1
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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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2
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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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3
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Aureille J, Prabhu SS, Barnett SF, Farrugia AJ, Arnal I, Lafanechère L, Low BC, Kanchanawong P, Mogilner A, Bershadsky AD. Focal adhesions are controlled by microtubules through local contractility regulation. EMBO J 2024; 43:2715-2732. [PMID: 38769437 PMCID: PMC11217342 DOI: 10.1038/s44318-024-00114-4] [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: 08/20/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/22/2024] Open
Abstract
Microtubules regulate cell polarity and migration via local activation of focal adhesion turnover, but the mechanism of this process is insufficiently understood. Molecular complexes containing KANK family proteins connect microtubules with talin, the major component of focal adhesions. Here, local optogenetic activation of KANK1-mediated microtubule/talin linkage promoted microtubule targeting to an individual focal adhesion and subsequent withdrawal, resulting in focal adhesion centripetal sliding and rapid disassembly. This sliding is preceded by a local increase of traction force due to accumulation of myosin-II and actin in the proximity of the focal adhesion. Knockdown of the Rho activator GEF-H1 prevented development of traction force and abolished sliding and disassembly of focal adhesions upon KANK1 activation. Other players participating in microtubule-driven, KANK-dependent focal adhesion disassembly include kinases ROCK, PAK, and FAK, as well as microtubules/focal adhesion-associated proteins kinesin-1, APC, and αTAT. Based on these data, we develop a mathematical model for a microtubule-driven focal adhesion disruption involving local GEF-H1/RhoA/ROCK-dependent activation of contractility, which is consistent with experimental data.
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Affiliation(s)
- Julien Aureille
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore.
| | - Srinivas S Prabhu
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Sam F Barnett
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Aaron J Farrugia
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Isabelle Arnal
- Grenoble institute of Neuroscience, University Grenoble Alpes, INSERM U1216, Grenoble, France
| | - Laurence Lafanechère
- University Grenoble Alpes, INSERM U1209, CNRS UMR5309, Institute for Advanced Biosciences, Grenoble, France
| | - Boon Chuan Low
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Pakorn Kanchanawong
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Alex Mogilner
- Courant Institute and Department of Biology, New York University, New York, USA
| | - Alexander D Bershadsky
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore.
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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4
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Kuwasako K, Dang W, He F, Takahashi M, Tsuda K, Nagata T, Tanaka A, Kobayashi N, Kigawa T, Güntert P, Shirouzu M, Yokoyama S, Muto Y. 1H, 13C, and 15N resonance assignments and solution structure of the N-terminal divergent calponin homology (NN-CH) domain of human intraflagellar transport protein 54. BIOMOLECULAR NMR ASSIGNMENTS 2024; 18:71-78. [PMID: 38551798 DOI: 10.1007/s12104-024-10170-w] [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: 11/28/2023] [Accepted: 03/13/2024] [Indexed: 05/12/2024]
Abstract
The intraflagellar transport (IFT) machinery plays a crucial role in the bidirectional trafficking of components necessary for ciliary signaling, such as the Hedgehog, Wnt/PCR, and cAMP/PKA systems. Defects in some components of the IFT machinery cause dysfunction, leading to a wide range of human diseases and developmental disorders termed ciliopathies, such as nephronophthisis. The IFT machinery comprises three sub-complexes: BBsome, IFT-A, and IFT-B. The IFT protein 54 (IFT54) is an important component of the IFT-B sub-complex. In anterograde movement, IFT54 binds to active kinesin-II, walking along the cilia microtubule axoneme and carrying the dynein-2 complex in an inactive state, which works for retrograde movement. Several mutations in IFT54 are known to cause Senior-Loken syndrome, a ciliopathy. IFT54 possesses a divergent Calponin Homology (CH) domain termed as NN-CH domain at its N-terminus. However, several aspects of the function of the NN-CH domain of IFT54 are still obscure. Here, we report the 1H, 15N, and 13C resonance assignments of the NN-CH domain of human IFT54 and its solution structure. The NN-CH domain of human IFT54 adopts essentially the α1-α2-α3-α4-α5 topology as that of mouse IFT54, whose structure was determined by X-ray crystallographic study. The structural information and assignments obtained in this study shed light on the molecular function of the NN-CH domain in IFT54.
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Affiliation(s)
- Kanako Kuwasako
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230- 0045, Japan
- Faculty of Pharmacy and Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, 202-8585, Japan
| | - Weirong Dang
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Fahu He
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Mari Takahashi
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230- 0045, Japan
| | - Kengo Tsuda
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Takashi Nagata
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
- Institute of Advanced Energy, Graduate School of Energy Science, Kyoto University, Gokasho, Kyoto, Uji, 611-0011, Japan
| | - Akiko Tanaka
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Naohiro Kobayashi
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
- RIKEN Yokohama NMR Facility, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takanori Kigawa
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230- 0045, Japan
| | - Peter Güntert
- Tatsuo Miyazawa Memorial Program, RIKEN Genomic Sciences Center, Yokohama, 230-0045, Japan
- Institute of Biophysical Chemistry, Goethe-University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany
- Institute of Molecular Physical Science, ETH Zurich, Vladimir-Prelog-Weg 2, Zurich, 8093, Switzerland
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo, 192- 0397, Japan
| | - Mikako Shirouzu
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230- 0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Yokohama, 230-0045, Japan.
| | - Yutaka Muto
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230- 0045, Japan.
- Faculty of Pharmacy and Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, 202-8585, Japan.
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5
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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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6
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Woo S, Saka SK, Xuan F, Yin P. Molecular robotic agents that survey molecular landscapes for information retrieval. Nat Commun 2024; 15:3293. [PMID: 38632239 PMCID: PMC11024175 DOI: 10.1038/s41467-024-46978-2] [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: 02/23/2023] [Accepted: 03/14/2024] [Indexed: 04/19/2024] Open
Abstract
DNA-based artificial motors have allowed the recapitulation of biological functions and the creation of new features. Here, we present a molecular robotic system that surveys molecular environments and reports spatial information in an autonomous and repeated manner. A group of molecular agents, termed 'crawlers', roam around and copy information from DNA-labeled targets, generating records that reflect their trajectories. Based on a mechanism that allows random crawling, we show that our system is capable of counting the number of subunits in example molecular complexes. Our system can also detect multivalent proximities by generating concatenated records from multiple local interactions. We demonstrate this capability by distinguishing colocalization patterns of three proteins inside fixed cells under different conditions. These mechanisms for examining molecular landscapes may serve as a basis towards creating large-scale detailed molecular interaction maps inside the cell with nanoscale resolution.
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Affiliation(s)
- Sungwook Woo
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Materials Science and Engineering, Pohang University of Science and Technology, Pohang, 37673, Korea.
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- European Molecular Biology Laboratory (EMBL), Heidelberg, Genome Biology Unit, 69117, Heidelberg, Germany
| | - Feng Xuan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Spear Bio Inc., Woburn, MA, 01801, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
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7
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Meier SM, Steinmetz MO, Barral Y. Microtubule specialization by +TIP networks: from mechanisms to functional implications. Trends Biochem Sci 2024; 49:318-332. [PMID: 38350804 DOI: 10.1016/j.tibs.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/23/2023] [Accepted: 01/12/2024] [Indexed: 02/15/2024]
Abstract
To fulfill their actual cellular role, individual microtubules become functionally specialized through a broad range of mechanisms. The 'search and capture' model posits that microtubule dynamics and functions are specified by cellular targets that they capture (i.e., a posteriori), independently of the microtubule-organizing center (MTOC) they emerge from. However, work in budding yeast indicates that MTOCs may impart a functional identity to the microtubules they nucleate, a priori. Key effectors in this process are microtubule plus-end tracking proteins (+TIPs), which track microtubule tips to regulate their dynamics and facilitate their targeted interactions. In this review, we discuss potential mechanisms of a priori microtubule specialization, focusing on recent findings indicating that +TIP networks may undergo liquid biomolecular condensation in different cell types.
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Affiliation(s)
- Sandro M Meier
- Institute of Biochemistry, Department of Biology, and Bringing Materials to Life Initiative, ETH Zürich, Switzerland; Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland; Bringing Materials to Life Initiative, ETH Zürich, Switzerland
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland; University of Basel, Biozentrum, CH-4056 Basel, Switzerland.
| | - Yves Barral
- Institute of Biochemistry, Department of Biology, and Bringing Materials to Life Initiative, ETH Zürich, Switzerland; Bringing Materials to Life Initiative, ETH Zürich, Switzerland.
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8
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Gonzalez SJ, Heckel JM, Goldblum RR, Reid TA, McClellan M, Gardner MK. Rapid binding to protofilament edge sites facilitates tip tracking of EB1 at growing microtubule plus-ends. eLife 2024; 13:e91719. [PMID: 38385657 PMCID: PMC10883673 DOI: 10.7554/elife.91719] [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: 08/08/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
EB1 is a key cellular protein that delivers regulatory molecules throughout the cell via the tip-tracking of growing microtubule plus-ends. Thus, it is important to understand the mechanism for how EB1 efficiently tracks growing microtubule plus-ends. It is widely accepted that EB1 binds with higher affinity to GTP-tubulin subunits at the growing microtubule tip, relative to GDP-tubulin along the microtubule length. However, it is unclear whether this difference in affinity alone is sufficient to explain the tip-tracking of EB1 at growing microtubule tips. Previously, we found that EB1 binds to exposed microtubule protofilament-edge sites at a ~70 fold faster rate than to closed-lattice sites, due to diffusional steric hindrance to binding. Thus, we asked whether rapid protofilament-edge binding could contribute to efficient EB1 tip tracking. A computational simulation with differential EB1 on-rates based on closed-lattice or protofilament-edge binding, and with EB1 off-rates that were dependent on the tubulin hydrolysis state, robustly recapitulated experimental EB1 tip tracking. To test this model, we used cell-free biophysical assays, as well as live-cell imaging, in combination with a Designed Ankyrin Repeat Protein (DARPin) that binds exclusively to protofilament-edge sites, and whose binding site partially overlaps with the EB1 binding site. We found that DARPin blocked EB1 protofilament-edge binding, which led to a decrease in EB1 tip tracking on dynamic microtubules. We conclude that rapid EB1 binding to microtubule protofilament-edge sites contributes to robust EB1 tip tracking at the growing microtubule plus-end.
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Affiliation(s)
- Samuel J Gonzalez
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Julia M Heckel
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Rebecca R Goldblum
- Department of Biophysics, Molecular Biology, and Biochemistry, University of Minnesota, Minneapolis, United States
- Medical Scientist Training Program, University of Minnesota, Minneapolis, United States
| | - Taylor A Reid
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Mark McClellan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Melissa K Gardner
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
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9
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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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10
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Volkov VA, Akhmanova A. Phase separation on microtubules: from droplet formation to cellular function? Trends Cell Biol 2024; 34:18-30. [PMID: 37453878 DOI: 10.1016/j.tcb.2023.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
Microtubules are cytoskeletal polymers that play important roles in numerous cellular processes, ranging from the control of cell shape and polarity to cell division and intracellular transport. Many of these roles rely on proteins that bind to microtubule ends and shafts, carry intrinsically disordered regions, and form complex multivalent interaction networks. A flurry of recent studies demonstrated that these properties allow diverse microtubule-binding proteins to undergo liquid-liquid phase separation (LLPS) in vitro. It is proposed that LLPS could potentially affect multiple microtubule-related processes, such as microtubule nucleation, control of microtubule dynamics and organization, and microtubule-based transport. Here, we discuss the evidence in favor and against the occurrence of LLPS and its functional significance for microtubule-based processes in cells.
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Affiliation(s)
- Vladimir A Volkov
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, UK.
| | - Anna Akhmanova
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands.
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11
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Valdez V, Ma M, Gouveia B, Zhang R, Petry S. HURP facilitates spindle assembly by stabilizing microtubules and working synergistically with TPX2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.571906. [PMID: 38187686 PMCID: PMC10769297 DOI: 10.1101/2023.12.18.571906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
In large vertebrate spindles, the majority of microtubules are formed via branching microtubule nucleation, whereby microtubules nucleate along the side of pre-existing microtubules. Hepatoma up-regulated protein (HURP) is a microtubule-associated protein that has been implicated in spindle assembly, but its mode of action is yet to be defined. In this study, we show that HURP is necessary for RanGTP-induced branching microtubule nucleation in Xenopus egg extract. Specifically, HURP stabilizes the microtubule lattice to promote microtubule formation from γ-TuRC. This function is shifted to promote branching microtubule nucleation in the presence of TPX2, another branching-promoting factor, as HURP's localization to microtubules is enhanced by TPX2 condensation. Lastly, we provide a structure of HURP on the microtubule lattice, revealing how HURP binding stabilizes the microtubule lattice. We propose a model in which HURP stabilizes microtubules during their formation, and TPX2 preferentially enriches HURP to microtubules to promote branching microtubule nucleation and thus spindle assembly.
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Affiliation(s)
- Venecia Valdez
- Princeton University, Department of Molecular Biology, Princeton, New Jersey, United States
| | - Meisheng Ma
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine (St. Louis, Missouri, United States)
- Present address: Department of Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology (Wuhan, Hubei, China)
| | - Bernardo Gouveia
- Princeton University, Department of Chemical and Biological Engineering, Princeton, New Jersey, United States
| | - Rui Zhang
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine (St. Louis, Missouri, United States)
| | - Sabine Petry
- Princeton University, Department of Molecular Biology, Princeton, New Jersey, United States
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12
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Lawrence EJ, Chatterjee S, Zanic M. More is different: Reconstituting complexity in microtubule regulation. J Biol Chem 2023; 299:105398. [PMID: 37898404 PMCID: PMC10694663 DOI: 10.1016/j.jbc.2023.105398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 10/30/2023] Open
Abstract
Microtubules are dynamic cytoskeletal filaments that undergo stochastic switching between phases of polymerization and depolymerization-a behavior known as dynamic instability. Many important cellular processes, including cell motility, chromosome segregation, and intracellular transport, require complex spatiotemporal regulation of microtubule dynamics. This coordinated regulation is achieved through the interactions of numerous microtubule-associated proteins (MAPs) with microtubule ends and lattices. Here, we review the recent advances in our understanding of microtubule regulation, focusing on results arising from biochemical in vitro reconstitution approaches using purified multiprotein ensembles. We discuss how the combinatory effects of MAPs affect both the dynamics of individual microtubule ends, as well as the stability and turnover of the microtubule lattice. In addition, we highlight new results demonstrating the roles of protein condensates in microtubule regulation. Our overall intent is to showcase how lessons learned from reconstitution approaches help unravel the regulatory mechanisms at play in complex cellular environments.
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Affiliation(s)
- Elizabeth J Lawrence
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Saptarshi Chatterjee
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Marija Zanic
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA.
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13
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Mosby LS, Straube A, Polin M. A general model for the motion of multivalent cargo interacting with substrates. J R Soc Interface 2023; 20:20230510. [PMID: 38016636 PMCID: PMC10684343 DOI: 10.1098/rsif.2023.0510] [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: 08/31/2023] [Accepted: 11/03/2023] [Indexed: 11/30/2023] Open
Abstract
Multivalent interactions are common in biology at many different length scales, and can result in the directional motion of multivalent cargo along substrates. Here, a general analytical model has been developed that can describe the directional motion of multivalent cargo as a response to position dependence in the binding and unbinding rates exhibited by their interaction sites. Cargo exhibit both an effective velocity, which acts in the direction of increasing cargo-substrate binding rate and decreasing cargo-substrate unbinding rate, and an effective diffusivity. This model can reproduce previously published experimental findings using only the binding and unbinding rate distributions of cargo interaction sites, and without any further parameter fitting. Extension of the cargo binding model to two dimensions reveals an effective velocity with the same properties as that derived for the one-dimensional case.
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Affiliation(s)
- L. S. Mosby
- Centre for Mechanochemical Cell Biology & Division of Biomedical Sciences, Warwick Medical School, Coventry CV4 7AL, UK
- Physics Department, University of Warwick, Coventry CV4 7AL, UK
- Institute of Advanced Study, University of Warwick, Coventry CV4 7AL, UK
| | - A. Straube
- Centre for Mechanochemical Cell Biology & Division of Biomedical Sciences, Warwick Medical School, Coventry CV4 7AL, UK
| | - M. Polin
- Centre for Mechanochemical Cell Biology & Division of Biomedical Sciences, Warwick Medical School, Coventry CV4 7AL, UK
- Physics Department, University of Warwick, Coventry CV4 7AL, UK
- Instituto Mediterráneo de Estudios Avanzados, IMEDEA, Esporles, Illes Balears 07190, Spain
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14
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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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15
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Park J, Xie Y, Miller KG, De Camilli P, Yogev S. End-binding protein 1 promotes specific motor-cargo association in the cell body prior to axonal delivery of dense core vesicles. Curr Biol 2023; 33:3851-3864.e7. [PMID: 37586371 PMCID: PMC10529979 DOI: 10.1016/j.cub.2023.07.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/25/2023] [Accepted: 07/25/2023] [Indexed: 08/18/2023]
Abstract
Axonal transport is key to neuronal function. Efficient transport requires specific motor-cargo association in the soma, yet the mechanisms regulating this early step remain poorly understood. We found that EBP-1, the C. elegans ortholog of the canonical-microtubule-end-binding protein EB1, promotes the specific association between kinesin-3/KIF1A/UNC-104 and dense core vesicles (DCVs) prior to their axonal delivery. Using single-neuron, in vivo labeling of endogenous cargo and EBs, we observed reduced axonal abundance and reduced secretion of DCV cargo, but not other KIF1A/UNC-104 cargoes, in ebp-1 mutants. This reduction could be traced back to fewer exit events from the cell body, where EBP-1 colocalized with the DCV sorting machinery at the trans Golgi, suggesting that this is the site of EBP-1 function. EBP-1 calponin homology (CH) domain was required for directing microtubule growth on the Golgi, and mammalian EB1 interacted with KIF1A in an EBH-domain-dependent manner. Loss- and gain-of-function experiments suggest a model in which both kinesin-3 binding and guidance of microtubule growth at the trans Golgi by EBP-1 promote motor-cargo association at sites of DCV biogenesis. In support of this model, tethering either EBP-1 or a kinesin-3/KIF1A/UNC-104-interacting domain from an unrelated protein to the Golgi restored the axonal abundance of DCV proteins in ebp-1 mutants. These results uncover an unexpected role for a microtubule-associated protein and provide insights into how specific kinesin-3 cargo is delivered to the axon.
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Affiliation(s)
- Junhyun Park
- Department of Neuroscience, Yale School of Medicine, 295 Congress Ave, New Haven, CT 06510, USA
| | - Yi Xie
- Department of Neuroscience, Yale School of Medicine, 295 Congress Ave, New Haven, CT 06510, USA
| | - Kenneth G Miller
- Genetic Models of Disease Laboratory, Oklahoma Medical Research Foundation, 825 N. E. 13th St, Oklahoma City, OK 73104, USA
| | - Pietro De Camilli
- Department of Neuroscience, Yale School of Medicine, 295 Congress Ave, New Haven, CT 06510, USA; Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven, CT 06510, USA; Howard Hughes Medical Institute, Yale University School of Medicine, 295 Congress Ave, New Haven, CT 06510, USA
| | - Shaul Yogev
- Department of Neuroscience, Yale School of Medicine, 295 Congress Ave, New Haven, CT 06510, USA; Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510, USA.
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16
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Yang S, Cai M, Huang J, Zhang S, Mo X, Jiang K, Cui H, Yuan J. EB1 decoration of microtubule lattice facilitates spindle-kinetochore lateral attachment in Plasmodium male gametogenesis. Nat Commun 2023; 14:2864. [PMID: 37208365 DOI: 10.1038/s41467-023-38516-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/04/2023] [Indexed: 05/21/2023] Open
Abstract
Faithful chromosome segregation of 8 duplicated haploid genomes into 8 daughter gametes is essential for male gametogenesis and mosquito transmission of Plasmodium. Plasmodium undergoes endomitosis in this multinucleated cell division, which is highly reliant on proper spindle-kinetochore attachment. However, the mechanisms underlying the spindle-kinetochore attachment remain elusive. End-binding proteins (EBs) are conserved microtubule (MT) plus-end binding proteins and play an important role in regulating MT plus-end dynamics. Here, we report that the Plasmodium EB1 is an orthologue distinct from the canonical eukaryotic EB1. Both in vitro and in vivo assays reveal that the Plasmodium EB1 losses MT plus-end tracking but possesses MT-lattice affinity. This MT-binding feature of Plasmodium EB1 is contributed by both CH domain and linker region. EB1-deficient parasites produce male gametocytes that develop to the anucleated male gametes, leading to defective mosquito transmission. EB1 is localized at the nucleoplasm of male gametocytes. During the gametogenesis, EB1 decorates the full-length of spindle MTs and regulates spindle structure. The kinetochores attach to spindle MTs laterally throughout endomitosis and this attachment is EB1-dependent. Consequently, impaired spindle-kinetochore attachment is observed in EB1-deficient parasites. These results indicate that a parasite-specific EB1 with MT-lattice binding affinity fulfills the spindle-kinetochore lateral attachment in male gametogenesis.
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Affiliation(s)
- Shuzhen Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China
| | - Mengya Cai
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China
| | - Junjie Huang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China
| | - Shengnan Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China
| | - Xiaoli Mo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China
| | - Kai Jiang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China.
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China.
| | - Huiting Cui
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China.
| | - Jing Yuan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China.
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17
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Carmona B, Marinho HS, Matos CL, Nolasco S, Soares H. Tubulin Post-Translational Modifications: The Elusive Roles of Acetylation. BIOLOGY 2023; 12:biology12040561. [PMID: 37106761 PMCID: PMC10136095 DOI: 10.3390/biology12040561] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/27/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023]
Abstract
Microtubules (MTs), dynamic polymers of α/β-tubulin heterodimers found in all eukaryotes, are involved in cytoplasm spatial organization, intracellular transport, cell polarity, migration and division, and in cilia biology. MTs functional diversity depends on the differential expression of distinct tubulin isotypes and is amplified by a vast number of different post-translational modifications (PTMs). The addition/removal of PTMs to α- or β-tubulins is catalyzed by specific enzymes and allows combinatory patterns largely enriching the distinct biochemical and biophysical properties of MTs, creating a code read by distinct proteins, including microtubule-associated proteins (MAPs), which allow cellular responses. This review is focused on tubulin-acetylation, whose cellular roles continue to generate debate. We travel through the experimental data pointing to α-tubulin Lys40 acetylation role as being a MT stabilizer and a typical PTM of long lived MTs, to the most recent data, suggesting that Lys40 acetylation enhances MT flexibility and alters the mechanical properties of MTs, preventing MTs from mechanical aging characterized by structural damage. Additionally, we discuss the regulation of tubulin acetyltransferases/desacetylases and their impacts on cell physiology. Finally, we analyze how changes in MT acetylation levels have been found to be a general response to stress and how they are associated with several human pathologies.
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Affiliation(s)
- Bruno Carmona
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Av. D. João II, Lote 4.69.01, 1990-096 Lisboa, Portugal
| | - H Susana Marinho
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Catarina Lopes Matos
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Sofia Nolasco
- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Av. D. João II, Lote 4.69.01, 1990-096 Lisboa, Portugal
- CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Helena Soares
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Av. D. João II, Lote 4.69.01, 1990-096 Lisboa, Portugal
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18
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Wethekam LC, Moore JK. Tubulin isotype regulation maintains asymmetric requirement for α-tubulin over β-tubulin. J Cell Biol 2023; 222:e202202102. [PMID: 36719400 PMCID: PMC9930134 DOI: 10.1083/jcb.202202102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 07/19/2022] [Accepted: 11/14/2022] [Indexed: 02/01/2023] Open
Abstract
How cells regulate α- and β-tubulin to meet the demand for αβ-heterodimers and avoid consequences of monomer imbalance is not understood. We investigate the role of gene copy number and how shifting expression of α- or β-tubulin genes impacts tubulin proteostasis and microtubule function in Saccharomyces cerevisiae. We find that α-tubulin gene copy number is important for maintaining excess α-tubulin protein compared to β-tubulin protein. Excess α-tubulin prevents accumulation of super-stoichiometric β-tubulin, which leads to loss of microtubules, formation of non-microtubule assemblies of tubulin, and disrupts cell proliferation. In contrast, sub-stoichiometric β-tubulin or overexpression of α-tubulin has minor effects. We provide evidence that yeast cells equilibrate α-tubulin protein concentration when α-tubulin isotype expression is increased. We propose an asymmetric relationship between α- and β-tubulins, in which α-tubulins are maintained in excess to supply αβ-heterodimers and limit the accumulation of β-tubulin monomers.
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Affiliation(s)
- Linnea C. Wethekam
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jeffrey K. Moore
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO, USA
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19
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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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20
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Park J, Miller KG, De Camilli P, Yogev S. End Binding protein 1 promotes specific motor-cargo association in the cell body prior to axonal delivery of Dense Core Vesicles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523768. [PMID: 36711860 PMCID: PMC9882160 DOI: 10.1101/2023.01.12.523768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Axonal transport is key to neuronal function. Efficient transport requires specific motor-cargo association in the soma, yet the mechanisms regulating this early step remain poorly understood. We found that EBP-1, the C. elegans ortholog of the canonical microtubule end binding protein EB1, promotes the specific association between kinesin-3/KIF1A/UNC-104 and Dense Core Vesicles (DCVs) prior to their axonal delivery. Using single-neuron, in vivo labelling of endogenous cargo and EBs, we observed reduced axonal abundance and reduced secretion of DCV cargo, but not other KIF1A/UNC-104 cargo, in ebp-1 mutants. This reduction could be traced back to fewer exit events from the cell body, where EBP-1 colocalized with the DCV sorting machinery at the trans Golgi, suggesting that this is the site of EBP-1 function. In addition to its microtubule binding CH domain, mammalian EB1 interacted with mammalian KIF1A in an EBH domain dependent manner, and expression of mammalian EB1 or the EBH domain was sufficient to rescue DCV transport in ebp-1 mutants. Our results suggest a model in which kinesin-3 binding and microtubule binding by EBP-1 cooperate to transiently enrich the motor near sites of DCV biogenesis to promote motor-cargo association. In support of this model, tethering either EBP-1 or a kinesin-3 KIF1A/UNC-104 interacting domain from an unrelated protein to the Golgi restored the axonal abundance of DCV proteins in ebp-1 mutants. These results uncover an unexpected role for a microtubule associated protein and provide insight into how specific kinesin-3 cargo are delivered to the axon.
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Affiliation(s)
- Junhyun Park
- Department of Neuroscience, Yale School of Medicine, 295 Congress Ave, New Haven, CT 06510
| | - Kenneth G. Miller
- Genetic Models of Disease Laboratory, Oklahoma Medical Research Foundation, 825 N. E. 13th St, Oklahoma City, OK 73104
| | - Pietro De Camilli
- Department of Neuroscience, Yale School of Medicine, 295 Congress Ave, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT06510
- Department of Cell Biology, Yale School of Medicine, 295 Congress Ave, New Haven CT 06510
- Howard Hughes Medical Institute
| | - Shaul Yogev
- Department of Neuroscience, Yale School of Medicine, 295 Congress Ave, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT06510
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21
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Luo W, Demidov V, Shen Q, Girão H, Chakraborty M, Maiorov A, Ataullakhanov FI, Lin C, Maiato H, Grishchuk EL. CLASP2 recognizes tubulins exposed at the microtubule plus-end in a nucleotide state-sensitive manner. SCIENCE ADVANCES 2023; 9:eabq5404. [PMID: 36598991 PMCID: PMC9812398 DOI: 10.1126/sciadv.abq5404] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 11/23/2022] [Indexed: 05/28/2023]
Abstract
CLASPs (cytoplasmic linker-associated proteins) are ubiquitous stabilizers of microtubule dynamics, but their molecular targets at the microtubule plus-end are not understood. Using DNA origami-based reconstructions, we show that clusters of human CLASP2 form a load-bearing bond with terminal non-GTP tubulins at the stabilized microtubule tip. This activity relies on the unconventional TOG2 domain of CLASP2, which releases its high-affinity bond with non-GTP dimers upon their conversion into polymerization-competent GTP-tubulins. The ability of CLASP2 to recognize nucleotide-specific tubulin conformation and stabilize the catastrophe-promoting non-GTP tubulins intertwines with the previously underappreciated exchange between GDP and GTP at terminal tubulins. We propose that TOG2-dependent stabilization of sporadically occurring non-GTP tubulins represents a distinct molecular mechanism to suppress catastrophe at the freely assembling microtubule ends and to promote persistent tubulin assembly at the load-bearing tethered ends, such as at the kinetochores in dividing cells.
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Affiliation(s)
- Wangxi Luo
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vladimir Demidov
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qi Shen
- Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT 06520, USA
- Nanobiology Institute, Yale University, West Haven, CT 06516, USA
| | - Hugo Girão
- Chromosome Instability & Dynamics Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Manas Chakraborty
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aleksandr Maiorov
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Fazly I. Ataullakhanov
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, 119991 Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russian Federation
| | - Chenxiang Lin
- Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT 06520, USA
- Nanobiology Institute, Yale University, West Haven, CT 06516, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - Helder Maiato
- Chromosome Instability & Dynamics Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Cell Division Group, Department of Biomedicine, Faculdade de Medicina, Universidade do Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Ekaterina L. Grishchuk
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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22
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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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23
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Farmer VJ, Zanic M. Beyond the GTP-cap: Elucidating the molecular mechanisms of microtubule catastrophe. Bioessays 2023; 45:e2200081. [PMID: 36398561 PMCID: PMC10648283 DOI: 10.1002/bies.202200081] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022]
Abstract
Almost 40 years since the discovery of microtubule dynamic instability, the molecular mechanisms underlying microtubule dynamics remain an area of intense research interest. The "standard model" of microtubule dynamics implicates a "cap" of GTP-bound tubulin dimers at the growing microtubule end as the main determinant of microtubule stability. Loss of the GTP-cap leads to microtubule "catastrophe," a switch-like transition from microtubule growth to shrinkage. However, recent studies, using biochemical in vitro reconstitution, cryo-EM, and computational modeling approaches, challenge the simple GTP-cap model. Instead, a new perspective on the mechanisms of microtubule dynamics is emerging. In this view, highly dynamic transitions between different structural conformations of the growing microtubule end - which may or may not be directly linked to the nucleotide content at the microtubule end - ultimately drive microtubule catastrophe.
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Affiliation(s)
- Veronica J. Farmer
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Marija Zanic
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biomolecular and Chemical Engineering, Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
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24
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Xie P. A model for the catalytic activity of microtubule polymerases. Cytoskeleton (Hoboken) 2023; 80:7-20. [PMID: 36305831 DOI: 10.1002/cm.21734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/04/2022] [Accepted: 10/22/2022] [Indexed: 11/07/2022]
Abstract
A XMAP215/Stu2/Alp14 polymerase can catalyze processively the tubulin addition to the microtubule (MT) plus end. In this work, a model is proposed for the underlying molecular mechanism of the polymerase activity, where the polymerase can not only catalyze processively the tubulin addition to but also promote the tubulin removal from the MT plus end. Based on the model the dynamics of both the wild-type and mutant polymerases is studied theoretically, explaining consistently and well various available experimental data. To further test the model, predicted results are provided.
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Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Science, Beijing, China
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25
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Cushion TD, Leca I, Keays DA. MAPping tubulin mutations. Front Cell Dev Biol 2023; 11:1136699. [PMID: 36875768 PMCID: PMC9975266 DOI: 10.3389/fcell.2023.1136699] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/02/2023] [Indexed: 02/17/2023] Open
Abstract
Microtubules are filamentous structures that play a critical role in a diverse array of cellular functions including, mitosis, nuclear translocation, trafficking of organelles and cell shape. They are composed of α/β-tubulin heterodimers which are encoded by a large multigene family that has been implicated in an umbrella of disease states collectively known as the tubulinopathies. De novo mutations in different tubulin genes are known to cause lissencephaly, microcephaly, polymicrogyria, motor neuron disease, and female infertility. The diverse clinical features associated with these maladies have been attributed to the expression pattern of individual tubulin genes, as well as their distinct Functional repertoire. Recent studies, however, have highlighted the impact of tubulin mutations on microtubule-associated proteins (MAPs). MAPs can be classified according to their effect on microtubules and include polymer stabilizers (e.g., tau, MAP2, doublecortin), destabilizers (e.g., spastin, katanin), plus-end binding proteins (e.g., EB1-3, XMAP215, CLASPs) and motor proteins (e.g., dyneins, kinesins). In this review we analyse mutation-specific disease mechanisms that influence MAP binding and their phenotypic consequences, and discuss methods by which we can exploit genetic variation to identify novel MAPs.
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Affiliation(s)
- Thomas D Cushion
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom.,Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Ines Leca
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - David A Keays
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom.,Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.,Division of Neurobiology, Department Biology II, Ludwig-Maximilians-University Munich, Munich, Germany
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26
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APC couples neuronal mRNAs to multiple kinesins, EB1, and shrinking microtubule ends for bidirectional mRNA motility. Proc Natl Acad Sci U S A 2022; 119:e2211536119. [PMID: 36469763 PMCID: PMC9897468 DOI: 10.1073/pnas.2211536119] [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] [Indexed: 12/12/2022] Open
Abstract
Understanding where in the cytoplasm mRNAs are translated is increasingly recognized as being as important as knowing the timing and level of protein expression. mRNAs are localized via active motor-driven transport along microtubules (MTs) but the underlying essential factors and dynamic interactions are largely unknown. Using biochemical in vitro reconstitutions with purified mammalian proteins, multicolor TIRF-microscopy, and interaction kinetics measurements, we show that adenomatous polyposis coli (APC) enables kinesin-1- and kinesin-2-based mRNA transport, and that APC is an ideal adaptor for long-range mRNA transport as it forms highly stable complexes with 3'UTR fragments of several neuronal mRNAs (APC-RNPs). The kinesin-1 KIF5A binds and transports several neuronal mRNP components such as FMRP, PURα and mRNA fragments weakly, whereas the transport frequency of the mRNA fragments is significantly increased by APC. APC-RNP-motor complexes can assemble on MTs, generating highly processive mRNA transport events. We further find that end-binding protein 1 (EB1) recruits APC-RNPs to dynamically growing MT ends and APC-RNPs track shrinking MTs, producing MT minus-end-directed RNA motility due to the high dwell times of APC on MTs. Our findings establish APC as a versatile mRNA-kinesin adaptor and a key factor for the assembly and bidirectional movement of neuronal transport mRNPs.
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27
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Guyomar C, Bousquet C, Ku S, Heumann JM, Guilloux G, Gaillard N, Heichette C, Duchesne L, Steinmetz MO, Gibeaux R, Chrétien D. Changes in seam number and location induce holes within microtubules assembled from porcine brain tubulin and in Xenopus egg cytoplasmic extracts. eLife 2022; 11:e83021. [PMID: 36503602 PMCID: PMC9788831 DOI: 10.7554/elife.83021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Microtubules are tubes of about 25 nm in diameter that are critically involved in a variety of cellular functions, including motility, compartmentalization, and division. They are considered as pseudo-helical polymers whose constituent αβ-tubulin heterodimers share lateral homotypic interactions, except at one unique region called the seam. Here, we used a segmented sub-tomogram averaging strategy to reassess this paradigm and analyze the organization of the αβ-tubulin heterodimers in microtubules assembled from purified porcine brain tubulin in the presence of GTP and GMPCPP, and in Xenopus egg cytoplasmic extracts. We find that in almost all conditions, microtubules incorporate variable protofilament and/or tubulin subunit helical-start numbers, as well as variable numbers of seams. Strikingly, the seam number and location vary along individual microtubules, generating holes of one to a few subunits in size within their lattices. Together, our results reveal that the formation of mixed and discontinuous microtubule lattices is an intrinsic property of tubulin that requires the formation of unique lateral interactions without longitudinal ones. They further suggest that microtubule assembly is tightly regulated in a cytoplasmic environment.
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Affiliation(s)
- Charlotte Guyomar
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, F-35000RennesFrance
| | - Clément Bousquet
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, F-35000RennesFrance
| | - Siou Ku
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, F-35000RennesFrance
| | - John M Heumann
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
| | - Gabriel Guilloux
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, F-35000RennesFrance
| | - Natacha Gaillard
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer InstituteVilligenSwitzerland
| | - Claire Heichette
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, F-35000RennesFrance
| | - Laurence Duchesne
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, F-35000RennesFrance
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer InstituteVilligenSwitzerland
- University of Basel, BiozentrumBaselSwitzerland
| | - Romain Gibeaux
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, F-35000RennesFrance
| | - Denis Chrétien
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, F-35000RennesFrance
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28
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Hoff KJ, Neumann AJ, Moore JK. The molecular biology of tubulinopathies: Understanding the impact of variants on tubulin structure and microtubule regulation. Front Cell Neurosci 2022; 16:1023267. [PMID: 36406756 PMCID: PMC9666403 DOI: 10.3389/fncel.2022.1023267] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/30/2022] [Indexed: 11/24/2022] Open
Abstract
Heterozygous, missense mutations in both α- and β-tubulin genes have been linked to an array of neurodevelopment disorders, commonly referred to as "tubulinopathies." To date, tubulinopathy mutations have been identified in three β-tubulin isotypes and one α-tubulin isotype. These mutations occur throughout the different genetic domains and protein structures of these tubulin isotypes, and the field is working to address how this molecular-level diversity results in different cellular and tissue-level pathologies. Studies from many groups have focused on elucidating the consequences of individual mutations; however, the field lacks comprehensive models for the molecular etiology of different types of tubulinopathies, presenting a major gap in diagnosis and treatment. This review highlights recent advances in understanding tubulin structural dynamics, the roles microtubule-associated proteins (MAPs) play in microtubule regulation, and how these are inextricably linked. We emphasize the value of investigating interactions between tubulin structures, microtubules, and MAPs to understand and predict the impact of tubulinopathy mutations at the cell and tissue levels. Microtubule regulation is multifaceted and provides a complex set of controls for generating a functional cytoskeleton at the right place and right time during neurodevelopment. Understanding how tubulinopathy mutations disrupt distinct subsets of those controls, and how that ultimately disrupts neurodevelopment, will be important for establishing mechanistic themes among tubulinopathies that may lead to insights in other neurodevelopment disorders and normal neurodevelopment.
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Affiliation(s)
| | | | - Jeffrey K. Moore
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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29
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Meiring JCM, Grigoriev I, Nijenhuis W, Kapitein LC, Akhmanova A. Opto-katanin, an optogenetic tool for localized, microtubule disassembly. Curr Biol 2022; 32:4660-4674.e6. [PMID: 36174574 DOI: 10.1016/j.cub.2022.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 08/01/2022] [Accepted: 09/06/2022] [Indexed: 11/30/2022]
Abstract
Microtubules are cytoskeletal polymers that separate chromosomes during mitosis and serve as rails for intracellular transport and organelle positioning. Manipulation of microtubules is widely used in cell and developmental biology, but tools for precise subcellular spatiotemporal control of microtubules are currently lacking. Here, we describe a light-activated system for localized recruitment of the microtubule-severing enzyme katanin. This system, named opto-katanin, uses targeted illumination with blue light to induce rapid, localized, and reversible microtubule depolymerization. This tool allows precise clearing of a subcellular region of microtubules while preserving the rest of the microtubule network, demonstrating that regulation of katanin recruitment to microtubules is sufficient to control its severing activity. The tool is not toxic in the absence of blue light and can be used to disassemble both dynamic and stable microtubules in primary neurons as well as in dividing cells. We show that opto-katanin can be used to locally block vesicle transport and to clarify the dependence of organelle morphology and dynamics on microtubules. Specifically, our data indicate that microtubules are not required for the maintenance of the Golgi stacks or the tubules of the endoplasmic reticulum but are needed for the formation of new membrane tubules. Finally, we demonstrate that this tool can be applied to study the contribution of microtubules to cell mechanics by showing that microtubule bundles can exert forces constricting the nucleus.
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Affiliation(s)
- Joyce C M Meiring
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Padualaan, Utrecht 3584 CS, the Netherlands
| | - Ilya Grigoriev
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Padualaan, Utrecht 3584 CS, the Netherlands
| | - Wilco Nijenhuis
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Padualaan, Utrecht 3584 CS, the Netherlands; Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, UMC Utrecht, Utrecht 3584 CB, the Netherlands
| | - Lukas C Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Padualaan, Utrecht 3584 CS, the Netherlands; Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, UMC Utrecht, Utrecht 3584 CB, the Netherlands
| | - Anna Akhmanova
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Padualaan, Utrecht 3584 CS, the Netherlands.
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30
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Zhong Y, Yan W, Ruan J, Fang M, Yu C, Du S, Rai G, Tao D, Henderson MJ, Fang S. XBP1 variant 1 promotes mitosis of cancer cells involving upregulation of the polyglutamylase TTLL6. Hum Mol Genet 2022; 31:2639-2654. [PMID: 35333353 PMCID: PMC9396943 DOI: 10.1093/hmg/ddac010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/19/2021] [Accepted: 01/10/2022] [Indexed: 11/15/2022] Open
Abstract
XBP1 variant 1 (Xv1) is the most abundant XBP1 variant and is highly enriched across cancer types but nearly none in normal tissues. Its expression is associated with poor patients' survival and is specifically required for survival of malignant cells, but the underlying mechanism is not known. Here we report that Xv1 upregulates the polyglutamylase tubulin tyrosine ligase-like 6 (TTLL6) and promotes mitosis of cancer cells. Like the canonical XBP1, Xv1 mRNA undergoes unconventional splicing by IRE1α under endoplasmic reticulum stress, but it is also constitutively spliced by IRE1β. The spliced Xv1 mRNA encodes the active form of Xv1 protein (Xv1s). RNA sequencing in HeLa cells revealed that Xv1s overexpression regulates expression of genes that are not involved in the canonical unfolded protein response, including TTLL6 as a highly upregulated gene. Gel shift assay and chromatin immunoprecipitation revealed that Xv1s bind to the TTLL6 promoter region. Knockdown of TTLL6 caused death of cancer cells but not benign and normal cells, similar to the effects of knocking down Xv1. Moreover, overexpression of TTLL6 partially rescued BT474 cells from apoptosis induced by either TTLL6 or Xv1 knockdown, supporting TTLL6 as an essential downstream effector of Xv1 in regulating cancer cell survival. TTLL6 is localized in the mitotic spindle of cancer cells. Xv1 or TTLL6 knockdown resulted in decreased spindle polyglutamylation and interpolar spindle, as well as congression failure, mitotic arrest and cell death. These findings suggest that Xv1 is essential for cancer cell mitosis, which is mediated, at least in part, by increasing TTLL6 expression.
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Affiliation(s)
- Yongwang Zhong
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Wenjing Yan
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jingjing Ruan
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Department of Pulmonary Medicine, Anhui Medical University First Affiliated Hospital, Hefei, Anhui 230032, China
| | - Mike Fang
- Population and Quantitative Health Sciences Department, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Changjun Yu
- Department of General surgery, Anhui Medical University First Affiliated Hospital, Hefei, Anhui 230032, China
| | - Shaojun Du
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Dingyin Tao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Mark J Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Shengyun Fang
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Program in Oncology, UM Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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31
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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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32
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Watson EE, Russo F, Moreau D, Winssinger N. Optochemical Control of Therapeutic Agents through Photocatalyzed Isomerization. Angew Chem Int Ed Engl 2022; 61:e202203390. [PMID: 35510306 PMCID: PMC9400970 DOI: 10.1002/anie.202203390] [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: 03/04/2022] [Indexed: 12/04/2022]
Abstract
A Ru(bpy)3Cl2 photocatalyst is applied to the rapid trans to cis isomerization of a range of alkene‐containing pharmacological agents, including combretastatin A‐4 (CA‐4), a clinical candidate in oncology, and resveratrol derivatives, switching their configuration from inactive substances to potent cytotoxic agents. Selective in cellulo activation of the CA‐4 analog Res‐3M is demonstrated, along with its potent cytotoxicity and inhibition of microtubule dynamics.
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Affiliation(s)
- Emma E. Watson
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
| | - Francesco Russo
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
| | - Dimitri Moreau
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
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33
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Watson EE, Russo F, Moreau D, Winssinger N. Optochemical Control of Therapeutic Agents through Photocatalyzed Isomerization. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Emma E. Watson
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
| | - Francesco Russo
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
| | - Dimitri Moreau
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Sciences University of Geneva 1211 Geneva Switzerland
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34
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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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35
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Molines AT, Lemière J, Gazzola M, Steinmark IE, Edrington CH, Hsu CT, Real-Calderon P, Suhling K, Goshima G, Holt LJ, Thery M, Brouhard GJ, Chang F. Physical properties of the cytoplasm modulate the rates of microtubule polymerization and depolymerization. Dev Cell 2022; 57:466-479.e6. [PMID: 35231427 PMCID: PMC9319896 DOI: 10.1016/j.devcel.2022.02.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 11/01/2021] [Accepted: 01/31/2022] [Indexed: 11/20/2022]
Abstract
The cytoplasm is a crowded, visco-elastic environment whose physical properties change according to physiological or developmental states. How the physical properties of the cytoplasm impact cellular functions in vivo remains poorly understood. Here, we probe the effects of cytoplasmic concentration on microtubules by applying osmotic shifts to fission yeast, moss, and mammalian cells. We show that the rates of both microtubule polymerization and depolymerization scale linearly and inversely with cytoplasmic concentration; an increase in cytoplasmic concentration decreases the rates of microtubule polymerization and depolymerization proportionally, whereas a decrease in cytoplasmic concentration leads to the opposite. Numerous lines of evidence indicate that these effects are due to changes in cytoplasmic viscosity rather than cellular stress responses or macromolecular crowding per se. We reconstituted these effects on microtubules in vitro by tuning viscosity. Our findings indicate that, even in normal conditions, the viscosity of the cytoplasm modulates the reactions that underlie microtubule dynamic behaviors.
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Affiliation(s)
- Arthur T Molines
- Department of Cell and Tissue Biology, University of California, San Francisco, USA; Marine Biological Laboratory, Woods Hole, MA 02543, USA.
| | - Joël Lemière
- Department of Cell and Tissue Biology, University of California, San Francisco, USA
| | - Morgan Gazzola
- University of Grenoble-Alpes, CEA, CNRS, INRA, Interdisciplinary Research Institute of Grenoble, Laboratoire de Phyiologie Cellulaire & Vegétale, CytoMorpho Lab, 38054 Grenoble, France
| | | | | | - Chieh-Ting Hsu
- Department of Physics, McGill University, Montréal, Quebec, Canada
| | - Paula Real-Calderon
- Department of Cell and Tissue Biology, University of California, San Francisco, USA
| | - Klaus Suhling
- Department of Physics, King's College London, London, UK
| | - Gohta Goshima
- Sugashima Marine Biological Laboratory and Division of Biological Science, Graduate School of Science, Nagoya University, Toba City, Mie, Japan; Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA; Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Manuel Thery
- University of Grenoble-Alpes, CEA, CNRS, INRA, Interdisciplinary Research Institute of Grenoble, Laboratoire de Phyiologie Cellulaire & Vegétale, CytoMorpho Lab, 38054 Grenoble, France; Université de Paris, INSERM, CEA, Institut de Recherche Saint Louis, U 976, CytoMorpho Lab, 75010 Paris, France
| | - Gary J Brouhard
- Department of Biology, McGill University, Montréal, Quebec, Canada
| | - Fred Chang
- Department of Cell and Tissue Biology, University of California, San Francisco, USA; Marine Biological Laboratory, Woods Hole, MA 02543, USA.
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36
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Foster HE, Ventura Santos C, Carter AP. A cryo-ET survey of microtubules and intracellular compartments in mammalian axons. J Cell Biol 2022; 221:e202103154. [PMID: 34878519 PMCID: PMC7612188 DOI: 10.1083/jcb.202103154] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 09/28/2021] [Accepted: 11/16/2021] [Indexed: 12/16/2022] Open
Abstract
The neuronal axon is packed with cytoskeletal filaments, membranes, and organelles, many of which move between the cell body and axon tip. Here, we used cryo-electron tomography to survey the internal components of mammalian sensory axons. We determined the polarity of the axonal microtubules (MTs) by combining subtomogram classification and visual inspection, finding MT plus and minus ends are structurally similar. Subtomogram averaging of globular densities in the MT lumen suggests they have a defined structure, which is surprising given they likely contain the disordered protein MAP6. We found the endoplasmic reticulum in axons is tethered to MTs through multiple short linkers. We surveyed membrane-bound cargos and describe unexpected internal features such as granules and broken membranes. In addition, we detected proteinaceous compartments, including numerous virus-like capsid particles. Our observations outline novel features of axonal cargos and MTs, providing a platform for identification of their constituents.
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37
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Kliuchnikov E, Klyshko E, Kelly MS, Zhmurov A, Dima RI, Marx KA, Barsegov V. Microtubule assembly and disassembly dynamics model: Exploring dynamic instability and identifying features of Microtubules' Growth, Catastrophe, Shortening, and Rescue. Comput Struct Biotechnol J 2022; 20:953-974. [PMID: 35242287 PMCID: PMC8861655 DOI: 10.1016/j.csbj.2022.01.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/21/2022] Open
Abstract
Microtubules (MTs), a cellular structure element, exhibit dynamic instability and can switch stochastically from growth to shortening; but the factors that trigger these processes at the molecular level are not understood. We developed a 3D Microtubule Assembly and Disassembly DYnamics (MADDY) model, based upon a bead-per-monomer representation of the αβ-tubulin dimers forming an MT lattice, stabilized by the lateral and longitudinal interactions between tubulin subunits. The model was parameterized against the experimental rates of MT growth and shortening, and pushing forces on the Dam1 protein complex due to protofilaments splaying out. Using the MADDY model, we carried out GPU-accelerated Langevin simulations to access dynamic instability behavior. By applying Machine Learning techniques, we identified the MT characteristics that distinguish simultaneously all four kinetic states: growth, catastrophe, shortening, and rescue. At the cellular 25 μM tubulin concentration, the most important quantities are the MT length L , average longitudinal curvatureκ long , MT tip width w , total energy of longitudinal interactions in MT latticeU long , and the energies of longitudinal and lateral interactions required to complete MT to full cylinderU long add andU lat add . At high 250 μM tubulin concentration, the most important characteristics are L ,κ long , number of hydrolyzed αβ-tubulin dimersn hyd and number of lateral interactions per helical pitchn lat in MT lattice, energy of lateral interactions in MT latticeU lat , and energy of longitudinal interactions in MT tipu long . These results allow greater insights into what brings about kinetic state stability and the transitions between states involved in MT dynamic instability behavior.
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Affiliation(s)
| | - Eugene Klyshko
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
| | - Maria S. Kelly
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Artem Zhmurov
- KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ruxandra I. Dima
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Kenneth A. Marx
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
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38
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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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39
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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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40
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Li S, Fernandez JJ, Fabritius AS, Agard DA, Winey M. Electron cryo-tomography structure of axonemal doublet microtubule from Tetrahymena thermophila. Life Sci Alliance 2022; 5:5/3/e202101225. [PMID: 34969817 PMCID: PMC8742875 DOI: 10.26508/lsa.202101225] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 11/24/2022] Open
Abstract
Doublet microtubules (DMTs) provide a scaffold for axoneme assembly in motile cilia. Aside from α/β tubulins, the DMT comprises a large number of non-tubulin proteins in the luminal wall of DMTs, collectively named the microtubule inner proteins (MIPs). We used cryoET to study axoneme DMT isolated from Tetrahymena We present the structures of DMT at nanometer and sub-nanometer resolution. The structures confirm that MIP RIB72A/B binds to the luminal wall of DMT by multiple DM10 domains. We found FAP115, an MIP-containing multiple EF-hand domains, located at the interface of four-tubulin dimers in the lumen of A-tubule. It contacts both lateral and longitudinal tubulin interfaces and playing a critical role in DMT stability. We observed substantial structure heterogeneity in DMT in an FAP115 knockout strain, showing extensive structural defects beyond the FAP115-binding site. The defects propagate along the axoneme. Finally, by comparing DMT structures from Tetrahymena and Chlamydomonas, we have identified a number of conserved MIPs as well as MIPs that are unique to each organism. This conservation and diversity of the DMT structures might be linked to their specific functions. Our work provides structural insights essential for understanding the roles of MIPs during motile cilium assembly and function, as well as their relationships to human ciliopathies.
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Affiliation(s)
- Sam Li
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Jose-Jesus Fernandez
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Health Research Institute of Asturias (ISPA), Oviedo, Spain
| | - Amy S Fabritius
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA, USA
| | - David A Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Mark Winey
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA, USA
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41
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Rafiei A, Schriemer DC. A Crosslinking Mass Spectrometry Protocol for the Structural Analysis of Microtubule-Associated Proteins. Methods Mol Biol 2022; 2456:211-222. [PMID: 35612744 DOI: 10.1007/978-1-0716-2124-0_14] [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: 11/25/2022]
Abstract
Microtubule-associated proteins (MAPs) engage microtubules (MTs) to regulate both the MT state and wide variety of cytoskeletal functions. A comprehensive understanding of MAPs function requires the structural characterization of physical contacts MAPs make with other proteins, particularly when engaged with the microtubule (MT) lattice. Most of the interaction between MAPs and MTs evade classical structural determination techniques, as the interactions can be both heterogenous and sub-stoichiometric. Crosslinking mass spectrometry (XL-MS) can aid in MAP-MT structure analysis by providing a wealth of residue-based distance restraints. This protocol provides an XL-MS workflow for accurate and unbiased sampling of an equilibrated MAP-MT interaction, involving modifications to the preparation and validation of a MAP-MT construct suitable for crosslinking with fast-sampling heterobifunctional crosslinkers. The distance restrains obtained by this protocol can be used to generate accurate models assembled with an integrative structural modeling approach.
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Affiliation(s)
- Atefeh Rafiei
- Department of Chemistry, University of Calgary, Calgary, AB, Canada
| | - David C Schriemer
- Department of Chemistry, University of Calgary, Calgary, AB, Canada.
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada.
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42
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Lattice defects induced by microtubule-stabilizing agents exert a long-range effect on microtubule growth by promoting catastrophes. Proc Natl Acad Sci U S A 2021; 118:2112261118. [PMID: 34916292 PMCID: PMC8713758 DOI: 10.1073/pnas.2112261118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2021] [Indexed: 11/18/2022] Open
Abstract
Microtubules are major cytoskeletal filaments important for cell division, growth, and differentiation. Microtubules can rapidly switch between phases of growth and shortening, and this dynamic behavior is essential for shaping microtubule arrays. To obtain insights into mechanisms controlling microtubule dynamics, here we used microtubule-stabilizing agents such as Taxol and their fluorescent analogs to manipulate microtubule protofilament number and generate stable defects in microtubule lattices that can be visualized using fluorescence microscopy. We show that microtubule polymerization rate increases with protofilament number and that drug-induced microtubule lattice discontinuities can promote plus-end catastrophes at a distance of several micrometers. Our data indicate that structural defects in the microtubule wall can have long-range propagating effects on microtubule tip dynamics. Microtubules are dynamic cytoskeletal polymers that spontaneously switch between phases of growth and shrinkage. The probability of transitioning from growth to shrinkage, termed catastrophe, increases with microtubule age, but the underlying mechanisms are poorly understood. Here, we set out to test whether microtubule lattice defects formed during polymerization can affect growth at the plus end. To generate microtubules with lattice defects, we used microtubule-stabilizing agents that promote formation of polymers with different protofilament numbers. By employing different agents during nucleation of stable microtubule seeds and the subsequent polymerization phase, we could reproducibly induce switches in protofilament number and induce stable lattice defects. Such drug-induced defects led to frequent catastrophes, which were not observed when microtubules were grown in the same conditions but without a protofilament number mismatch. Microtubule severing at the site of the defect was sufficient to suppress catastrophes. We conclude that structural defects within the microtubule lattice can exert effects that can propagate over long distances and affect the dynamic state of the microtubule end.
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43
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Asthana J, Cade NI, Normanno D, Lim WM, Surrey T. Gradual compaction of the central spindle decreases its dynamicity in PRC1 and EB1 gene-edited cells. Life Sci Alliance 2021; 4:4/12/e202101222. [PMID: 34580180 PMCID: PMC8500333 DOI: 10.26508/lsa.202101222] [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: 09/01/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 11/24/2022] Open
Abstract
Although different anaphase proteins bind with characteristically different strength to the central spindle, the overall central spindle dynamicity slows down as mitosis proceeds. During mitosis, the spindle undergoes morphological and dynamic changes. It reorganizes at the onset of the anaphase when the antiparallel bundler PRC1 accumulates and recruits central spindle proteins to the midzone. Little is known about how the dynamic properties of the central spindle change during its morphological changes in human cells. Using gene editing, we generated human cells that express from their endogenous locus fluorescent PRC1 and EB1 to quantify their native spindle distribution and binding/unbinding turnover. EB1 plus end tracking revealed a general slowdown of microtubule growth, whereas PRC1, similar to its yeast orthologue Ase1, binds increasingly strongly to compacting antiparallel microtubule overlaps. KIF4A and CLASP1 bind more dynamically to the central spindle, but also show slowing down turnover. These results show that the central spindle gradually becomes more stable during mitosis, in agreement with a recent “bundling, sliding, and compaction” model of antiparallel midzone bundle formation in the central spindle during late mitosis.
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Affiliation(s)
- Jayant Asthana
- The Francis Crick Institute, London, UK.,Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | - Davide Normanno
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Wei Ming Lim
- The Francis Crick Institute, London, UK.,Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Thomas Surrey
- The Francis Crick Institute, London, UK .,Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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44
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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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45
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Farmer V, Arpağ G, Hall SL, Zanic M. XMAP215 promotes microtubule catastrophe by disrupting the growing microtubule end. J Cell Biol 2021; 220:212518. [PMID: 34324632 PMCID: PMC8327381 DOI: 10.1083/jcb.202012144] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 05/11/2021] [Accepted: 07/08/2021] [Indexed: 01/13/2023] Open
Abstract
The GTP-tubulin cap is widely accepted to protect microtubules against catastrophe. The GTP-cap size is thought to increase with the microtubule growth rate, presumably endowing fast-growing microtubules with enhanced stability. It is unknown what GTP-cap properties permit frequent microtubule catastrophe despite fast growth. Here, we investigate microtubules growing in the presence and absence of the polymerase XMAP215. Using EB1 as a GTP-cap marker, we find that GTP-cap size increases regardless of whether growth acceleration is achieved by increasing tubulin concentration or by XMAP215. Despite increased mean GTP-cap size, microtubules grown with XMAP215 display increased catastrophe frequency, in contrast to microtubules grown with more tubulin, for which catastrophe is abolished. However, microtubules polymerized with XMAP215 have large fluctuations in growth rate; display tapered and curled ends; and undergo catastrophe at faster growth rates and with higher EB1 end-localization. Our results suggest that structural perturbations induced by XMAP215 override the protective effects of the GTP-cap, ultimately driving microtubule catastrophe.
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Affiliation(s)
- Veronica Farmer
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Göker Arpağ
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Sarah L Hall
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Marija Zanic
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN.,Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN.,Department of Biochemistry, Vanderbilt University, Nashville, TN
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46
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Rodrigues EC, Grawenhoff J, Baumann SJ, Lorenzon N, Maurer SP. Mammalian Neuronal mRNA Transport Complexes: The Few Knowns and the Many Unknowns. Front Integr Neurosci 2021; 15:692948. [PMID: 34211375 PMCID: PMC8239176 DOI: 10.3389/fnint.2021.692948] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Hundreds of messenger RNAs (mRNAs) are transported into neurites to provide templates for the assembly of local protein networks. These networks enable a neuron to configure different cellular domains for specialized functions. According to current evidence, mRNAs are mostly transported in rather small packages of one to three copies, rarely containing different transcripts. This opens up fascinating logistic problems: how are hundreds of different mRNA cargoes sorted into distinct packages and how are they coupled to and released from motor proteins to produce the observed mRNA distributions? Are all mRNAs transported by the same transport machinery, or are there different adaptors or motors for different transcripts or classes of mRNAs? A variety of often indirect evidence exists for the involvement of proteins in mRNA localization, but relatively little is known about the essential activities required for the actual transport process. Here, we summarize the different types of available evidence for interactions that connect mammalian mRNAs to motor proteins to highlight at which point further research is needed to uncover critical missing links. We further argue that a combination of discovery approaches reporting direct interactions, in vitro reconstitution, and fast perturbations in cells is an ideal future strategy to unravel essential interactions and specific functions of proteins in mRNA transport processes.
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Affiliation(s)
- Elsa C. Rodrigues
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Julia Grawenhoff
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Sebastian J. Baumann
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Nicola Lorenzon
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Sebastian P. Maurer
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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47
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Mühlethaler T, Gioia D, Prota AE, Sharpe ME, Cavalli A, Steinmetz MO. Comprehensive Analysis of Binding Sites in Tubulin. Angew Chem Int Ed Engl 2021; 60:13331-13342. [PMID: 33951246 PMCID: PMC8251789 DOI: 10.1002/anie.202100273] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Indexed: 01/01/2023]
Abstract
Tubulin plays essential roles in vital cellular activities and is the target of a wide range of proteins and ligands. Here, using a combined computational and crystallographic fragment screening approach, we addressed the question of how many binding sites exist in tubulin. We identified 27 distinct sites, of which 11 have not been described previously, and analyzed their relationship to known tubulin-protein and tubulin-ligand interactions. We further observed an intricate pocket communication network and identified 56 chemically diverse fragments that bound to 10 distinct tubulin sites. Our results offer a unique structural basis for the development of novel small molecules for use as tubulin modulators in basic research applications or as drugs. Furthermore, our method lays down a framework that may help to discover new pockets in other pharmaceutically important targets and characterize them in terms of chemical tractability and allosteric modulation.
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Affiliation(s)
- Tobias Mühlethaler
- Laboratory of Biomolecular ResearchDepartment of Biology and ChemistryPaul Scherrer Institut5232Villigen PSISwitzerland
| | - Dario Gioia
- Computational & Chemical BiologyIstituto Italiano di Tecnologiavia Morego, 3016163GenovaItaly
| | - Andrea E. Prota
- Laboratory of Biomolecular ResearchDepartment of Biology and ChemistryPaul Scherrer Institut5232Villigen PSISwitzerland
| | - May E. Sharpe
- Swiss Light SourcePaul Scherrer Institut5232Villigen PSISwitzerland
| | - Andrea Cavalli
- Computational & Chemical BiologyIstituto Italiano di Tecnologiavia Morego, 3016163GenovaItaly
- Department of Pharmacy and BiotechnologyAlma Mater StudiorumUniversity of Bolognavia Belmeloro 640126BolognaItaly
| | - Michel O. Steinmetz
- Laboratory of Biomolecular ResearchDepartment of Biology and ChemistryPaul Scherrer Institut5232Villigen PSISwitzerland
- University of BaselBiozentrum4056BaselSwitzerland
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48
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Feng C, Cleary JM, Kothe GO, Stone MC, Weiner AT, Hertzler JI, Hancock WO, Rolls MM. Trim9 and Klp61F promote polymerization of new dendritic microtubules along parallel microtubules. J Cell Sci 2021; 134:jcs258437. [PMID: 34096607 PMCID: PMC8214762 DOI: 10.1242/jcs.258437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/04/2021] [Indexed: 02/03/2023] Open
Abstract
Axons and dendrites are distinguished by microtubule polarity. In Drosophila, dendrites are dominated by minus-end-out microtubules, whereas axons contain plus-end-out microtubules. Local nucleation in dendrites generates microtubules in both orientations. To understand why dendritic nucleation does not disrupt polarity, we used live imaging to analyze the fate of microtubules generated at branch points. We found that they had different rates of success exiting the branch based on orientation: correctly oriented minus-end-out microtubules succeeded in leaving about twice as often as incorrectly oriented microtubules. Increased success relied on other microtubules in a parallel orientation. From a candidate screen, we identified Trim9 and kinesin-5 (Klp61F) as machinery that promoted growth of new microtubules. In S2 cells, Eb1 recruited Trim9 to microtubules. Klp61F promoted microtubule growth in vitro and in vivo, and could recruit Trim9 in S2 cells. In summary, the data argue that Trim9 and kinesin-5 act together at microtubule plus ends to help polymerizing microtubules parallel to pre-existing ones resist catastrophe.
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Affiliation(s)
- Chengye Feng
- Biochemistry and Molecular Biology Department and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Joseph M. Cleary
- Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Gregory O. Kothe
- Biochemistry and Molecular Biology Department and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Michelle C. Stone
- Biochemistry and Molecular Biology Department and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Alexis T. Weiner
- Biochemistry and Molecular Biology Department and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - James I. Hertzler
- Biochemistry and Molecular Biology Department and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - William O. Hancock
- Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Melissa M. Rolls
- Biochemistry and Molecular Biology Department and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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49
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Mühlethaler T, Gioia D, Prota AE, Sharpe ME, Cavalli A, Steinmetz MO. Comprehensive Analysis of Binding Sites in Tubulin. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tobias Mühlethaler
- Laboratory of Biomolecular Research Department of Biology and Chemistry Paul Scherrer Institut 5232 Villigen PSI Switzerland
| | - Dario Gioia
- Computational & Chemical Biology Istituto Italiano di Tecnologia via Morego, 30 16163 Genova Italy
| | - Andrea E. Prota
- Laboratory of Biomolecular Research Department of Biology and Chemistry Paul Scherrer Institut 5232 Villigen PSI Switzerland
| | - May E. Sharpe
- Swiss Light Source Paul Scherrer Institut 5232 Villigen PSI Switzerland
| | - Andrea Cavalli
- Computational & Chemical Biology Istituto Italiano di Tecnologia via Morego, 30 16163 Genova Italy
- Department of Pharmacy and Biotechnology Alma Mater Studiorum University of Bologna via Belmeloro 6 40126 Bologna Italy
| | - Michel O. Steinmetz
- Laboratory of Biomolecular Research Department of Biology and Chemistry Paul Scherrer Institut 5232 Villigen PSI Switzerland
- University of Basel Biozentrum 4056 Basel Switzerland
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50
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Minagawa M, Shirato M, Toya M, Sato M. Dual Impact of a Benzimidazole Resistant β-Tubulin on Microtubule Behavior in Fission Yeast. Cells 2021; 10:1042. [PMID: 33925026 PMCID: PMC8145593 DOI: 10.3390/cells10051042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 11/17/2022] Open
Abstract
The cytoskeleton microtubule consists of polymerized αβ-tubulin dimers and plays essential roles in many cellular events. Reagents that inhibit microtubule behaviors have been developed as antifungal, antiparasitic, and anticancer drugs. Benzimidazole compounds, including thiabendazole (TBZ), carbendazim (MBC), and nocodazole, are prevailing microtubule poisons that target β-tubulin and inhibit microtubule polymerization. The molecular basis, however, as to how the drug acts on β-tubulin remains controversial. Here, we characterize the S. pombe β-tubulin mutant nda3-TB101, which was previously isolated as a mutant resistance to benzimidazole. The mutation site tyrosine at position 50 is located in the interface of two lateral β-tubulin proteins and at the gate of a putative binging pocket for benzimidazole. Our observation revealed two properties of the mutant tubulin. First, the dynamics of cellular microtubules comprising the mutant β-tubulin were stabilized in the absence of benzimidazole. Second, the mutant protein reduced the affinity to benzimidazole in vitro. We therefore conclude that the mutant β-tubulin Nda3-TB101 exerts a dual effect on microtubule behaviors: the mutant β-tubulin stabilizes microtubules and is insensitive to benzimidazole drugs. This notion fine-tunes the current elusive molecular model regarding binding of benzimidazole to β-tubulin.
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Affiliation(s)
- Mamika Minagawa
- Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo 162-8480, Japan; (M.M.); (M.S.); (M.T.)
| | - Minamo Shirato
- Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo 162-8480, Japan; (M.M.); (M.S.); (M.T.)
| | - Mika Toya
- Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo 162-8480, Japan; (M.M.); (M.S.); (M.T.)
- Faculty of Science and Engineering, Global Center for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Masamitsu Sato
- Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo 162-8480, Japan; (M.M.); (M.S.); (M.T.)
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Institute for Medical-Oriented Structural Biology, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo 162-8480, Japan
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