1
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Kubo T, Sasaki R, Oda T. Tubulin glycylation controls ciliary motility through modulation of outer-arm dyneins. Mol Biol Cell 2024; 35:ar90. [PMID: 38758663 PMCID: PMC11244163 DOI: 10.1091/mbc.e24-04-0154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2024] Open
Abstract
Tubulins undergo several kinds of posttranslational modifications (PTMs) including glutamylation and glycylation. The contribution of these PTMs to the motilities of cilia and flagella is still unclear. Here, we investigated the role of tubulin glycylation by examining a novel Chlamydomonas mutant lacking TTLL3, an enzyme responsible for initiating glycylation. Immunostaining of cells and flagella revealed that glycylation is only restricted to the axonemal tubulin composing the outer-doublet but not the central-pair microtubules. Furthermore, the flagellar localization of TTLL3 was found to be dependent on intraflagellar transport. The mutant, ttll3(ex5), completely lacks glycylation and consequently exhibits slower swimming velocity compared with the wild-type strain. By combining the ttll3(ex5) mutation with multiple axonemal dynein-deficient mutants, we found that the lack of glycylation does not affect the motility of the outer-arm dynein lacking mutations. Sliding disintegration assay using isolated axonemes revealed that the lack of glycylation decreases microtubule sliding velocity in the normal axoneme but not in the axoneme lacking the outerarm dyneins. Based on our recent study that glycylation occurs exclusively on β-tubulin in Chlamydomonas, these findings suggest that tubulin glycylation controls flagellar motility through modulating outer-arm dyneins, presumably by neutralizing the negative charges of glutamate residues at the C-terminus region of β-tubulin.
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Affiliation(s)
- Tomohiro Kubo
- Department of Anatomy and Structural Biology, Graduate School of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Rinka Sasaki
- Department of Anatomy and Structural Biology, Graduate School of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Toshiyuki Oda
- Department of Anatomy and Structural Biology, Graduate School of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
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2
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Viar GA, Pigino G. Tubulin posttranslational modifications through the lens of new technologies. Curr Opin Cell Biol 2024; 88:102362. [PMID: 38701611 DOI: 10.1016/j.ceb.2024.102362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 05/05/2024]
Abstract
The Tubulin Code revolutionizes our understanding of microtubule dynamics and functions, proposing a nuanced system governed by tubulin isotypes, posttranslational modifications (PTMs) and microtubule-associated proteins (MAPs). Tubulin isotypes, diverse across species, contribute structural complexity, and are thought to influence microtubule functions. PTMs encode dynamic information on microtubules, which are read by several microtubule interacting proteins and impact on cellular processes. Here we discuss recent technological and methodological advances, such as in genome engineering, live cell imaging, expansion microscopy, and cryo-electron microscopy that reveal new elements and levels of complexity of the tubulin code, including new modifying enzymes and nanopatterns of PTMs on individual microtubules. The Tubulin Code's exploration holds transformative potential, guiding therapeutic strategies and illuminating connections to diseases like cancer and neurodegenerative disorders, underscoring its relevance in decoding fundamental cellular language.
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Affiliation(s)
| | - Gaia Pigino
- Human Technopole, via Rita Levi Montalcini 1, Milan, Italy.
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3
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Walton T, Doran MH, Brown A. Structural determination and modeling of ciliary microtubules. Acta Crystallogr D Struct Biol 2024; 80:220-231. [PMID: 38451206 PMCID: PMC10994176 DOI: 10.1107/s2059798324001815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 02/24/2024] [Indexed: 03/08/2024] Open
Abstract
The axoneme, a microtubule-based array at the center of every cilium, has been the subject of structural investigations for decades, but only recent advances in cryo-EM and cryo-ET have allowed a molecular-level interpretation of the entire complex to be achieved. The unique properties of the nine doublet microtubules and central pair of singlet microtubules that form the axoneme, including the highly decorated tubulin lattice and the docking of massive axonemal complexes, provide opportunities and challenges for sample preparation, 3D reconstruction and atomic modeling. Here, the approaches used for cryo-EM and cryo-ET of axonemes are reviewed, while highlighting the unique opportunities provided by the latest generation of AI-guided tools that are transforming structural biology.
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Affiliation(s)
- Travis Walton
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew H. Doran
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Alan Brown
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
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4
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Brody SL, Pan J, Huang T, Xu J, Xu H, Koenitizer J, Brennan SK, Nanjundappa R, Saba TG, Berical A, Hawkins FJ, Wang X, Zhang R, Mahjoub MR, Horani A, Dutcher SK. Loss of an extensive ciliary connectome induces proteostasis and cell fate switching in a severe motile ciliopathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585965. [PMID: 38562900 PMCID: PMC10983967 DOI: 10.1101/2024.03.20.585965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Motile cilia have essential cellular functions in development, reproduction, and homeostasis. Genetic causes for motile ciliopathies have been identified, but the consequences on cellular functions beyond impaired motility remain unknown. Variants in CCDC39 and CCDC40 cause severe disease not explained by loss of motility. Using human cells with pathological variants in these genes, Chlamydomonas genetics, cryo-electron microscopy, single cell RNA transcriptomics, and proteomics, we identified perturbations in multiple cilia-independent pathways. Absence of the axonemal CCDC39/CCDC40 heterodimer results in loss of a connectome of over 90 proteins. The undocked connectome activates cell quality control pathways, switches multiciliated cell fate, impairs microtubule architecture, and creates a defective periciliary barrier. Both cilia-dependent and independent defects are likely responsible for the disease severity. Our findings provide a foundation for reconsidering the broad cellular impact of pathologic variants in ciliopathies and suggest new directions for therapies.
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Affiliation(s)
- Steven L Brody
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Jiehong Pan
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Tao Huang
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Jian Xu
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Huihui Xu
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Jeffrey Koenitizer
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Steven K Brennan
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Rashmi Nanjundappa
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Thomas G Saba
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, 48108, USA
| | - Andrew Berical
- Center for Regenerative Medicine, Boston University, Boston, MA, 02118, USA
| | - Finn J Hawkins
- Center for Regenerative Medicine, Boston University, Boston, MA, 02118, USA
| | - Xiangli Wang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Rui Zhang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Moe R Mahjoub
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
- Department of Cell Biology and Physisology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Amjad Horani
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, 48108, USA
- Department of Cell Biology and Physisology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Susan K Dutcher
- Department of Cell Biology and Physisology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, 63110, USA
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5
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Hwang J, Yanagisawa H, Davis KC, Hunter EL, Fox LA, Jimenez AR, Goodwin RE, Gordon SA, Stuart CDE, Bower R, Porter ME, Dutcher SK, Sale WS, Lechtreck KF, Alford LM. Assembly of FAP93 at the proximal axoneme in Chlamydomonas cilia. Cytoskeleton (Hoboken) 2024. [PMID: 38224153 DOI: 10.1002/cm.21818] [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: 09/19/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 01/16/2024]
Abstract
To identify proteins specific to the proximal ciliary axoneme, we used iTRAQ to compare short (~2 μm) and full-length (~11 μm) axonemes of Chlamydomonas. Known compoents of the proximal axoneme such as minor dynein heavy chains and LF5 kinase as well as the ciliary tip proteins FAP256 (CEP104) and EB1 were enriched in short axonemes whereas proteins present along the length of the axoneme were of similar abundance in both samples. The iTRAQ analysis revealed that FAP93, a protein of unknown function, and protein phosphatase 2A (PP2A) are enriched in the short axonemes. Consistently, immunoblots show enrichment of FAP93 and PP2A in short axonemes and immunofluorescence confirms the localization of FAP93 and enrichment of PP2A at the proximal axoneme. Ciliary regeneration reveals that FAP93 assembles continuously but more slowly than other axonemal structures and terminates at 1.03 μm in steady-state axonemes. The length of FAP93 assembly correlates with ciliary length, demonstrating ciliary length-dependent assembly of FAP93. Dikaryon rescue experiments show that FAP93 can assemble independently of IFT transport. In addition, FRAP analysis of GFP-tagged FAP93 demonstrates that FAP93 is stably anchored in axoneme. FAP93 may function as a scaffold for assembly of other specific proteins at the proximal axoneme.
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Affiliation(s)
- Juyeon Hwang
- Department of Cell Biology, Emory University, Atlanta, Georgia, USA
| | | | - Keira C Davis
- Department of Cell Biology, Emory University, Atlanta, Georgia, USA
- College of Arts & Sciences, Clayton State University, Morrow, Georgia, USA
| | - Emily L Hunter
- Department of Cell Biology, Emory University, Atlanta, Georgia, USA
- Science Communication Group, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Laura A Fox
- Department of Cell Biology, Emory University, Atlanta, Georgia, USA
| | - Ariana R Jimenez
- Division of Natural Sciences, Oglethorpe University, Atlanta, Georgia, USA
| | - Reagan E Goodwin
- Division of Natural Sciences, Oglethorpe University, Atlanta, Georgia, USA
| | - Sarah A Gordon
- Division of Natural Sciences, Oglethorpe University, Atlanta, Georgia, USA
| | | | - Raqual Bower
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Mary E Porter
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Susan K Dutcher
- Department of Genetics, Washington University St. Louis, St. Louis, Missouri, USA
| | - Winfield S Sale
- Department of Cell Biology, Emory University, Atlanta, Georgia, USA
| | - Karl F Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Lea M Alford
- Division of Natural Sciences, Oglethorpe University, Atlanta, Georgia, USA
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6
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Kanamaru T, Neuner A, Kurtulmus B, Pereira G. Balancing the length of the distal tip by septins is key for stability and signalling function of primary cilia. EMBO J 2022; 41:e108843. [PMID: 34981518 PMCID: PMC8724769 DOI: 10.15252/embj.2021108843] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/19/2021] [Accepted: 10/26/2021] [Indexed: 01/08/2023] Open
Abstract
Primary cilia are antenna-like organelles required for signalling transduction. How cilia structure is mechanistically maintained at steady-state to promote signalling is largely unknown. Here, we define that mammalian primary cilia axonemes are formed by proximal segment (PS) and distal segment (DS) delineated by tubulin polyglutamylation-rich and -poor regions, respectively. The analysis of proximal/distal segmentation indicated that perturbations leading to cilia over-elongation influenced PS or DS length with a different impact on cilia behaviour. We identified septins as novel repressors of DS growth. We show that septins control the localisation of MKS3 and CEP290 required for a functional transition zone (TZ), and the cilia tip accumulation of the microtubule-capping kinesin KIF7, a cilia-growth inhibitor. Live-cell imaging and analysis of sonic-hedgehog (SHH) signalling activation established that DS over-extension increased cilia ectocytosis events and decreased SHH activation. Our data underlines the importance of understanding cilia segmentation for length control and cilia-dependent signalling.
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Affiliation(s)
- Taishi Kanamaru
- Centre for Organismal Studies (COS)University of HeidelbergHeidelbergGermany
- German Cancer Research Centre (DKFZ)DKFZ‐ZMBH AllianceHeidelbergGermany
- Centre for Molecular Biology (ZMBH)University of HeidelbergHeidelbergGermany
| | - Annett Neuner
- Centre for Molecular Biology (ZMBH)University of HeidelbergHeidelbergGermany
| | - Bahtiyar Kurtulmus
- Centre for Organismal Studies (COS)University of HeidelbergHeidelbergGermany
- German Cancer Research Centre (DKFZ)DKFZ‐ZMBH AllianceHeidelbergGermany
- Centre for Molecular Biology (ZMBH)University of HeidelbergHeidelbergGermany
| | - Gislene Pereira
- Centre for Organismal Studies (COS)University of HeidelbergHeidelbergGermany
- German Cancer Research Centre (DKFZ)DKFZ‐ZMBH AllianceHeidelbergGermany
- Centre for Molecular Biology (ZMBH)University of HeidelbergHeidelbergGermany
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7
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Mathieu H, Patten SA, Aragon-Martin JA, Ocaka L, Simpson M, Child A, Moldovan F. Genetic variant of TTLL11 gene and subsequent ciliary defects are associated with idiopathic scoliosis in a 5-generation UK family. Sci Rep 2021; 11:11026. [PMID: 34040021 PMCID: PMC8155187 DOI: 10.1038/s41598-021-90155-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 05/04/2021] [Indexed: 02/07/2023] Open
Abstract
Idiopathic scoliosis (IS) is a complex 3D deformation of the spine with a strong genetic component, most commonly found in adolescent girls. Adolescent idiopathic scoliosis (AIS) affects around 3% of the general population. In a 5-generation UK family, linkage analysis identified the locus 9q31.2-q34.2 as a candidate region for AIS; however, the causative gene remained unidentified. Here, using exome sequencing we identified a rare insertion c.1569_1570insTT in the tubulin tyrosine ligase like gene, member 11 (TTLL11) within that locus, as the IS causative gene in this British family. Two other TTLL11 mutations were also identified in two additional AIS cases in the same cohort. Analyses of primary cells of individuals carrying the c.1569_1570insTT (NM_194252) mutation reveal a defect at the primary cilia level, which is less present, smaller and less polyglutamylated compared to control. Further, in a zebrafish, the knock down of ttll11, and the mutated ttll11 confirmed its role in spine development and ciliary function in the fish retina. These findings provide evidence that mutations in TTLL11, a ciliary gene, contribute to the pathogenesis of IS.
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Affiliation(s)
- Hélène Mathieu
- CHU Sainte-Justine Research Center, 3175 Côte Sainte-Catherine, 2.17.026, Montreal, QC, H3T 1C5, Canada
| | - Shunmoogum A Patten
- INRS-Centre Armand-Frappier Santé et Biotechnologie, Laval, QC, H7V1B7, Canada
| | | | - Louise Ocaka
- Centre for Translational Omics-GOSgene, Department of Genetics and Genomic Medicine, UCL GOSH Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
| | - Michael Simpson
- Genetics and Molecular Medicine, King's College London, SE1 1UL, London, UK
| | - Anne Child
- Marfan Trust, NHLI, Imperial College, Guy Scadding Building, London, SW3 6LY, UK.
| | - Florina Moldovan
- CHU Sainte-Justine Research Center, 3175 Côte Sainte-Catherine, 2.17.026, Montreal, QC, H3T 1C5, Canada.
- Faculty of Dentistry, Université de Montréal, Montreal, QC, H3T 1J4, Canada.
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8
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Song K, Shang Z, Fu X, Lou X, Grigorieff N, Nicastro D. In situ structure determination at nanometer resolution using TYGRESS. Nat Methods 2020; 17:201-208. [PMID: 31768058 PMCID: PMC7004880 DOI: 10.1038/s41592-019-0651-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/20/2019] [Accepted: 10/11/2019] [Indexed: 02/06/2023]
Abstract
The resolution of subtomogram averages calculated from cryo-electron tomograms (cryo-ET) of crowded cellular environments is often limited owing to signal loss in, and misalignment of, the subtomograms. By contrast, single-particle cryo-electron microscopy (SP-cryo-EM) routinely reaches near-atomic resolution of isolated complexes. We report a method called 'tomography-guided 3D reconstruction of subcellular structures' (TYGRESS) that is a hybrid of cryo-ET and SP-cryo-EM, and is able to achieve close-to-nanometer resolution of complexes inside crowded cellular environments. TYGRESS combines the advantages of SP-cryo-EM (images with good signal-to-noise ratio and contrast, as well as minimal radiation damage) and subtomogram averaging (three-dimensional alignment of macromolecules in a complex sample). Using TYGRESS, we determined the structure of the intact ciliary axoneme with up to resolution of 12 Å. These results reveal many structural details that were not visible by cryo-ET alone. TYGRESS is generally applicable to cellular complexes that are amenable to subtomogram averaging.
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Affiliation(s)
- Kangkang Song
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cryo-EM Core Facility, University of Massachusetts Medical School, Worcester, MA, USA
| | - Zhiguo Shang
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaofeng Fu
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Biological Science Imaging Resource, Florida State University, Tallahassee, FL, USA
| | - Xiaochu Lou
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nikolaus Grigorieff
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Daniela Nicastro
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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9
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Scaffold subunits support associated subunit assembly in the Chlamydomonas ciliary nexin-dynein regulatory complex. Proc Natl Acad Sci U S A 2019; 116:23152-23162. [PMID: 31659045 DOI: 10.1073/pnas.1910960116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The nexin-dynein regulatory complex (N-DRC) in motile cilia and flagella functions as a linker between neighboring doublet microtubules, acts to stabilize the axonemal core structure, and serves as a central hub for the regulation of ciliary motility. Although the N-DRC has been studied extensively using genetic, biochemical, and structural approaches, the precise arrangement of the 11 (or more) N-DRC subunits remains unknown. Here, using cryo-electron tomography, we have compared the structure of Chlamydomonas wild-type flagella to that of strains with specific DRC subunit deletions or rescued strains with tagged DRC subunits. Our results show that DRC7 is a central linker subunit that helps connect the N-DRC to the outer dynein arms. DRC11 is required for the assembly of DRC8, and DRC8/11 form a subcomplex in the proximal lobe of the linker domain that is required to form stable contacts to the neighboring B-tubule. Gold labeling of tagged subunits determines the precise locations of the previously ambiguous N terminus of DRC4 and C terminus of DRC5. DRC4 is now shown to contribute to the core scaffold of the N-DRC. Our results reveal the overall architecture of N-DRC, with the 3 subunits DRC1/2/4 forming a core complex that serves as the scaffold for the assembly of the "functional subunits," namely DRC3/5-8/11. These findings shed light on N-DRC assembly and its role in regulating flagellar beating.
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10
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Osinka A, Poprzeczko M, Zielinska MM, Fabczak H, Joachimiak E, Wloga D. Ciliary Proteins: Filling the Gaps. Recent Advances in Deciphering the Protein Composition of Motile Ciliary Complexes. Cells 2019; 8:cells8070730. [PMID: 31319499 PMCID: PMC6678824 DOI: 10.3390/cells8070730] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/12/2019] [Accepted: 07/16/2019] [Indexed: 12/15/2022] Open
Abstract
Cilia are highly evolutionarily conserved, microtubule-based cell protrusions present in eukaryotic organisms from protists to humans, with the exception of fungi and higher plants. Cilia can be broadly divided into non-motile sensory cilia, called primary cilia, and motile cilia, which are locomotory organelles. The skeleton (axoneme) of primary cilia is formed by nine outer doublet microtubules distributed on the cilium circumference. In contrast, the skeleton of motile cilia is more complex: in addition to outer doublets, it is composed of two central microtubules and several diverse multi-protein complexes that are distributed periodically along both types of microtubules. For many years, researchers have endeavored to fully characterize the protein composition of ciliary macro-complexes and the molecular basis of signal transduction between these complexes. Genetic and biochemical analyses have suggested that several hundreds of proteins could be involved in the assembly and function of motile cilia. Within the last several years, the combined efforts of researchers using cryo-electron tomography, genetic and biochemical approaches, and diverse model organisms have significantly advanced our knowledge of the ciliary structure and protein composition. Here, we summarize the recent progress in the identification of the subunits of ciliary complexes, their precise intraciliary localization determined by cryo-electron tomography data, and the role of newly identified proteins in cilia.
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Affiliation(s)
- Anna Osinka
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Martyna Poprzeczko
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Magdalena M Zielinska
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Hanna Fabczak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland.
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland.
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11
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Kubo T, Oda T. Chlamydomonas as a tool to study tubulin polyglutamylation. Microscopy (Oxf) 2019; 68:80-91. [PMID: 30364995 DOI: 10.1093/jmicro/dfy044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/11/2018] [Accepted: 10/10/2018] [Indexed: 12/15/2022] Open
Abstract
The diversity of α- and β-tubulin is facilitated by various post-translational modifications (PTMs), such as acetylation, tyrosination, glycylation, glutamylation, phosphorylation and methylation. These PTMs affect the stability and structure of microtubules as well as the interaction between microtubules and microtubule-associated proteins, including molecular motors. Therefore, it is extremely important to investigate the roles of tubulin PTMs for understanding the cell cycle, cell motility and intracellular trafficking. Tubulin PTMs were first studied in the 1980s, and considerable progress has been made since then; it is likely that additional mechanisms remain yet to be elucidated. Here, we discuss one such modification, tubulin glutamylation, and introduce our research on the eukaryotic flagellum of the unicellular green alga Chlamydomonas reinhardtii.
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Affiliation(s)
- Tomohiro Kubo
- Department of Anatomy and Structural Biology, Graduate School of Medicine, University of Yamanashi, Shimokato, Chuo, Yamanashi, Japan
| | - Toshiyuki Oda
- Department of Anatomy and Structural Biology, Graduate School of Medicine, University of Yamanashi, Shimokato, Chuo, Yamanashi, Japan
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12
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Hong SR, Wang CL, Huang YS, Chang YC, Chang YC, Pusapati GV, Lin CY, Hsu N, Cheng HC, Chiang YC, Huang WE, Shaner NC, Rohatgi R, Inoue T, Lin YC. Spatiotemporal manipulation of ciliary glutamylation reveals its roles in intraciliary trafficking and Hedgehog signaling. Nat Commun 2018; 9:1732. [PMID: 29712905 PMCID: PMC5928066 DOI: 10.1038/s41467-018-03952-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 03/22/2018] [Indexed: 12/22/2022] Open
Abstract
Tubulin post-translational modifications (PTMs) occur spatiotemporally throughout cells and are suggested to be involved in a wide range of cellular activities. However, the complexity and dynamic distribution of tubulin PTMs within cells have hindered the understanding of their physiological roles in specific subcellular compartments. Here, we develop a method to rapidly deplete tubulin glutamylation inside the primary cilia, a microtubule-based sensory organelle protruding on the cell surface, by targeting an engineered deglutamylase to the cilia in minutes. This rapid deglutamylation quickly leads to altered ciliary functions such as kinesin-2-mediated anterograde intraflagellar transport and Hedgehog signaling, along with no apparent crosstalk to other PTMs such as acetylation and detyrosination. Our study offers a feasible approach to spatiotemporally manipulate tubulin PTMs in living cells. Future expansion of the repertoire of actuators that regulate PTMs may facilitate a comprehensive understanding of how diverse tubulin PTMs encode ciliary as well as cellular functions. Tubulin post-translational modifications (PTMs) occur spatiotemporally throughout cells, therefore assessing the physiological roles in specific subcellular compartments has been challenging. Here the authors develop a method to rapidly deplete tubulin glutamylation inside the primary cilia by targeting an engineered deglutamylase to the axoneme.
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Affiliation(s)
- Shi-Rong Hong
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Cuei-Ling Wang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yao-Shen Huang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yu-Chen Chang
- Department of Life Science, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Ya-Chu Chang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Ganesh V Pusapati
- Departments of Medicine and Biochemistry, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Chun-Yu Lin
- Department of Medical Science, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Ning Hsu
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Hsiao-Chi Cheng
- Department of Medical Science, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yueh-Chen Chiang
- Interdisciplinary Program of Science, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Wei-En Huang
- Department of Life Science, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Nathan C Shaner
- Department of Photobiology and Bioimaging, The Scintillon Institute, San Diego, 92121, CA, USA
| | - Rajat Rohatgi
- Departments of Medicine and Biochemistry, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Takanari Inoue
- Department of Cell Biology, Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, 21205, MD, USA.
| | - Yu-Chun Lin
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 30013, Taiwan. .,Department of Medical Science, National Tsing Hua University, Hsinchu, 30013, Taiwan.
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13
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Bower R, Tritschler D, Mills KV, Heuser T, Nicastro D, Porter ME. DRC2/CCDC65 is a central hub for assembly of the nexin-dynein regulatory complex and other regulators of ciliary and flagellar motility. Mol Biol Cell 2017; 29:137-153. [PMID: 29167384 PMCID: PMC5909927 DOI: 10.1091/mbc.e17-08-0510] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/13/2017] [Accepted: 11/15/2017] [Indexed: 02/01/2023] Open
Abstract
DRC2 is a subunit of the nexin–dynein regulatory complex linked to primary ciliary dyskinesia. Little is known about the impact of drc2 mutations on axoneme composition and structure. We used proteomic and structural approaches to reveal that DRC2 coassembles with DRC1 to attach the N-DRC to the A-tubule and mediate interactions with other regulatory structures. The nexin–dynein regulatory complex (N-DRC) plays a central role in the regulation of ciliary and flagellar motility. In most species, the N-DRC contains at least 11 subunits, but the specific function of each subunit is unknown. Mutations in three subunits (DRC1, DRC2/CCDC65, DRC4/GAS8) have been linked to defects in ciliary motility in humans and lead to a ciliopathy known as primary ciliary dyskinesia (PCD). Here we characterize the biochemical, structural, and motility phenotypes of two mutations in the DRC2 gene of Chlamydomonas. Using high-resolution proteomic and structural approaches, we find that the C-terminal region of DRC2 is critical for the coassembly of DRC2 and DRC1 to form the base plate of N-DRC and its attachment to the outer doublet microtubule. Loss of DRC2 in drc2 mutants disrupts the assembly of several other N-DRC subunits and also destabilizes the assembly of several closely associated structures such as the inner dynein arms, the radial spokes, and the calmodulin- and spoke-associated complex. Our study provides new insights into the range of ciliary defects that can lead to PCD.
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Affiliation(s)
- Raqual Bower
- Department of Genetics, Cell Biology, and Development, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Douglas Tritschler
- Department of Genetics, Cell Biology, and Development, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Kristyn VanderWaal Mills
- Department of Genetics, Cell Biology, and Development, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Thomas Heuser
- Biology Department and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454.,Vienna Biocenter Core Facilities, 1030 Vienna, Austria
| | - Daniela Nicastro
- Biology Department and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454.,Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Mary E Porter
- Department of Genetics, Cell Biology, and Development, University of Minnesota Medical School, Minneapolis, MN 55455
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14
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Oda T. Three-dimensional structural labeling microscopy of cilia and flagella. Microscopy (Oxf) 2017; 66:234-244. [PMID: 28541401 DOI: 10.1093/jmicro/dfx018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/13/2017] [Indexed: 06/07/2023] Open
Abstract
Locating a molecule within a cell using protein-tagging and immunofluorescence is a fundamental technique in cell biology, whereas in three-dimensional electron microscopy, locating a subunit within a macromolecular complex remains challenging. Recently, we developed a new structural labeling method for cryo-electron tomography by taking advantage of the biotin-streptavidin system, and have intensively used this method to locate a number of proteins and protein domains in cilia and flagella. In this review, we summarize our findings on the three-dimensional architecture of the axoneme, especially the importance of coiled-coil proteins. In addition, we provide an overview of the technical aspects of our structural labeling method.
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Affiliation(s)
- Toshiyuki Oda
- Department of Anatomy and Structural Biology, Graduate School of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898, Japan
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15
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Viswanadha R, Sale WS, Porter ME. Ciliary Motility: Regulation of Axonemal Dynein Motors. Cold Spring Harb Perspect Biol 2017; 9:9/8/a018325. [PMID: 28765157 DOI: 10.1101/cshperspect.a018325] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Ciliary motility is crucial for the development and health of many organisms. Motility depends on the coordinated activity of multiple dynein motors arranged in a precise pattern on the outer doublet microtubules. Although significant progress has been made in elucidating the composition and organization of the dyneins, a comprehensive understanding of dynein regulation is lacking. Here, we focus on two conserved signaling complexes located at the base of the radial spokes. These include the I1/f inner dynein arm associated with radial spoke 1 and the calmodulin- and spoke-associated complex and the nexin-dynein regulatory complex associated with radial spoke 2. Current research is focused on understanding how these two axonemal hubs coordinate and regulate the dynein motors and ciliary motility.
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Affiliation(s)
- Rasagnya Viswanadha
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Winfield S Sale
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Mary E Porter
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455
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16
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Kubo T, Oda T. Electrostatic interaction between polyglutamylated tubulin and the nexin-dynein regulatory complex regulates flagellar motility. Mol Biol Cell 2017. [PMID: 28637765 PMCID: PMC5555654 DOI: 10.1091/mbc.e17-05-0285] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The 3D localization of polyglutamylated tubulin in eukaryotic flagella is identified. Polyglutamylated tubulins are located on the interface between the microtubule and its cross-bridging structure, the N-DRC. Flagellar motility is regulated by electrostatic interaction between negatively charged tubulins and positively charged N-DRC. Tubulins undergo various posttranslational modifications. Among them, polyglutamylation is involved in the motility of eukaryotic flagella and the stability of the axonemal microtubules. However, it remains unclear where polyglutamylated tubulin localizes precisely within the axoneme and how tubulin polyglutamylation affects flagellar motility. In this study, we identified the three-dimensional localization of the polyglutamylated tubulin in Chlamydomonas flagella using antibody labeling and cryo–electron tomography. Polyglutamylated tubulins specifically located in close proximity to a microtubule-cross-bridging structure called the nexin–dynein regulatory complex (N-DRC). Because N-DRC is positively charged, we hypothesized that there is an electrostatic interaction between the polyglutamylated tubulin and the N-DRC, and therefore we mutated the amino acid sequences of DRC4 to modify the charge of the N-DRC. We found that both augmentation and reduction of the positive charge on DRC4 resulted in reduced flagellar motility. Moreover, reduced motility in a mutant with a structurally defective N-DRC was partially restored by increasing the positive charge on DRC4. These results clearly indicate that beating motion of flagella is maintained by the electrostatic cross-bridge formed between the negatively charged polyglutamylated tubulins and the positively charged N-DRC.
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Affiliation(s)
- Tomohiro Kubo
- Department of Anatomy and Structural Biology, Graduate School of Medical Science, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Toshiyuki Oda
- Department of Anatomy and Structural Biology, Graduate School of Medical Science, University of Yamanashi, Yamanashi 409-3898, Japan
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17
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Wloga D, Joachimiak E, Louka P, Gaertig J. Posttranslational Modifications of Tubulin and Cilia. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a028159. [PMID: 28003186 DOI: 10.1101/cshperspect.a028159] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Tubulin undergoes several highly conserved posttranslational modifications (PTMs) including acetylation, detyrosination, glutamylation, and glycylation. These PTMs accumulate on a subset of microtubules that are long-lived, including those in the basal bodies and axonemes. Tubulin PTMs are distributed nonuniformly. In the outer doublet microtubules of the axoneme, the B-tubules are highly enriched in the detyrosinated, polyglutamylated, and polyglycylated tubulin, whereas the A-tubules contain mostly unmodified tubulin. The nonuniform patterns of tubulin PTMs may functionalize microtubules in a position-dependent manner. Recent studies indicate that tubulin PTMs contribute to the assembly, disassembly, maintenance, and motility of cilia. In particular, tubulin glutamylation has emerged as a key PTM that affects ciliary motility through regulation of axonemal dynein arms and controls the stability and length of the axoneme.
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Affiliation(s)
- Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Department of Cell Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Department of Cell Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Panagiota Louka
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602
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