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Gao J, Tong M, Lee C, Gaertig J, Legal T, Bui KH. DomainFit: Identification of protein domains in cryo-EM maps at intermediate resolution using AlphaFold2-predicted models. Structure 2024; 32:1248-1259.e5. [PMID: 38754431 PMCID: PMC11316655 DOI: 10.1016/j.str.2024.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/18/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Cryoelectron microscopy (cryo-EM) has revolutionized the structural determination of macromolecular complexes. With the paradigm shift to structure determination of highly complex endogenous macromolecular complexes ex vivo and in situ structural biology, there are an increasing number of structures of native complexes. These complexes often contain unidentified proteins, related to different cellular states or processes. Identifying proteins at resolutions lower than 4 Å remains challenging because side chains cannot be visualized reliably. Here, we present DomainFit, a program for semi-automated domain-level protein identification from cryo-EM maps, particularly at resolutions lower than 4 Å. By fitting domains from AlphaFold2-predicted models into cryo-EM maps, the program performs statistical analyses and attempts to identify the domains and protein candidates forming the density. Using DomainFit, we identified two microtubule inner proteins, one of which contains a CCDC81 domain and is exclusively localized in the proximal region of the doublet microtubule in Tetrahymena thermophila.
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Affiliation(s)
- Jerry Gao
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC H3A 0C7, Canada; Centre de recherche en biologie structurale, McGill University, Montréal, QC H3G 0B1, Canada
| | - Maxwell Tong
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC H3A 0C7, Canada; Centre de recherche en biologie structurale, McGill University, Montréal, QC H3G 0B1, Canada
| | - Chinkyu Lee
- Department of Cellular Biology, University of Georgia, Athens 30602-2607, GA, USA
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens 30602-2607, GA, USA
| | - Thibault Legal
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC H3A 0C7, Canada; Centre de recherche en biologie structurale, McGill University, Montréal, QC H3G 0B1, Canada.
| | - Khanh Huy Bui
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC H3A 0C7, Canada; Centre de recherche en biologie structurale, McGill University, Montréal, QC H3G 0B1, Canada.
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Lee C, Maier W, Jiang YY, Nakano K, Lechtreck KF, Gaertig J. Global and local functions of the Fused kinase ortholog CdaH in intracellular patterning in Tetrahymena. J Cell Sci 2024; 137:jcs261256. [PMID: 37667859 PMCID: PMC10565251 DOI: 10.1242/jcs.261256] [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: 04/19/2023] [Accepted: 08/29/2023] [Indexed: 09/06/2023] Open
Abstract
Ciliates assemble numerous microtubular structures into complex cortical patterns. During ciliate division, the pattern is duplicated by intracellular segmentation that produces a tandem of daughter cells. In Tetrahymena thermophila, the induction and positioning of the division boundary involves two mutually antagonistic factors: posterior CdaA (cyclin E) and anterior CdaI (Hippo kinase). Here, we characterized the related cdaH-1 allele, which confers a pleiotropic patterning phenotype including an absence of the division boundary and an anterior-posterior mispositioning of the new oral apparatus. CdaH is a Fused or Stk36 kinase ortholog that localizes to multiple sites that correlate with the effects of its loss, including the division boundary and the new oral apparatus. CdaH acts downstream of CdaA to induce the division boundary and drives asymmetric cytokinesis at the tip of the posterior daughter. CdaH both maintains the anterior-posterior position of the new oral apparatus and interacts with CdaI to pattern ciliary rows within the oral apparatus. Thus, CdaH acts at multiple scales, from induction and positioning of structures on the cell-wide polarity axis to local organelle-level patterning.
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Affiliation(s)
- Chinkyu Lee
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Wolfgang Maier
- Bioinformatics, University of Freiburg, 79110 Freiburg, Germany
| | - Yu-Yang Jiang
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Kentaro Nakano
- Degree Programs in Biology, Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Karl F Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
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Gao J, Tong M, Lee C, Gaertig J, Legal T, Bui KH. DomainFit: Identification of Protein Domains in cryo-EM maps at Intermediate Resolution using AlphaFold2-predicted Models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569001. [PMID: 38077012 PMCID: PMC10705406 DOI: 10.1101/2023.11.28.569001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Cryo-electron microscopy (cryo-EM) has revolutionized our understanding of macromolecular complexes, enabling high-resolution structure determination. With the paradigm shift to in situ structural biology recently driven by the ground-breaking development of cryo-focused ion beam milling and cryo-electron tomography, there are an increasing number of structures at sub-nanometer resolution of complexes solved directly within their cellular environment. These cellular complexes often contain unidentified proteins, related to different cellular states or processes. Identifying proteins at resolutions lower than 4 Å remains challenging because the side chains cannot be visualized reliably. Here, we present DomainFit, a program for automated domain-level protein identification from cryo-EM maps at resolutions lower than 4 Å. By fitting domains from artificial intelligence-predicted models such as AlphaFold2-predicted models into cryo-EM maps, the program performs statistical analyses and attempts to identify the proteins forming the density. Using DomainFit, we identified two microtubule inner proteins, one of them, a CCDC81 domain-containing protein, is exclusively localized in the proximal region of the doublet microtubule from the ciliate Tetrahymena thermophila. The flexibility and capability of DomainFit makes it a valuable tool for analyzing in situ structures.
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Affiliation(s)
- Jerry Gao
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
- Centre de recherche en biologie structurale, McGill University, Montréal, Quebec, Canada
| | - Max Tong
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
- Centre de recherche en biologie structurale, McGill University, Montréal, Quebec, Canada
| | - Chinkyu Lee
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Thibault Legal
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
- Centre de recherche en biologie structurale, McGill University, Montréal, Quebec, Canada
| | - Khanh Huy Bui
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
- Centre de recherche en biologie structurale, McGill University, Montréal, Quebec, Canada
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4
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Legal T, Parra M, Tong M, Black CS, Joachimiak E, Valente-Paterno M, Lechtreck K, Gaertig J, Bui KH. CEP104/FAP256 and associated cap complex maintain stability of the ciliary tip. J Cell Biol 2023; 222:e202301129. [PMID: 37756660 PMCID: PMC10522465 DOI: 10.1083/jcb.202301129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 07/13/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Cilia are essential organelles that protrude from the cell body. Cilia are made of a microtubule-based structure called the axoneme. In most types of cilia, the ciliary tip is distinct from the rest of the cilium. Here, we used cryo-electron tomography and subtomogram averaging to obtain the structure of the ciliary tip of the ciliate Tetrahymena thermophila. We show that the microtubules at the tip are highly crosslinked with each other and stabilized by luminal proteins, plugs, and cap proteins at the plus ends. In the tip region, the central pair lacks typical projections and twists significantly. By analyzing cells lacking a ciliary tip-enriched protein CEP104/FAP256 by cryo-electron tomography and proteomics, we discovered candidates for the central pair cap complex and explained the potential functions of CEP104/FAP256. These data provide new insights into the function of the ciliary tip and the mechanisms of ciliary assembly and length regulation.
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Affiliation(s)
- Thibault Legal
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
| | - Mireya Parra
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Maxwell Tong
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
| | - Corbin S. Black
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Melissa Valente-Paterno
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
| | - Karl Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Khanh Huy Bui
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
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McCafferty CL, Papoulas O, Lee C, Bui KH, Taylor DW, Marcotte EM, Wallingford JB. An amino acid-resolution interactome for motile cilia illuminates the structure and function of ciliopathy protein complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.09.548259. [PMID: 37781579 PMCID: PMC10541116 DOI: 10.1101/2023.07.09.548259] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Motile cilia are ancient, evolutionarily conserved organelles whose dysfunction underlies motile ciliopathies, a broad class of human diseases. Motile cilia contain myriad different proteins that assemble into an array of distinct machines, so understanding the interactions and functional hierarchies among them presents an important challenge. Here, we defined the protein interactome of motile axonemes using cross-linking mass spectrometry (XL/MS) in Tetrahymena thermophila. From over 19,000 XLs, we identified 4,757 unique amino acid interactions among 1,143 distinct proteins, providing both macromolecular and atomic-scale insights into diverse ciliary machines, including the Intraflagellar Transport system, axonemal dynein arms, radial spokes, the 96 nm ruler, and microtubule inner proteins, among others. Guided by this dataset, we used vertebrate multiciliated cells to reveal novel functional interactions among several poorly-defined human ciliopathy proteins. The dataset therefore provides a powerful resource for studying the basic biology of an ancient organelle and the molecular etiology of human genetic disease.
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Affiliation(s)
- Caitlyn L. McCafferty
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Ophelia Papoulas
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Chanjae Lee
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Khanh Huy Bui
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences McGill University, Québec, Canada
| | - David W. Taylor
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Edward M. Marcotte
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - John B. Wallingford
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
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McCafferty CL, Pennington EL, Papoulas O, Taylor DW, Marcotte EM. Does AlphaFold2 model proteins' intracellular conformations? An experimental test using cross-linking mass spectrometry of endogenous ciliary proteins. Commun Biol 2023; 6:421. [PMID: 37061613 PMCID: PMC10105775 DOI: 10.1038/s42003-023-04773-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/28/2023] [Indexed: 04/17/2023] Open
Abstract
A major goal in structural biology is to understand protein assemblies in their biologically relevant states. Here, we investigate whether AlphaFold2 structure predictions match native protein conformations. We chemically cross-linked proteins in situ within intact Tetrahymena thermophila cilia and native ciliary extracts, identifying 1,225 intramolecular cross-links within the 100 best-sampled proteins, providing a benchmark of distance restraints obeyed by proteins in their native assemblies. The corresponding structure predictions were highly concordant, positioning 86.2% of cross-linked residues within Cɑ-to-Cɑ distances of 30 Å, consistent with the cross-linker length. 43% of proteins showed no violations. Most inconsistencies occurred in low-confidence regions or between domains. Overall, AlphaFold2 predictions with lower predicted aligned error corresponded to more correct native structures. However, we observe cases where rigid body domains are oriented incorrectly, as for ciliary protein BBC118, suggesting that combining structure prediction with experimental information will better reveal biologically relevant conformations.
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Affiliation(s)
- Caitlyn L McCafferty
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA.
| | - Erin L Pennington
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA
| | - Ophelia Papoulas
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA
| | - David W Taylor
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA.
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA.
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7
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Leggere JC, Hibbard JVK, Papoulas O, Lee C, Pearson CG, Marcotte EM, Wallingford JB. Label-free proteomic comparison reveals ciliary and non-ciliary phenotypes of IFT-A mutants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.08.531778. [PMID: 36945534 PMCID: PMC10028850 DOI: 10.1101/2023.03.08.531778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
DIFFRAC is a powerful method for systematically comparing proteome content and organization between samples in a high-throughput manner. By subjecting control and experimental protein extracts to native chromatography and quantifying the contents of each fraction using mass spectrometry, it enables the quantitative detection of alterations to protein complexes and abundances. Here, we applied DIFFRAC to investigate the consequences of genetic loss of Ift122, a subunit of the intraflagellar transport-A (IFT-A) protein complex that plays a vital role in the formation and function of cilia and flagella, on the proteome of Tetrahymena thermophila . A single DIFFRAC experiment was sufficient to detect changes in protein behavior that mirrored known effects of IFT-A loss and revealed new biology. We uncovered several novel IFT-A-regulated proteins, which we validated through live imaging in Xenopus multiciliated cells, shedding new light on both the ciliary and non-ciliary functions of IFT-A. Our findings underscore the robustness of DIFFRAC for revealing proteomic changes in response to genetic or biochemical perturbation.
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McCafferty CL, Papoulas O, Jordan MA, Hoogerbrugge G, Nichols C, Pigino G, Taylor DW, Wallingford JB, Marcotte EM. Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex. eLife 2022; 11:e81977. [PMID: 36346217 PMCID: PMC9674347 DOI: 10.7554/elife.81977] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/07/2022] [Indexed: 11/10/2022] Open
Abstract
Intraflagellar transport (IFT) is a conserved process of cargo transport in cilia that is essential for development and homeostasis in organisms ranging from algae to vertebrates. In humans, variants in genes encoding subunits of the cargo-adapting IFT-A and IFT-B protein complexes are a common cause of genetic diseases known as ciliopathies. While recent progress has been made in determining the atomic structure of IFT-B, little is known of the structural biology of IFT-A. Here, we combined chemical cross-linking mass spectrometry and cryo-electron tomography with AlphaFold2-based prediction of both protein structures and interaction interfaces to model the overall architecture of the monomeric six-subunit IFT-A complex, as well as its polymeric assembly within cilia. We define monomer-monomer contacts and membrane-associated regions available for association with transported cargo, and we also use this model to provide insights into the pleiotropic nature of human ciliopathy-associated genetic variants in genes encoding IFT-A subunits. Our work demonstrates the power of integration of experimental and computational strategies both for multi-protein structure determination and for understanding the etiology of human genetic disease.
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Affiliation(s)
- Caitlyn L McCafferty
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of TexasAustinUnited States
| | - Ophelia Papoulas
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of TexasAustinUnited States
| | - Mareike A Jordan
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Gabriel Hoogerbrugge
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of TexasAustinUnited States
| | - Candice Nichols
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of TexasAustinUnited States
| | | | - David W Taylor
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of TexasAustinUnited States
| | - John B Wallingford
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of TexasAustinUnited States
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of TexasAustinUnited States
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Niziolek M, Bicka M, Osinka A, Samsel Z, Sekretarska J, Poprzeczko M, Bazan R, Fabczak H, Joachimiak E, Wloga D. PCD Genes-From Patients to Model Organisms and Back to Humans. Int J Mol Sci 2022; 23:ijms23031749. [PMID: 35163666 PMCID: PMC8836003 DOI: 10.3390/ijms23031749] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 01/27/2023] Open
Abstract
Primary ciliary dyskinesia (PCD) is a hereditary genetic disorder caused by the lack of motile cilia or the assembxly of dysfunctional ones. This rare human disease affects 1 out of 10,000-20,000 individuals and is caused by mutations in at least 50 genes. The past twenty years brought significant progress in the identification of PCD-causative genes and in our understanding of the connections between causative mutations and ciliary defects observed in affected individuals. These scientific advances have been achieved, among others, due to the extensive motile cilia-related research conducted using several model organisms, ranging from protists to mammals. These are unicellular organisms such as the green alga Chlamydomonas, the parasitic protist Trypanosoma, and free-living ciliates, Tetrahymena and Paramecium, the invertebrate Schmidtea, and vertebrates such as zebrafish, Xenopus, and mouse. Establishing such evolutionarily distant experimental models with different levels of cell or body complexity was possible because both basic motile cilia ultrastructure and protein composition are highly conserved throughout evolution. Here, we characterize model organisms commonly used to study PCD-related genes, highlight their pros and cons, and summarize experimental data collected using these models.
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Affiliation(s)
- Michal Niziolek
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Marta Bicka
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
- Faculty of Chemistry, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Anna Osinka
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Zuzanna Samsel
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Justyna Sekretarska
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Martyna Poprzeczko
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
- Laboratory of Immunology, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawinskiego Street, 02-106 Warsaw, Poland
| | - Rafal Bazan
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Hanna Fabczak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
- Correspondence: (E.J.); (D.W.); Tel.: +48-22-58-92-338 (E.J. & D.W.)
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
- Correspondence: (E.J.); (D.W.); Tel.: +48-22-58-92-338 (E.J. & D.W.)
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10
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Black C, Dai DC, Peri K, Ichikawa M, Bui KH. Preparation of Doublet Microtubule Fraction for Single ParticleCryo-electron Microscopy. Bio Protoc 2021; 11:e4041. [PMID: 34250207 PMCID: PMC8249912 DOI: 10.21769/bioprotoc.4041] [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: 07/13/2020] [Revised: 02/03/2021] [Accepted: 02/08/2021] [Indexed: 11/02/2022] Open
Abstract
Over the years, studying the ultrastructure of the eukaryotic cilia/flagella using electron microscopy (EM) has contributed significantly toward our understanding of ciliary function. Major complexes in the cilia, such as inner and outer dynein arms, radial spokes, and dynein regulatory complexes, were originally discovered by EM. Classical resin-embedding EM or cryo-electron tomography can be performed directly on the isolated cilia or in some cases, cilia directly attached to the cell body. Recently, single particle cryo-EM has emerged as a powerful structural technique to elucidate high-resolution structures of macromolecular complexes; however, single particle cryo-EM requires non-overlapping complexes, i.e., the doublet microtubule of the cilia. Here, we present a protocol to separate the doublet microtubule from the isolated cilia bundle of two species, Tetrahymena thermophila and Chlamydomonas reinhardtii, using ATP reactivation and sonication. Our approach produces good distribution and random orientation of the doublet microtubule fragments, which is suitable for single particle cryo-EM analysis.
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Affiliation(s)
- Corbin Black
- Department of Anatomy and Cell Biology, McGill University, Montréal, Canada
| | - Daniel Chen Dai
- Department of Anatomy and Cell Biology, McGill University, Montréal, Canada
| | - Katya Peri
- Department of Anatomy and Cell Biology, McGill University, Montréal, Canada
| | - Muneyoshi Ichikawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama-cho, Ikoma, Nara, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Khanh Huy Bui
- Department of Anatomy and Cell Biology, McGill University, Montréal, Canada
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11
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Composition and function of the C1b/C1f region in the ciliary central apparatus. Sci Rep 2021; 11:11760. [PMID: 34083607 PMCID: PMC8175508 DOI: 10.1038/s41598-021-90996-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/19/2021] [Indexed: 02/04/2023] Open
Abstract
Motile cilia are ultrastructurally complex cell organelles with the ability to actively move. The highly conserved central apparatus of motile 9 × 2 + 2 cilia is composed of two microtubules and several large microtubule-bound projections, including the C1b/C1f supercomplex. The composition and function of C1b/C1f subunits has only recently started to emerge. We show that in the model ciliate Tetrahymena thermophila, C1b/C1f contains several evolutionarily conserved proteins: Spef2A, Cfap69, Cfap246/LRGUK, Adgb/androglobin, and a ciliate-specific protein Tt170/TTHERM_00205170. Deletion of genes encoding either Spef2A or Cfap69 led to a loss of the entire C1b projection and resulted in an abnormal vortex motion of cilia. Loss of either Cfap246 or Adgb caused only minor alterations in ciliary motility. Comparative analyses of wild-type and C1b-deficient mutant ciliomes revealed that the levels of subunits forming the adjacent C2b projection but not C1d projection are greatly reduced, indicating that C1b stabilizes C2b. Moreover, the levels of several IFT and BBS proteins, HSP70, and enzymes that catalyze the final steps of the glycolytic pathway: enolase ENO1 and pyruvate kinase PYK1, are also reduced in the C1b-less mutants.
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12
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Hazime KS, Zhou Z, Joachimiak E, Bulgakova NA, Wloga D, Malicki JJ. STORM imaging reveals the spatial arrangement of transition zone components and IFT particles at the ciliary base in Tetrahymena. Sci Rep 2021; 11:7899. [PMID: 33846423 PMCID: PMC8041816 DOI: 10.1038/s41598-021-86909-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/22/2021] [Indexed: 11/17/2022] Open
Abstract
The base of the cilium comprising the transition zone (TZ) and transition fibers (TF) acts as a selecting gate to regulate the intraflagellar transport (IFT)-dependent trafficking of proteins to and from cilia. Before entering the ciliary compartment, IFT complexes and transported cargoes accumulate at or near the base of the cilium. The spatial organization of IFT proteins at the cilia base is key for understanding cilia formation and function. Using stochastic optical reconstruction microscopy (STORM) and computational averaging, we show that seven TZ, nine IFT, three Bardet–Biedl syndrome (BBS), and one centrosomal protein, form 9-clustered rings at the cilium base of a ciliate Tetrahymena thermophila. In the axial dimension, analyzed TZ proteins localize to a narrow region of about 30 nm while IFT proteins dock approximately 80 nm proximal to TZ. Moreover, the IFT-A subcomplex is positioned peripheral to the IFT-B subcomplex and the investigated BBS proteins localize near the ciliary membrane. The positioning of the HA-tagged N- and C-termini of the selected proteins enabled the prediction of the spatial orientation of protein particles and likely cargo interaction sites. Based on the obtained data, we built a comprehensive 3D-model showing the arrangement of the investigated ciliary proteins.
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Affiliation(s)
- Khodor S Hazime
- Bateson Centre and the Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| | - Zhu Zhou
- Bateson Centre and the Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, 3 Pasteur Street, 02-093, Warsaw, Poland
| | - Natalia A Bulgakova
- Bateson Centre and the Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, 3 Pasteur Street, 02-093, Warsaw, Poland.
| | - Jarema J Malicki
- Bateson Centre and the Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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13
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Bazan R, Schröfel A, Joachimiak E, Poprzeczko M, Pigino G, Wloga D. Ccdc113/Ccdc96 complex, a novel regulator of ciliary beating that connects radial spoke 3 to dynein g and the nexin link. PLoS Genet 2021; 17:e1009388. [PMID: 33661892 PMCID: PMC7987202 DOI: 10.1371/journal.pgen.1009388] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/23/2021] [Accepted: 01/28/2021] [Indexed: 11/19/2022] Open
Abstract
Ciliary beating requires the coordinated activity of numerous axonemal complexes. The protein composition and role of radial spokes (RS), nexin links (N-DRC) and dyneins (ODAs and IDAs) is well established. However, how information is transmitted from the central apparatus to the RS and across other ciliary structures remains unclear. Here, we identify a complex comprising the evolutionarily conserved proteins Ccdc96 and Ccdc113, positioned parallel to N-DRC and forming a connection between RS3, dynein g, and N-DRC. Although Ccdc96 and Ccdc113 can be transported to cilia independently, their stable docking and function requires the presence of both proteins. Deletion of either CCDC113 or CCDC96 alters cilia beating frequency, amplitude and waveform. We propose that the Ccdc113/Ccdc96 complex transmits signals from RS3 and N-DRC to dynein g and thus regulates its activity and the ciliary beat pattern.
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Affiliation(s)
- Rafał Bazan
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Adam Schröfel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Martyna Poprzeczko
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Gaia Pigino
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Human Technopole, Milan, Italy
- * E-mail: (GP); (DW)
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
- * E-mail: (GP); (DW)
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14
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Rao VG, Kulkarni SS. Xenopus to the rescue: A model to validate and characterize candidate ciliopathy genes. Genesis 2021; 59:e23414. [PMID: 33576572 DOI: 10.1002/dvg.23414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 12/14/2022]
Abstract
Cilia are present on most vertebrate cells and play a central role in development, growth, and homeostasis. Thus, cilia dysfunction can manifest into an array of diseases, collectively termed ciliopathies, affecting millions of lives worldwide. Yet, our understanding of the gene regulatory networks that control cilia assembly and functions remain incomplete. With the advances in next-generation sequencing technologies, we can now rapidly predict pathogenic variants from hundreds of ciliopathy patients. While the pace of candidate gene discovery is exciting, most of these genes have never been previously implicated in cilia assembly or function. This makes assigning the disease causality difficult. This review discusses how Xenopus, a genetically tractable and high-throughput vertebrate model, has played a central role in identifying, validating, and characterizing candidate ciliopathy genes. The review is focused on multiciliated cells (MCCs) and diseases associated with MCC dysfunction. MCCs harbor multiple motile cilia on their apical surface to generate extracellular fluid flow inside the airway, the brain ventricles, and the oviduct. In Xenopus, these cells are external and present on the embryonic epidermal epithelia, facilitating candidate genes analysis in MCC development in vivo. The ability to introduce patient variants to study their effects on disease progression makes Xenopus a powerful model to improve our understanding of the underlying disease mechanisms and explain the patient phenotype.
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Affiliation(s)
- Venkatramanan G Rao
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Saurabh S Kulkarni
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia, USA.,Department of Biology, University of Virginia, Charlottesville, Virginia, USA
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15
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Jiang YY, Maier W, Chukka UN, Choromanski M, Lee C, Joachimiak E, Wloga D, Yeung W, Kannan N, Frankel J, Gaertig J. Mutual antagonism between Hippo signaling and cyclin E drives intracellular pattern formation. J Cell Biol 2020; 219:e202002077. [PMID: 32642758 PMCID: PMC7480119 DOI: 10.1083/jcb.202002077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/11/2020] [Accepted: 06/04/2020] [Indexed: 11/23/2022] Open
Abstract
Not much is known about how organelles organize into patterns. In ciliates, the cortical pattern is propagated during "tandem duplication," a cell division that remodels the parental cell into two daughter cells. A key step is the formation of the division boundary along the cell's equator. In Tetrahymena thermophila, the cdaA alleles prevent the formation of the division boundary. We find that the CDAA gene encodes a cyclin E that accumulates in the posterior cell half, concurrently with accumulation of CdaI, a Hippo/Mst kinase, in the anterior cell half. The division boundary forms between the margins of expression of CdaI and CdaA, which exclude each other from their own cortical domains. The activities of CdaA and CdaI must be balanced to initiate the division boundary and to position it along the cell's equator. CdaA and CdaI cooperate to position organelles near the new cell ends. Our data point to an intracellular positioning mechanism involving antagonistic Hippo signaling and cyclin E.
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Affiliation(s)
- Yu-Yang Jiang
- Department of Cellular Biology, University of Georgia, Athens, GA
| | - Wolfgang Maier
- Bioinformatics, University of Freiburg, Freiburg, Germany
| | | | | | - Chinkyu Lee
- Department of Cellular Biology, University of Georgia, Athens, GA
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA
| | - Joseph Frankel
- Department of Biology, University of Iowa, Iowa City, IA
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, GA
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16
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Soares H, Sunter JD, Wloga D, Joachimiak E, Miceli C. Trypanosoma, Paramecium and Tetrahymena: From genomics to flagellar and ciliary structures and cytoskeleton dynamics. Eur J Protistol 2020; 76:125722. [PMID: 32679518 DOI: 10.1016/j.ejop.2020.125722] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/06/2020] [Accepted: 05/11/2020] [Indexed: 02/06/2023]
Abstract
Cilia and flagella play an important role in motility, sensory perception, and the life cycles of eukaryotes, from protists to humans. However, much critical information concerning cilia structure and function remains elusive. The vast majority of ciliary and flagellar proteins analyzed so far are evolutionarily conserved and play a similar role in protozoa and vertebrates. This makes protozoa attractive biological models for studying cilia biology. Research conducted on ciliated or flagellated protists may improve our general understanding of cilia protein composition, of cilia beating, and can shed light on the molecular basis of the human disorders caused by motile cilia dysfunction. The Symposium "From genomics to flagellar and ciliary structures and cytoskeleton dynamics" at ECOP2019 in Rome presented the latest discoveries about cilia biogenesis and the molecular mechanisms of ciliary and flagellum motility based on studies in Paramecium, Tetrahymena, and Trypanosoma. Here, we review the most relevant aspects presented and discussed during the symposium and add our perspectives for future research.
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Affiliation(s)
- Helena Soares
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisboa, Portugal
| | - Jack D Sunter
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Cristina Miceli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy.
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17
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Heydeck W, Bayless BA, Stemm-Wolf AJ, O'Toole ET, Fabritius AS, Ozzello C, Nguyen M, Winey M. Tetrahymena Poc5 is a transient basal body component that is important for basal body maturation. J Cell Sci 2020; 133:jcs.240838. [PMID: 32350068 DOI: 10.1242/jcs.240838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 04/06/2020] [Indexed: 01/26/2023] Open
Abstract
Basal bodies (BBs) are microtubule-based organelles that act as a template for and stabilize cilia at the cell surface. Centrins ubiquitously associate with BBs and function in BB assembly, maturation and stability. Human POC5 (hPOC5) is a highly conserved centrin-binding protein that binds centrins through Sfi1p-like repeats and is required for building full-length, mature centrioles. Here, we use the BB-rich cytoskeleton of Tetrahymena thermophila to characterize Poc5 BB functions. Tetrahymena Poc5 (TtPoc5) uniquely incorporates into assembling BBs and is then removed from mature BBs prior to ciliogenesis. Complete genomic knockout of TtPOC5 leads to a significantly increased production of BBs, yet a markedly reduced ciliary density, both of which are rescued by reintroduction of TtPoc5. A second Tetrahymena POC5-like gene, SFR1, is similarly implicated in modulating BB production. When TtPOC5 and SFR1 are co-deleted, cell viability is compromised and BB overproduction is exacerbated. Overproduced BBs display defective transition zone formation and a diminished capacity for ciliogenesis. This study uncovers a requirement for Poc5 in building mature BBs, providing a possible functional link between hPOC5 mutations and impaired cilia.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Westley Heydeck
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Brian A Bayless
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Alexander J Stemm-Wolf
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Eileen T O'Toole
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Amy S Fabritius
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Courtney Ozzello
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Marina Nguyen
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Mark Winey
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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18
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Rare Human Diseases: Model Organisms in Deciphering the Molecular Basis of Primary Ciliary Dyskinesia. Cells 2019; 8:cells8121614. [PMID: 31835861 PMCID: PMC6952885 DOI: 10.3390/cells8121614] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/02/2019] [Accepted: 12/10/2019] [Indexed: 12/17/2022] Open
Abstract
Primary ciliary dyskinesia (PCD) is a recessive heterogeneous disorder of motile cilia, affecting one per 15,000-30,000 individuals; however, the frequency of this disorder is likely underestimated. Even though more than 40 genes are currently associated with PCD, in the case of approximately 30% of patients, the genetic cause of the manifested PCD symptoms remains unknown. Because motile cilia are highly evolutionarily conserved organelles at both the proteomic and ultrastructural levels, analyses in the unicellular and multicellular model organisms can help not only to identify new proteins essential for cilia motility (and thus identify new putative PCD-causative genes), but also to elucidate the function of the proteins encoded by known PCD-causative genes. Consequently, studies involving model organisms can help us to understand the molecular mechanism(s) behind the phenotypic changes observed in the motile cilia of PCD affected patients. Here, we summarize the current state of the art in the genetics and biology of PCD and emphasize the impact of the studies conducted using model organisms on existing knowledge.
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19
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Two Antagonistic Hippo Signaling Circuits Set the Division Plane at the Medial Position in the Ciliate Tetrahymena. Genetics 2018; 211:651-663. [PMID: 30593491 DOI: 10.1534/genetics.118.301889] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 12/21/2018] [Indexed: 12/17/2022] Open
Abstract
In a single cell, ciliates maintain a complex pattern of cortical organelles that are arranged along the anteroposterior and circumferential axes. The underlying molecular mechanisms of intracellular pattern formation in ciliates are largely unknown. Ciliates divide by tandem duplication, a process that remodels the parental cell into two daughters aligned head-to-tail. In the elo1-1 mutant of Tetrahymena thermophila, the segmentation boundary/division plane forms too close to the posterior end of the parental cell, producing a large anterior and a small posterior daughter cell, respectively. We show that ELO1 encodes a Lats/NDR kinase that marks the posterior segment of the cell cortex, where the division plane does not form in the wild-type. Elo1 acts independently of CdaI, a Hippo/Mst kinase that marks the anterior half of the parental cell, and whose loss shifts the division plane anteriorly. We propose that, in Tetrahymena, two antagonistic Hippo circuits focus the segmentation boundary/division plane at the equatorial position, by excluding divisional morphogenesis from the cortical areas that are too close to cell ends.
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20
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Louka P, Vasudevan KK, Guha M, Joachimiak E, Wloga D, Tomasi RFX, Baroud CN, Dupuis-Williams P, Galati DF, Pearson CG, Rice LM, Moresco JJ, Yates JR, Jiang YY, Lechtreck K, Dentler W, Gaertig J. Proteins that control the geometry of microtubules at the ends of cilia. J Cell Biol 2018; 217:4298-4313. [PMID: 30217954 PMCID: PMC6279374 DOI: 10.1083/jcb.201804141] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/25/2018] [Accepted: 08/31/2018] [Indexed: 11/22/2022] Open
Abstract
Cilia, essential motile and sensory organelles, have several compartments: the basal body, transition zone, and the middle and distal axoneme segments. The distal segment accommodates key functions, including cilium assembly and sensory activities. While the middle segment contains doublet microtubules (incomplete B-tubules fused to complete A-tubules), the distal segment contains only A-tubule extensions, and its existence requires coordination of microtubule length at the nanometer scale. We show that three conserved proteins, two of which are mutated in the ciliopathy Joubert syndrome, determine the geometry of the distal segment, by controlling the positions of specific microtubule ends. FAP256/CEP104 promotes A-tubule elongation. CHE-12/Crescerin and ARMC9 act as positive and negative regulators of B-tubule length, respectively. We show that defects in the distal segment dimensions are associated with motile and sensory deficiencies of cilia. Our observations suggest that abnormalities in distal segment organization cause a subset of Joubert syndrome cases.
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Affiliation(s)
- Panagiota Louka
- Department of Cellular Biology, University of Georgia, Athens, GA
| | | | - Mayukh Guha
- Department of Cellular Biology, University of Georgia, Athens, GA
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Raphaël F-X Tomasi
- Department of Mechanics, LadHyX, Ecole Polytechnique-Centre National de la Recherche Scientifique, Palaiseau, France
| | - Charles N Baroud
- Department of Mechanics, LadHyX, Ecole Polytechnique-Centre National de la Recherche Scientifique, Palaiseau, France
| | - Pascale Dupuis-Williams
- UMR-S1174 Institut National de la Santé et de la Recherche Médicale, Université Paris-Sud, Bat 443, Orsay, France
- École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris, Paris, France
| | - Domenico F Galati
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Chad G Pearson
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Luke M Rice
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA
| | - Yu-Yang Jiang
- Department of Cellular Biology, University of Georgia, Athens, GA
| | - Karl Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA
| | - William Dentler
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, GA
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21
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Reynolds MJ, Phetruen T, Fisher RL, Chen K, Pentecost BT, Gomez G, Ounjai P, Sui H. The Developmental Process of the Growing Motile Ciliary Tip Region. Sci Rep 2018; 8:7977. [PMID: 29789632 PMCID: PMC5964098 DOI: 10.1038/s41598-018-26111-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/01/2018] [Indexed: 11/09/2022] Open
Abstract
Eukaryotic motile cilia/flagella play vital roles in various physiological processes in mammals and some protists. Defects in cilia formation underlie multiple human disorders, known as ciliopathies. The detailed processes of cilia growth and development are still far from clear despite extensive studies. In this study, we characterized the process of cilium formation (ciliogenesis) by investigating the newly developed motile cilia of deciliated protists using complementary techniques in electron microscopy and image analysis. Our results demonstrated that the distal tip region of motile cilia exhibit progressive morphological changes as cilia develop. This developmental process is time-dependent and continues after growing cilia reach their full lengths. The structural analysis of growing ciliary tips revealed that B-tubules of axonemal microtubule doublets terminate far away from the tip end, which is led by the flagellar tip complex (FTC), demonstrating that the FTC might not directly mediate the fast turnover of intraflagellar transport (IFT).
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Affiliation(s)
- Matthew J Reynolds
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201, USA
- Biology Department, University of Scranton, Scranton, PA, 18510, USA
| | - Tanaporn Phetruen
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201, USA
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Rebecca L Fisher
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201, USA
| | - Ke Chen
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201, USA
| | - Brian T Pentecost
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201, USA
| | - George Gomez
- Biology Department, University of Scranton, Scranton, PA, 18510, USA
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Haixin Sui
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201, USA.
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, 12201, USA.
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22
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Jiang YY, Maier W, Baumeister R, Minevich G, Joachimiak E, Ruan Z, Kannan N, Clarke D, Frankel J, Gaertig J. The Hippo Pathway Maintains the Equatorial Division Plane in the Ciliate Tetrahymena. Genetics 2017; 206:873-888. [PMID: 28413159 PMCID: PMC5499192 DOI: 10.1534/genetics.117.200766] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/29/2017] [Indexed: 12/30/2022] Open
Abstract
The mechanisms that govern pattern formation within the cell are poorly understood. Ciliates carry on their surface an elaborate pattern of cortical organelles that are arranged along the anteroposterior and circumferential axes by largely unknown mechanisms. Ciliates divide by tandem duplication: the cortex of the predivision cell is remodeled into two similarly sized and complete daughters. In the conditional cdaI-1 mutant of Tetrahymena thermophila, the division plane migrates from its initially correct equatorial position toward the cell's anterior, resulting in unequal cell division, and defects in nuclear divisions and cytokinesis. We used comparative whole genome sequencing to identify the cause of cdaI-1 as a mutation in a Hippo/Mst kinase. CdaI is a cortical protein with a cell cycle-dependent, highly polarized localization. Early in cell division, CdaI marks the anterior half of the cell, and later concentrates at the posterior end of the emerging anterior daughter. Despite the strong association of CdaI with the new posterior cell end, the cdaI-1 mutation does not affect the patterning of the new posterior cortical organelles. We conclude that, in Tetrahymena, the Hippo pathway maintains an equatorial position of the fission zone, and, by this activity, specifies the relative dimensions of the anterior and posterior daughter cell.
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Affiliation(s)
- Yu-Yang Jiang
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602
| | - Wolfgang Maier
- Bio3/Bioinformatics and Molecular Genetics (Faculty of Biology) and ZMBZ (Faculty of Medicine)
| | - Ralf Baumeister
- Bio3/Bioinformatics and Molecular Genetics (Faculty of Biology) and ZMBZ (Faculty of Medicine)
- Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University of Freiburg, 79104 Germany
| | - Gregory Minevich
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Department of Cell Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Zheng Ruan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Diamond Clarke
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602
| | - Joseph Frankel
- Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602
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23
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Jiang YY, Lechtreck K, Gaertig J. Total internal reflection fluorescence microscopy of intraflagellar transport in Tetrahymena thermophila. Methods Cell Biol 2015; 127:445-56. [PMID: 25837403 DOI: 10.1016/bs.mcb.2015.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Live imaging has become a powerful tool in studies of ciliary proteins. Tetrahymena thermophila is an established ciliated model with well-developed genetic and biochemical approaches, but its large size, complex shape, and the large number of short and overlapping cilia, have made live imaging of ciliary proteins challenging. Here we describe a method that combines paralysis of cilia by nickel ions and total internal reflection microscopy for live imaging of fluorescent proteins inside cilia of Tetrahymena. Using this method, we quantitatively documented the intraflagellar transport in Tetrahymena.
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Affiliation(s)
- Yu-Yang Jiang
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Karl Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
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Vasudevan KK, Song K, Alford LM, Sale WS, Dymek EE, Smith EF, Hennessey T, Joachimiak E, Urbanska P, Wloga D, Dentler W, Nicastro D, Gaertig J. FAP206 is a microtubule-docking adapter for ciliary radial spoke 2 and dynein c. Mol Biol Cell 2014; 26:696-710. [PMID: 25540426 PMCID: PMC4325840 DOI: 10.1091/mbc.e14-11-1506] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Radial spokes are conserved macromolecular complexes that are essential for ciliary motility. Little is known about the assembly and functions of the three individual radial spokes, RS1, RS2, and RS3. In Tetrahymena, a conserved ciliary protein, FAP206, docks RS2 and dynein c to the doublet microtubule. Radial spokes are conserved macromolecular complexes that are essential for ciliary motility. A triplet of three radial spokes, RS1, RS2, and RS3, repeats every 96 nm along the doublet microtubules. Each spoke has a distinct base that docks to the doublet and is linked to different inner dynein arms. Little is known about the assembly and functions of individual radial spokes. A knockout of the conserved ciliary protein FAP206 in the ciliate Tetrahymena resulted in slow cell motility. Cryo–electron tomography showed that in the absence of FAP206, the 96-nm repeats lacked RS2 and dynein c. Occasionally, RS2 assembled but lacked both the front prong of its microtubule base and dynein c, whose tail is attached to the front prong. Overexpressed GFP-FAP206 decorated nonciliary microtubules in vivo. Thus FAP206 is likely part of the front prong and docks RS2 and dynein c to the microtubule.
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Affiliation(s)
| | - Kangkang Song
- Department of Biology, Rosenstiel Center, Brandeis University, Waltham, MA 02454
| | - Lea M Alford
- Department of Cell Biology, Emory University, Atlanta, GA 30303
| | - Winfield S Sale
- Department of Cell Biology, Emory University, Atlanta, GA 30303
| | - Erin E Dymek
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
| | - Elizabeth F Smith
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
| | - Todd Hennessey
- Department of Biological Sciences, State University of New York, Buffalo, NY 14260
| | - Ewa Joachimiak
- Department of Cell Biology, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland Department of Animal Physiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Paulina Urbanska
- Department of Cell Biology, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland
| | - Dorota Wloga
- Department of Cell Biology, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland
| | - William Dentler
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045
| | - Daniela Nicastro
- Department of Biology, Rosenstiel Center, Brandeis University, Waltham, MA 02454
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, GA 30602
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Vasudevan KK, Jiang YY, Lechtreck KF, Kushida Y, Alford LM, Sale WS, Hennessey T, Gaertig J. Kinesin-13 regulates the quantity and quality of tubulin inside cilia. Mol Biol Cell 2014; 26:478-94. [PMID: 25501369 PMCID: PMC4310739 DOI: 10.1091/mbc.e14-09-1354] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Kinesin-13, a microtubule-end depolymerase, has been shown to affect the length of cilia, but its ciliary function is unclear. In Tetrahymena thermophila, kinesin-13 positively regulates the axoneme length, influences the properties of ciliary tubulin, and affects the ciliary dynein-dependent motility. Kinesin-13, an end depolymerizer of cytoplasmic and spindle microtubules, also affects the length of cilia. However, in different models, depletion of kinesin-13 either lengthens or shortens cilia, and therefore the exact function of kinesin-13 in cilia remains unclear. We generated null mutations of all kinesin-13 paralogues in the ciliate Tetrahymena. One of the paralogues, Kin13Ap, localizes to the nuclei and is essential for nuclear divisions. The remaining two paralogues, Kin13Bp and Kin13Cp, localize to the cell body and inside assembling cilia. Loss of both Kin13Bp and Kin13Cp resulted in slow cell multiplication and motility, overgrowth of cell body microtubules, shortening of cilia, and synthetic lethality with either paclitaxel or a deletion of MEC-17/ATAT1, the α-tubulin acetyltransferase. The mutant cilia assembled slowly and contained abnormal tubulin, characterized by altered posttranslational modifications and hypersensitivity to paclitaxel. The mutant cilia beat slowly and axonemes showed reduced velocity of microtubule sliding. Thus kinesin-13 positively regulates the axoneme length, influences the properties of ciliary tubulin, and likely indirectly, through its effects on the axonemal microtubules, affects the ciliary dynein-dependent motility.
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Affiliation(s)
| | - Yu-Yang Jiang
- Department of Cellular Biology, University of Georgia, Athens, GA 30602
| | - Karl F Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA 30602
| | - Yasuharu Kushida
- Department of Structural Biosciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Lea M Alford
- Department of Cell Biology, Emory University, Atlanta, GA 30303
| | - Winfield S Sale
- Department of Cell Biology, Emory University, Atlanta, GA 30303
| | - Todd Hennessey
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, GA 30602;
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