1
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Aher A, Urnavicius L, Xue A, Neselu K, Kapoor TM. Structure of the γ-tubulin ring complex-capped microtubule. Nat Struct Mol Biol 2024; 31:1124-1133. [PMID: 38609661 PMCID: PMC11257807 DOI: 10.1038/s41594-024-01264-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/04/2024] [Indexed: 04/14/2024]
Abstract
Microtubules are composed of α-tubulin and β-tubulin dimers positioned head-to-tail to form protofilaments that associate laterally in varying numbers. It is not known how cellular microtubules assemble with the canonical 13-protofilament architecture, resulting in micrometer-scale α/β-tubulin tracks for intracellular transport that align with, rather than spiral along, the long axis of the filament. We report that the human ~2.3 MDa γ-tubulin ring complex (γ-TuRC), an essential regulator of microtubule formation that contains 14 γ-tubulins, selectively nucleates 13-protofilament microtubules. Cryogenic electron microscopy reconstructions of γ-TuRC-capped microtubule minus ends reveal the extensive intra-domain and inter-domain motions of γ-TuRC subunits that accommodate luminal bridge components and establish lateral and longitudinal interactions between γ-tubulins and α-tubulins. Our structures suggest that γ-TuRC, an inefficient nucleation template owing to its splayed conformation, can transform into a compacted cap at the microtubule minus end and set the lattice architecture of cellular microtubules.
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Affiliation(s)
- Amol Aher
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA
| | - Linas Urnavicius
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA
| | - Allen Xue
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA
| | - Kasahun Neselu
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA.
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2
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Chen J, Zehr EA, Gruschus JM, Szyk A, Liu Y, Tanner ME, Tjandra N, Roll-Mecak A. Tubulin code eraser CCP5 binds branch glutamates by substrate deformation. Nature 2024; 631:905-912. [PMID: 39020174 DOI: 10.1038/s41586-024-07699-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 06/11/2024] [Indexed: 07/19/2024]
Abstract
Microtubule function is modulated by the tubulin code, diverse posttranslational modifications that are altered dynamically by writer and eraser enzymes1. Glutamylation-the addition of branched (isopeptide-linked) glutamate chains-is the most evolutionarily widespread tubulin modification2. It is introduced by tubulin tyrosine ligase-like enzymes and erased by carboxypeptidases of the cytosolic carboxypeptidase (CCP) family1. Glutamylation homeostasis, achieved through the balance of writers and erasers, is critical for normal cell function3-9, and mutations in CCPs lead to human disease10-13. Here we report cryo-electron microscopy structures of the glutamylation eraser CCP5 in complex with the microtubule, and X-ray structures in complex with transition-state analogues. Combined with NMR analysis, these analyses show that CCP5 deforms the tubulin main chain into a unique turn that enables lock-and-key recognition of the branch glutamate in a cationic pocket that is unique to CCP family proteins. CCP5 binding of the sequences flanking the branch point primarily through peptide backbone atoms enables processing of diverse tubulin isotypes and non-tubulin substrates. Unexpectedly, CCP5 exhibits inefficient processing of an abundant β-tubulin isotype in the brain. This work provides an atomistic view into glutamate branch recognition and resolution, and sheds light on homeostasis of the tubulin glutamylation syntax.
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Affiliation(s)
- Jiayi Chen
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Elena A Zehr
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - James M Gruschus
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Agnieszka Szyk
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Yanjie Liu
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin E Tanner
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nico Tjandra
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA.
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3
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Eibauer M, Weber MS, Kronenberg-Tenga R, Beales CT, Boujemaa-Paterski R, Turgay Y, Sivagurunathan S, Kraxner J, Köster S, Goldman RD, Medalia O. Vimentin filaments integrate low-complexity domains in a complex helical structure. Nat Struct Mol Biol 2024; 31:939-949. [PMID: 38632361 PMCID: PMC11189308 DOI: 10.1038/s41594-024-01261-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 03/01/2024] [Indexed: 04/19/2024]
Abstract
Intermediate filaments (IFs) are integral components of the cytoskeleton. They provide cells with tissue-specific mechanical properties and are involved in numerous cellular processes. Due to their intricate architecture, a 3D structure of IFs has remained elusive. Here we use cryo-focused ion-beam milling, cryo-electron microscopy and tomography to obtain a 3D structure of vimentin IFs (VIFs). VIFs assemble into a modular, intertwined and flexible helical structure of 40 α-helices in cross-section, organized into five protofibrils. Surprisingly, the intrinsically disordered head domains form a fiber in the lumen of VIFs, while the intrinsically disordered tails form lateral connections between the protofibrils. Our findings demonstrate how protein domains of low sequence complexity can complement well-folded protein domains to construct a biopolymer with striking mechanical strength and stretchability.
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Affiliation(s)
- Matthias Eibauer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
| | - Miriam S Weber
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Charlie T Beales
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Yagmur Turgay
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Suganya Sivagurunathan
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Julia Kraxner
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
- MDC Berlin-Buch, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
| | - Robert D Goldman
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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4
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Conboy JP, Istúriz Petitjean I, van der Net A, Koenderink GH. How cytoskeletal crosstalk makes cells move: Bridging cell-free and cell studies. BIOPHYSICS REVIEWS 2024; 5:021307. [PMID: 38840976 PMCID: PMC11151447 DOI: 10.1063/5.0198119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/13/2024] [Indexed: 06/07/2024]
Abstract
Cell migration is a fundamental process for life and is highly dependent on the dynamical and mechanical properties of the cytoskeleton. Intensive physical and biochemical crosstalk among actin, microtubules, and intermediate filaments ensures their coordination to facilitate and enable migration. In this review, we discuss the different mechanical aspects that govern cell migration and provide, for each mechanical aspect, a novel perspective by juxtaposing two complementary approaches to the biophysical study of cytoskeletal crosstalk: live-cell studies (often referred to as top-down studies) and cell-free studies (often referred to as bottom-up studies). We summarize the main findings from both experimental approaches, and we provide our perspective on bridging the two perspectives to address the open questions of how cytoskeletal crosstalk governs cell migration and makes cells move.
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Affiliation(s)
- James P. Conboy
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Irene Istúriz Petitjean
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Anouk van der Net
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Gijsje H. Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
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5
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Perez-Bertoldi JM, Zhao Y, Thawani A, Yildiz A, Nogales E. Molecular interplay between HURP and Kif18A in mitotic spindle regulation. RESEARCH SQUARE 2024:rs.3.rs-4249615. [PMID: 38854046 PMCID: PMC11160874 DOI: 10.21203/rs.3.rs-4249615/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
During mitosis, microtubule dynamics are regulated to ensure proper alignment and segregation of chromosomes. The dynamics of kinetochore-attached microtubules are regulated by hepatoma-upregulated protein (HURP) and the mitotic kinesin-8 Kif18A, but the underlying mechanism remains elusive. Using single-molecule imaging in vitro, we demonstrate that Kif18A motility is regulated by HURP. While sparse decoration of HURP activates the motor, higher concentrations hinder processive motility. To shed light on this behavior, we determined the binding mode of HURP to microtubules using Cryo-EM. The structure reveals that one HURP motif spans laterally across β-tubulin, while a second motif binds between adjacent protofilaments. HURP partially overlaps with the microtubule-binding site of the Kif18A motor domain, indicating that excess HURP inhibits Kif18A motility by steric exclusion. We also observed that HURP and Kif18A function together to suppress dynamics of the microtubule plus-end, providing a mechanistic basis for how they collectively serve in spindle length control.
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Affiliation(s)
| | - Yuanchang Zhao
- Physics Department, University of California, Berkeley, CA, USA
| | - Akanksha Thawani
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Ahmet Yildiz
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
- Physics Department, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
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6
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Perez-Bertoldi JM, Zhao Y, Thawani A, Yildiz A, Nogales E. Molecular interplay between HURP and Kif18A in mitotic spindle regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.589088. [PMID: 38645125 PMCID: PMC11030443 DOI: 10.1101/2024.04.11.589088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
During mitosis, microtubule dynamics are regulated to ensure proper alignment and segregation of chromosomes. The dynamics of kinetochore-attached microtubules are regulated by hepatoma-upregulated protein (HURP) and the mitotic kinesin-8 Kif18A, but the underlying mechanism remains elusive. Using single-molecule imaging in vitro , we demonstrate that Kif18A motility is regulated by HURP. While sparse decoration of HURP activates the motor, higher concentrations hinder processive motility. To shed light on this behavior, we determined the binding mode of HURP to microtubules using Cryo-EM. The structure reveals that one HURP motif spans laterally across β-tubulin, while a second motif binds between adjacent protofilaments. HURP partially overlaps with the microtubule-binding site of the Kif18A motor domain, indicating that excess HURP inhibits Kif18A motility by steric exclusion. We also observed that HURP and Kif18A function together to suppress dynamics of the microtubule plus-end, providing a mechanistic basis for how they collectively serve in spindle length control.
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7
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Adler A, Bangera M, Beugelink JW, Bahri S, van Ingen H, Moores CA, Baldus M. A structural and dynamic visualization of the interaction between MAP7 and microtubules. Nat Commun 2024; 15:1948. [PMID: 38431715 PMCID: PMC10908866 DOI: 10.1038/s41467-024-46260-5] [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: 06/02/2023] [Accepted: 02/21/2024] [Indexed: 03/05/2024] Open
Abstract
Microtubules (MTs) are key components of the eukaryotic cytoskeleton and are essential for intracellular organization, organelle trafficking and mitosis. MT tasks depend on binding and interactions with MT-associated proteins (MAPs). MT-associated protein 7 (MAP7) has the unusual ability of both MT binding and activating kinesin-1-mediated cargo transport along MTs. Additionally, the protein is reported to stabilize MTs with its 112 amino-acid long MT-binding domain (MTBD). Here we investigate the structural basis of the interaction of MAP7 MTBD with the MT lattice. Using a combination of solid and solution-state nuclear magnetic resonance (NMR) spectroscopy with electron microscopy, fluorescence anisotropy and isothermal titration calorimetry, we shed light on the binding mode of MAP7 to MTs at an atomic level. Our results show that a combination of interactions between MAP7 and MT lattice extending beyond a single tubulin dimer and including tubulin C-terminal tails contribute to formation of the MAP7-MT complex.
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Affiliation(s)
- Agnes Adler
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Mamata Bangera
- Institute of Structural and Molecular Biology, School of Natural Sciences, Birkbeck, University of London, London, WC1E 7HX, UK
| | - J Wouter Beugelink
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Salima Bahri
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Hugo van Ingen
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Carolyn A Moores
- Institute of Structural and Molecular Biology, School of Natural Sciences, Birkbeck, University of London, London, WC1E 7HX, UK.
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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8
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Ori-McKenney KM, McKenney RJ. Tau oligomerization on microtubules in health and disease. Cytoskeleton (Hoboken) 2024; 81:35-40. [PMID: 37747123 PMCID: PMC10841430 DOI: 10.1002/cm.21785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023]
Affiliation(s)
- Kassandra M Ori-McKenney
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, California, USA
| | - Richard J McKenney
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, California, USA
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9
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Valdez V, Ma M, Gouveia B, Zhang R, Petry S. HURP facilitates spindle assembly by stabilizing microtubules and working synergistically with TPX2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.571906. [PMID: 38187686 PMCID: PMC10769297 DOI: 10.1101/2023.12.18.571906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
In large vertebrate spindles, the majority of microtubules are formed via branching microtubule nucleation, whereby microtubules nucleate along the side of pre-existing microtubules. Hepatoma up-regulated protein (HURP) is a microtubule-associated protein that has been implicated in spindle assembly, but its mode of action is yet to be defined. In this study, we show that HURP is necessary for RanGTP-induced branching microtubule nucleation in Xenopus egg extract. Specifically, HURP stabilizes the microtubule lattice to promote microtubule formation from γ-TuRC. This function is shifted to promote branching microtubule nucleation in the presence of TPX2, another branching-promoting factor, as HURP's localization to microtubules is enhanced by TPX2 condensation. Lastly, we provide a structure of HURP on the microtubule lattice, revealing how HURP binding stabilizes the microtubule lattice. We propose a model in which HURP stabilizes microtubules during their formation, and TPX2 preferentially enriches HURP to microtubules to promote branching microtubule nucleation and thus spindle assembly.
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Affiliation(s)
- Venecia Valdez
- Princeton University, Department of Molecular Biology, Princeton, New Jersey, United States
| | - Meisheng Ma
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine (St. Louis, Missouri, United States)
- Present address: Department of Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology (Wuhan, Hubei, China)
| | - Bernardo Gouveia
- Princeton University, Department of Chemical and Biological Engineering, Princeton, New Jersey, United States
| | - Rui Zhang
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine (St. Louis, Missouri, United States)
| | - Sabine Petry
- Princeton University, Department of Molecular Biology, Princeton, New Jersey, United States
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10
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Aher A, Urnavicius L, Xue A, Neselu K, Kapoor TM. Structure of the γ-tubulin ring complex-capped microtubule. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567916. [PMID: 38045257 PMCID: PMC10690160 DOI: 10.1101/2023.11.20.567916] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Microtubules are composed of α/β-tubulin dimers positioned head-to-tail to form protofilaments that associate laterally in varying numbers. It is not known how cellular microtubules assemble with the canonical 13-protofilament architecture, resulting in micrometer-scale α/β-tubulin tracks for intracellular transport that align with, rather than spiral along, the filament's long-axis. We report that the human ∼2.3MDa γ-tubulin ring complex (γ-TuRC), an essential regulator of microtubule formation that contains 14 γ-tubulins, selectively nucleates 13-protofilament microtubules. Cryo-EM reconstructions of γ-TuRC-capped microtubule minus-ends reveal the extensive intra- and inter-domain motions of γ-TuRC subunits that accommodate its actin-containing luminal bridge and establish lateral and longitudinal interactions between γ- and α-tubulins. Our structures reveal how free γ-TuRC, an inefficient nucleation template due to its splayed conformation, transforms into a stable cap that blocks addition or loss of α/β-tubulins from minus-ends and sets the lattice architecture of cellular microtubules. One Sentence Summary Structural insights into how the γ-tubulin ring complex nucleates and caps a 13-protofilament microtubule.
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11
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Shen Y, Ori-McKenney KM. Macromolecular Crowding Tailors the Microtubule Cytoskeleton Through Tubulin Modifications and Microtubule-Associated Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544846. [PMID: 37398431 PMCID: PMC10312695 DOI: 10.1101/2023.06.14.544846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Cells remodel their cytoskeletal networks to adapt to their environment. Here, we analyze the mechanisms utilized by the cell to tailor its microtubule landscape in response to changes in osmolarity that alter macromolecular crowding. By integrating live cell imaging, ex vivo enzymatic assays, and in vitro reconstitution, we probe the impact of acute perturbations in cytoplasmic density on microtubule-associated proteins (MAPs) and tubulin posttranslational modifications (PTMs), unraveling the molecular underpinnings of cellular adaptation via the microtubule cytoskeleton. We find that cells respond to fluctuations in cytoplasmic density by modulating microtubule acetylation, detyrosination, or MAP7 association, without differentially affecting polyglutamylation, tyrosination, or MAP4 association. These MAP-PTM combinations alter intracellular cargo transport, enabling the cell to respond to osmotic challenges. We further dissect the molecular mechanisms governing tubulin PTM specification, and find that MAP7 promotes acetylation by biasing the conformation of the microtubule lattice, and directly inhibits detyrosination. Acetylation and detyrosination can therefore be decoupled and utilized for distinct cellular purposes. Our data reveal that the MAP code dictates the tubulin code, resulting in remodeling of the microtubule cytoskeleton and alteration of intracellular transport as an integrated mechanism of cellular adaptation.
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Affiliation(s)
- Yusheng Shen
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Kassandra M Ori-McKenney
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
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12
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Liu H, Shima T. Preference of CAMSAP3 for expanded microtubule lattice contributes to stabilization of the minus end. Life Sci Alliance 2023; 6:e202201714. [PMID: 36894175 PMCID: PMC9998277 DOI: 10.26508/lsa.202201714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 03/11/2023] Open
Abstract
CAMSAPs are proteins that show microtubule minus-end-specific localization, decoration, and stabilization. Although the mechanism for minus-end recognition via their C-terminal CKK domain has been well described in recent studies, it is unclear how CAMSAPs stabilize microtubules. Our several binding assays revealed that the D2 region of CAMSAP3 specifically binds to microtubules with the expanded lattice. To investigate the relationship between this preference and the stabilization effect of CAMSAP3, we precisely measured individual microtubule lengths and found that D2 binding expanded the microtubule lattice by ∼3%. Consistent with the notion that the expanded lattice is a common feature of stable microtubules, the presence of D2 slowed the microtubule depolymerization rate to ∼1/20, suggesting that the D2-triggered lattice expansion stabilizes microtubules. Combining these results, we propose that CAMSAP3 stabilizes microtubules by lattice expansion upon D2 binding, which further accelerates the recruitment of other CAMSAP3 molecules. Because only CAMSAP3 has D2 and the highest microtubule-stabilizing effect among mammalian CAMSAPs, our model also explains the molecular basis for the functional diversity of CAMSAP family members.
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Affiliation(s)
- Hanjin Liu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tomohiro Shima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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13
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Beckett D, Voth GA. Unveiling the Catalytic Mechanism of GTP Hydrolysis in Microtubules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.01.538927. [PMID: 37205601 PMCID: PMC10187240 DOI: 10.1101/2023.05.01.538927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Microtubules (MTs) are large cytoskeletal polymers, composed of αβ-tubulin heterodimers, capable of stochastically converting from polymerizing to depolymerizing states and vice-versa. Depolymerization is coupled with hydrolysis of GTP within β-tubulin. Hydrolysis is favored in the MT lattice compared to free heterodimer with an experimentally observed rate increase of 500 to 700 fold, corresponding to an energetic barrier lowering of 3.8 to 4.0 kcal/mol. Mutagenesis studies have implicated α-tubulin residues, α:E254 and α:D251, as catalytic residues completing the β-tubulin active site of the lower heterodimer in the MT lattice. The mechanism for GTP hydrolysis in the free heterodimer, however, is not understood. Additionally, there has been debate concerning whether the GTP-state lattice is expanded or compacted relative to the GDP-state and whether a "compacted" GDP-state lattice is required for hydrolysis. In this work, extensive QM/MM simulations with transition-tempered metadynamics free energy sampling of compacted and expanded inter-dimer complexes, as well as free heterodimer, have been carried out to provide clear insight into the GTP hydrolysis mechanism. α:E254 was found to be the catalytic residue in a compacted lattice, while in the expanded lattice disruption of a key salt bridge interaction renders α:E254 less effective. The simulations reveal a barrier decrease of 3.8 ± 0.5 kcal/mol for the compacted lattice compared to free heterodimer, in good agreement with experimental kinetic measurements. Additionally, the expanded lattice barrier was found to be 6.3 ± 0.5 kcal/mol higher than compacted, demonstrating that GTP hydrolysis is variable with lattice state and slower at the MT tip. Significance Statement Microtubules (MTs) are large and dynamic components of the eukaryotic cytoskeleton with the ability to stochastically convert from a polymerizing to a depolymerizing state and vice-versa. Depolymerization is coupled to the hydrolysis of guanosine-5'-triphosphate (GTP), which is orders of magnitude faster in the MT lattice than in free tubulin heterodimers. Our results computationally ascertain the catalytic residue contacts in the MT lattice that accelerate GTP hydrolysis compared to the free heterodimer as well as confirm that a compacted MT lattice is necessary for hydrolysis while a more expanded lattice is unable to form the necessary contacts and thereby hydrolyze GTP.
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14
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Kalra A, Benny A, Travis SM, Zizzi EA, Morales-Sanchez A, Oblinsky DG, Craddock TJA, Hameroff SR, MacIver MB, Tuszyński JA, Petry S, Penrose R, Scholes GD. Electronic Energy Migration in Microtubules. ACS CENTRAL SCIENCE 2023; 9:352-361. [PMID: 36968538 PMCID: PMC10037452 DOI: 10.1021/acscentsci.2c01114] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Indexed: 05/29/2023]
Abstract
The repeating arrangement of tubulin dimers confers great mechanical strength to microtubules, which are used as scaffolds for intracellular macromolecular transport in cells and exploited in biohybrid devices. The crystalline order in a microtubule, with lattice constants short enough to allow energy transfer between amino acid chromophores, is similar to synthetic structures designed for light harvesting. After photoexcitation, can these amino acid chromophores transfer excitation energy along the microtubule like a natural or artificial light-harvesting system? Here, we use tryptophan autofluorescence lifetimes to probe energy hopping between aromatic residues in tubulin and microtubules. By studying how the quencher concentration alters tryptophan autofluorescence lifetimes, we demonstrate that electronic energy can diffuse over 6.6 nm in microtubules. We discover that while diffusion lengths are influenced by tubulin polymerization state (free tubulin versus tubulin in the microtubule lattice), they are not significantly altered by the average number of protofilaments (13 versus 14). We also demonstrate that the presence of the anesthetics etomidate and isoflurane reduce exciton diffusion. Energy transport as explained by conventional Förster theory (accommodating for interactions between tryptophan and tyrosine residues) does not sufficiently explain our observations. Our studies indicate that microtubules are, unexpectedly, effective light harvesters.
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Affiliation(s)
- Aarat
P. Kalra
- Department
of Chemistry, New Frick Chemistry Building, Princeton University, Princeton, New Jersey08544, United States
| | - Alfy Benny
- Department
of Chemistry, New Frick Chemistry Building, Princeton University, Princeton, New Jersey08544, United States
| | - Sophie M. Travis
- Department
of Molecular Biology, Schultz Laboratory, Princeton University, Princeton, New Jersey08544, United States
| | - Eric A. Zizzi
- Department
of Mechanical and Aerospace Engineering (DIMEAS), Politecnico di Torino, Torino10129, Italy
| | - Austin Morales-Sanchez
- Department
of Chemistry, New Frick Chemistry Building, Princeton University, Princeton, New Jersey08544, United States
| | - Daniel G. Oblinsky
- Department
of Chemistry, New Frick Chemistry Building, Princeton University, Princeton, New Jersey08544, United States
| | - Travis J. A. Craddock
- Departments
of Psychology & Neuroscience, Computer Science, and Clinical Immunology, Nova Southeastern University, Ft. Lauderdale, Florida33314, United States
| | - Stuart R. Hameroff
- Department
of Anesthesiology, Center for Consciousness Studies, University of Arizona, Tucson, Arizona85721, United States
| | - M. Bruce MacIver
- Department
of Anesthesiology, Stanford University School
of Medicine, Stanford, California94305, United States
| | - Jack A. Tuszyński
- Department
of Mechanical and Aerospace Engineering (DIMEAS), Politecnico di Torino, Torino10129, Italy
- Department
of Physics, University of Alberta, Edmonton, AlbertaT6G 2E1, Canada
- Department
of Oncology, University of Alberta, Edmonton, AlbertaT6G 1Z2, Canada
| | - Sabine Petry
- Department
of Molecular Biology, Schultz Laboratory, Princeton University, Princeton, New Jersey08544, United States
| | - Roger Penrose
- Mathematical
Institute, Andrew Wiles Building, University
of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, United
Kingdom
| | - Gregory D. Scholes
- Department
of Chemistry, New Frick Chemistry Building, Princeton University, Princeton, New Jersey08544, United States
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15
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Oliva M, Gago F, Kamimura S, Díaz JF. Alternative Approaches to Understand Microtubule Cap Morphology and Function. ACS OMEGA 2023; 8:3540-3550. [PMID: 36743020 PMCID: PMC9893253 DOI: 10.1021/acsomega.2c06926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/26/2022] [Indexed: 06/18/2023]
Abstract
Microtubules (MTs) are essential cellular machines built from concatenated αβ-tubulin heterodimers. They are responsible for two central and opposite functions from the dynamic point of view: scaffolding (static filaments) and force generation (dynamic MTs). These roles engage multiple physiological processes, including cell shape, polarization, division and movement, and intracellular long-distance transport. At the most basic level, the MT regulation is chemical because GTP binding and hydrolysis have the ability to promote assembly and disassembly in the absence of any other constraint. Due to the stochastic GTP hydrolysis, a chemical gradient from GTP-bound to GDP-bound tubulin is created at the MT growing end (GTP cap), which is translated into a cascade of structural regulatory changes known as MT maturation. This is an area of intense research, and several models have been proposed based on information mostly gathered from macromolecular crystallography and cryo-electron microscopy studies. However, these classical structural biology methods lack temporal resolution and can be complemented, as shown in this mini-review, by other approaches such as time-resolved fiber diffraction and computational modeling. Together with studies on structurally similar tubulins from the prokaryotic world, these inputs can provide novel insights on MT assembly, dynamics, and the GTP cap.
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Affiliation(s)
- María
Ángela Oliva
- Unidad
de Desarrollo de Fármacos Biológicos, Inmunológicos
y Químicos, Centro de Investigaciones
Biológicas Margarita Salas - Consejo Superior de Investigaciones
Científicas, E-28040 Madrid, Spain
| | - Federico Gago
- Department
of Biomedical Sciences and IQM-UAH Associate Unit, University of Alcalá, E-28805 Alcalá de Henares, Spain
| | - Shinji Kamimura
- Department
of Biological Sciences, Faculty of Science and Engineering, Chuo University, 112-8551 Tokyo, Japan
| | - J. Fernando Díaz
- Unidad
de Desarrollo de Fármacos Biológicos, Inmunológicos
y Químicos, Centro de Investigaciones
Biológicas Margarita Salas - Consejo Superior de Investigaciones
Científicas, E-28040 Madrid, Spain
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16
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Kubo S, Bui KH. Regulatory mechanisms of the dynein-2 motility by post-translational modification revealed by MD simulation. Sci Rep 2023; 13:1477. [PMID: 36702893 PMCID: PMC9879972 DOI: 10.1038/s41598-023-28026-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/11/2023] [Indexed: 01/27/2023] Open
Abstract
Intraflagellar transport for ciliary assembly and maintenance is driven by dynein and kinesins specific to the cilia. It has been shown that anterograde and retrograde transports run on different regions of the doublet microtubule, i.e., separate train tracks. However, little is known about the regulatory mechanism of this selective process. Since the doublet microtubule is known to display specific post-translational modifications of tubulins, i.e., "tubulin code", for molecular motor regulations, we investigated the motility of ciliary specific dynein-2 under different post-translational modification by coarse-grained molecular dynamics. Our setup allows us to simulate the landing behaviors of dynein-2 on un-modified, detyrosinated, poly-glutamylated and poly-glycylated microtubules in silico. Our study revealed that poly-glutamylation can play an inhibitory effect on dynein-2 motility. Our result indicates that poly-glutamylation of the B-tubule of the doublet microtubule can be used as an efficient means to target retrograde intraflagellar transport onto the A-tubule.
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Affiliation(s)
- Shintaroh Kubo
- Department of Anatomy and Cell Biology, McGill University, Montréal, Québec, H3A 0C7, Canada. .,Department of Biological Science, Grad. Sch. of Sci, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Khanh Huy Bui
- Department of Anatomy and Cell Biology, McGill University, Montréal, Québec, H3A 0C7, Canada. .,Centre de Recherche en Biologie Structurale, McGill University, Montréal, Québec, H3A 0C7, Canada.
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17
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Nair A, Greeny A, Rajendran R, Abdelgawad MA, Ghoneim MM, Raghavan RP, Sudevan ST, Mathew B, Kim H. KIF1A-Associated Neurological Disorder: An Overview of a Rare Mutational Disease. Pharmaceuticals (Basel) 2023; 16:147. [PMID: 37259299 PMCID: PMC9962247 DOI: 10.3390/ph16020147] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 10/03/2023] Open
Abstract
KIF1A-associated neurological diseases (KANDs) are a group of inherited conditions caused by changes in the microtubule (MT) motor protein KIF1A as a result of KIF1A gene mutations. Anterograde transport of membrane organelles is facilitated by the kinesin family protein encoded by the MT-based motor gene KIF1A. Variations in the KIF1A gene, which primarily affect the motor domain, disrupt its ability to transport synaptic vesicles containing synaptophysin and synaptotagmin leading to various neurological pathologies such as hereditary sensory neuropathy, autosomal dominant and recessive forms of spastic paraplegia, and different neurological conditions. These mutations are frequently misdiagnosed because they result from spontaneous, non-inherited genomic alterations. Whole-exome sequencing (WES), a cutting-edge method, assists neurologists in diagnosing the illness and in planning and choosing the best course of action. These conditions are simple to be identified in pediatric and have a life expectancy of 5-7 years. There is presently no permanent treatment for these illnesses, and researchers have not yet discovered a medicine to treat them. Scientists have more hope in gene therapy since it can be used to cure diseases brought on by mutations. In this review article, we discussed some of the experimental gene therapy methods, including gene replacement, gene knockdown, symptomatic gene therapy, and cell suicide gene therapy. It also covered its clinical symptoms, pathogenesis, current diagnostics, therapy, and research advances currently occurring in the field of KAND-related disorders. This review also explained the impact that gene therapy can be designed in this direction and afford the remarkable benefits to the patients and society.
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Affiliation(s)
- Ayushi Nair
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Amrita Health Science Campus, Kochi 682041, India
| | - Alosh Greeny
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Amrita Health Science Campus, Kochi 682041, India
| | - Rajalakshmi Rajendran
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Amrita Health Science Campus, Kochi 682041, India
| | - Mohamed A. Abdelgawad
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Al Jouf 72341, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt
| | - Mohammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia
| | - Roshni Pushpa Raghavan
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Amrita Health Science Campus, Kochi 682041, India
| | - Sachithra Thazhathuveedu Sudevan
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi 682 041, India
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi 682 041, India
| | - Hoon Kim
- Department of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea
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18
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Pyrpassopoulos S, Gicking AM, Zaniewski TM, Hancock WO, Ostap EM. KIF1A is kinetically tuned to be a superengaging motor under hindering loads. Proc Natl Acad Sci U S A 2023; 120:e2216903120. [PMID: 36598948 PMCID: PMC9926277 DOI: 10.1073/pnas.2216903120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/04/2022] [Indexed: 01/05/2023] Open
Abstract
KIF1A is a highly processive vesicle transport motor in the kinesin-3 family. Mutations in KIF1A lead to neurodegenerative diseases including hereditary spastic paraplegia. We applied optical tweezers to study the ability of KIF1A to generate and sustain force against hindering loads. We used both the three-bead assay, where force is oriented parallel to the microtubule, and the traditional single-bead assay, where force is directed along the radius of the bead, resulting in a vertical force component. The average force and attachment duration of KIF1A in the three-bead assay were substantially greater than those observed in the single-bead assay. Thus, vertical forces accelerate termination of force ramps of KIF1A. Average KIF1A termination forces were slightly lower than the kinesin-1 KIF5B, and the median attachment duration of KIF1A was >10-fold shorter than KIF5B under hindering loads. KIF1A rapidly reengages with microtubules after detachment, as observed previously. Strikingly, quantification enabled by the three-bead assay shows that reengagement largely occurs within 2 ms of detachment, indicating that KIF1A has a nearly 10-fold faster reengagement rate than KIF5B. We found that rapid microtubule reengagement is not due to KIF1A's positively charged loop-12; however, removal of charge from this loop diminished the unloaded run length at near physiological ionic strength. Both loop-12 and the microtubule nucleotide state have modulatory effects on reengagement under load, suggesting a role for the microtubule lattice in KIF1A reengagement. Our results reveal adaptations of KIF1A that lead to a model of superengaging transport under load.
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Affiliation(s)
- Serapion Pyrpassopoulos
- The Pennsylvania Muscle Institute, Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Center for Engineering Mechanobiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Allison M. Gicking
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802
| | - Taylor M. Zaniewski
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802
- Department of Chemistry, Pennsylvania State University, University Park, PA16802
| | - William O. Hancock
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802
- Department of Chemistry, Pennsylvania State University, University Park, PA16802
| | - E. Michael Ostap
- The Pennsylvania Muscle Institute, Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Center for Engineering Mechanobiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
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19
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Iwanski MK, Kapitein LC. Cellular cartography: Towards an atlas of the neuronal microtubule cytoskeleton. Front Cell Dev Biol 2023; 11:1052245. [PMID: 37035244 PMCID: PMC10073685 DOI: 10.3389/fcell.2023.1052245] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/28/2023] [Indexed: 04/11/2023] Open
Abstract
Microtubules, one of the major components of the cytoskeleton, play a crucial role during many aspects of neuronal development and function, such as neuronal polarization and axon outgrowth. Consequently, the microtubule cytoskeleton has been implicated in many neurodevelopmental and neurodegenerative disorders. The polar nature of microtubules is quintessential for their function, allowing them to serve as tracks for long-distance, directed intracellular transport by kinesin and dynein motors. Most of these motors move exclusively towards either the plus- or minus-end of a microtubule and some have been shown to have a preference for either dynamic or stable microtubules, those bearing a particular post-translational modification or those decorated by a specific microtubule-associated protein. Thus, it becomes important to consider the interplay of these features and their combinatorial effects on transport, as well as how different types of microtubules are organized in the cell. Here, we discuss microtubule subsets in terms of tubulin isotypes, tubulin post-translational modifications, microtubule-associated proteins, microtubule stability or dynamicity, and microtubule orientation. We highlight techniques used to study these features of the microtubule cytoskeleton and, using the information from these studies, try to define the composition, role, and organization of some of these subsets in neurons.
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20
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Abstract
Cilia are cell-surface organelles with cytoskeletons formed by different microtubule types. These microtubules are decorated inside and out by proteins that alter microtubule stability and elasticity and allow cilia to beat. Mutations in these proteins are associated with human ciliopathies such as primary ciliary dyskinesia. Here, we used cryo-EM to reveal the structures of two distinct types of human ciliary microtubule: the doublet microtubules of respiratory tract cilia and the distal singlet microtubules of the sperm tail. Among the microtubule-binding proteins identified is SPACA9, which we show is capable of forming both spirals and striations within human ciliary microtubules. The ability to resolve human ciliary microtubule composition improves our understanding of ciliary complexes and the potential causes of human ciliopathies. The cilium-centrosome complex contains triplet, doublet, and singlet microtubules. The lumenal surfaces of each microtubule within this diverse array are decorated by microtubule inner proteins (MIPs). Here, we used single-particle cryo-electron microscopy methods to build atomic models of two types of human ciliary microtubule: the doublet microtubules of multiciliated respiratory cells and the distal singlet microtubules of monoflagellated human spermatozoa. We discover that SPACA9 is a polyspecific MIP capable of binding both microtubule types. SPACA9 forms intralumenal striations in the B tubule of respiratory doublet microtubules and noncontinuous spirals in sperm singlet microtubules. By acquiring new and reanalyzing previous cryo-electron tomography data, we show that SPACA9-like intralumenal striations are common features of different microtubule types in animal cilia. Our structures provide detailed references to help rationalize ciliopathy-causing mutations and position cryo-EM as a tool for the analysis of samples obtained directly from ciliopathy patients.
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21
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Sulimenko V, Dráberová E, Dráber P. γ-Tubulin in microtubule nucleation and beyond. Front Cell Dev Biol 2022; 10:880761. [PMID: 36158181 PMCID: PMC9503634 DOI: 10.3389/fcell.2022.880761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Microtubules composed of αβ-tubulin dimers are dynamic cytoskeletal polymers that play key roles in essential cellular processes such as cell division, organelle positioning, intracellular transport, and cell migration. γ-Tubulin is a highly conserved member of the tubulin family that is required for microtubule nucleation. γ-Tubulin, together with its associated proteins, forms the γ-tubulin ring complex (γ-TuRC), that templates microtubules. Here we review recent advances in the structure of γ-TuRC, its activation, and centrosomal recruitment. This provides new mechanistic insights into the molecular mechanism of microtubule nucleation. Accumulating data suggest that γ-tubulin also has other, less well understood functions. We discuss emerging evidence that γ-tubulin can form oligomers and filaments, has specific nuclear functions, and might be involved in centrosomal cross-talk between microtubules and microfilaments.
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Affiliation(s)
| | | | - Pavel Dráber
- *Correspondence: Vadym Sulimenko, ; Pavel Dráber,
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22
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Siahaan V, Tan R, Humhalova T, Libusova L, Lacey SE, Tan T, Dacy M, Ori-McKenney KM, McKenney RJ, Braun M, Lansky Z. Microtubule lattice spacing governs cohesive envelope formation of tau family proteins. Nat Chem Biol 2022; 18:1224-1235. [PMID: 35996000 PMCID: PMC9613621 DOI: 10.1038/s41589-022-01096-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/24/2022] [Indexed: 01/28/2023]
Abstract
Tau is an intrinsically disordered microtubule-associated protein (MAP) implicated in neurodegenerative disease. On microtubules, tau molecules segregate into two kinetically distinct phases, consisting of either independently diffusing molecules or interacting molecules that form cohesive 'envelopes' around microtubules. Envelopes differentially regulate lattice accessibility for other MAPs, but the mechanism of envelope formation remains unclear. Here we find that tau envelopes form cooperatively, locally altering the spacing of tubulin dimers within the microtubule lattice. Envelope formation compacted the underlying lattice, whereas lattice extension induced tau envelope disassembly. Investigating other members of the tau family, we find that MAP2 similarly forms envelopes governed by lattice spacing, whereas MAP4 cannot. Envelopes differentially biased motor protein movement, suggesting that tau family members could spatially divide the microtubule surface into functionally distinct regions. We conclude that the interdependent allostery between lattice spacing and cooperative envelope formation provides the molecular basis for spatial regulation of microtubule-based processes by tau and MAP2.
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Affiliation(s)
- Valerie Siahaan
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Prague West, Czech Republic
| | - Ruensern Tan
- Department of Molecular and Cellular Biology, University of California - Davis, Davis, CA, USA.,Department of Molecular and Cellular Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Tereza Humhalova
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Lenka Libusova
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Samuel E Lacey
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK.,Human Technopole, Milan, Italy
| | - Tracy Tan
- Department of Molecular and Cellular Biology, University of California - Davis, Davis, CA, USA
| | - Mariah Dacy
- Department of Molecular and Cellular Biology, University of California - Davis, Davis, CA, USA
| | | | - Richard J McKenney
- Department of Molecular and Cellular Biology, University of California - Davis, Davis, CA, USA.
| | - Marcus Braun
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Prague West, Czech Republic.
| | - Zdenek Lansky
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Prague West, Czech Republic.
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23
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An overview on the exploring the interaction of inorganic nanoparticles with microtubules for the advancement of cancer therapeutics. Int J Biol Macromol 2022; 212:358-369. [PMID: 35618086 DOI: 10.1016/j.ijbiomac.2022.05.150] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/17/2022] [Accepted: 05/21/2022] [Indexed: 01/01/2023]
Abstract
Targeting microtubules (MTs), dynamic and stable proteins in cells, by different ligands have been reported to be a potential strategy to combat cancer cells. Inorganic nanoparticles (NPs) have been widely used as anticancer, antibacterial, and free radical scavenging agents, where the come in contact with biological macromolecules. The interaction between the NPs and biological macromolecules like MTs frequently occurs through different mechanisms. A prerequisite for a detailed exploration of MT structures and functions for biomedical applications like cancer therapy is to investigate profoundly the mechanisms involved in MT-NP interactions, for which the full explanation and characterization of the parameters that are responsible for the formation of a NP-protein complex are crucial. Therefore, in view of the fact that the goal of the rational NP-based future drug design and new therapies is to rely on the information of the structural details and protein-NPs binding mechanisms to manipulate the process of developing new potential drugs, a comprehensive investigation of the essence of the molecular recognition/interaction is also of considerable importance. In the present review, first, the microtubule (MT) structure and its binding sites upon interaction with MT stabilizing agents (MSAs) and MT destabilizing agents (MDAs) are introduced and rationalized. Next, MT targeting in cancer therapy and interaction of NPs with MTs are discussed. Furthermore, interaction of NPs with proteins and the manipulation of protein corona (PC), experimental techniques, and direct interaction of NPs with MTs, are discussed, and finally the challenges and future perspective of the field are introduced. We envision this review can provide useful information on the manipulation of the MT lattice for the progress of cancer nanomedicine.
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24
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Ciliary central apparatus structure reveals mechanisms of microtubule patterning. Nat Struct Mol Biol 2022; 29:483-492. [PMID: 35578023 PMCID: PMC9930914 DOI: 10.1038/s41594-022-00770-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 03/30/2022] [Indexed: 02/05/2023]
Abstract
A pair of extensively modified microtubules form the central apparatus (CA) of the axoneme of most motile cilia, where they regulate ciliary motility. The external surfaces of both CA microtubules are patterned asymmetrically with large protein complexes that repeat every 16 or 32 nm. The composition of these projections and the mechanisms that establish asymmetry and longitudinal periodicity are unknown. Here, by determining cryo-EM structures of the CA microtubules, we identify 48 different CA-associated proteins, which in turn reveal mechanisms for asymmetric and periodic protein binding to microtubules. We identify arc-MIPs, a novel class of microtubule inner protein, that bind laterally across protofilaments and remodel tubulin structure and lattice contacts. The binding mechanisms utilized by CA proteins may be generalizable to other microtubule-associated proteins. These structures establish a foundation to elucidate the contributions of individual CA proteins to ciliary motility and ciliopathies.
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25
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Vu HT, Zhang Z, Tehver R, Thirumalai D. Plus and minus ends of microtubules respond asymmetrically to kinesin binding by a long-range directionally driven allosteric mechanism. SCIENCE ADVANCES 2022; 8:eabn0856. [PMID: 35417226 PMCID: PMC9007332 DOI: 10.1126/sciadv.abn0856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
Although it is known that majority of kinesin motors walk predominantly toward the plus end of microtubules (MTs) in a hand-over-hand manner, the structural origin of the stepping directionality is not understood. To resolve this issue, we modeled the structures of kinesin-1 (Kin1), MT, and the Kin1-MT complex using the elastic network model and calculated the residue-dependent responses to a local perturbation in the constructs. Kin1 binding elicits an asymmetric response that is pronounced in α/β-tubulin dimers in the plus end of the MT. Kin1 opens the clefts of multiple plus end α/β-tubulin dimers, creating binding-competent conformations, which is required for processivity. Reciprocally, MT induces correlations between switches I and II in the motor and enhances fluctuations in adenosine 5'-diphosphate and the residues in the binding pocket. Our findings explain both the directionality of stepping and MT effects on a key step in the catalytic cycle of kinesin.
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Affiliation(s)
- Huong T. Vu
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry CV4 7AL, UK
| | - Zhechun Zhang
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Riina Tehver
- Department of Physics, Denison University, Granville, OH 43023, USA
| | - D. Thirumalai
- Department of Chemistry, University of Texas, Austin, TX 78702, USA
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26
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Akıl C, Ali S, Tran LT, Gaillard J, Li W, Hayashida K, Hirose M, Kato T, Oshima A, Fujishima K, Blanchoin L, Narita A, Robinson RC. Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution. SCIENCE ADVANCES 2022; 8:eabm2225. [PMID: 35333570 PMCID: PMC8956254 DOI: 10.1126/sciadv.abm2225] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Tubulins are critical for the internal organization of eukaryotic cells, and understanding their emergence is an important question in eukaryogenesis. Asgard archaea are the closest known prokaryotic relatives to eukaryotes. Here, we elucidated the apo and nucleotide-bound x-ray structures of an Asgard tubulin from hydrothermal living Odinarchaeota (OdinTubulin). The guanosine 5'-triphosphate (GTP)-bound structure resembles a microtubule protofilament, with GTP bound between subunits, coordinating the "+" end subunit through a network of water molecules and unexpectedly by two cations. A water molecule is located suitable for GTP hydrolysis. Time course crystallography and electron microscopy revealed conformational changes on GTP hydrolysis. OdinTubulin forms tubules at high temperatures, with short curved protofilaments coiling around the tubule circumference, more similar to FtsZ, rather than running parallel to its length, as in microtubules. Thus, OdinTubulin represents an evolutionary stage intermediate between prokaryotic FtsZ and eukaryotic microtubule-forming tubulins.
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Affiliation(s)
- Caner Akıl
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
- Tokyo Institute of Technology, Earth-Life Science Institute (ELSI), Tokyo 152-8551, Japan
| | - Samson Ali
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Linh T. Tran
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Jérémie Gaillard
- University of Grenoble-Alpes, CEA, CNRS, INRA, Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, 38054 Grenoble, France
| | - Wenfei Li
- National Laboratory of Solid State Microstructure, Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210093 Nanjing, China
| | - Kenichi Hayashida
- Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Mika Hirose
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Takayuki Kato
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Atsunori Oshima
- Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Kosuke Fujishima
- Tokyo Institute of Technology, Earth-Life Science Institute (ELSI), Tokyo 152-8551, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Laurent Blanchoin
- University of Grenoble-Alpes, CEA, CNRS, INRA, Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, 38054 Grenoble, France
- Université de Paris, INSERM, CEA, Institut de Recherche Saint Louis, U 976, CytoMorpho Lab, 75010 Paris, France
| | - Akihiro Narita
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Robert C. Robinson
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
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27
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Abstract
The mechanochemical basis of microtubule growth, which is essential for the normal function and division of eukaryotic cells, has remained elusive and controversial, despite extensive work. In particular, recent findings have created the paradox that the microtubule plus-end tips look very similar during both growing and shrinking phases, thereby challenging the traditional textbook picture. Our large-scale atomistic simulations resolve this paradox and explain microtubule growth and shrinkage dynamics as a process governed by energy barriers between protofilament conformations, the heights of which are in turn fine-tuned by different nucleotide states, thus implementing an information-driven Brownian ratchet. Microtubules (MTs), mesoscopic cellular filaments, grow primarily by the addition of GTP-bound tubulin dimers at their dynamic flaring plus-end tips. They operate as chemomechanical energy transducers with stochastic transitions to an astounding shortening motion upon hydrolyzing GTP to GDP. Time-resolved dynamics of the MT tip—a key determinant of this behavior—as a function of nucleotide state, internal lattice strain, and stabilizing lateral interactions have not been fully understood. Here we use atomistic simulations to study the spontaneous relaxation of complete GTP-MT and GDP-MT tip models from unfavorable straight to relaxed splayed conformations and to comprehensively characterize the elasticity of MT tips. Our simulations reveal the dominance of viscoelastic dynamics of MT protofilaments during the relaxation process, driven by the stored bending-torsional strain and counterbalanced by the interprotofilament interactions. We show that the posthydrolysis MT tip is exposed to higher activation energy barriers for straight lattice formation, which translates into its inability to elongate. Our study provides an information-driven Brownian ratchet mechanism for the elastic energy conversion and release by MT tips and offers insights into the mechanoenzymatics of MTs.
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28
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Ruiz FM, Huecas S, Santos-Aledo A, Prim EA, Andreu JM, Fernández-Tornero C. FtsZ filament structures in different nucleotide states reveal the mechanism of assembly dynamics. PLoS Biol 2022; 20:e3001497. [PMID: 35312677 PMCID: PMC8936486 DOI: 10.1371/journal.pbio.3001497] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/21/2022] [Indexed: 11/19/2022] Open
Abstract
Treadmilling protein filaments perform essential cellular functions by growing from one end while shrinking from the other, driven by nucleotide hydrolysis. Bacterial cell division relies on the primitive tubulin homolog FtsZ, a target for antibiotic discovery that assembles into single treadmilling filaments that hydrolyse GTP at an active site formed upon subunit association. We determined high-resolution filament structures of FtsZ from the pathogen Staphylococcus aureus in complex with different nucleotide analogs and cations, including mimetics of the ground and transition states of catalysis. Together with mutational and biochemical analyses, our structures reveal interactions made by the GTP γ-phosphate and Mg2+ at the subunit interface, a K+ ion stabilizing loop T7 for co-catalysis, new roles of key residues at the active site and a nearby crosstalk area, and rearrangements of a dynamic water shell bridging adjacent subunits upon GTP hydrolysis. We propose a mechanistic model that integrates nucleotide hydrolysis signaling with assembly-associated conformational changes and filament treadmilling. Equivalent assembly mechanisms may apply to more complex tubulin and actin cytomotive filaments that share analogous features with FtsZ. Bacterial cell division critically relies on the tubulin homolog FtsZ, which assembles into filaments that treadmill, fuelled by GTP hydrolysis. This structural and biochemical study of FtsZ from Staphylocuccus aureus reveals the mechanism of GTP hydrolysis and its connection with filament dynamics.
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Affiliation(s)
- Federico M. Ruiz
- Centro de Investigaciones Biológicas Margarita Salas CSIC, Madrid, Spain
| | - Sonia Huecas
- Centro de Investigaciones Biológicas Margarita Salas CSIC, Madrid, Spain
| | | | - Elena A. Prim
- Centro de Investigaciones Biológicas Margarita Salas CSIC, Madrid, Spain
| | - José M. Andreu
- Centro de Investigaciones Biológicas Margarita Salas CSIC, Madrid, Spain
- * E-mail: (JMA); (CFT)
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29
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Kinesin-14 motors participate in a force balance at microtubule plus-ends to regulate dynamic instability. Proc Natl Acad Sci U S A 2022; 119:2108046119. [PMID: 35173049 PMCID: PMC8872730 DOI: 10.1073/pnas.2108046119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2022] [Indexed: 01/08/2023] Open
Abstract
Kinesin-14 motors represent an essential class of molecular motors that bind to microtubules and then walk toward the microtubule minus-end. However, whether these motors can interact with growing plus-ends of microtubules to impact the lengthening of microtubules remains unknown. We found that Kinesin-14 motors could bind to a protein that resides at growing microtubule plus-ends and then pull this protein away from the growing end. This interaction acted to disrupt microtubule growth and decrease microtubule lengths in cells, likely by exerting minus-end–directed forces at the microtubule tip to alter the configuration of the growing microtubule plus-end. This work demonstrates general principles for the diverse roles that force-generating molecular motors can play in regulating cellular processes. Kinesin-14 molecular motors represent an essential class of proteins that bind microtubules and walk toward their minus-ends. Previous studies have described important roles for Kinesin-14 motors at microtubule minus-ends, but their role in regulating plus-end dynamics remains controversial. Kinesin-14 motors have been shown to bind the EB family of microtubule plus-end binding proteins, suggesting that these minus-end–directed motors could interact with growing microtubule plus-ends. In this work, we explored the role of minus-end–directed Kinesin-14 motor forces in controlling plus-end microtubule dynamics. In cells, a Kinesin-14 mutant with reduced affinity to EB proteins led to increased microtubule lengths. Cell-free biophysical microscopy assays were performed using Kinesin-14 motors and an EB family marker of growing microtubule plus-ends, Mal3, which revealed that when Kinesin-14 motors bound to Mal3 at growing microtubule plus-ends, the motors subsequently walked toward the minus-end, and Mal3 was pulled away from the growing microtubule tip. Strikingly, these interactions resulted in an approximately twofold decrease in the expected postinteraction microtubule lifetime. Furthermore, generic minus-end–directed tension forces, generated by tethering growing plus-ends to the coverslip using λ-DNA, led to an approximately sevenfold decrease in the expected postinteraction microtubule growth length. In contrast, the inhibition of Kinesin-14 minus-end–directed motility led to extended tip interactions and to an increase in the expected postinteraction microtubule lifetime, indicating that plus-ends were stabilized by nonmotile Kinesin-14 motors. Together, we find that Kinesin-14 motors participate in a force balance at microtubule plus-ends to regulate microtubule lengths in cells.
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30
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Garnett JA, Atherton J. Structure Determination of Microtubules and Pili: Past, Present, and Future Directions. Front Mol Biosci 2022; 8:830304. [PMID: 35096976 PMCID: PMC8795688 DOI: 10.3389/fmolb.2021.830304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/28/2021] [Indexed: 11/30/2022] Open
Abstract
Historically proteins that form highly polymeric and filamentous assemblies have been notoriously difficult to study using high resolution structural techniques. This has been due to several factors that include structural heterogeneity, their large molecular mass, and available yields. However, over the past decade we are now seeing a major shift towards atomic resolution insight and the study of more complex heterogenous samples and in situ/ex vivo examination of multi-subunit complexes. Although supported by developments in solid state nuclear magnetic resonance spectroscopy (ssNMR) and computational approaches, this has primarily been due to advances in cryogenic electron microscopy (cryo-EM). The study of eukaryotic microtubules and bacterial pili are good examples, and in this review, we will give an overview of the technical innovations that have enabled this transition and highlight the advancements that have been made for these two systems. Looking to the future we will also describe systems that remain difficult to study and where further technical breakthroughs are required.
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Affiliation(s)
- James A. Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral and Craniofacial Sciences, King’s College London, London, United Kingdom
| | - Joseph Atherton
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
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31
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Structural transitions in the GTP cap visualized by cryo-electron microscopy of catalytically inactive microtubules. Proc Natl Acad Sci U S A 2022; 119:2114994119. [PMID: 34996871 PMCID: PMC8764682 DOI: 10.1073/pnas.2114994119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2021] [Indexed: 01/27/2023] Open
Abstract
Microtubules (MTs) are polymers of αβ-tubulin heterodimers that stochastically switch between growth and shrinkage phases. This dynamic instability is critically important for MT function. It is believed that GTP hydrolysis within the MT lattice is accompanied by destabilizing conformational changes and that MT stability depends on a transiently existing GTP cap at the growing MT end. Here, we use cryo-electron microscopy and total internal reflection fluorescence microscopy of GTP hydrolysis-deficient MTs assembled from mutant recombinant human tubulin to investigate the structure of a GTP-bound MT lattice. We find that the GTP-MT lattice of two mutants in which the catalytically active glutamate in α-tubulin was substituted by inactive amino acids (E254A and E254N) is remarkably plastic. Undecorated E254A and E254N MTs with 13 protofilaments both have an expanded lattice but display opposite protofilament twists, making these lattices distinct from the compacted lattice of wild-type GDP-MTs. End-binding proteins of the EB family have the ability to compact both mutant GTP lattices and to stabilize a negative twist, suggesting that they promote this transition also in the GTP cap of wild-type MTs, thereby contributing to the maturation of the MT structure. We also find that the MT seam appears to be stabilized in mutant GTP-MTs and destabilized in GDP-MTs, supporting the proposal that the seam plays an important role in MT stability. Together, these structures of catalytically inactive MTs add mechanistic insight into the GTP state of MTs, the stability of the GTP- and GDP-bound lattice, and our overall understanding of MT dynamic instability.
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32
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Lattice defects induced by microtubule-stabilizing agents exert a long-range effect on microtubule growth by promoting catastrophes. Proc Natl Acad Sci U S A 2021; 118:2112261118. [PMID: 34916292 PMCID: PMC8713758 DOI: 10.1073/pnas.2112261118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2021] [Indexed: 11/18/2022] Open
Abstract
Microtubules are major cytoskeletal filaments important for cell division, growth, and differentiation. Microtubules can rapidly switch between phases of growth and shortening, and this dynamic behavior is essential for shaping microtubule arrays. To obtain insights into mechanisms controlling microtubule dynamics, here we used microtubule-stabilizing agents such as Taxol and their fluorescent analogs to manipulate microtubule protofilament number and generate stable defects in microtubule lattices that can be visualized using fluorescence microscopy. We show that microtubule polymerization rate increases with protofilament number and that drug-induced microtubule lattice discontinuities can promote plus-end catastrophes at a distance of several micrometers. Our data indicate that structural defects in the microtubule wall can have long-range propagating effects on microtubule tip dynamics. Microtubules are dynamic cytoskeletal polymers that spontaneously switch between phases of growth and shrinkage. The probability of transitioning from growth to shrinkage, termed catastrophe, increases with microtubule age, but the underlying mechanisms are poorly understood. Here, we set out to test whether microtubule lattice defects formed during polymerization can affect growth at the plus end. To generate microtubules with lattice defects, we used microtubule-stabilizing agents that promote formation of polymers with different protofilament numbers. By employing different agents during nucleation of stable microtubule seeds and the subsequent polymerization phase, we could reproducibly induce switches in protofilament number and induce stable lattice defects. Such drug-induced defects led to frequent catastrophes, which were not observed when microtubules were grown in the same conditions but without a protofilament number mismatch. Microtubule severing at the site of the defect was sufficient to suppress catastrophes. We conclude that structural defects within the microtubule lattice can exert effects that can propagate over long distances and affect the dynamic state of the microtubule end.
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33
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Guichard P, Laporte MH, Hamel V. The centriolar tubulin code. Semin Cell Dev Biol 2021; 137:16-25. [PMID: 34896019 DOI: 10.1016/j.semcdb.2021.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 11/25/2022]
Abstract
Centrioles are microtubule-based cell organelles present in most eukaryotes. They participate in the control of cell division as part of the centrosome, the major microtubule-organizing center of the cell, and are also essential for the formation of primary and motile cilia. During centriole assembly as well as across its lifetime, centriolar tubulin display marks defined by post-translational modifications (PTMs), such as glutamylation or acetylation. To date, the functions of these PTMs at centrioles are not well understood, although pioneering experiments suggest a role in the stability of this organelle. Here, we review the current knowledge regarding PTMs at centrioles with a particular focus on a possible link between these modifications and centriole's architecture, and propose possible hypothesis regarding centriolar tubulin PTMs's function.
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Affiliation(s)
- Paul Guichard
- University of Geneva, Department of Cell Biology, Geneva, Switzerland.
| | - Marine H Laporte
- University of Geneva, Department of Cell Biology, Geneva, Switzerland
| | - Virginie Hamel
- University of Geneva, Department of Cell Biology, Geneva, Switzerland.
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34
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Crotonylation directs the spindle. Nat Chem Biol 2021; 17:1217-1218. [PMID: 34608294 DOI: 10.1038/s41589-021-00881-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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35
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Regulation of microtubule dynamics, mechanics and function through the growing tip. Nat Rev Mol Cell Biol 2021; 22:777-795. [PMID: 34408299 DOI: 10.1038/s41580-021-00399-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2021] [Indexed: 02/07/2023]
Abstract
Microtubule dynamics and their control are essential for the normal function and division of all eukaryotic cells. This plethora of functions is, in large part, supported by dynamic microtubule tips, which can bind to various intracellular targets, generate mechanical forces and couple with actin microfilaments. Here, we review progress in the understanding of microtubule assembly and dynamics, focusing on new information about the structure of microtubule tips. First, we discuss evidence for the widely accepted GTP cap model of microtubule dynamics. Next, we address microtubule dynamic instability in the context of structural information about assembly intermediates at microtubule tips. Three currently discussed models of microtubule assembly and dynamics are reviewed. These are considered in the context of established facts and recent data, which suggest that some long-held views must be re-evaluated. Finally, we review structural observations about the tips of microtubules in cells and describe their implications for understanding the mechanisms of microtubule regulation by associated proteins, by mechanical forces and by microtubule-targeting drugs, prominently including cancer chemotherapeutics.
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36
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Ciorîță A, Bugiel M, Sudhakar S, Schäffer E, Jannasch A. Single depolymerizing and transport kinesins stabilize microtubule ends. Cytoskeleton (Hoboken) 2021; 78:177-184. [PMID: 34310069 DOI: 10.1002/cm.21681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/14/2021] [Accepted: 07/19/2021] [Indexed: 11/07/2022]
Abstract
Microtubules are highly dynamic cellular filaments and an accurate control of their length is important for many intracellular processes like cell division. Among other factors, microtubule length is actively modulated by motors from the kinesin superfamily. For example, yeast kinesin-8, Kip3, motors depolymerize microtubules by a cooperative, force- and length-dependent mechanism. However, whether single motors can also depolymerize microtubules is unclear. Here, we measured how single kinesin motors influenced the stability of microtubules in an in vitro assay. Using label-free interference reflection microscopy, we determined the spontaneous microtubule depolymerization rate of stabilized microtubules in the presence of kinesins. Surprisingly, we found that both single Kip3 and nondepolymerizing kinesin-1 transport motors, used as a control, stabilized microtubules further. For Kip3, this behavior is contrary to the collective force-dependent depolymerization activity of multiple motors. Because of the control measurement, the finding may hint at a more general stabilization mechanism. The complex, concentration-dependent interaction with microtubule ends provides new insights into the molecular mechanism of kinesin-8 and its regulatory function of microtubule length.
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Affiliation(s)
- Alexandra Ciorîță
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany.,National Institute for Research and Development of Isotopic and Molecular Technologies, Integrated Electron Microscopy Laboratory, Cluj-Napoca, Romania
| | - Michael Bugiel
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Swathi Sudhakar
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany.,MRC London Institute of Medical Science, Imperial College London, London, UK
| | - Erik Schäffer
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Anita Jannasch
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
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37
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Chen J, Kholina E, Szyk A, Fedorov VA, Kovalenko I, Gudimchuk N, Roll-Mecak A. α-tubulin tail modifications regulate microtubule stability through selective effector recruitment, not changes in intrinsic polymer dynamics. Dev Cell 2021; 56:2016-2028.e4. [PMID: 34022132 PMCID: PMC8476856 DOI: 10.1016/j.devcel.2021.05.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/26/2021] [Accepted: 05/05/2021] [Indexed: 10/21/2022]
Abstract
Microtubules are non-covalent polymers of αβ-tubulin dimers. Posttranslational processing of the intrinsically disordered C-terminal α-tubulin tail produces detyrosinated and Δ2-tubulin. Although these are widely employed as proxies for stable cellular microtubules, their effect (and of the α-tail) on microtubule dynamics remains uncharacterized. Using recombinant, engineered human tubulins, we now find that neither detyrosinated nor Δ2-tubulin affect microtubule dynamics, while the α-tubulin tail is an inhibitor of microtubule growth. Consistent with the latter, molecular dynamics simulations show the α-tubulin tail transiently occluding the longitudinal microtubule polymerization interface. The marked differential in vivo stabilities of the modified microtubule subpopulations, therefore, must result exclusively from selective effector recruitment. We find that tyrosination quantitatively tunes CLIP-170 density at the growing plus end and that CLIP170 and EB1 synergize to selectively upregulate the dynamicity of tyrosinated microtubules. Modification-dependent recruitment of regulators thereby results in microtubule subpopulations with distinct dynamics, a tenet of the tubulin code hypothesis.
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Affiliation(s)
- Jiayi Chen
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - Ekaterina Kholina
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Agnieszka Szyk
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - Vladimir A Fedorov
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia; Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya Kovalenko
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia; Astrakhan State University, Astrakhan 414056, Russia; Sechenov University, Moscow 119991, Russia
| | - Nikita Gudimchuk
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia; Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia; Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA; Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, Bethesda, MD 20892, USA.
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38
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Zhou H, Isozaki N, Fujimoto K, Yokokawa R. Growth rate-dependent flexural rigidity of microtubules influences pattern formation in collective motion. J Nanobiotechnology 2021; 19:218. [PMID: 34281555 PMCID: PMC8287809 DOI: 10.1186/s12951-021-00960-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 07/11/2021] [Indexed: 11/10/2022] Open
Abstract
Background Microtubules (MTs) are highly dynamic tubular cytoskeleton filaments that are essential for cellular morphology and intracellular transport. In vivo, the flexural rigidity of MTs can be dynamically regulated depending on their intracellular function. In the in vitro reconstructed MT-motor system, flexural rigidity affects MT gliding behaviors and trajectories. Despite the importance of flexural rigidity for both biological functions and in vitro applications, there is no clear interpretation of the regulation of MT flexural rigidity, and the results of many studies are contradictory. These discrepancies impede our understanding of the regulation of MT flexural rigidity, thereby challenging its precise manipulation. Results Here, plausible explanations for these discrepancies are provided and a new method to evaluate the MT rigidity is developed. Moreover, a new relationship of the dynamic and mechanic of MTs is revealed that MT flexural rigidity decreases through three phases with the growth rate increases, which offers a method of designing MT flexural rigidity by regulating its growth rate. To test the validity of this method, the gliding performances of MTs with different flexural rigidities polymerized at different growth rates are examined. The growth rate-dependent flexural rigidity of MTs is experimentally found to influence the pattern formation in collective motion using gliding motility assay, which is further validated using machine learning. Conclusion Our study establishes a robust quantitative method for measurement and design of MT flexural rigidity to study its influences on MT gliding assays, collective motion, and other biological activities in vitro. The new relationship about the growth rate and rigidity of MTs updates current concepts on the dynamics and mechanics of MTs and provides comparable data for investigating the regulation mechanism of MT rigidity in vivo in the future. Graphic Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12951-021-00960-y.
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Affiliation(s)
- Hang Zhou
- Department of Micro Engineering, Kyoto University, Kyoto Daigaku-Katsura, Nishikyo-ku, Kyoto, 615-8540, Japan
| | - Naoto Isozaki
- Department of Micro Engineering, Kyoto University, Kyoto Daigaku-Katsura, Nishikyo-ku, Kyoto, 615-8540, Japan
| | - Kazuya Fujimoto
- Department of Micro Engineering, Kyoto University, Kyoto Daigaku-Katsura, Nishikyo-ku, Kyoto, 615-8540, Japan
| | - Ryuji Yokokawa
- Department of Micro Engineering, Kyoto University, Kyoto Daigaku-Katsura, Nishikyo-ku, Kyoto, 615-8540, Japan.
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39
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Abstract
Microtubules are dynamic cytoskeletal filaments composed of αβ-tubulin heterodimers. Historically, the dynamics of single tubulin interactions at the growing microtubule tip have been inferred from steady-state growth kinetics. However, recent advances in the production of recombinant tubulin and in high-resolution optical and cryo-electron microscopies have opened new windows into understanding the impacts of specific intermolecular interactions during growth. The microtubule lattice is held together by lateral and longitudinal tubulin-tubulin interactions, and these interactions are in turn regulated by the GTP hydrolysis state of the tubulin heterodimer. Furthermore, tubulin can exist in either an extended or a compacted state in the lattice. Growing evidence has led to the suggestion that binding of microtubule-associated proteins (MAPs) or motors can induce changes in tubulin conformation and that this information can be communicated through the microtubule lattice. Progress in understanding how dynamic tubulin-tubulin interactions control dynamic instability has benefitted from visualizing structures of growing microtubule plus ends and through stochastic biochemical models constrained by experimental data. Here, we review recent insights into the molecular basis of microtubule growth and discuss how MAPs and regulatory proteins alter tubulin-tubulin interactions to exert their effects on microtubule growth and stability.
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Affiliation(s)
- Joseph M Cleary
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
| | - William O Hancock
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
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40
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Wang X, Fu Y, Beatty WL, Ma M, Brown A, Sibley LD, Zhang R. Cryo-EM structure of cortical microtubules from human parasite Toxoplasma gondii identifies their microtubule inner proteins. Nat Commun 2021; 12:3065. [PMID: 34031406 PMCID: PMC8144581 DOI: 10.1038/s41467-021-23351-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 04/21/2021] [Indexed: 02/04/2023] Open
Abstract
In living cells, microtubules (MTs) play pleiotropic roles, which require very different mechanical properties. Unlike the dynamic MTs found in the cytoplasm of metazoan cells, the specialized cortical MTs from Toxoplasma gondii, a prevalent human pathogen, are extraordinarily stable and resistant to detergent and cold treatments. Using single-particle cryo-EM, we determine their ex vivo structure and identify three proteins (TrxL1, TrxL2 and SPM1) as bona fide microtubule inner proteins (MIPs). These three MIPs form a mesh on the luminal surface and simultaneously stabilize the tubulin lattice in both longitudinal and lateral directions. Consistent with previous observations, deletion of the identified MIPs compromises MT stability and integrity under challenges by chemical treatments. We also visualize a small molecule like density at the Taxol-binding site of β-tubulin. Our results provide the structural basis to understand the stability of cortical MTs and suggest an evolutionarily conserved mechanism of MT stabilization from the inside.
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Affiliation(s)
- Xiangli Wang
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Yong Fu
- Department of Molecular Microbiology, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Wandy L Beatty
- Department of Molecular Microbiology, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Meisheng Ma
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Alan Brown
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - L David Sibley
- Department of Molecular Microbiology, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA.
| | - Rui Zhang
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA.
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41
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Ulyanov EV, Vinogradov DS, McIntosh JR, Gudimchuk NB. Brownian dynamics simulation of protofilament relaxation during rapid freezing. PLoS One 2021; 16:e0247022. [PMID: 33577570 PMCID: PMC7880439 DOI: 10.1371/journal.pone.0247022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/31/2021] [Indexed: 11/18/2022] Open
Abstract
Electron cryo-microscopy (Cryo-EM) is a powerful method for visualizing biological objects with up to near-angstrom resolution. Instead of chemical fixation, the method relies on very rapid freezing to immobilize the sample. Under these conditions, crystalline ice does not have time to form and distort structure. For many practical applications, the rate of cooling is fast enough to consider sample immobilization instantaneous, but in some cases, a more rigorous analysis of structure relaxation during freezing could be essential. This difficult yet important problem has been significantly under-reported in the literature, despite spectacular recent developments in Cryo-EM. Here we use Brownian dynamics modeling to examine theoretically the possible effects of cryo-immobilization on the apparent shapes of biological polymers. The main focus of our study is on tubulin protofilaments. These structures are integral parts of microtubules, which in turn are key elements of the cellular skeleton, essential for intracellular transport, maintenance of cell shape, cell division and migration. We theoretically examine the extent of protofilament relaxation within the freezing time as a function of the cooling rate, the filament's flexural rigidity, and the effect of cooling on water's viscosity. Our modeling suggests that practically achievable cooling rates are not rapid enough to capture tubulin protofilaments in conformations that are incompletely relaxed, suggesting that structures seen by cryo-EM are good approximations to physiological shapes. This prediction is confirmed by our analysis of curvatures of tubulin protofilaments, using samples, prepared and visualized with a variety of methods. We find, however, that cryofixation may capture incompletely relaxed shapes of more flexible polymers, and it may affect Cryo-EM-based measurements of their persistence lengths. This analysis will be valuable for understanding of structures of different types of biopolymers, observed with Cryo-EM.
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Affiliation(s)
- Evgeniy V. Ulyanov
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
| | | | - J. Richard McIntosh
- Department of MCD Biology, University of Colorado, Boulder, CO, United States of America
| | - Nikita B. Gudimchuk
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
- Department of MCD Biology, University of Colorado, Boulder, CO, United States of America
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
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42
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Ayukawa R, Iwata S, Imai H, Kamimura S, Hayashi M, Ngo KX, Minoura I, Uchimura S, Makino T, Shirouzu M, Shigematsu H, Sekimoto K, Gigant B, Muto E. GTP-dependent formation of straight tubulin oligomers leads to microtubule nucleation. J Cell Biol 2021; 220:211760. [PMID: 33544140 PMCID: PMC7871348 DOI: 10.1083/jcb.202007033] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/23/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022] Open
Abstract
Nucleation of microtubules (MTs) is essential for cellular activities, but its mechanism is unknown because of the difficulty involved in capturing rare stochastic events in the early stage of polymerization. Here, combining rapid flush negative stain electron microscopy (EM) and kinetic analysis, we demonstrate that the formation of straight oligomers of critical size is essential for nucleation. Both GDP and GTP tubulin form single-stranded oligomers with a broad range of curvatures, but upon nucleation, the curvature distribution of GTP oligomers is shifted to produce a minor population of straight oligomers. With tubulin having the Y222F mutation in the β subunit, the proportion of straight oligomers increases and nucleation accelerates. Our results support a model in which GTP binding generates a minor population of straight oligomers compatible with lateral association and further growth to MTs. This study suggests that cellular factors involved in nucleation promote it via stabilization of straight oligomers.
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Affiliation(s)
- Rie Ayukawa
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Seigo Iwata
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Hiroshi Imai
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Shinji Kamimura
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Masahito Hayashi
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Kien Xuan Ngo
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Itsushi Minoura
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Seiichi Uchimura
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Tsukasa Makino
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Hideki Shigematsu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Ken Sekimoto
- Matière et Systèmes Complexes (MSC), CNRS UMR 7057, Université de Paris, Paris, France.,Gulliver, CNRS UMR 7083, ESPCI Paris and Université Paris Sciences et Lettres, Paris, France
| | - Benoît Gigant
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Etsuko Muto
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
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43
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Atomistic Basis of Microtubule Dynamic Instability Assessed Via Multiscale Modeling. Ann Biomed Eng 2021; 49:1716-1734. [PMID: 33537926 PMCID: PMC8302526 DOI: 10.1007/s10439-020-02715-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023]
Abstract
Microtubule “dynamic instability,” the abrupt switching from assembly to disassembly caused by the hydrolysis of GTP to GDP within the β subunit of the αβ-tubulin heterodimer, is necessary for vital cellular processes such as mitosis and migration. Despite existing high-resolution structural data, the key mechanochemical differences between the GTP and GDP states that mediate dynamic instability behavior remain unclear. Starting with a published atomic-level structure as an input, we used multiscale modeling to find that GTP hydrolysis results in both longitudinal bond weakening (~ 4 kBT) and an outward bending preference (~ 1.5 kBT) to both drive dynamic instability and give rise to the microtubule tip structures previously observed by light and electron microscopy. More generally, our study provides an example where atomic level structural information is used as the sole input to predict cellular level dynamics without parameter adjustment.
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44
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Boiarska Z, Passarella D. Microtubule-targeting agents and neurodegeneration. Drug Discov Today 2020; 26:604-615. [PMID: 33279455 DOI: 10.1016/j.drudis.2020.11.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/17/2020] [Accepted: 11/28/2020] [Indexed: 11/25/2022]
Abstract
The association of microtubule (MT) breakdown with neurodegeneration and neurotoxicity has provided an emerging therapeutic approach for neurodegenerative diseases. Tubulin binders are able to modulate MT dynamics and, as a result, are of particular interest both as potential therapeutics and experimental tools used to validate this strategy. Here, we provide a comprehensive overview of current knowledge and recent advancements regarding MT-targeting approaches for neurodegeneration and evaluate the potential application of MT-targeting agents (MTAs) based on available preclinical and clinical data.
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Affiliation(s)
- Zlata Boiarska
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Daniele Passarella
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy.
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45
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Kiesel P, Alvarez Viar G, Tsoy N, Maraspini R, Gorilak P, Varga V, Honigmann A, Pigino G. The molecular structure of mammalian primary cilia revealed by cryo-electron tomography. Nat Struct Mol Biol 2020; 27:1115-1124. [PMID: 32989303 PMCID: PMC7610599 DOI: 10.1038/s41594-020-0507-4] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/12/2020] [Indexed: 01/09/2023]
Abstract
Primary cilia are microtubule-based organelles that are important for signaling and sensing in eukaryotic cells. Unlike the thoroughly studied motile cilia, the three-dimensional architecture and molecular composition of primary cilia are largely unexplored. Yet, studying these aspects is necessary to understand how primary cilia function in health and disease. We developed an enabling method for investigating the structure of primary cilia isolated from MDCK-II cells at molecular resolution by cryo-electron tomography. We show that the textbook '9 + 0' arrangement of microtubule doublets is only present at the primary cilium base. A few microns out, the architecture changes into an unstructured bundle of EB1-decorated microtubules and actin filaments, putting an end to a long debate on the presence or absence of actin filaments in primary cilia. Our work provides a plethora of insights into the molecular structure of primary cilia and offers a methodological framework to study these important organelles.
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Affiliation(s)
- Petra Kiesel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Nikolai Tsoy
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Riccardo Maraspini
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Peter Gorilak
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Vladimir Varga
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alf Honigmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Gaia Pigino
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Human Technopole, Milan, Italy.
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46
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Ku S, Messaoudi C, Guyomar C, Kervrann C, Chrétien D. Determination of Microtubule Lattice Parameters from Cryo-electron Microscope Images Using TubuleJ. Bio Protoc 2020; 10:e3814. [PMID: 33659467 DOI: 10.21769/bioprotoc.3814] [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: 03/31/2020] [Revised: 09/20/2020] [Accepted: 10/14/2020] [Indexed: 11/02/2022] Open
Abstract
The α-β tubulin heterodimer undergoes subtle conformational changes during microtubule assembly. These can be modulated by external factors, whose effects on microtubule structure can be characterized on 2D views obtained by cryo-electron microscopy. Analysis of microtubule images is facilitated if they are straight enough to interpret and filter their image Fourier transform, which provide useful information concerning the arrangement of tubulin molecules inside the microtubule lattice. Here, we describe the use of the TubuleJ software to straighten microtubules and determine their lattice parameters. Basic 3D reconstructions can be performed to evaluate the relevance of these parameters. This approach can be used to analyze the effects of nucleotide analogues, drugs or MAPs on microtubule structure, or to select microtubule images prior to high-resolution 3D reconstructions.
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Affiliation(s)
- Siou Ku
- Univ Rennes, CNRS, IGDR (Institut de genetique et developpement de Rennes) - UMR 6290, F-35000 Rennes, France
| | - Cédric Messaoudi
- Institut Curie, PSL Research University, CNRS UMS 2016, F-91401 Orsay, France.,Université Paris-Saclay, INSERM US43, F-91401 Orsay, France
| | - Charlotte Guyomar
- Univ Rennes, CNRS, IGDR (Institut de genetique et developpement de Rennes) - UMR 6290, F-35000 Rennes, France
| | - Charles Kervrann
- Inria-Centre de Rennes Bretagne Atlantique, Campus Universitaire de Beaulieu, 35042 Rennes, France
| | - Denis Chrétien
- Univ Rennes, CNRS, IGDR (Institut de genetique et developpement de Rennes) - UMR 6290, F-35000 Rennes, France
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47
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Knossow M, Campanacci V, Khodja LA, Gigant B. The Mechanism of Tubulin Assembly into Microtubules: Insights from Structural Studies. iScience 2020; 23:101511. [PMID: 32920486 PMCID: PMC7491153 DOI: 10.1016/j.isci.2020.101511] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/03/2020] [Accepted: 08/25/2020] [Indexed: 11/26/2022] Open
Abstract
Microtubules are cytoskeletal components involved in pivotal eukaryotic functions such as cell division, ciliogenesis, and intracellular trafficking. They assemble from αβ-tubulin heterodimers and disassemble in a process called dynamic instability, which is driven by GTP hydrolysis. Structures of the microtubule and of soluble tubulin have been determined by cryo-EM and by X-ray crystallography, respectively. Altogether, these data define the mechanism of tubulin assembly-disassembly at atomic or near-atomic level. We review here the structural changes that occur during assembly, tubulin switching from a curved conformation in solution to a straight one in the microtubule core. We also present more subtle changes associated with GTP binding, leading to tubulin activation for assembly. Finally, we show how cryo-EM and X-ray crystallography are complementary methods to characterize the interaction of tubulin with proteins involved either in intracellular transport or in microtubule dynamics regulation.
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Affiliation(s)
- Marcel Knossow
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Valérie Campanacci
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Liza Ammar Khodja
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Benoît Gigant
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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48
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Paul DM, Mantell J, Borucu U, Coombs J, Surridge KJ, Squire JM, Verkade P, Dodding MP. In situ cryo-electron tomography reveals filamentous actin within the microtubule lumen. J Cell Biol 2020; 219:e201911154. [PMID: 32478855 PMCID: PMC7480112 DOI: 10.1083/jcb.201911154] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/16/2020] [Accepted: 05/13/2020] [Indexed: 11/22/2022] Open
Abstract
Microtubules and filamentous (F-) actin engage in complex interactions to drive many cellular processes from subcellular organization to cell division and migration. This is thought to be largely controlled by proteins that interface between the two structurally distinct cytoskeletal components. Here, we use cryo-electron tomography to demonstrate that the microtubule lumen can be occupied by extended segments of F-actin in small molecule-induced, microtubule-based, cellular projections. We uncover an unexpected versatility in cytoskeletal form that may prompt a significant development of our current models of cellular architecture and offer a new experimental approach for the in situ study of microtubule structure and contents.
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Affiliation(s)
- Danielle M. Paul
- School of Physiology, Pharmacology and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Judith Mantell
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Ufuk Borucu
- GW4 Facility for High-Resolution Electron Cryo-Microscopy, University of Bristol, Bristol, United Kingdom
| | - Jennifer Coombs
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Katherine J. Surridge
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - John M. Squire
- School of Physiology, Pharmacology and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
- Department of Metabolism, Digestion and Reproduction, Imperial College, London, United Kingdom
| | - Paul Verkade
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Mark P. Dodding
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
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49
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Microtubules pull the strings: disordered sequences as efficient couplers of microtubule-generated force. Essays Biochem 2020; 64:371-382. [PMID: 32502246 DOI: 10.1042/ebc20190078] [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: 03/05/2020] [Revised: 05/01/2020] [Accepted: 05/14/2020] [Indexed: 11/17/2022]
Abstract
Microtubules are dynamic polymers that grow and shrink through addition or loss of tubulin subunits at their ends. Microtubule ends generate mechanical force that moves chromosomes and cellular organelles, and provides mechanical tension. Recent literature describes a number of proteins and protein complexes that couple dynamics of microtubule ends to movements of their cellular cargoes. These 'couplers' are quite diverse in their microtubule-binding domains (MTBDs), while sharing similarity in function, but a systematic understanding of the principles underlying their activity is missing. Here, I review various types of microtubule couplers, focusing on their essential activities: ability to follow microtubule ends and capture microtubule-generated force. Most of the couplers require presence of unstructured positively charged sequences and multivalency in their microtubule-binding sites to efficiently convert the microtubule-generated force into useful connection to a cargo. An overview of the microtubule features supporting end-tracking and force-coupling, and the experimental methods to assess force-coupling properties is also provided.
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50
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Igaev M, Grubmüller H. Microtubule instability driven by longitudinal and lateral strain propagation. PLoS Comput Biol 2020; 16:e1008132. [PMID: 32877399 PMCID: PMC7467311 DOI: 10.1371/journal.pcbi.1008132] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 07/09/2020] [Indexed: 12/21/2022] Open
Abstract
Tubulin dimers associate longitudinally and laterally to form metastable microtubules (MTs). MT disassembly is preceded by subtle structural changes in tubulin fueled by GTP hydrolysis. These changes render the MT lattice unstable, but it is unclear exactly how they affect lattice energetics and strain. We performed long-time atomistic simulations to interrogate the impacts of GTP hydrolysis on tubulin lattice conformation, lateral inter-dimer interactions, and (non-)local lateral coordination of dimer motions. The simulations suggest that most of the hydrolysis energy is stored in the lattice in the form of longitudinal strain. While not significantly affecting lateral bond stability, the stored elastic energy results in more strongly confined and correlated dynamics of GDP-tubulins, thereby entropically destabilizing the MT lattice.
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Affiliation(s)
- Maxim Igaev
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Helmut Grubmüller
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
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