seda
- Genetics and Genomic Medicine Programmes, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - David A Long
- Developmental Biology and Cancer, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Dagan Jenkins
- Genetics and Genomic Medicine Programmes, Great Ormond Street Institute of Child Health, University College London, London, UK.
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22
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Chlamydomonas Basal Bodies as Flagella Organizing Centers. Cells 2018; 7:cells7070079. [PMID: 30018231 PMCID: PMC6070942 DOI: 10.3390/cells7070079] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 11/17/2022] Open
Abstract
During ciliogenesis, centrioles convert to membrane-docked basal bodies, which initiate the formation of cilia/flagella and template the nine doublet microtubules of the flagellar axoneme. The discovery that many human diseases and developmental disorders result from defects in flagella has fueled a strong interest in the analysis of flagellar assembly. Here, we will review the structure, function, and development of basal bodies in the unicellular green alga Chlamydomonas reinhardtii, a widely used model for the analysis of basal bodies and flagella. Intraflagellar transport (IFT), a flagella-specific protein shuttle critical for ciliogenesis, was first described in C. reinhardtii. A focus of this review will be on the role of the basal bodies in organizing the IFT machinery.
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