1
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Cannariato M, Zizzi EA, Tuszynski JA, Deriu MA. Multiscale Computational Analysis of the Effect of Taxol on Microtubule Mechanics. ACS Biomater Sci Eng 2024; 10:5666-5674. [PMID: 39166920 DOI: 10.1021/acsbiomaterials.4c00847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Microtubules (MTs) are widely recognized as targets for cancer therapies. They are directly related to unique mechanical properties, closely dependent on MT architecture and tubulin molecular features. Taxol is known to affect tubulin interactions resulting in the stabilization of the MT lattice, and thus the hierarchical organization stability, mechanics, and function. A deeper understanding of the molecular mechanisms through which taxol modulates intertubulin interactions in the MT lattice, and consequently, its stability and mechanical response is crucial to characterize how MT properties are regulated by environmental factors, such as interacting ligands. In this study, a computational analysis of the effect of taxol on the MT was performed at different scales, combining molecular dynamics simulation, dynamical network analysis, and elastic network modeling. The results show that the taxol-induced conformational differences at the M-loop region increase the stability of the lateral interactions and the amount of surface in contact between laterally coupled tubulins. Moreover, the conformational rearrangements in the taxane binding site result in a different structural communication pattern. Finally, the different conformation of the tubulin heterodimers and the stabilized lateral interactions resulted in a tendency toward higher deformation of the vibrating MT in the presence of taxol. Overall, this work provides additional insights into taxol-induced stabilization and relates the conformational changes at the tubulin level to the MT mechanics. Besides providing useful insights into taxol effect on MT mechanics, a methodological framework that could be used to characterize the effects of other MT stabilizing agents is presented.
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Affiliation(s)
- Marco Cannariato
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin 10129, Italy
| | - Eric A Zizzi
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin 10129, Italy
| | - Jacek A Tuszynski
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin 10129, Italy
| | - Marco A Deriu
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin 10129, Italy
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2
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Bagdadi N, Wu J, Delaroche J, Serre L, Delphin C, De Andrade M, Carcel M, Nawabi H, Pinson B, Vérin C, Couté Y, Gory-Fauré S, Andrieux A, Stoppin-Mellet V, Arnal I. Stable GDP-tubulin islands rescue dynamic microtubules. J Cell Biol 2024; 223:e202307074. [PMID: 38758215 PMCID: PMC11101955 DOI: 10.1083/jcb.202307074] [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: 07/18/2023] [Revised: 02/26/2024] [Accepted: 05/04/2024] [Indexed: 05/18/2024] Open
Abstract
Microtubules are dynamic polymers that interconvert between phases of growth and shrinkage, yet they provide structural stability to cells. Growth involves hydrolysis of GTP-tubulin to GDP-tubulin, which releases energy that is stored within the microtubule lattice and destabilizes it; a GTP cap at microtubule ends is thought to prevent GDP subunits from rapidly dissociating and causing catastrophe. Here, using in vitro reconstitution assays, we show that GDP-tubulin, usually considered inactive, can itself assemble into microtubules, preferentially at the minus end, and promote persistent growth. GDP-tubulin-assembled microtubules are highly stable, displaying no detectable spontaneous shrinkage. Strikingly, islands of GDP-tubulin within dynamic microtubules stop shrinkage events and promote rescues. Microtubules thus possess an intrinsic capacity for stability, independent of accessory proteins. This finding provides novel mechanisms to explain microtubule dynamics.
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Affiliation(s)
- Nassiba Bagdadi
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Juliette Wu
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Julie Delaroche
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Laurence Serre
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Christian Delphin
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Manon De Andrade
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Marion Carcel
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Homaira Nawabi
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Benoît Pinson
- Metabolic Analyses Service, TBMCore—Université de Bordeaux—CNRS UAR 3427—INSERM US005, Bordeaux, France
| | - Claire Vérin
- Université Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, FR2048, Grenoble, France
| | - Yohann Couté
- Université Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, FR2048, Grenoble, France
| | - Sylvie Gory-Fauré
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Annie Andrieux
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Virginie Stoppin-Mellet
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
| | - Isabelle Arnal
- Université Grenoble Alpes, INSERM, U1216, CNRS, CEA, Grenoble Institut Neurosciences (GIN), Grenoble, France
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3
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Wood LM, Moore JK. β3 accelerates microtubule plus end maturation through a divergent lateral interface. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.603993. [PMID: 39071388 PMCID: PMC11275713 DOI: 10.1101/2024.07.17.603993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
β-tubulin isotypes exhibit similar sequences but different activities, suggesting that limited sequence divergence is functionally important. We investigated this hypothesis for TUBB3/β3, a β-tubulin linked to aggressive cancers and chemoresistance in humans. We created mutant yeast strains with β-tubulin alleles that mimic variant residues in β3 and find that residues at the lateral interface are sufficient to alter microtubule dynamics and response to microtubule targeting agents. In HeLa cells, β3 overexpression decreases the lifetime of microtubule growth, and this requires residues at the lateral interface. These microtubules exhibit a shorter region of EB binding at the plus end, suggesting faster lattice maturation, and resist stabilization by paclitaxel. Resistance requires the H1-S2 and H2-S3 regions at the lateral interface of β3. Our results identify the mechanistic origins of the unique activity of β3 tubulin and suggest that tubulin isotype expression may tune the rate of lattice maturation at growing microtubule plus ends in cells.
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Affiliation(s)
- Lisa M Wood
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jeffrey K Moore
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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4
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Dendooven T, Yatskevich S, Burt A, Chen ZA, Bellini D, Rappsilber J, Kilmartin JV, Barford D. Structure of the native γ-tubulin ring complex capping spindle microtubules. Nat Struct Mol Biol 2024; 31:1134-1144. [PMID: 38609662 PMCID: PMC11257966 DOI: 10.1038/s41594-024-01281-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/19/2024] [Indexed: 04/14/2024]
Abstract
Microtubule (MT) filaments, composed of α/β-tubulin dimers, are fundamental to cellular architecture, function and organismal development. They are nucleated from MT organizing centers by the evolutionarily conserved γ-tubulin ring complex (γTuRC). However, the molecular mechanism of nucleation remains elusive. Here we used cryo-electron tomography to determine the structure of the native γTuRC capping the minus end of a MT in the context of enriched budding yeast spindles. In our structure, γTuRC presents a ring of γ-tubulin subunits to seed nucleation of exclusively 13-protofilament MTs, adopting an active closed conformation to function as a perfect geometric template for MT nucleation. Our cryo-electron tomography reconstruction revealed that a coiled-coil protein staples the first row of α/β-tubulin of the MT to alternating positions along the γ-tubulin ring of γTuRC. This positioning of α/β-tubulin onto γTuRC suggests a role for the coiled-coil protein in augmenting γTuRC-mediated MT nucleation. Based on our results, we describe a molecular model for budding yeast γTuRC activation and MT nucleation.
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Affiliation(s)
| | - Stanislau Yatskevich
- MRC Laboratory of Molecular Biology, Cambridge, UK.
- Genentech, South San Francisco, CA, USA.
| | - Alister Burt
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Genentech, South San Francisco, CA, USA
| | - Zhuo A Chen
- Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany
| | - Dom Bellini
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Juri Rappsilber
- Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany
- Si-M/'Der Simulierte Mensch', Technische Universität Berlin and Charité, Universitätsmedizin Berlin, Berlin, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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5
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Vermeulen BJ, Böhler A, Gao Q, Neuner A, Župa E, Chu Z, Würtz M, Jäkle U, Gruss OJ, Pfeffer S, Schiebel E. γ-TuRC asymmetry induces local protofilament mismatch at the RanGTP-stimulated microtubule minus end. EMBO J 2024; 43:2062-2085. [PMID: 38600243 PMCID: PMC11099078 DOI: 10.1038/s44318-024-00087-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
The γ-tubulin ring complex (γ-TuRC) is a structural template for de novo microtubule assembly from α/β-tubulin units. The isolated vertebrate γ-TuRC assumes an asymmetric, open structure deviating from microtubule geometry, suggesting that γ-TuRC closure may underlie regulation of microtubule nucleation. Here, we isolate native γ-TuRC-capped microtubules from Xenopus laevis egg extract nucleated through the RanGTP-induced pathway for spindle assembly and determine their cryo-EM structure. Intriguingly, the microtubule minus end-bound γ-TuRC is only partially closed and consequently, the emanating microtubule is locally misaligned with the γ-TuRC and asymmetric. In the partially closed conformation of the γ-TuRC, the actin-containing lumenal bridge is locally destabilised, suggesting lumenal bridge modulation in microtubule nucleation. The microtubule-binding protein CAMSAP2 specifically binds the minus end of γ-TuRC-capped microtubules, indicating that the asymmetric minus end structure may underlie recruitment of microtubule-modulating factors for γ-TuRC release. Collectively, we reveal a surprisingly asymmetric microtubule minus end protofilament organisation diverging from the regular microtubule structure, with direct implications for the kinetics and regulation of nucleation and subsequent modulation of microtubules during spindle assembly.
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Affiliation(s)
- Bram Ja Vermeulen
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Anna Böhler
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Qi Gao
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Annett Neuner
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Erik Župa
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Zhenzhen Chu
- Institut für Genetik, Universität Bonn, Bonn, Germany
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Lymphoma Department, Peking University Cancer Hospital & Institute, Beijing, China
| | - Martin Würtz
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Ursula Jäkle
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | | | - Stefan Pfeffer
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany.
| | - Elmar Schiebel
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany.
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6
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Mahalingan KK, Grotjahn DA, Li Y, Lander GC, Zehr EA, Roll-Mecak A. Structural basis for α-tubulin-specific and modification state-dependent glutamylation. Nat Chem Biol 2024:10.1038/s41589-024-01599-0. [PMID: 38658656 DOI: 10.1038/s41589-024-01599-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 03/06/2024] [Indexed: 04/26/2024]
Abstract
Microtubules have spatiotemporally complex posttranslational modification patterns. Tubulin tyrosine ligase-like (TTLL) enzymes introduce the most prevalent modifications on α-tubulin and β-tubulin. How TTLLs specialize for specific substrate recognition and ultimately modification-pattern generation is largely unknown. TTLL6, a glutamylase implicated in ciliopathies, preferentially modifies tubulin α-tails in microtubules. Cryo-electron microscopy, kinetic analysis and single-molecule biochemistry reveal an unprecedented quadrivalent recognition that ensures simultaneous readout of microtubule geometry and posttranslational modification status. By binding to a β-tubulin subunit, TTLL6 modifies the α-tail of the longitudinally adjacent tubulin dimer. Spanning two tubulin dimers along and across protofilaments (PFs) ensures fidelity of recognition of both the α-tail and the microtubule. Moreover, TTLL6 reads out and is stimulated by glutamylation of the β-tail of the laterally adjacent tubulin dimer, mediating crosstalk between α-tail and β-tail. This positive feedback loop can generate localized microtubule glutamylation patterns. Our work uncovers general principles that generate tubulin chemical and topographic complexity.
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Affiliation(s)
- Kishore K Mahalingan
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Danielle A Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute La Jolla, La Jolla, CA, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute La Jolla, La Jolla, CA, USA
| | - Elena A Zehr
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
- Biochemistry & Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA.
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7
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Cannariato M, Zizzi EA, Pallante L, Miceli M, Deriu MA. Mechanical communication within the microtubule through network-based analysis of tubulin dynamics. Biomech Model Mechanobiol 2024; 23:569-579. [PMID: 38060156 PMCID: PMC10963519 DOI: 10.1007/s10237-023-01792-5] [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: 07/24/2023] [Accepted: 11/11/2023] [Indexed: 12/08/2023]
Abstract
The identification of the mechanisms underlying the transfer of mechanical vibrations in protein complexes is crucial to understand how these super-assemblies are stabilized to perform specific functions within the cell. In this context, the study of the structural communication and the propagation of mechanical stimuli within the microtubule (MT) is important given the pivotal role of the latter in cell viability. In this study, we employed molecular modelling and the dynamical network analysis approaches to analyse the MT. The results highlight that β -tubulin drives the transfer of mechanical information between protofilaments (PFs), which is altered at the seam due to a different interaction pattern. Moreover, while the key residues involved in the structural communication along the PF are generally conserved, a higher diversity was observed for amino acids mediating the lateral communication. Taken together, these results might explain why MTs with different PF numbers are formed in different organisms or with different β -tubulin isotypes.
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Affiliation(s)
- Marco Cannariato
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Eric A Zizzi
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Lorenzo Pallante
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Marcello Miceli
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Marco A Deriu
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy.
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8
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McCormick LA, Cleary JM, Hancock WO, Rice LM. Interface-acting nucleotide controls polymerization dynamics at microtubule plus- and minus-ends. eLife 2024; 12:RP89231. [PMID: 38180336 PMCID: PMC10945504 DOI: 10.7554/elife.89231] [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] [Indexed: 01/06/2024] Open
Abstract
GTP-tubulin is preferentially incorporated at growing microtubule ends, but the biochemical mechanism by which the bound nucleotide regulates the strength of tubulin:tubulin interactions is debated. The 'self-acting' (cis) model posits that the nucleotide (GTP or GDP) bound to a particular tubulin dictates how strongly that tubulin interacts, whereas the 'interface-acting' (trans) model posits that the nucleotide at the interface of two tubulin dimers is the determinant. We identified a testable difference between these mechanisms using mixed nucleotide simulations of microtubule elongation: with a self-acting nucleotide, plus- and minus-end growth rates decreased in the same proportion to the amount of GDP-tubulin, whereas with interface-acting nucleotide, plus-end growth rates decreased disproportionately. We then experimentally measured plus- and minus-end elongation rates in mixed nucleotides and observed a disproportionate effect of GDP-tubulin on plus-end growth rates. Simulations of microtubule growth were consistent with GDP-tubulin binding at and 'poisoning' plus-ends but not at minus-ends. Quantitative agreement between simulations and experiments required nucleotide exchange at terminal plus-end subunits to mitigate the poisoning effect of GDP-tubulin there. Our results indicate that the interfacial nucleotide determines tubulin:tubulin interaction strength, thereby settling a longstanding debate over the effect of nucleotide state on microtubule dynamics.
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Affiliation(s)
- Lauren A McCormick
- Department of Biophysics and Biochemistry, the University of Texas Southwestern Medical CenterDallasUnited States
| | - Joseph M Cleary
- Department of Biomedical Engineering, Pennsylvania State UniversityState CollegeUnited States
| | - William O Hancock
- Department of Biomedical Engineering, Pennsylvania State UniversityState CollegeUnited States
| | - Luke M Rice
- Department of Biophysics and Biochemistry, the University of Texas Southwestern Medical CenterDallasUnited States
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9
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Hussain A, Nguyen VT, Reigan P, McMurray M. Evolutionary degeneration of septins into pseudoGTPases: impacts on a hetero-oligomeric assembly interface. Front Cell Dev Biol 2023; 11:1296657. [PMID: 38125875 PMCID: PMC10731463 DOI: 10.3389/fcell.2023.1296657] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023] Open
Abstract
The septin family of eukaryotic proteins comprises distinct classes of sequence-related monomers that associate in a defined order into linear hetero-oligomers, which are capable of polymerizing into cytoskeletal filaments. Like actin and ⍺ and β tubulin, most septin monomers require binding of a nucleotide at a monomer-monomer interface (the septin "G" interface) for assembly into higher-order structures. Like ⍺ and β tubulin, where GTP is bound by both subunits but only the GTP at the ⍺-β interface is subject to hydrolysis, the capacity of certain septin monomers to hydrolyze their bound GTP has been lost during evolution. Thus, within septin hetero-oligomers and filaments, certain monomers remain permanently GTP-bound. Unlike tubulins, loss of septin GTPase activity-creating septin "pseudoGTPases"-occurred multiple times in independent evolutionary trajectories, accompanied in some cases by non-conservative substitutions in highly conserved residues in the nucleotide-binding pocket. Here, we used recent septin crystal structures, AlphaFold-generated models, phylogenetics and in silico nucleotide docking to investigate how in some organisms the septin G interface evolved to accommodate changes in nucleotide occupancy. Our analysis suggests that yeast septin monomers expressed only during meiosis and sporulation, when GTP is scarce, are evolving rapidly and might not bind GTP or GDP. Moreover, the G dimerization partners of these sporulation-specific septins appear to carry compensatory changes in residues that form contacts at the G interface to help retain stability despite the absence of bound GDP or GTP in the facing subunit. During septin evolution in nematodes, apparent loss of GTPase activity was also accompanied by changes in predicted G interface contacts. Overall, our observations support the conclusion that the primary function of nucleotide binding and hydrolysis by septins is to ensure formation of G interfaces that impose the proper subunit-subunit order within the hetero-oligomer.
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Affiliation(s)
- Alya Hussain
- Program in Structural Biology and Biochemistry, Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Vu T. Nguyen
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Philip Reigan
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Michael McMurray
- Program in Structural Biology and Biochemistry, Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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10
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Duan D, Lyu W, Chai P, Ma S, Wu K, Wu C, Xiong Y, Sestan N, Zhang K, Koleske AJ. Abl2 repairs microtubules and phase separates with tubulin to promote microtubule nucleation. Curr Biol 2023; 33:4582-4598.e10. [PMID: 37858340 PMCID: PMC10877310 DOI: 10.1016/j.cub.2023.09.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 07/07/2023] [Accepted: 09/06/2023] [Indexed: 10/21/2023]
Abstract
Abl family kinases are evolutionarily conserved regulators of cell migration and morphogenesis. Genetic experiments in Drosophila suggest that Abl family kinases interact functionally with microtubules to regulate axon guidance and neuronal morphogenesis. Vertebrate Abl2 binds to microtubules and promotes their plus-end elongation, both in vitro and in cells, but the molecular mechanisms by which Abl2 regulates microtubule (MT) dynamics are unclear. We report here that Abl2 regulates MT assembly via condensation and direct interactions with both the MT lattice and tubulin dimers. We find that Abl2 promotes MT nucleation, which is further facilitated by the ability of the Abl2 C-terminal half to undergo liquid-liquid phase separation (LLPS) and form co-condensates with tubulin. Abl2 binds to regions adjacent to MT damage, facilitates MT repair via fresh tubulin recruitment, and increases MT rescue frequency and lifetime. Cryo-EM analyses strongly support a model in which Abl2 engages tubulin C-terminal tails along an extended MT lattice conformation at damage sites to facilitate repair via fresh tubulin recruitment. Abl2Δ688-790, which closely mimics a naturally occurring splice isoform, retains binding to the MT lattice but does not bind tubulin, promote MT nucleation, or increase rescue frequency. In COS-7 cells, MT reassembly after nocodazole treatment is greatly slowed in Abl2 knockout COS-7 cells compared with wild-type cells, and these defects are rescued by re-expression of Abl2, but not Abl2Δ688-790. We propose that Abl2 locally concentrates tubulin to promote MT nucleation and recruits it to defects in the MT lattice to enable repair and rescue.
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Affiliation(s)
- Daisy Duan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Wanqing Lyu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Pengxin Chai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Kuanlin Wu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Chunxiang Wu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA; Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Psychiatry, Yale School of Medicine, New Haven, CT 06510, USA; Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT 06510, USA; Yale Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Kai Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Anthony J Koleske
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA; Department of Neuroscience, Yale University, New Haven, CT 06510, USA.
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11
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Yue Y, Hotta T, Higaki T, Verhey KJ, Ohi R. Microtubule detyrosination by VASH1/SVBP is regulated by the conformational state of tubulin in the lattice. Curr Biol 2023; 33:4111-4123.e7. [PMID: 37716348 PMCID: PMC10592207 DOI: 10.1016/j.cub.2023.07.062] [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: 03/16/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 09/18/2023]
Abstract
Tubulin, a heterodimer of α- and β-tubulin, is a GTPase that assembles into microtubule (MT) polymers whose dynamic properties are intimately coupled to nucleotide hydrolysis. In cells, the organization and dynamics of MTs are further tuned by post-translational modifications (PTMs), which control the ability of MT-associated proteins (MAPs) and molecular motors to engage MTs. Detyrosination is a PTM of α-tubulin, wherein its C-terminal tyrosine residue is enzymatically removed by either the vasohibin (VASH) or MT-associated tyrosine carboxypeptidase (MATCAP) peptidases. How these enzymes generate specific patterns of MT detyrosination in cells is not known. Here, we use a novel antibody-based probe to visualize the formation of detyrosinated MTs in real time and employ single-molecule imaging of VASH1 bound to its regulatory partner small-vasohibin binding protein (SVBP) to understand the process of MT detyrosination in vitro and in cells. We demonstrate that the activity, but not binding, of VASH1/SVBP is much greater on mimics of guanosine triphosphate (GTP)-MTs than on guanosine diphosphate (GDP)-MTs. Given emerging data showing that tubulin subunits in GTP-MTs are in expanded conformation relative to tubulin subunits in GDP-MTs, we reasoned that the lattice conformation of MTs is a key factor that gates the activity of VASH1/SVBP. We show that Taxol, a drug known to expand the MT lattice, promotes MT detyrosination and that CAMSAP2 and CAMSAP3 are two MAPs that spatially regulate detyrosination in cells. Collectively, our work shows that VASH1/SVBP detyrosination is regulated by the conformational state of tubulin in the MT lattice and that this is spatially determined in cells by the activity of MAPs.
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Affiliation(s)
- Yang Yue
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Takashi Hotta
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Takumi Higaki
- Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan; International Research Organization in Advanced Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Ryoma Ohi
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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12
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Eren E, Watts NR, Randazzo D, Palmer I, Sackett DL, Wingfield PT. Structural basis of microtubule depolymerization by the kinesin-like activity of HIV-1 Rev. Structure 2023; 31:1233-1246.e5. [PMID: 37572662 PMCID: PMC10592302 DOI: 10.1016/j.str.2023.07.009] [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: 08/17/2022] [Revised: 04/07/2023] [Accepted: 07/18/2023] [Indexed: 08/14/2023]
Abstract
HIV-1 Rev is an essential regulatory protein that transports unspliced and partially spliced viral mRNAs from the nucleus to the cytoplasm for the expression of viral structural proteins. During its nucleocytoplasmic shuttling, Rev interacts with several host proteins to use the cellular machinery for the advantage of the virus. Here, we report the 3.5 Å cryo-EM structure of a 4.8 MDa Rev-tubulin ring complex. Our structure shows that Rev's arginine-rich motif (ARM) binds to both the acidic surfaces and the C-terminal tails of α/β-tubulin. The Rev-tubulin interaction is functionally homologous to that of kinesin-13, potently destabilizing microtubules at sub-stoichiometric levels. Expression of Rev in astrocytes and HeLa cells shows that it can modulate the microtubule cytoskeleton within the cellular environment. These results show a previously undefined regulatory role of Rev.
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Affiliation(s)
- Elif Eren
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Norman R Watts
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Davide Randazzo
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ira Palmer
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dan L Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul T Wingfield
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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13
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McCormick LA, Cleary JM, Hancock WO, Rice LM. Interface-acting nucleotide controls polymerization dynamics at microtubule plus- and minus-ends. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539131. [PMID: 37205370 PMCID: PMC10187237 DOI: 10.1101/2023.05.03.539131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
GTP-tubulin is preferentially incorporated at growing microtubule ends, but the biochemical mechanism by which the bound nucleotide regulates the strength of tubulin:tubulin interactions is debated. The 'self-acting' (cis) model posits that the nucleotide (GTP or GDP) bound to a particular tubulin dictates how strongly that tubulin interacts, whereas the 'interface-acting' (trans) model posits that the nucleotide at the interface of two tubulin dimers is the determinant. We identified a testable difference between these mechanisms using mixed nucleotide simulations of microtubule elongation: with self-acting nucleotide, plus- and minus-end growth rates decreased in the same proportion to the amount of GDP-tubulin, whereas with interface-acting nucleotide, plus-end growth rates decreased disproportionately. We then experimentally measured plus- and minus-end elongation rates in mixed nucleotides and observed a disproportionate effect of GDP-tubulin on plus-end growth rates. Simulations of microtubule growth were consistent with GDP-tubulin binding at and 'poisoning' plus-ends but not at minus-ends. Quantitative agreement between simulations and experiments required nucleotide exchange at terminal plus-end subunits to mitigate the poisoning effect of GDP-tubulin there. Our results indicate that the interfacial nucleotide determines tubulin:tubulin interaction strength, thereby settling a longstanding debate over the effect of nucleotide state on microtubule dynamics.
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Affiliation(s)
- Lauren A McCormick
- Department of Biophysics and Biochemistry, the University of Texas Southwestern Medical Center, Dallas, TX
| | - Joseph M Cleary
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA
| | - William O Hancock
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA
| | - Luke M Rice
- Department of Biophysics and Biochemistry, the University of Texas Southwestern Medical Center, Dallas, TX
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14
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Zhou J, Wang A, Song Y, Liu N, Wang J, Li Y, Liang X, Li G, Chu H, Wang HW. Structural insights into the mechanism of GTP initiation of microtubule assembly. Nat Commun 2023; 14:5980. [PMID: 37749104 PMCID: PMC10519996 DOI: 10.1038/s41467-023-41615-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 09/08/2023] [Indexed: 09/27/2023] Open
Abstract
In eukaryotes, the dynamic assembly of microtubules (MT) plays an important role in numerous cellular processes. The underlying mechanism of GTP triggering MT assembly is still unknown. Here, we present cryo-EM structures of tubulin heterodimer at their GTP- and GDP-bound states, intermediate assembly states of GTP-tubulin, and final assembly stages of MT. Both GTP- and GDP-tubulin heterodimers adopt similar curved conformations with subtle flexibility differences. In head-to-tail oligomers of tubulin heterodimers, the inter-dimer interface of GDP-tubulin exhibits greater flexibility, particularly in tangential bending. Cryo-EM of the intermediate assembly states reveals two types of tubulin lateral contacts, "Tube-bond" and "MT-bond". Further, molecular dynamics (MD) simulations show that GTP triggers lateral contact formation in MT assembly in multiple sequential steps, gradually straightening the curved tubulin heterodimers. Therefore, we propose a flexible model of GTP-initiated MT assembly, including the formation of longitudinal and lateral contacts, to explain the nucleation and assembly of MT.
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Affiliation(s)
- Ju Zhou
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
- University of California Berkeley, Berkeley, CA, USA
| | - Anhui Wang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Yinlong Song
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Nan Liu
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
| | - Jia Wang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
| | - Yan Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Xin Liang
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China.
| | - Hong-Wei Wang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China.
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15
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Chew YM, Cross RA. Taxol acts differently on different tubulin isotypes. Commun Biol 2023; 6:946. [PMID: 37717119 PMCID: PMC10505170 DOI: 10.1038/s42003-023-05306-y] [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: 03/20/2023] [Accepted: 08/31/2023] [Indexed: 09/18/2023] Open
Abstract
Taxol is a small molecule effector that allosterically locks tubulin into the microtubule lattice. We show here that taxol has different effects on different single-isotype microtubule lattices. Using in vitro reconstitution, we demonstrate that single-isotype α1β4 GDP-tubulin lattices are stabilised and expanded by 10 µM taxol, as reported by accelerated microtubule gliding in kinesin motility assays, whereas single-isotype α1β3 GDP-tubulin lattices are stabilised but not expanded. This isotype-specific action of taxol drives gliding of segmented-isotype GDP-taxol microtubules along convoluted, sinusoidal paths, because their expanded α1β4 segments try to glide faster than their compacted α1β3 segments. In GMPCPP, single-isotype α1β3 and α1β4 lattices both show accelerated gliding, indicating that both can in principle be driven to expand. We therefore propose that taxol-induced lattice expansion requires a higher taxol occupancy than taxol-induced stabilisation, and that higher taxol occupancies are accessible to α1β4 but not α1β3 single-isotype lattices.
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Affiliation(s)
- Yean Ming Chew
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, CV4 7LA, UK
| | - Robert A Cross
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, CV4 7LA, UK.
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16
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Minckley TF, Salvagio LA, Fudge DH, Verhey K, Markus SM, Qin Y. Zn2+ decoration of microtubules arrests axonal transport and displaces tau, doublecortin, and MAP2C. J Cell Biol 2023; 222:e202208121. [PMID: 37326602 PMCID: PMC10276529 DOI: 10.1083/jcb.202208121] [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: 08/22/2022] [Revised: 03/31/2023] [Accepted: 05/11/2023] [Indexed: 06/17/2023] Open
Abstract
Intracellular Zn2+ concentrations increase via depolarization-mediated influx or intracellular release, but the immediate effects of Zn2+ signals on neuron function are not fully understood. By simultaneous recording of cytosolic Zn2+ and organelle motility, we find that elevated Zn2+ (IC50 ≈ 5-10 nM) reduces both lysosomal and mitochondrial motility in primary rat hippocampal neurons and HeLa cells. Using live-cell confocal microscopy and in vitro single-molecule TIRF imaging, we reveal that Zn2+ inhibits activity of motor proteins (kinesin and dynein) without disrupting their microtubule binding. Instead, Zn2+ directly binds to microtubules and selectively promotes detachment of tau, DCX, and MAP2C, but not MAP1B, MAP4, MAP7, MAP9, or p150glued. Bioinformatic predictions and structural modeling show that the Zn2+ binding sites on microtubules partially overlap with the microtubule binding sites of tau, DCX, dynein, and kinesin. Our results reveal that intraneuronal Zn2+ regulates axonal transport and microtubule-based processes by interacting with microtubules.
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Affiliation(s)
- Taylor F. Minckley
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | | | - Dylan H. Fudge
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Kristen Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Steven M. Markus
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Yan Qin
- Department of Biological Sciences, University of Denver, Denver, CO, USA
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17
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Verhey KJ, Ohi R. Causes, costs and consequences of kinesin motors communicating through the microtubule lattice. J Cell Sci 2023; 136:293511. [PMID: 36866642 PMCID: PMC10022682 DOI: 10.1242/jcs.260735] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023] Open
Abstract
Microtubules are critical for a variety of important functions in eukaryotic cells. During intracellular trafficking, molecular motor proteins of the kinesin superfamily drive the transport of cellular cargoes by stepping processively along the microtubule surface. Traditionally, the microtubule has been viewed as simply a track for kinesin motility. New work is challenging this classic view by showing that kinesin-1 and kinesin-4 proteins can induce conformational changes in tubulin subunits while they are stepping. These conformational changes appear to propagate along the microtubule such that the kinesins can work allosterically through the lattice to influence other proteins on the same track. Thus, the microtubule is a plastic medium through which motors and other microtubule-associated proteins (MAPs) can communicate. Furthermore, stepping kinesin-1 can damage the microtubule lattice. Damage can be repaired by the incorporation of new tubulin subunits, but too much damage leads to microtubule breakage and disassembly. Thus, the addition and loss of tubulin subunits are not restricted to the ends of the microtubule filament but rather, the lattice itself undergoes continuous repair and remodeling. This work leads to a new understanding of how kinesin motors and their microtubule tracks engage in allosteric interactions that are critical for normal cell physiology.
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Affiliation(s)
- Kristen J. Verhey
- Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Author for correspondence ()
| | - Ryoma Ohi
- Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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18
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Shemesh A, Ghareeb H, Dharan R, Levi-Kalisman Y, Metanis N, Ringel I, Raviv U. Effect of tubulin self-association on GTP hydrolysis and nucleotide exchange reactions. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140869. [PMID: 36400388 DOI: 10.1016/j.bbapap.2022.140869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 10/13/2022] [Accepted: 11/08/2022] [Indexed: 11/17/2022]
Abstract
We investigated how the self-association of isolated tubulin dimers affects the rate of GTP hydrolysis and the equilibrium of nucleotide exchange. Both reactions are relevant for microtubule (MT) dynamics. We used HPLC to determine the concentrations of GDP and GTP and thereby the GTPase activity of SEC-eluted tubulin dimers in assembly buffer solution, free of glycerol and tubulin aggregates. When GTP hydrolysis was negligible, the nucleotide exchange mechanism was studied by determining the concentrations of tubulin-free and tubulin-bound GTP and GDP. We observed no GTP hydrolysis below the critical conditions for MT assembly (either below the critical tubulin concentration and/or at low temperature), despite the assembly of tubulin 1D curved oligomers and single-rings, showing that their assembly did not involve GTP hydrolysis. Under conditions enabling spontaneous slow MT assembly, a slow pseudo-first-order GTP hydrolysis kinetics was detected, limited by the rate of MT assembly. Cryo-TEM images showed that GTP-tubulin 1D oligomers were curved also at 36 °C. Nucleotide exchange depended on the total tubulin concentration and the molar ratio between tubulin-free GDP and GTP. We used a thermodynamic model of isodesmic tubulin self-association, terminated by the formation of tubulin single-rings to determine the molar fractions of dimers with exposed and buried nucleotide exchangeable sites (E-sites). Our analysis shows that the GDP to GTP exchange reaction equilibrium constant was an order-of-magnitude larger for tubulin dimers with exposed E-sites than for assembled dimers with buried E-sites. This conclusion may have implications on the dynamics at the tip of the MT plus end.
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Affiliation(s)
- Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Hiba Ghareeb
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Raviv Dharan
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Yael Levi-Kalisman
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Norman Metanis
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Israel Ringel
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, 9112102 Jerusalem, Israel
| | - Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel.
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19
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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: 1] [Impact Index Per Article: 1.0] [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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20
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Estévez-Gallego J, Álvarez-Bernad B, Pera B, Wullschleger C, Raes O, Menche D, Martínez JC, Lucena-Agell D, Prota AE, Bonato F, Bargsten K, Cornelus J, Giménez-Abián JF, Northcote P, Steinmetz MO, Kamimura S, Altmann KH, Paterson I, Gago F, Van der Eycken J, Díaz JF, Oliva MÁ. Chemical modulation of microtubule structure through the laulimalide/peloruside site. Structure 2023; 31:88-99.e5. [PMID: 36462501 DOI: 10.1016/j.str.2022.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/23/2022] [Accepted: 11/08/2022] [Indexed: 12/05/2022]
Abstract
Taxanes are microtubule-stabilizing agents used in the treatment of many solid tumors, but they often involve side effects affecting the peripheral nervous system. It has been proposed that this could be related to structural modifications on the filament upon drug binding. Alternatively, laulimalide and peloruside bind to a different site also inducing stabilization, but they have not been exploited in clinics. Here, we use a combination of the parental natural compounds and derived analogs to unravel the stabilization mechanism through this site. These drugs settle lateral interactions without engaging the M loop, which is part of the key and lock involved in the inter-protofilament contacts. Importantly, these drugs can modulate the angle between protofilaments, producing microtubules of different diameters. Among the compounds studied, we have found some showing low cytotoxicity and able to induce stabilization without compromising microtubule native structure. This opens the window of new applications for microtubule-stabilizing agents beyond cancer treatment.
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Affiliation(s)
- Juan Estévez-Gallego
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - Beatriz Álvarez-Bernad
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - Benet Pera
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - Christoph Wullschleger
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences - ETH Zurich, Zürich 8093, Switzerland
| | - Olivier Raes
- Department of Organic and Macromolecular Chemistry, Ghent University, Gent 9000, Belgium
| | - Dirk Menche
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | | | - Daniel Lucena-Agell
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - Andrea E Prota
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen 5232, Switzerland
| | - Francesca Bonato
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - Katja Bargsten
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen 5232, Switzerland
| | - Jelle Cornelus
- Department of Organic and Macromolecular Chemistry, Ghent University, Gent 9000, Belgium
| | - Juan Francisco Giménez-Abián
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - Peter Northcote
- Ferrier Research Institute, University of Wellington, Lower Hutt 5010, New Zealand
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen 5232, Switzerland; University of Basel, Biozentrum, Basel 4056, Switzerland
| | - Shinji Kamimura
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo 192-0393, Japan
| | - Karl-Heinz Altmann
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences - ETH Zurich, Zürich 8093, Switzerland
| | - Ian Paterson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Federico Gago
- Department of Biomedical Sciences and Associated Unit IQM-UAH, Universidad de Alcalá, Alcalá de Henares 28805, Spain
| | - Johan Van der Eycken
- Department of Organic and Macromolecular Chemistry, Ghent University, Gent 9000, Belgium
| | - J Fernando Díaz
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - María Ángela Oliva
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain.
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21
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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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Yan W, Li Y, Liu Y, Wen Y, Pei H, Yang J, Chen L. Crystal structure of tubulin-barbigerone complex enables rational design of potent anticancer agents with isoflavone skeleton. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 109:154550. [PMID: 36610121 DOI: 10.1016/j.phymed.2022.154550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Isoflavones possess many biological activities, including anti-inflammatory and anticancer effects. Microtubules (composed of αβ-tubulin heterodimers) are described as one possible cellular target of some of these isoflavones. However, the binding of tubulin to isoflavones has not been extensively studied, and until now, no crystal structure of the tubulin-isoflavone complex has been solved, and details of the isoflavone-tubulin interaction remain elusive. PURPOSE Barbigerone is an isoflavone mainly found in the genus Milletti, such as the edible leguminous plant Millettia ferruginea, with anticancer activity. This study aims to confirm the cellular target of barbigerone and to study its anticancer mechanism. METHOD Surface plasmon resonance assays and X-ray crystallography were used to study the interaction of barbigerone with tubulin protein. Immunofluorescence, in-cell and in vitro tubulin polymerization assays were employed to investigate the mechanism. MTT assays, cell clonal formation assays, wound healing assays, tube formation assays and H460 xenograft models were conducted to evaluate the in vitro and in vivo anticancer activities of barbigerone and one of its derivatives, 0412. RESULTS Here, we found that barbigerone binds to tubulin to inhibit tubulin polymerization. Moreover, we solved the X-ray crystal structure of the tubulin-barbigerone complex at 2.33 Å resolution, which unambiguously determined the orientation and position of barbigerone in the colchicine-binding site. Illuminated by the X-ray data, we synthetized and obtained a more active isoflavone, 0412. Both barbigerone and 0412 inhibit cancer cell proliferation, tubulin polymerization, migration of HeLa cells and capillary-like tube formation of HUVECs, induce G2/M phase cell cycle arrest and apoptosis, and exhibit anticancer activity in an H460 xenograft model. CONCLUSION In all, through biochemical and X-ray crystal structure results, we identified tubulin as the cellular target of one isoflavone, barbigerone, and proved that the tubulin-barbigerone complex plays a guiding role in obtaining a more active compound, 0412. These studies provide a crucial research basis for the development of isoflavones as anticancer candidate compounds.
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Affiliation(s)
- Wei Yan
- Laboratory of Natural and targeted small molecule drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yong Li
- Laboratory of Natural and targeted small molecule drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yan Liu
- Laboratory of Natural and targeted small molecule drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yi Wen
- Laboratory of Natural and targeted small molecule drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Heying Pei
- Laboratory of Natural and targeted small molecule drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Jianhong Yang
- Laboratory of Natural and targeted small molecule drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China.
| | - Lijuan Chen
- Laboratory of Natural and targeted small molecule drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China.
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23
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Úsuga-Acevedo B, García Y, Díaz CF, Jiménez VA. Rational Discovery of Microtubule-Stabilizing Peptides. J Chem Inf Model 2022; 62:6844-6856. [PMID: 36074453 DOI: 10.1021/acs.jcim.2c00849] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Microtubule (MT) stabilization is an attractive pharmacological strategy to hamper the progress of neurodegenerative diseases. In this regard, seeking peptides with MT-stabilizing properties has awoken great interest. This work reports the rational discovery of two structurally related MT-stabilizing octapeptides using a combination of protein-peptide docking, conventional molecular dynamics, Gaussian accelerated molecular dynamics (GaMD), and tubulin polymerization assays. FASTA sequences for ∼1000 peptides were crafted from single and double mutants of davunetide (NAP) and docked against the Taxol (TX) site on an octameric MT model representing a portion of the MT wall. Docked peptides were rescored after MM minimization and binding free energy refinement through single-point MM/GBSA calculations. The 60 best-ranked peptides were subjected to 50 ns MD simulations on peptide-MT complexes at the terminal TX site in the octameric Tau-MT model resulting in 11 complexes with occupancies greater than 99% and peptide-protein binding free energies less than -40 kcal/mol. Selected peptides were then examined through 300 ns GaMD simulations in complexes containing two identical ligands at the terminal and intermediate TX sites in the Tau-MT model to account for the differential association of MT-binding peptides to different regions of the MT structure. Six candidates showed a favorable MT-binding potential based on the analysis of interaction frequencies and relative mobilities of the complex components, suggesting a pivotal role of Arg278, Gln281, and Arg369 residues for peptides recognition. Four candidates were predicted to preserve an adequate balance of longitudinal and lateral interactions between tubulin dimers in peptide-MT complexes such that MT-stabilizing effects could be expected. MT polymerization experiments confirmed that four peptides (HAPVSIHQ, NYPVSIHQ, NWPVSIWQ, HAPVSIIQ) exhibit MT-stabilizing activity in vitro with NWPVSIWQ (P43) and HAPVSIIQ (P52) being the most active. Tryptophan quenching assays verified that P43 and P52 bind to nonpolymeric tubulin, whereas viability experiments on HEK cells confirmed their safety to pursue future pharmacological studies. The results herein presented are valuable to making progress in the rational design of MT-stabilizing peptides.
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Affiliation(s)
- Brandon Úsuga-Acevedo
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Sede Concepción, Autopista Concepción-Talcahuano 7100, Talcahuano, Chile 4300866
| | - Yadiris García
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Sede Concepción, Autopista Concepción-Talcahuano 7100, Talcahuano, Chile 4300866
| | - Carola F Díaz
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Sede Concepción, Autopista Concepción-Talcahuano 7100, Talcahuano, Chile 4300866
| | - Verónica A Jiménez
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Sede Concepción, Autopista Concepción-Talcahuano 7100, Talcahuano, Chile 4300866
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24
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The augmin complex architecture reveals structural insights into microtubule branching. Nat Commun 2022; 13:5635. [PMID: 36163468 PMCID: PMC9512787 DOI: 10.1038/s41467-022-33228-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/05/2022] [Indexed: 11/24/2022] Open
Abstract
In mitosis, the augmin complex binds to spindle microtubules to recruit the γ-tubulin ring complex (γ-TuRC), the principal microtubule nucleator, for the formation of branched microtubules. Our understanding of augmin-mediated microtubule branching is hampered by the lack of structural information on the augmin complex. Here, we elucidate the molecular architecture and conformational plasticity of the augmin complex using an integrative structural biology approach. The elongated structure of the augmin complex is characterised by extensive coiled-coil segments and comprises two structural elements with distinct but complementary functions in γ-TuRC and microtubule binding, linked by a flexible hinge. The augmin complex is recruited to microtubules via a composite microtubule binding site comprising a positively charged unordered extension and two calponin homology domains. Our study provides the structural basis for augmin function in branched microtubule formation, decisively fostering our understanding of spindle formation in mitosis. The formation of branched microtubule networks in mitotic spindles depends on the augmin complex. Zupa, Würtz et al. elucidate the molecular architecture and conformational plasticity of the augmin complex using integrative structural biology, providing structural insights into microtubule branching.
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25
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Inaba H, Sueki Y, Ichikawa M, Kabir AMR, Iwasaki T, Shigematsu H, Kakugo A, Sada K, Tsukazaki T, Matsuura K. Generation of stable microtubule superstructures by binding of peptide-fused tetrameric proteins to inside and outside. SCIENCE ADVANCES 2022; 8:eabq3817. [PMID: 36070375 PMCID: PMC9451167 DOI: 10.1126/sciadv.abq3817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/22/2022] [Indexed: 05/24/2023]
Abstract
Microtubules play important roles in biological functions by forming superstructures, such as doublets and branched structures, in vivo. Despite the importance, it is challenging to construct these superstructures in vitro. Here, we designed a tetrameric fluorescent protein Azami-Green (AG) fused with His-tag and Tau-derived peptide (TP), TP-AG, to generate the superstructures. Main binding sites of TP-AG can be controlled to the inside and outside of microtubules by changing the polymerization conditions. The binding of TP-AG to the inside promoted microtubule formation and generated rigid and stable microtubules. The binding of TP-AG to the outside induced various microtubule superstructures, including doublets, multiplets, branched structures, and extremely long microtubules by recruiting tubulins to microtubules. Motile microtubule aster structures were also constructed by TP-AG. The generation of various microtubule superstructures by a single type of exogenous protein is a new concept for understanding the functions of microtubules and constructing microtubule-based nanomaterials.
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Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
| | - Yurina Sueki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Muneyoshi Ichikawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | | | - Takashi Iwasaki
- Department of Bioresources Science, Graduate School of Agricultural Sciences, Tottori University, Tottori 680-8553, Japan
| | | | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Kazuki Sada
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Tomoya Tsukazaki
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
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26
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Castrogiovanni C, Inchingolo AV, Harrison JU, Dudka D, Sen O, Burroughs NJ, McAinsh AD, Meraldi P. Evidence for a HURP/EB free mixed-nucleotide zone in kinetochore-microtubules. Nat Commun 2022; 13:4704. [PMID: 35948594 PMCID: PMC9365851 DOI: 10.1038/s41467-022-32421-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 07/28/2022] [Indexed: 12/02/2022] Open
Abstract
Current models infer that the microtubule-based mitotic spindle is built from GDP-tubulin with small GTP caps at microtubule plus-ends, including those that attach to kinetochores, forming the kinetochore-fibres. Here we reveal that kinetochore-fibres additionally contain a dynamic mixed-nucleotide zone that reaches several microns in length. This zone becomes visible in cells expressing fluorescently labelled end-binding proteins, a known marker for GTP-tubulin, and endogenously-labelled HURP - a protein which we show to preferentially bind the GDP microtubule lattice in vitro and in vivo. We find that in mitotic cells HURP accumulates on the kinetochore-proximal region of depolymerising kinetochore-fibres, whilst avoiding recruitment to nascent polymerising K-fibres, giving rise to a growing "HURP-gap". The absence of end-binding proteins in the HURP-gaps leads us to postulate that they reflect a mixed-nucleotide zone. We generate a minimal quantitative model based on the preferential binding of HURP to GDP-tubulin to show that such a mixed-nucleotide zone is sufficient to recapitulate the observed in vivo dynamics of HURP-gaps.
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Affiliation(s)
- Cédric Castrogiovanni
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211, Geneva 4, Switzerland
- Translational Research Centre in Onco-hematology, Faculty of Medicine, University of Geneva, 1211, Geneva 4, Switzerland
| | - Alessio V Inchingolo
- Centre for Mechanochemical Cell Biology, University of Warwick, Coventry, UK
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Jonathan U Harrison
- Centre for Mechanochemical Cell Biology, University of Warwick, Coventry, UK
- Mathematics Institute, University of Warwick, Coventry, UK
| | - Damian Dudka
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211, Geneva 4, Switzerland
- Translational Research Centre in Onco-hematology, Faculty of Medicine, University of Geneva, 1211, Geneva 4, Switzerland
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Onur Sen
- Centre for Mechanochemical Cell Biology, University of Warwick, Coventry, UK
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Nigel J Burroughs
- Centre for Mechanochemical Cell Biology, University of Warwick, Coventry, UK
- Mathematics Institute, University of Warwick, Coventry, UK
| | - Andrew D McAinsh
- Centre for Mechanochemical Cell Biology, University of Warwick, Coventry, UK.
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK.
| | - Patrick Meraldi
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211, Geneva 4, Switzerland.
- Translational Research Centre in Onco-hematology, Faculty of Medicine, University of Geneva, 1211, Geneva 4, Switzerland.
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Rafiei A, Cruz Tetlalmatzi S, Edrington CH, Lee L, Crowder DA, Saltzberg DJ, Sali A, Brouhard G, Schriemer DC. Doublecortin engages the microtubule lattice through a cooperative binding mode involving its C-terminal domain. eLife 2022; 11:66975. [PMID: 35485925 PMCID: PMC9122500 DOI: 10.7554/elife.66975] [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] [Received: 01/28/2021] [Accepted: 04/07/2022] [Indexed: 11/17/2022] Open
Abstract
Doublecortin (DCX) is a microtubule (MT)-associated protein that regulates MT structure and function during neuronal development and mutations in DCX lead to a spectrum of neurological disorders. The structural properties of MT-bound DCX that explain these disorders are incompletely determined. Here, we describe the molecular architecture of the DCX–MT complex through an integrative modeling approach that combines data from X-ray crystallography, cryo-electron microscopy, and a high-fidelity chemical crosslinking method. We demonstrate that DCX interacts with MTs through its N-terminal domain and induces a lattice-dependent self-association involving the C-terminal structured domain and its disordered tail, in a conformation that favors an open, domain-swapped state. The networked state can accommodate multiple different attachment points on the MT lattice, all of which orient the C-terminal tails away from the lattice. As numerous disease mutations cluster in the C-terminus, and regulatory phosphorylations cluster in its tail, our study shows that lattice-driven self-assembly is an important property of DCX.
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Affiliation(s)
- Atefeh Rafiei
- Department of Chemistry, University of Calgary, Calgary, Canada
| | | | | | - Linda Lee
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - D Alex Crowder
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Daniel J Saltzberg
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Gary Brouhard
- Department of Biology, McGill University, Montreal, Canada
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
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28
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Akhmanova A, Kapitein LC. Mechanisms of microtubule organization in differentiated animal cells. Nat Rev Mol Cell Biol 2022; 23:541-558. [PMID: 35383336 DOI: 10.1038/s41580-022-00473-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2022] [Indexed: 02/08/2023]
Abstract
Microtubules are polarized cytoskeletal filaments that serve as tracks for intracellular transport and form a scaffold that positions organelles and other cellular components and modulates cell shape and mechanics. In animal cells, the geometry, density and directionality of microtubule networks are major determinants of cellular architecture, polarity and proliferation. In dividing cells, microtubules form bipolar spindles that pull chromosomes apart, whereas in interphase cells, microtubules are organized in a cell type-specific fashion, which strongly correlates with cell physiology. In motile cells, such as fibroblasts and immune cells, microtubules are organized as radial asters, whereas in immotile epithelial and neuronal cells and in muscles, microtubules form parallel or antiparallel arrays and cortical meshworks. Here, we review recent work addressing how the formation of such microtubule networks is driven by the plethora of microtubule regulatory proteins. These include proteins that nucleate or anchor microtubule ends at different cellular structures and those that sever or move microtubules, as well as regulators of microtubule elongation, stability, bundling or modifications. The emerging picture, although still very incomplete, shows a remarkable diversity of cell-specific mechanisms that employ conserved building blocks to adjust microtubule organization in order to facilitate different cellular functions.
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Affiliation(s)
- Anna Akhmanova
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands.
| | - Lukas C Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands.
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29
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Igaev M, Grubmüller H. Bending-torsional elasticity and energetics of the plus-end microtubule tip. Proc Natl Acad Sci U S A 2022; 119:e2115516119. [PMID: 35302883 PMCID: PMC8944587 DOI: 10.1073/pnas.2115516119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/10/2022] [Indexed: 11/18/2022] Open
Abstract
SignificanceThe 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.
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Affiliation(s)
- Maxim Igaev
- Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, D-37077 Göttingen, Germany
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, D-37077 Göttingen, Germany
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30
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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: 5] [Impact Index Per Article: 2.5] [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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31
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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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32
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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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Liu J, Li L, Zou Y, Fu L, Ma X, Zhang H, Xu Y, Xu J, Zhang J, Li M, Hu X, Li Z, Wang X, Sun H, Zheng H, Zhu L, Guo J. Role of microtubule dynamics in Wallerian degeneration and nerve regeneration after peripheral nerve injury. Neural Regen Res 2022; 17:673-681. [PMID: 34380909 PMCID: PMC8504388 DOI: 10.4103/1673-5374.320997] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Wallerian degeneration, the progressive disintegration of distal axons and myelin that occurs after peripheral nerve injury, is essential for creating a permissive microenvironment for nerve regeneration, and involves cytoskeletal reconstruction. However, it is unclear whether microtubule dynamics play a role in this process. To address this, we treated cultured sciatic nerve explants, an in vitro model of Wallerian degeneration, with the microtubule-targeting agents paclitaxel and nocodazole. We found that paclitaxel-induced microtubule stabilization promoted axon and myelin degeneration and Schwann cell dedifferentiation, whereas nocodazole-induced microtubule destabilization inhibited these processes. Evaluation of an in vivo model of peripheral nerve injury showed that treatment with paclitaxel or nocodazole accelerated or attenuated axonal regeneration, as well as functional recovery of nerve conduction and target muscle and motor behavior, respectively. These results suggest that microtubule dynamics participate in peripheral nerve regeneration after injury by affecting Wallerian degeneration. This study was approved by the Animal Care and Use Committee of Southern Medical University, China (approval No. SMU-L2015081) on October 15, 2015.
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Affiliation(s)
- Jingmin Liu
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Lixia Li
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Ying Zou
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Lanya Fu
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Xinrui Ma
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Haowen Zhang
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Yizhou Xu
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University; Department of Spine Orthopedics, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong Province, China
| | - Jiawei Xu
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Jiaqi Zhang
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Mi Li
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Xiaofang Hu
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Zhenlin Li
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Xianghai Wang
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong Province, China
| | - Hao Sun
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong Province, China
| | - Hui Zheng
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong Province, China
| | - Lixin Zhu
- Department of Spine Orthopedics, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong Province, China
| | - Jiasong Guo
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering; Department of Spine Orthopedics, Zhujiang Hospital of Southern Medical University; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory); Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangzhou, Guangdong Province, China
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34
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Park K, Hoff KJ, Wethekam L, Stence N, Saenz M, Moore JK. Kinetically Stabilizing Mutations in Beta Tubulins Create Isotype-Specific Brain Malformations. Front Cell Dev Biol 2021; 9:765992. [PMID: 34869359 PMCID: PMC8637541 DOI: 10.3389/fcell.2021.765992] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Mutations in the family of genes encoding the tubulin subunits of microtubules are associated with a spectrum of human brain malformations known as tubulinopathies. How these mutations impact tubulin activity to give rise to distinct developmental consequences is poorly understood. Here we report two patients exhibiting brain malformations characteristic of tubulinopathies and heterozygous T178M missense mutations in different β-tubulin genes, TUBB2A or TUBB3. RNAseq analysis indicates that both TUBB2A and TUBB3 are expressed in the brain during development, but only TUBB2A maintains high expression in neurons into adulthood. The T178 residue is highly conserved in β-tubulins and located in the exchangeable GTP-binding pocket of β-tubulin. To determine the impact of T178M on β-tubulin function we created an analogous mutation in the β-tubulin of budding yeast and show that the substitution acts dominantly to produce kinetically stabilized microtubules that assemble and disassemble slowly, with fewer transitions between these states. In vitro experiments with purified mutant tubulin demonstrate that T178M decreases the intrinsic assembly activity of β-tubulin and forms microtubules that rarely transition to disassembly. We provide evidence that the T178M substitution disrupts GTPase-dependent conformational changes in tubulin, providing a mechanistic explanation for kinetic stabilization. Our findings demonstrate the importance of tubulin’s GTPase activity during brain development, and indicate that tubulin isotypes play different, important roles during brain development.
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Affiliation(s)
- Kristen Park
- Department of Pediatrics and Neurology, Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Katelyn J Hoff
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Linnea Wethekam
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Nicholas Stence
- Section of Pediatric Radiology, Department of Radiology, Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Margarita Saenz
- Section of Genetics, Department of Pediatrics, Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jeffrey K Moore
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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35
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Rice LM, Moritz M, Agard DA. Microtubules form by progressively faster tubulin accretion, not by nucleation-elongation. J Cell Biol 2021; 220:211894. [PMID: 33734292 PMCID: PMC7980253 DOI: 10.1083/jcb.202012079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 01/14/2023] Open
Abstract
Microtubules are dynamic polymers that play fundamental roles in all eukaryotes. Despite their importance, how new microtubules form is poorly understood. Textbooks have focused on variations of a nucleation–elongation mechanism in which monomers rapidly equilibrate with an unstable oligomer (nucleus) that limits the rate of polymer formation; once formed, the polymer then elongates efficiently from this nucleus by monomer addition. Such models faithfully describe actin assembly, but they fail to account for how more complex polymers like hollow microtubules assemble. Here, we articulate a new model for microtubule formation that has three key features: (1) microtubules initiate via rectangular, sheet-like structures that grow faster the larger they become; (2) the dominant pathway proceeds via accretion, the stepwise addition of longitudinal or lateral layers; and (3) a “straightening penalty” to account for the energetic cost of tubulin’s curved-to-straight conformational transition. This model can quantitatively fit experimental assembly data, providing new insights into biochemical determinants and assembly pathways for microtubule nucleation.
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Affiliation(s)
- Luke M Rice
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Michelle Moritz
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco CA
| | - David A Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco CA
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36
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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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37
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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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38
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Jana B, Barman S, Roy R, Das G, Mukherjee N, Adak A, Ghosh S. Fluorine Substituted Proline Enhances the Tubulin Binding Potential of a Tetrapeptide at the GTP Binding Pocket Causing the Inhibition of Microtubule Motility and an Antimitotic Effect. J Phys Chem B 2021; 125:8768-8780. [PMID: 34328335 DOI: 10.1021/acs.jpcb.1c04323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The microtubule is regarded as the key target for designing anticancer and neurotherapeutic drugs due to its functional importance in eukaryotic cells including neurons. The microtubule is a dynamic hollow polymer tube consisting of α,β-tubulin heterodimer. Polymerization of α,β-tubulin heterodimer resulted in microtubule formation. GTP plays a crucial role in microtubule polymerization. It binds at the exchangeable binding site of the β-tubulin heterodimer, and it is one of the most crucial therapeutic hot spots for designing anticancer therapeutics. In this manuscript, we have shown using an in silico strategy and various in vitro and cellular experiments that the binding affinity to the tubulin and cancer therapeutic potential of an exchangeable GTP/GDP binding antimitotic tetrapeptide (SP: Ser-Leu-Arg-Pro) is increased through changing proline with the multifluorine substituted proline. This study showcases the importance of the proline amino acid and its pyrrolidine ring in the regulation of binding with tubulin at the GTP binding pocket.
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Affiliation(s)
- Batakrishna Jana
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Surajit Barman
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Rajsekhar Roy
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Surpura Bypass Road, Karwar, Rajasthan 342037, India
| | - Gaurav Das
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Nabanita Mukherjee
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Surpura Bypass Road, Karwar, Rajasthan 342037, India
| | - Anindyasundar Adak
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Surajit Ghosh
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India.,Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Surpura Bypass Road, Karwar, Rajasthan 342037, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
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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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Kubota R, Tanaka W, Hamachi I. Microscopic Imaging Techniques for Molecular Assemblies: Electron, Atomic Force, and Confocal Microscopies. Chem Rev 2021; 121:14281-14347. [DOI: 10.1021/acs.chemrev.0c01334] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Wataru Tanaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8530, Japan
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41
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Průša J, Ayoub AT, Chafai DE, Havelka D, Cifra M. Electro-opening of a microtubule lattice in silico. Comput Struct Biotechnol J 2021; 19:1488-1496. [PMID: 33815687 PMCID: PMC7985272 DOI: 10.1016/j.csbj.2021.02.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 11/28/2022] Open
Abstract
Modulation of the structure and function of biomaterials is essential for advancing bio-nanotechnology and biomedicine. Microtubules (MTs) are self-assembled protein polymers that are essential for fundamental cellular processes and key model compounds for the design of active bio-nanomaterials. In this in silico study, a 0.5 μs-long all-atom molecular dynamics simulation of a complete MT with approximately 1.2 million atoms in the system indicated that a nanosecond-scale intense electric field can induce the longitudinal opening of the cylindrical shell of the MT lattice, modifying the structure of the MT. This effect is field-strength- and temperature-dependent and occurs on the cathode side. A model was formulated to explain the opening on the cathode side, which resulted from an electric-field-induced imbalance between electric torque on tubulin dipoles and cohesive forces between tubulin heterodimers. Our results open new avenues for electromagnetic modulation of biological and artificial materials through action on noncovalent molecular interactions.
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Affiliation(s)
- Jiří Průša
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague 18251, Czech Republic
| | - Ahmed Taha Ayoub
- Biomolecular Simulation Center, Department of Chemistry, Faculty of Pharmacy, Heliopolis University, Cairo 11777, Egypt
| | - Djamel Eddine Chafai
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague 18251, Czech Republic
| | - Daniel Havelka
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague 18251, Czech Republic
| | - Michal Cifra
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague 18251, Czech Republic
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42
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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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43
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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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44
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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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45
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Feng W, Liu R, Xie X, Diao L, Gao N, Cheng J, Zhang X, Li Y, Bao L. SUMOylation of α-tubulin is a novel modification regulating microtubule dynamics. J Mol Cell Biol 2021; 13:91-103. [PMID: 33394042 PMCID: PMC8104938 DOI: 10.1093/jmcb/mjaa076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/02/2020] [Accepted: 12/14/2020] [Indexed: 11/13/2022] Open
Abstract
Microtubules (MTs) are regulated by a number of known posttranslational modifications (PTMs) on α/β-tubulin to fulfill diverse cellular functions. Here, we showed that SUMOylation is a novel PTM on α-tubulin in vivo and in vitro. The SUMOylation on α-tubulin mainly occurred at Lys 96 (K96), K166, and K304 of soluble α-tubulin and could be removed by small ubiquitin-related modifier (SUMO)-specific peptidase 1. In vitro experiments showed that tubulin SUMOylation could reduce interprotofilament interaction, promote MT catastrophe, and impede MT polymerization. In cells, mutation of the SUMOylation sites on α-tubulin reduced catastrophe frequency and increased the proportion of polymerized α-tubulin, while upregulation of SUMOylation with fusion of SUMO1 reduced α-tubulin assembly into MTs. Additionally, overexpression of SUMOylation-deficient α-tubulin attenuated the neurite extension in Neuro-2a cells. Thus, SUMOylation on α-tubulin represents a new player in the regulation of MT properties.
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Affiliation(s)
- Wenfeng Feng
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science/Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Institute of Brain-Intelligence Technology, Zhangjiang Laboratory; Shanghai Research Center for Brain Science & Brain-Inspired Intelligence, Shanghai 201210, China
| | - Rong Liu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science/Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xuan Xie
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science/Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lei Diao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science/Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Nannan Gao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science/Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jinke Cheng
- Discipline of Neuroscience and Department of Biochemistry, Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xu Zhang
- Institute of Brain-Intelligence Technology, Zhangjiang Laboratory; Shanghai Research Center for Brain Science & Brain-Inspired Intelligence, Shanghai 201210, China.,Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yong Li
- Discipline of Neuroscience and Department of Biochemistry, Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lan Bao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science/Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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46
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Manka SW, Moores CA. Pseudo-repeats in doublecortin make distinct mechanistic contributions to microtubule regulation. EMBO Rep 2020; 21:e51534. [PMID: 33051979 PMCID: PMC7726794 DOI: 10.15252/embr.202051534] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 11/16/2022] Open
Abstract
Doublecortin (DCX) is a neuronal microtubule-associated protein (MAP) indispensable for brain development. Its flexibly linked doublecortin (DC) domains-NDC and CDC-mediate microtubule (MT) nucleation and stabilization, but it is unclear how. Using high-resolution time-resolved cryo-EM, we mapped NDC and CDC interactions with tubulin at different MT polymerization stages and studied their functional effects on MT dynamics using TIRF microscopy. Although coupled, each DC repeat within DCX appears to have a distinct role in MT nucleation and stabilization: CDC is a conformationally plastic module that appears to facilitate MT nucleation and stabilize tubulin-tubulin contacts in the nascent MT lattice, while NDC appears to be favored along the mature lattice, providing MT stabilization. Our structures of MT-bound DC domains also explain in unprecedented detail the DCX mutation-related brain defects observed in the clinic. This modular composition of DCX reflects a common design principle among MAPs where pseudo-repeats of tubulin/MT binding elements chaperone or stabilize distinct conformational transitions to regulate distinct stages of MT dynamic instability.
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Affiliation(s)
- Szymon W Manka
- Institute of Structural and Molecular BiologyDepartment of Biological Sciences, BirkbeckUniversity of LondonLondonUK
| | - Carolyn A Moores
- Institute of Structural and Molecular BiologyDepartment of Biological Sciences, BirkbeckUniversity of LondonLondonUK
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47
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Kode J, Kovvuri J, Nagaraju B, Jadhav S, Barkume M, Sen S, Kasinathan NK, Chaudhari P, Mohanty BS, Gour J, Sigalapalli DK, Ganesh Kumar C, Pradhan T, Banerjee M, Kamal A. Synthesis, biological evaluation, and molecular docking analysis of phenstatin based indole linked chalcones as anticancer agents and tubulin polymerization inhibitors. Bioorg Chem 2020; 105:104447. [PMID: 33207276 DOI: 10.1016/j.bioorg.2020.104447] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 02/08/2023]
Abstract
A library of new phenstatin based indole linked chalcone compounds (9a-z and 9aa-ad) were designed and synthesized. Of these, compound 9a with 1-methyl, 2- and 3-methoxy substituents in the aromatic ring was efficacious against the human oral cancer cell line SCC-29B, spheroids, and in a mouse xenograft model of oral cancer AW13516. Compound 9a exhibited anti-cancer activity through disrupting cellular integrity and affecting glucose metabolism-which is a hallmark of cancer. The cellular architecture was affected by inhibition of tubulin polymerization as observed by an immunofluorescence assay on 9a-treated SCC-29B cells. An in vitro tubulin polymerization kinetics assay provided evidence of direct interaction of 9a with tubulin. This physical interaction between tubulin and compound 9a was further confirmed by Surface Plasmon Resonance (SPR) analysis. Molecular docking experiments and validations revealed that compound 9a interacts and binds at the colchicine binding site of tubulin and at active sites of key enzymes in the glucose metabolism pathway. Based on in silico modeling, biophysical interactions, and pre-clinical observations, 9a consisting of phenstatin based indole-chalcone scaffolds, can be considered as an attractive tubulin polymerization inhibitor candidate for developing anti-cancer therapeutics.
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Affiliation(s)
- Jyoti Kode
- Anti-Cancer Drug Screening Facility (ACDSF), Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India; Tumor Immunology & Immunotherapy Group, Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India; Homi Bhabha National Institute (HBNI), Training School Complex, Anushakti Nagar, Mumbai 400085, India.
| | - Jeshma Kovvuri
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi 110025, India; Department of Humanities and Sciences, Vardhaman College of Engineering (Autonomous), Shamshabad, Hyderabad, Telangana 501218, India.
| | - Burri Nagaraju
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi 110025, India.
| | - Shailesh Jadhav
- Anti-Cancer Drug Screening Facility (ACDSF), Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India.
| | - Madan Barkume
- Anti-Cancer Drug Screening Facility (ACDSF), Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India.
| | - Subrata Sen
- Anti-Cancer Drug Screening Facility (ACDSF), Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India.
| | - Nirmal Kumar Kasinathan
- Anti-Cancer Drug Screening Facility (ACDSF), Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India.
| | - Pradip Chaudhari
- Homi Bhabha National Institute (HBNI), Training School Complex, Anushakti Nagar, Mumbai 400085, India; Small Animal Imaging Facility, Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India.
| | - Bhabani Shankar Mohanty
- Small Animal Imaging Facility, Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India.
| | - Jitendra Gour
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India.
| | - Dilep Kumar Sigalapalli
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India.
| | - C Ganesh Kumar
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi 110025, India.
| | - Trupti Pradhan
- Tumor Immunology & Immunotherapy Group, Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India.
| | - Manisha Banerjee
- Homi Bhabha National Institute (HBNI), Training School Complex, Anushakti Nagar, Mumbai 400085, India; Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India.
| | - Ahmed Kamal
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi 110025, India; Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India; School of Pharmaceutical Education and Research (SPER), Jamia Hamdard, New Delhi 110062, India.
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48
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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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49
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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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50
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Abstract
Directed cell migration is critical for embryogenesis and organ development, wound healing and the immune response. Microtubules are dynamic polymers that control directional migration through a number of coordinated processes: microtubules are the tracks for long-distance intracellular transport, crucial for delivery of new membrane components and signalling molecules to the leading edge of a migrating cell and the recycling of adhesion receptors. Microtubules act as force generators and compressive elements to support sustained cell protrusions. The assembly and disassembly of microtubules is coupled to Rho GTPase signalling, thereby controlling actin polymerisation, myosin-driven contractility and the turnover of cellular adhesions locally. Cross-talk of actin and microtubule dynamics is mediated through a number of common binding proteins and regulators. Furthermore, cortical microtubule capture sites are physically linked to focal adhesions, facilitating the delivery of secretory vesicles and efficient cross-talk. Here we summarise the diverse functions of microtubules during cell migration, aiming to show how they contribute to the spatially and temporally coordinated sequence of events that permit efficient, directional and persistent migration.
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