1
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Zheng T, Cai S. Recent Technical Advances in Cellular Cryo-Electron Tomography. Int J Biochem Cell Biol 2024:106648. [PMID: 39181502 DOI: 10.1016/j.biocel.2024.106648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 08/20/2024] [Accepted: 08/20/2024] [Indexed: 08/27/2024]
Abstract
Understanding the in situ structure, organization, and interactions of macromolecules is essential for elucidating their functions and mechanisms of action. Cellular cryo-electron tomography (cryo-ET) is a cutting-edge technique that reveals in situ molecular-resolution architectures of macromolecules in their lifelike states. It also provides insights into the three-dimensional distribution of macromolecules and their spatial relationships with various subcellular structures. Thus, cellular cryo-ET bridges the gap between structural biology and cell biology. With rapid advancements, this technique achieved substantial improvements in throughput, automation, and resolution. This review presents the fundamental principles and methodologies of cellular cryo-ET, highlighting recent developments in sample preparation, data collection, and image processing. We also discuss emerging trends and potential future directions. As cellular cryo-ET continues to develop, it is set to play an increasingly vital role in structural cell biology.
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Affiliation(s)
- Tianyu Zheng
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shujun Cai
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen 518055, China
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2
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Abstract
Cilia are tail-like organelles responsible for motility, transportation, and sensory functions in eukaryotic cells. Cilia research has been providing multifaceted questions, attracting biologists of various areas and inducing interdisciplinary studies. In this chapter, we mainly focus on efforts to elucidate the molecular mechanism of ciliary beating motion, a field of research that has a long history and is still ongoing. We also overview topics closely related to the motility mechanism, such as ciliogenesis, cilia-related diseases, and sensory cilia. Subnanometer-scale to submillimeter-scale 3D imaging of the axoneme and the basal body resulted in a wide variety of insights into these questions.
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Affiliation(s)
- Takashi Ishikawa
- Department of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland.
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3
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A. Abd El Samad A. Transmission Electron Tomography: Intracellular Insight for the Future of Medicine. ELECTRON MICROSCOPY - NOVEL MICROSCOPY TRENDS 2019. [DOI: 10.5772/intechopen.84977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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4
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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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5
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Grotjahn DA, Lander GC. Setting the dynein motor in motion: New insights from electron tomography. J Biol Chem 2019; 294:13202-13217. [PMID: 31285262 DOI: 10.1074/jbc.rev119.003095] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Dyneins are ATP-fueled macromolecular machines that power all minus-end microtubule-based transport processes of molecular cargo within eukaryotic cells and play essential roles in a wide variety of cellular functions. These complex and fascinating motors have been the target of countless structural and biophysical studies. These investigations have elucidated the mechanism of ATP-driven force production and have helped unravel the conformational rearrangements associated with the dynein mechanochemical cycle. However, despite decades of research, it remains unknown how these molecular motions are harnessed to power massive cellular reorganization and what are the regulatory mechanisms that drive these processes. Recent advancements in electron tomography imaging have enabled researchers to visualize dynein motors in their transport environment with unprecedented detail and have led to exciting discoveries regarding dynein motor function and regulation. In this review, we will highlight how these recent structural studies have fundamentally propelled our understanding of the dynein motor and have revealed some unexpected, unifying mechanisms of regulation.
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Affiliation(s)
- Danielle A Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037.
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6
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Sasaki K, Shiba K, Nakamura A, Kawano N, Satouh Y, Yamaguchi H, Morikawa M, Shibata D, Yanase R, Jokura K, Nomura M, Miyado M, Takada S, Ueno H, Nonaka S, Baba T, Ikawa M, Kikkawa M, Miyado K, Inaba K. Calaxin is required for cilia-driven determination of vertebrate laterality. Commun Biol 2019; 2:226. [PMID: 31240264 PMCID: PMC6586612 DOI: 10.1038/s42003-019-0462-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 05/14/2019] [Indexed: 12/24/2022] Open
Abstract
Calaxin is a Ca2+-binding dynein-associated protein that regulates flagellar and ciliary movement. In ascidians, calaxin plays essential roles in chemotaxis of sperm. However, nothing has been known for the function of calaxin in vertebrates. Here we show that the mice with a null mutation in Efcab1, which encodes calaxin, display typical phenotypes of primary ciliary dyskinesia, including hydrocephalus, situs inversus, and abnormal motility of trachea cilia and sperm flagella. Strikingly, both males and females are viable and fertile, indicating that calaxin is not essential for fertilization in mice. The 9 + 2 axonemal structures of epithelial multicilia and sperm flagella are normal, but the formation of 9 + 0 nodal cilia is significantly disrupted. Knockout of calaxin in zebrafish also causes situs inversus due to the irregular ciliary beating of Kupffer's vesicle cilia, although the 9 + 2 axonemal structure appears to remain normal.
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Affiliation(s)
- Keita Sasaki
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, 415-0025 Japan
| | - Kogiku Shiba
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, 415-0025 Japan
| | - Akihiro Nakamura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, 415-0025 Japan
- Department of Reproductive Biology, National Center for Child Health and Development, Tokyo, 157-8535 Japan
| | - Natsuko Kawano
- Department of Life Science, School of Agriculture, Meiji University, Kanagawa, 214-8574 Japan
| | - Yuhkoh Satouh
- Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871 Japan
| | - Hiroshi Yamaguchi
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Motohiro Morikawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Daisuke Shibata
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, 415-0025 Japan
| | - Ryuji Yanase
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, 415-0025 Japan
| | - Kei Jokura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, 415-0025 Japan
| | - Mami Nomura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, 415-0025 Japan
| | - Mami Miyado
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535 Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, 157-8535 Japan
| | - Hironori Ueno
- Molecular Function & Life Sciences, Aichi University of Education, Aichi, 448-8542 Japan
| | - Shigenori Nonaka
- Spatiotemporal Regulations Group, Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, 444-8585 Japan
- Laboratory for Spatiotemporal Regulations, National Institute for Basic Biology, Okazaki, 444-8585 Japan
| | - Tadashi Baba
- Faculty of Life and Environmental Sciences, and Life Science Center for Survival Dynamics Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, 305-8577 Japan
| | - Masahito Ikawa
- Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871 Japan
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Kenji Miyado
- Department of Reproductive Biology, National Center for Child Health and Development, Tokyo, 157-8535 Japan
| | - Kazuo Inaba
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, 415-0025 Japan
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7
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Bottier M, Thomas KA, Dutcher SK, Bayly PV. How Does Cilium Length Affect Beating? Biophys J 2019; 116:1292-1304. [PMID: 30878201 PMCID: PMC6451027 DOI: 10.1016/j.bpj.2019.02.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/23/2019] [Accepted: 02/13/2019] [Indexed: 12/21/2022] Open
Abstract
The effects of cilium length on the dynamics of cilia motion were investigated by high-speed video microscopy of uniciliated mutants of the swimming alga, Chlamydomonas reinhardtii. Cells with short cilia were obtained by deciliating cells via pH shock and allowing cilia to reassemble for limited times. The frequency of cilia beating was estimated from the motion of the cell body and of the cilium. Key features of the ciliary waveform were quantified from polynomial curves fitted to the cilium in each image frame. Most notably, periodic beating did not emerge until the cilium reached a critical length between 2 and 4 μm. Surprisingly, in cells that exhibited periodic beating, the frequency of beating was similar for all lengths with only a slight decrease in frequency as length increased from 4 μm to the normal length of 10-12 μm. The waveform average curvature (rad/μm) was also conserved as the cilium grew. The mechanical metrics of ciliary propulsion (force, torque, and power) all increased in proportion to length. The mechanical efficiency of beating appeared to be maximal at the normal wild-type length of 10-12 μm. These quantitative features of ciliary behavior illuminate the biophysics of cilia motion and, in future studies, may help distinguish competing hypotheses of the underlying mechanism of oscillation.
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Affiliation(s)
- Mathieu Bottier
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, Missouri; Department of Genetics, Washington University in St. Louis, St. Louis, Missouri
| | - Kyle A Thomas
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, Missouri
| | - Susan K Dutcher
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri
| | - Philip V Bayly
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, Missouri.
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8
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Abstract
Motility of cilia (also known as flagella in some eukaryotes) is based on axonemal doublet microtubule sliding that is driven by the dynein molecular motors. Dyneins are organized into intricately patterned inner and outer rows of arms, whose collective activity is to produce inter-microtubule movement. However, to generate a ciliary bend, not all dyneins can be active simultaneously. The switch point model accounts, in part, for how dynein motors are regulated during ciliary movement. On the basis of this model, supported by key direct experimental observations as well as more recent theoretical and structural studies, we are now poised to understand the mechanics of how ciliary dynein coordination controls axonemal bend formation and propagation.
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Affiliation(s)
- Stephen M King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030-3305
| | - Winfield S Sale
- Department of Cell Biology, Emory University, Atlanta, GA 30322
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9
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Peabody JE, Shei RJ, Bermingham BM, Phillips SE, Turner B, Rowe SM, Solomon GM. Seeing cilia: imaging modalities for ciliary motion and clinical connections. Am J Physiol Lung Cell Mol Physiol 2018; 314:L909-L921. [PMID: 29493257 DOI: 10.1152/ajplung.00556.2017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The respiratory tract is lined with multiciliated epithelial cells that function to move mucus and trapped particles via the mucociliary transport apparatus. Genetic and acquired ciliopathies result in diminished mucociliary clearance, contributing to disease pathogenesis. Recent innovations in imaging technology have advanced our understanding of ciliary motion in health and disease states. Application of imaging modalities including transmission electron microscopy, high-speed video microscopy, and micron-optical coherence tomography could improve diagnostics and be applied for precision medicine. In this review, we provide an overview of ciliary motion, imaging modalities, and ciliopathic diseases of the respiratory system including primary ciliary dyskinesia, cystic fibrosis, chronic obstructive pulmonary disease, and idiopathic pulmonary fibrosis.
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Affiliation(s)
- Jacelyn E Peabody
- Department of Medicine, University of Alabama at Birmingham, Alabama.,Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham , Birmingham, Alabama
| | - Ren-Jay Shei
- Department of Medicine, University of Alabama at Birmingham, Alabama.,Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham , Birmingham, Alabama
| | | | - Scott E Phillips
- Department of Medicine, University of Alabama at Birmingham, Alabama
| | - Brett Turner
- Departments of Pediatrics and Cell Developmental and Integrative Biology, University of Alabama at Birmingham, Alabama
| | - Steven M Rowe
- Department of Medicine, University of Alabama at Birmingham, Alabama.,Departments of Pediatrics and Cell Developmental and Integrative Biology, University of Alabama at Birmingham, Alabama.,Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham , Birmingham, Alabama
| | - George M Solomon
- Department of Medicine, University of Alabama at Birmingham, Alabama.,Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham , Birmingham, Alabama
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10
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Hu T, Bayly PV. Finite element models of flagella with sliding radial spokes and interdoublet links exhibit propagating waves under steady dynein loading. Cytoskeleton (Hoboken) 2018; 75:185-200. [PMID: 29316355 DOI: 10.1002/cm.21432] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 12/21/2017] [Accepted: 12/22/2017] [Indexed: 12/11/2022]
Abstract
It remains unclear how flagella generate propulsive, oscillatory waveforms. While it is well known that dynein motors, in combination with passive cytoskeletal elements, drive the bending of the axoneme by applying shearing forces and bending moments to microtubule doublets, the origin of rhythmicity is still mysterious. Most conceptual models of flagellar oscillation involve dynein regulation or switching, so that dynein activity first on one side of the axoneme, then the other, drives bending. In contrast, a "viscoelastic flutter" mechanism has recently been proposed, based on a dynamic structural instability. Simple mathematical models of coupled elastic beams in viscous fluid, subjected to steady, axially distributed, dynein forces of sufficient magnitude, can exhibit oscillatory motion without any switching or dynamic regulation. Here we introduce more realistic finite element (FE) models of 6-doublet and 9-doublet flagella, with radial spokes and interdoublet links that slide along the central pair or corresponding doublet. These models demonstrate the viscoelastic flutter mechanism. Above a critical force threshold, these models exhibit an abrupt onset of propulsive, wavelike oscillations typical of flutter instability. Changes in the magnitude and spatial distribution of steady dynein force, or to viscous resistance, lead to behavior qualitatively consistent with experimental observations. This study demonstrates the ability of FE models to simulate nonlinear interactions between axonemal components during flagellar beating, and supports the plausibility of viscoelastic flutter as a mechanism of flagellar oscillation.
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Affiliation(s)
- Tianchen Hu
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, Missouri
| | - Philip V Bayly
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, Missouri
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11
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Kirima J, Oiwa K. Flagellar-associated Protein FAP85 Is a Microtubule Inner Protein That Stabilizes Microtubules. Cell Struct Funct 2017; 43:1-14. [PMID: 29311430 DOI: 10.1247/csf.17023] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Genomics and proteomics studies in Chlamydomonas have revealed that an axoneme is composed of 200-600 types of proteins, including uncharacterized proteins collectively named flagellar-associated proteins (FAPs). Nine FAPs contain the EF-hand motif; however, they have not yet been well characterized. To find components responsible for Chlamydomonas-specific waveform changes coupled with intracellular Ca2+ concentrations, we focused on FAP85, an EF-hand motif-containing FAP specific to Chlamydomonas and its relatives. We cloned the cDNA encoding FAP85, expressed it in Escherichia coli cells, and generated a polyclonal antibody against the expressed protein. Immunoblotting showed that FAP85 was present in every axoneme of several flagellar mutants lacking major axonemal components. Immuno-electron microscopy revealed that anti-FAP85 antibodies were found only on the inner wall of A-tubules of the doublets exposed by N-lauroylsarcosine (Sarkosyl) treatment. The zero-length cross-linker 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) applied to 0.6 M KCl-extracted axonemes generated a 75-kDa complex containing β-tubulin and FAP85. Further characterization of FAP85 and its effects on microtubule dynamics showed that FAP85 binds to tubulin and stabilized microtubules. According to these results, we conclude that FAP85 is a novel member of microtubule-binding proteins, localizing on the inner wall of the A-tubule and stabilizing microtubules.Key words: Chlamydomonas, flagella, doublet microtubule, microtubule inner proteins.
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Affiliation(s)
- Junya Kirima
- Department of Picobiology, Graduate School of Life Science, University of Hyogo
| | - Kazuhiro Oiwa
- Department of Picobiology, Graduate School of Life Science, University of Hyogo.,Advanced ICT Research Institute, National Institute of Information and Communications Technology
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12
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Schroeder JA. Application of laboratory and digital techniques for visual enhancement during the ultrastructural assessment of cilia. Ultrastruct Pathol 2017; 41:399-407. [DOI: 10.1080/01913123.2017.1363335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Josef A. Schroeder
- Central EM-Lab, Department of Pathology, University Hospital Regensburg, Regensburg, Germany
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13
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Stepp WL, Merck G, Mueller-Planitz F, Ökten Z. Kinesin-2 motors adapt their stepping behavior for processive transport on axonemes and microtubules. EMBO Rep 2017; 18:1947-1956. [PMID: 28887322 DOI: 10.15252/embr.201744097] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 08/11/2017] [Accepted: 08/14/2017] [Indexed: 11/09/2022] Open
Abstract
Two structurally distinct filamentous tracks, namely singlet microtubules in the cytoplasm and axonemes in the cilium, serve as railroads for long-range transport processes in vivo In all organisms studied so far, the kinesin-2 family is essential for long-range transport on axonemes. Intriguingly, in higher eukaryotes, kinesin-2 has been adapted to work on microtubules in the cytoplasm as well. Here, we show that heterodimeric kinesin-2 motors distinguish between axonemes and microtubules. Unlike canonical kinesin-1, kinesin-2 takes directional, off-axis steps on microtubules, but it resumes a straight path when walking on the axonemes. The inherent ability of kinesin-2 to side-track on the microtubule lattice restricts the motor to one side of the doublet microtubule in axonemes. The mechanistic features revealed here provide a molecular explanation for the previously observed partitioning of oppositely moving intraflagellar transport trains to the A- and B-tubules of the same doublet microtubule. Our results offer first mechanistic insights into why nature may have co-evolved the heterodimeric kinesin-2 with the ciliary machinery to work on the specialized axonemal surface for two-way traffic.
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Affiliation(s)
- Willi L Stepp
- Physik Department E22, Technische Universität München, Garching, Germany
| | - Georg Merck
- Physik Department E22, Technische Universität München, Garching, Germany
| | - Felix Mueller-Planitz
- Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Zeynep Ökten
- Physik Department E22, Technische Universität München, Garching, Germany .,Munich Center for Integrated Protein Science, Munich, Germany
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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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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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16
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Abstract
Electron cryotomography (ECT) provides three-dimensional views of macromolecular complexes inside cells in a native frozen-hydrated state. Over the last two decades, ECT has revealed the ultrastructure of cells in unprecedented detail. It has also allowed us to visualize the structures of macromolecular machines in their native context inside intact cells. In many cases, such machines cannot be purified intact for in vitro study. In other cases, the function of a structure is lost outside the cell, so that the mechanism can be understood only by observation in situ. In this review, we describe the technique and its history and provide examples of its power when applied to cell biology. We also discuss the integration of ECT with other techniques, including lower-resolution fluorescence imaging and higher-resolution atomic structure determination, to cover the full scale of cellular processes.
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Affiliation(s)
- Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125; ,
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125; , .,Howard Hughes Medical Institute, Pasadena, California 91125
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17
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Abstract
This is a history of cilia research before and after the discovery of intraflagellar transport (IFT) and the link between primary cilia ciliogenesis and polycystic kidney disease (PKD). Before IFT, ca. the beginning of the new millennium, although sensory and primary cilia were well described, research was largely focused on motile cilia, their structure, movement, and biogenesis. After IFT and the link to PKD, although work on motile cilia has continued to progress, research on primary cilia has exploded, leading to new insights into the role of cilia in cell signaling and development. Genomics, proteomics, and new imaging techniques have unified the field and pointed out the critical role of cilia as a restricted cell organellar compartment, functionally integrated with other cell organelles including the autophagosome and the nucleus.
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Affiliation(s)
- Peter Satir
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY USA
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18
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Abstract
The axoneme is the main extracellular part of cilia and flagella in eukaryotes. It consists of a microtubule cytoskeleton, which normally comprises nine doublets. In motile cilia, dynein ATPase motor proteins generate sliding motions between adjacent microtubules, which are integrated into a well-orchestrated beating or rotational motion. In primary cilia, there are a number of sensory proteins functioning on membranes surrounding the axoneme. In both cases, as the study of proteomics has elucidated, hundreds of proteins exist in this compartmentalized biomolecular system. In this article, we review the recent progress of structural studies of the axoneme and its components using electron microscopy and X-ray crystallography, mainly focusing on motile cilia. Structural biology presents snapshots (but not live imaging) of dynamic structural change and gives insights into the force generation mechanism of dynein, ciliary bending mechanism, ciliogenesis, and evolution of the axoneme.
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Affiliation(s)
- Takashi Ishikawa
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland.,Department of Biology, ETH Zurich, 5232 Villigen PSI, Switzerland
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19
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Kollmar M. Fine-Tuning Motile Cilia and Flagella: Evolution of the Dynein Motor Proteins from Plants to Humans at High Resolution. Mol Biol Evol 2016; 33:3249-3267. [PMID: 27880711 PMCID: PMC5100056 DOI: 10.1093/molbev/msw213] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The flagellum is a key innovation linked to eukaryogenesis. It provides motility by regulated cycles of bending and bend propagation, which are thought to be controlled by a complex arrangement of seven distinct dyneins in repeated patterns of outer- (OAD) and inner-arm dynein (IAD) complexes. Electron tomography showed high similarity of this axonemal repeat pattern across ciliates, algae, and animals, but the diversity of dynein sequences across the eukaryotes has not yet comprehensively been resolved and correlated with structural data. To shed light on the evolution of the axoneme I performed an exhaustive analysis of dyneins using the available sequenced genome data. Evidence from motor domain phylogeny allowed expanding the current set of nine dynein subtypes by eight additional isoforms with, however, restricted taxonomic distributions. I confirmed the presence of the nine dyneins in all eukaryotic super-groups indicating their origin predating the last eukaryotic common ancestor. The comparison of the N-terminal tail domains revealed a most likely axonemal dynein origin of the new classes, a group of chimeric dyneins in plants/algae and Stramenopiles, and the unique domain architecture and origin of the outermost OADs present in green algae and ciliates but not animals. The correlation of sequence and structural data suggests the single-headed class-8 and class-9 dyneins to localize to the distal end of the axonemal repeat and the class-7 dyneins filling the region up to the proximal heterodimeric IAD. Tracing dynein gene duplications across the eukaryotes indicated ongoing diversification and fine-tuning of flagellar functions in extant taxa and species.
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Affiliation(s)
- Martin Kollmar
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany
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Verhey KJ, Yang W. Permeability barriers for generating a unique ciliary protein and lipid composition. Curr Opin Cell Biol 2016; 41:109-16. [PMID: 27232950 DOI: 10.1016/j.ceb.2016.05.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 05/04/2016] [Accepted: 05/10/2016] [Indexed: 01/08/2023]
Abstract
Cilia (and flagella) are microtubule-based protrusions that are found in single or multiple copies on the surface of most eukaryotic cells. Defects in cilia formation and/or function have now been correlated with an expanding spectrum of human genetic diseases termed ciliopathies. Recent work indicates that cilia are indeed a bona fide organelle with a unique protein and lipid content that enables specific cellular functions. Despite the physiological and clinical relevance of cilia, our understanding of how a unique protein and lipid composition is generated for this organelle remains poor. Here we review recent work on the mechanisms that determine the protein and lipid content, and thus the functional outputs, of this unique organelle.
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Affiliation(s)
- Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
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21
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Lesich KA, dePinho TG, Pelle DW, Lindemann CB. Mechanics of the eukaryotic flagellar axoneme: Evidence for structural distortion during bending. Cytoskeleton (Hoboken) 2016; 73:233-45. [PMID: 27001352 DOI: 10.1002/cm.21296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 03/18/2016] [Accepted: 03/18/2016] [Indexed: 11/08/2022]
Abstract
The sliding doublet mechanism is the established explanation that allows us to understand the process of ciliary and flagellar bending. In this study, we apply the principles of the sliding doublet mechanism to analyze the mechanics of the counterbend phenomenon in sea urchin sperm flagella. When a passive, vanadate-treated, flagellum is forced into a bend with a glass microprobe, the portion of the flagellum distal to the probe exhibits a bend of opposite curvature (counterbend) to the imposed bend. This phenomenon was shown to be caused by the induction of inter-doublet shear and is dependent on the presence of an inter-doublet shear resistance. Here we report that in sea urchin flagella there is systematically less shear induced in the distal flagellum than is predicted by the sliding doublet mechanism, if we follow the assumption that the diameter of the flagellum is uniform. To account for the reduced shear that is observed, the likeliest and most direct interpretation is that the portion of the axoneme that is forced to bend undergoes substantial compression of the axoneme in the bending plane. A compression of 30-50 nm would be sufficient to account for the shear reduction from a bend of 2 radians. A compression of this magnitude would require considerable flexibility in the axoneme structure. This would necessitate that the radial spokes and/or the central pair apparatus are easily compressed by transverse stress. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Kathleen A Lesich
- Department of Biological Sciences, Oakland University, Rochester, Michigan
| | - Tania G dePinho
- Department of Biological Sciences, Oakland University, Rochester, Michigan
| | - Dominic W Pelle
- Department of Orthopaedic Surgery, Michigan State University/Grand Rapids Medical Education Partners, Grand Rapids, Michigan.,Van Andel Institute, Center for Skeletal Disease and Tumor Microenvironment, Grand Rapids, Michigan
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22
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Monroe N, Hill CP. Meiotic Clade AAA ATPases: Protein Polymer Disassembly Machines. J Mol Biol 2015; 428:1897-911. [PMID: 26555750 DOI: 10.1016/j.jmb.2015.11.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/03/2015] [Accepted: 11/04/2015] [Indexed: 12/20/2022]
Abstract
Meiotic clade AAA ATPases (ATPases associated with diverse cellular activities), which were initially grouped on the basis of phylogenetic classification of their AAA ATPase cassette, include four relatively well characterized family members, Vps4, spastin, katanin and fidgetin. These enzymes all function to disassemble specific polymeric protein structures, with Vps4 disassembling the ESCRT-III polymers that are central to the many membrane-remodeling activities of the ESCRT (endosomal sorting complexes required for transport) pathway and spastin, katanin p60 and fidgetin affecting multiple aspects of cellular dynamics by severing microtubules. They share a common domain architecture that features an N-terminal MIT (microtubule interacting and trafficking) domain followed by a single AAA ATPase cassette. Meiotic clade AAA ATPases function as hexamers that can cycle between the active assembly and inactive monomers/dimers in a regulated process, and they appear to disassemble their polymeric substrates by translocating subunits through the central pore of their hexameric ring. Recent studies with Vps4 have shown that nucleotide-induced asymmetry is a requirement for substrate binding to the pore loops and that recruitment to the protein lattice via MIT domains also relieves autoinhibition and primes the AAA ATPase cassettes for substrate binding. The most striking, unifying feature of meiotic clade AAA ATPases may be their MIT domain, which is a module that is found in a wide variety of proteins that localize to ESCRT-III polymers. Spastin also displays an adjacent microtubule binding sequence, and the presence of both ESCRT-III and microtubule binding elements may underlie the recent findings that the ESCRT-III disassembly function of Vps4 and the microtubule-severing function of spastin, as well as potentially katanin and fidgetin, are highly coordinated.
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Affiliation(s)
- Nicole Monroe
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112-5650, USA
| | - Christopher P Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112-5650, USA.
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