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Multiple roles for the cytoskeleton in ALS. Exp Neurol 2022; 355:114143. [PMID: 35714755 PMCID: PMC10163623 DOI: 10.1016/j.expneurol.2022.114143] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 11/20/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease caused by more than sixty genes identified through classic linkage analysis and new sequencing methods. Yet no clear mechanism of onset, cure, or effective treatment is known. Popular discourse classifies the proteins encoded from ALS-related genes into four disrupted processes: proteostasis, mitochondrial function and ROS, nucleic acid regulation, and cytoskeletal dynamics. Surprisingly, the mechanisms detailing the contribution of the neuronal cytoskeletal in ALS are the least explored, despite involvement in these cell processes. Eight genes directly regulate properties of cytoskeleton function and are essential for the health and survival of motor neurons, including: TUBA4A, SPAST, KIF5A, DCTN1, NF, PRPH, ALS2, and PFN1. Here we review the properties and studies exploring the contribution of each of these genes to ALS.
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2
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Ti SC. Reconstituting Microtubules: A Decades-Long Effort From Building Block Identification to the Generation of Recombinant α/β-Tubulin. Front Cell Dev Biol 2022; 10:861648. [PMID: 35573669 PMCID: PMC9096264 DOI: 10.3389/fcell.2022.861648] [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: 01/24/2022] [Accepted: 04/18/2022] [Indexed: 11/13/2022] Open
Abstract
Microtubules are cytoskeletal filaments underlying the morphology and functions of all eukaryotic cells. In higher eukaryotes, the basic building blocks of these non-covalent polymers, ɑ- and β-tubulins, are encoded by expanded tubulin family genes (i.e., isotypes) at distinct loci in the genome. While ɑ/β-tubulin heterodimers have been isolated and examined for more than 50 years, how tubulin isotypes contribute to the microtubule organization and functions that support diverse cellular architectures remains a fundamental question. To address this knowledge gap, in vitro reconstitution of microtubules with purified ɑ/β-tubulin proteins has been employed for biochemical and biophysical characterization. These in vitro assays have provided mechanistic insights into the regulation of microtubule dynamics, stability, and interactions with other associated proteins. Here we survey the evolving strategies of generating purified ɑ/β-tubulin heterodimers and highlight the advances in tubulin protein biochemistry that shed light on the roles of tubulin isotypes in determining microtubule structures and properties.
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3
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Jain K, Basu J, Roy M, Yadav J, Patil S, Athale CA. Polymerization kinetics of tubulin from mung seedlings modeled as a competition between nucleation and GTP-hydrolysis rates. Cytoskeleton (Hoboken) 2022; 78:436-447. [PMID: 35233933 DOI: 10.1002/cm.21694] [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: 09/25/2021] [Revised: 02/10/2022] [Accepted: 02/21/2022] [Indexed: 11/07/2022]
Abstract
Microtubules (MTs) form physiologically important cytoskeletal structures that assemble by tubulin polymerization in a nucleation- and GTP-dependent manner. GTP-hydrolysis competes with the addition of monomers, to determine the GTP-cap size, and onset of shrinkage, which alternates with growth. Multiple theoretical models of MT polymerization dynamics have been reconciled to the kinetics of animal brain tubulins, but more recently rapid kinetics seen in Arabidopsis tubulin polymerization suggest the need to sample a wider diversity in tubulin polymerization kinetics and reconcile it to theory. Here, we have isolated tubulin from seedlings of Vigna sp. (mung bean), compared polymerization kinetics to animal brain tubulin and used a computational model to understand the di_erences. We _nd that activity isolated mung tubulin polymerizes in a nucleation-dependent manner, based on turbidimetry, qualitatively similar to brain tubulin, but with a ten-fold smaller critical critical concentration. GTP-dependent polymerization kinetics also appear to be transient, indicative of high rates of GTP-hydrolysis. Computational modeling of tubulin nucleation and vectorial GTP-hydrolysis to examine the e_ect of high nucleation and GTP-hydrolysis rates predicts a dominance of the latter in determining MT lengths and numbers. Microscopy of mung tubulin _laments stabilized by GMPCPP or taxol result in few and short MTs, compared to the many long MTs arising from goat tubulin, qualitatively matching the model predictions. We _nd GTP-hydrolysis outcompetes nucleation rates in determining MT lengths and numbers. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Kunalika Jain
- Division of Biology, IISER Pune, Pune, Maharashtra, India
| | - Jashaswi Basu
- Division of Biology, IISER Pune, Pune, Maharashtra, India
| | - Megha Roy
- Division of Biology, IISER Pune, Pune, Maharashtra, India
| | - Jyoti Yadav
- Department of Chemistry, IISER Pune, Pune, Maharashtra, India
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4
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Fukuda S, Ando T. Faster high-speed atomic force microscopy for imaging of biomolecular processes. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2021; 92:033705. [PMID: 33820001 DOI: 10.1063/5.0032948] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
High-speed atomic force microscopy (HS-AFM) has enabled observing protein molecules during their functional activity at rates of 1-12.5 frames per second (fps), depending on the imaging conditions, sample height, and fragility. To meet the increasing demand for the great expansion of observable dynamic molecular processes, faster HS-AFM with less disturbance is imperatively needed. However, even a 50% improvement in the speed performance imposes tremendous challenges, as the optimization of major rate-limiting components for their fast response is nearly matured. This paper proposes an alternative method that can lower the feedback control error and thereby enhance the imaging rate. This method can be implemented in any HS-AFM system by minor modifications of the software and hardware. The resulting faster and less-disturbing imaging capabilities are demonstrated by the imaging of relatively fragile actin filaments and microtubules near the video rate, and of actin polymerization that occurs through weak intermolecular interactions, at ∼8 fps.
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Affiliation(s)
- Shingo Fukuda
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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5
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Abstract
α/β-tubulin heterodimers, which can harbor diverse isotypes and post-translational modifications, polymerize into microtubules that are fundamental to many cellular processes. Due to long-standing challenges in generating recombinant tubulin, however, it has been difficult to examine the properties of specific tubulin isotypes. Here, we provide a protocol for purifying milligrams of affinity tag-free, isotypically pure recombinant tubulin. Our method can be applicable to any tubulin of interest, opening the door to dissecting how tubulin diversity regulates microtubule function. For complete details on the use and execution of this protocol, please see Ti et al. (2018). Strategy to generate isotypically pure affinity tag-free recombinant tubulin Strategy is generally applicable to any desired tubulin sequence Purified tubulin has no detectable post-translational modifications Recombinant tubulin is of sufficient yield for biochemical and biophysical assays
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6
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Howes SC, Geyer EA, LaFrance B, Zhang R, Kellogg EH, Westermann S, Rice LM, Nogales E. Structural and functional differences between porcine brain and budding yeast microtubules. Cell Cycle 2018; 17:278-287. [PMID: 29278985 PMCID: PMC5914886 DOI: 10.1080/15384101.2017.1415680] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The cytoskeleton of eukaryotic cells relies on microtubules to perform many essential functions. We have previously shown that, in spite of the overall conservation in sequence and structure of tubulin subunits across species, there are differences between mammalian and budding yeast microtubules with likely functional consequences for the cell. Here we expand our structural and function comparison of yeast and porcine microtubules to show different distribution of protofilament number in microtubules assembled in vitro from these two species. The different geometry at lateral contacts between protofilaments is likely due to a more polar interface in yeast. We also find that yeast tubulin forms longer and less curved oligomers in solution, suggesting stronger tubulin:tubulin interactions along the protofilament. Finally, we observed species-specific plus-end tracking activity for EB proteins: yeast Bim1 tracked yeast but not mammalian MTs, and human EB1 tracked mammalian but not yeast MTs. These findings further demonstrate that subtle sequence differences in tubulin sequence can have significant structural and functional consequences in microtubule structure and behavior.
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Affiliation(s)
- Stuart C Howes
- a Biophysics Graduate Group , UC Berkeley , CA 94720 , USA and Department of Molecular Cell Biology , Leiden University Medical Center , 2333 ZC Leiden , Netherlands
| | - Elisabeth A Geyer
- b UT Southwestern Medical Center , Departments of Biophysics and Biochemistry , Dallas , TX 75390 , USA
| | - Benjamin LaFrance
- c Molecular and Cell Biology Graduate Program , UC Berkeley , CA 94720 , USA
| | - Rui Zhang
- d Molecular Biophysics and Integrated Bioimaging , Lawrence Berkeley National Laboratory , CA 94720 , USA.,e Howard Hughes Medical Institute , UC Berkeley , CA 94720-3220 , USA.,f Department of Biochemistry and Molecular Biophysics , Washington University School of Medicine , St. Louis , MO 63110 , USA
| | - Elizabeth H Kellogg
- d Molecular Biophysics and Integrated Bioimaging , Lawrence Berkeley National Laboratory , CA 94720 , USA.,e Howard Hughes Medical Institute , UC Berkeley , CA 94720-3220 , USA
| | - Stefan Westermann
- g Research Institute of Molecular Pathology , Dr. Bohr-Gasse 7, 1030 Vienna , Austria
| | - Luke M Rice
- b UT Southwestern Medical Center , Departments of Biophysics and Biochemistry , Dallas , TX 75390 , USA
| | - Eva Nogales
- d Molecular Biophysics and Integrated Bioimaging , Lawrence Berkeley National Laboratory , CA 94720 , USA.,e Howard Hughes Medical Institute , UC Berkeley , CA 94720-3220 , USA.,h Molecular and Cell Biology Department and QB3 Institute , UC Berkeley , CA 94720 , USA
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7
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Howes SC, Geyer EA, LaFrance B, Zhang R, Kellogg EH, Westermann S, Rice LM, Nogales E. Structural differences between yeast and mammalian microtubules revealed by cryo-EM. J Cell Biol 2017; 216:2669-2677. [PMID: 28652389 PMCID: PMC5584162 DOI: 10.1083/jcb.201612195] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 03/31/2017] [Accepted: 05/30/2017] [Indexed: 01/03/2023] Open
Abstract
Yeast MTs do not appear to undergo the lattice compaction seen in mammalian MTs upon GTP hydrolysis. Binding of the +TIP Bim1, both between and within αβ-tubulin dimers, causes compaction of yeast MTs and their rapid disassembly. Microtubules are polymers of αβ-tubulin heterodimers essential for all eukaryotes. Despite sequence conservation, there are significant structural differences between microtubules assembled in vitro from mammalian or budding yeast tubulin. Yeast MTs were not observed to undergo compaction at the interdimer interface as seen for mammalian microtubules upon GTP hydrolysis. Lack of compaction might reflect slower GTP hydrolysis or a different degree of allosteric coupling in the lattice. The microtubule plus end–tracking protein Bim1 binds yeast microtubules both between αβ-tubulin heterodimers, as seen for other organisms, and within tubulin dimers, but binds mammalian tubulin only at interdimer contacts. At the concentrations used in cryo-electron microscopy, Bim1 causes the compaction of yeast microtubules and induces their rapid disassembly. Our studies demonstrate structural differences between yeast and mammalian microtubules that likely underlie their differing polymerization dynamics. These differences may reflect adaptations to the demands of different cell size or range of physiological growth temperatures.
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Affiliation(s)
- Stuart C Howes
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA
| | - Elisabeth A Geyer
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Benjamin LaFrance
- Molecular and Cell Biology Graduate Program, University of California, Berkeley, Berkeley, CA
| | - Rui Zhang
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Elizabeth H Kellogg
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Stefan Westermann
- Department of Molecular Genetics, Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Luke M Rice
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Eva Nogales
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA .,Department of Molecular Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA
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8
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Minoura I. Towards an understanding of the isotype-specific functions of tubulin in neurons: Technical advances in tubulin expression and purification. Neurosci Res 2017; 122:1-8. [PMID: 28412269 DOI: 10.1016/j.neures.2017.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/29/2017] [Accepted: 04/07/2017] [Indexed: 12/20/2022]
Abstract
Microtubules are cytoskeletal filaments critical for determining the complex morphology of neurons, as well as the basic architecture and organization of mitosis in all eukaryotic cells. Microtubules in humans are composed of 8 α- and 9 β-tubulin isotypes, each of which is encoded by different members of a multi-gene family. The expression pattern of tubulin isotypes, in addition to isotype-specific post-translational modifications, is thought to be critical for the morphogenesis of axons and dendrites. Recent studies revealed that several neurodevelopmental disorders are caused by mutations of specific tubulin isotypes, suggesting that each tubulin isotype has distinct functions. Therefore, in vitro and in vivo functional analyses of tubulin isotypes are important to understand the pathogenesis of developmental disorders. Likewise, analysis of developmental disorders may clarify the function of different tubulin isotypes. In this respect, both the preparation of specific tubulin isotypes and of specific mutant tubulin proteins is critical to understanding the function of tubulin. In the last 20 years, various methods have been developed to study functional differences between tubulin isotypes and the functional defects caused by tubulin mutations. These technical achievements have been discussed in this review. The function of tubulin/microtubules in neuronal morphogenesis as revealed through these techniques has also been described.
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Affiliation(s)
- Itsushi Minoura
- Laboratory for Molecular Biophysics, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Goryo Chemical Inc., Earee Bldg. 5F, Kita 8 Nishi 18-35-100, Chuo-ku, Sapporo 060-0008, Japan.
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9
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Piedra FA, Kim T, Garza ES, Geyer EA, Burns A, Ye X, Rice LM. GDP-to-GTP exchange on the microtubule end can contribute to the frequency of catastrophe. Mol Biol Cell 2016; 27:3515-3525. [PMID: 27146111 PMCID: PMC5221584 DOI: 10.1091/mbc.e16-03-0199] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 04/26/2016] [Indexed: 11/11/2022] Open
Abstract
Microtubules are dynamic polymers of αβ-tubulin that have essential roles in chromosome segregation and organization of the cytoplasm. Catastrophe-the switch from growing to shrinking-occurs when a microtubule loses its stabilizing GTP cap. Recent evidence indicates that the nucleotide on the microtubule end controls how tightly an incoming subunit will be bound (trans-acting GTP), but most current models do not incorporate this information. We implemented trans-acting GTP into a computational model for microtubule dynamics. In simulations, growing microtubules often exposed terminal GDP-bound subunits without undergoing catastrophe. Transient GDP exposure on the growing plus end slowed elongation by reducing the number of favorable binding sites on the microtubule end. Slower elongation led to erosion of the GTP cap and an increase in the frequency of catastrophe. Allowing GDP-to-GTP exchange on terminal subunits in simulations mitigated these effects. Using mutant αβ-tubulin or modified GTP, we showed experimentally that a more readily exchangeable nucleotide led to less frequent catastrophe. Current models for microtubule dynamics do not account for GDP-to-GTP exchange on the growing microtubule end, so our findings provide a new way of thinking about the molecular events that initiate catastrophe.
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Affiliation(s)
- Felipe-Andrés Piedra
- Departments of Biophysics and Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390
| | - Tae Kim
- Departments of Biophysics and Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390
| | - Emily S Garza
- Departments of Biophysics and Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390
| | - Elisabeth A Geyer
- Departments of Biophysics and Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390
| | - Alexander Burns
- Departments of Biophysics and Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390
| | - Xuecheng Ye
- Departments of Biophysics and Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390
| | - Luke M Rice
- Departments of Biophysics and Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390
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10
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Uchimura S, Fujii T, Takazaki H, Ayukawa R, Nishikawa Y, Minoura I, Hachikubo Y, Kurisu G, Sutoh K, Kon T, Namba K, Muto E. A flipped ion pair at the dynein-microtubule interface is critical for dynein motility and ATPase activation. ACTA ACUST UNITED AC 2015; 208:211-22. [PMID: 25583999 PMCID: PMC4298687 DOI: 10.1083/jcb.201407039] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Dynein is a motor protein that moves on microtubules (MTs) using the energy of adenosine triphosphate (ATP) hydrolysis. To understand its motility mechanism, it is crucial to know how the signal of MT binding is transmitted to the ATPase domain to enhance ATP hydrolysis. However, the molecular basis of signal transmission at the dynein-MT interface remains unclear. Scanning mutagenesis of tubulin identified two residues in α-tubulin, R403 and E416, that are critical for ATPase activation and directional movement of dynein. Electron cryomicroscopy and biochemical analyses revealed that these residues form salt bridges with the residues in the dynein MT-binding domain (MTBD) that work in concert to induce registry change in the stalk coiled coil and activate the ATPase. The R403-E3390 salt bridge functions as a switch for this mechanism because of its reversed charge relative to other residues at the interface. This study unveils the structural basis for coupling between MT binding and ATPase activation and implicates the MTBD in the control of directional movement.
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Affiliation(s)
- Seiichi Uchimura
- Laboratory for Molecular Biophysics, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Takashi Fujii
- Graduate School of Frontier Biosciences and Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, Kawaguchi, Saitama 332-0012, Japan Quantitative Biology Center, Institute of Physical and Chemical Research, Suita, Osaka 565-0871, Japan
| | - Hiroko Takazaki
- Laboratory for Molecular Biophysics, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Rie Ayukawa
- Laboratory for Molecular Biophysics, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Yosuke Nishikawa
- Graduate School of Frontier Biosciences and Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Itsushi Minoura
- Laboratory for Molecular Biophysics, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - You Hachikubo
- Laboratory for Molecular Biophysics, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Genji Kurisu
- Graduate School of Frontier Biosciences and Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Kazuo Sutoh
- Research Institute for Science and Engineering, Waseda University, Toshima-ku, Tokyo 171-0033, Japan
| | - Takahide Kon
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, Kawaguchi, Saitama 332-0012, Japan Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan Department of Frontier Bioscience, Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences and Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan Quantitative Biology Center, Institute of Physical and Chemical Research, Suita, Osaka 565-0871, Japan
| | - Etsuko Muto
- Laboratory for Molecular Biophysics, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
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Podolski M, Mahamdeh M, Howard J. Stu2, the budding yeast XMAP215/Dis1 homolog, promotes assembly of yeast microtubules by increasing growth rate and decreasing catastrophe frequency. J Biol Chem 2014; 289:28087-93. [PMID: 25172511 DOI: 10.1074/jbc.m114.584300] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Stu2 is the budding yeast member of the XMAP215/Dis1 family of microtubule polymerases. It is essential in cell division, allowing proper spindle orientation and metaphase chromosome alignment, as well as spindle elongation during anaphase. Despite Stu2 having a phenotype that suggests it promotes microtubule growth, like the other members of the XMAP215/Dis1 family, previous studies with purified Stu2 indicate only that it antagonizes microtubule growth. One potential explanation for these contradictory findings is that the assays were performed with mammalian brain tubulin, which may not be the right substrate to test the activity of Stu2 given that yeast and brain tubulins are quite divergent in sequence and that the vertebrate tubulins are subject to many post-translational modifications. To test this possibility, we reconstituted the activity of Stu2 with purified budding yeast tubulin. We found that Stu2 accelerated microtubule growth in yeast tubulin by severalfold, similar to the acceleration reported for XMAP215 in porcine brain tubulin. Furthermore, Stu2 accelerated polymerization in yeast tubulin to a much greater extent than in porcine brain tubulin, and the concentration of Stu2 required to reach 50% maximum activity in yeast tubulin was nearly 2 orders of magnitude lower than that in porcine brain tubulin. We conclude that Stu2 is a microtubule polymerase, like its relatives, and that its activity is considerably higher in yeast tubulin compared with mammalian brain tubulin. The biochemical properties of Stu2 reported here account for many of the phenotypes of Stu2 observed in cells.
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Affiliation(s)
- Marija Podolski
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Mohammed Mahamdeh
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Jonathon Howard
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
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12
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Minoura I, Hachikubo Y, Yamakita Y, Takazaki H, Ayukawa R, Uchimura S, Muto E. Overexpression, purification, and functional analysis of recombinant human tubulin dimer. FEBS Lett 2013; 587:3450-5. [PMID: 24021646 DOI: 10.1016/j.febslet.2013.08.032] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 08/26/2013] [Accepted: 08/26/2013] [Indexed: 12/19/2022]
Abstract
Microtubules consisting of tubulin dimers play essential roles in various cellular functions. Investigating the structure-function relationship of tubulin dimers requires a method to prepare sufficient quantities of recombinant tubulin. To this end, we simultaneously expressed human α1- and β3-tubulin using a baculovirus-insect cell expression system that enabled the purification of 5mg recombinant tubulin per litre of cell culture. The purified recombinant human tubulin could be polymerized into microtubules that glide on a kinesin-coated glass surface. The method provides a powerful tool for in vitro functional analyses of microtubules.
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Affiliation(s)
- Itsushi Minoura
- Laboratory for Molecular Biophysics, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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13
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Abstract
The alpha-beta tubulin heterodimer is the subunit from which microtubules are assembled. The pathway leading to correctly folded alpha- and beta-tubulins is unusually complex: it involves cycles of ATP-dependent interaction of newly synthesized tubulin subunits with cytosolic chaperonin, resulting in the production of quasi-native folding intermediates, which must then be acted upon by additional protein cofactors. These cofactors form a supercomplex containing both alpha- and beta-tubulin polypeptides, from which native heterodimer is released in a GTP-dependent reaction. Here, we discuss the current state of our understanding of the function of cytosolic chaperonin and cofactors in tubulin folding.
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14
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Johnson V, Ayaz P, Huddleston P, Rice LM. Design, overexpression, and purification of polymerization-blocked yeast αβ-tubulin mutants. Biochemistry 2011; 50:8636-44. [PMID: 21888381 DOI: 10.1021/bi2005174] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microtubule dynamics play essential roles in intracellular organization and cell division. They result from structural and biochemical properties of αβ-tubulin heterodimers and how these polymerizing subunits interact with themselves and with regulatory proteins. A broad understanding of the underlying mechanisms has been established, but fundamental questions remain unresolved. The lack of routine access to recombinant αβ-tubulin represents an obstacle to deeper insight into αβ-tubulin structure, biochemistry, and recognition. Indeed, the widespread reliance on animal brain αβ-tubulin means that very few in vitro studies have taken advantage of powerful and ordinarily routine techniques like site-directed mutagenesis. Here we report new methods for purifying wild-type or mutant yeast αβ-tubulin from inducibly overexpressing strains of Saccharomyces cerevisiae. Inducible overexpression is an improvement over existing approaches that rely on constitutive expression: it provides higher yields while also allowing otherwise lethal mutants to be purified. We also designed and purified polymerization-blocked αβ-tubulin mutants. These "blocked" forms of αβ-tubulin give a dominant lethal phenotype when expressed in cells; they cannot form microtubules in vitro and when present in mixtures inhibit the polymerization of wild-type αβ-tubulin. The effects of blocking mutations are very specific, because purified mutants exhibit normal hydrodynamic properties, bind GTP, and interact with a tubulin-binding domain. The ability to overexpress and purify wild-type αβ-tubulin, or mutants like the ones we report here, creates new opportunities for structural studies of αβ-tubulin and its complexes with regulatory proteins, and for biochemical and functional studies of microtubule dynamics and its regulation.
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Affiliation(s)
- Vinu Johnson
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
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15
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Drummond DR, Kain S, Newcombe A, Hoey C, Katsuki M, Cross RA. Purification of tubulin from the fission yeast Schizosaccharomyces pombe. Methods Mol Biol 2011; 777:29-55. [PMID: 21773919 DOI: 10.1007/978-1-61779-252-6_3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The fission yeast Schizosaccharomyces pombe is an attractive source of tubulin for biochemical experiments as it contains few tubulin isoforms and is amenable to genetic manipulation. We describe the preparation of milligram quantities of highly purified native tubulin from S. pombe suitable for use in microtubule dynamics assays as well as structural and other biochemical studies. S. pombe cells are grown in bulk in a fermenter and then lysed using a bead mill. The soluble protein fraction is bound to anion-exchange chromatography resin by batch binding, packed in a -chromatography column and eluted by a salt gradient. The tubulin-containing fraction is ammonium sulphate precipitated to further concentrate and purify the protein. A round of high-resolution anion-exchange chromatography is carried out before a cycle of polymerisation and depolymerisation to select functional tubulin. Gel filtration is used to remove residual contaminants before a final desalting step. The purified tubulin is concentrated, and then frozen and stored in liquid nitrogen.
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Affiliation(s)
- Douglas R Drummond
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Coventry, UK.
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16
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Abstract
Microtubules are cytoskeletal structures built of alpha- and beta-tubulins. Although tubulins are highly conserved throughout evolution, microtubules can be adapted to a range of different functions. A powerful mechanism that could regulate the functional specialization of microtubules is the posttranslational modification of tubulin molecules. Two tubulin modifications, polyglutamylation and polyglycylation, generate amino acid side chains of different length on tubulin. These modifications are thought to regulate interactions between microtubules and their associated proteins; however, detailed studies of this potential mechanism have not been performed. The investigation of the potential regulatory role of polyglutamylation requires in vitro tools to visualize the molecular events that could be affected by this modification. Classically, in vitro work with microtubules is performed with tubulin from brain tissue; however, this tubulin is highly posttranslationally modified. Here, we describe a method for the purification of tubulin carrying controlled levels of polyglutamylation, which can be used in basic in vitro assays.
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17
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α-Tubulin mutations alter oryzalin affinity and microtubule assembly properties to confer dinitroaniline resistance. EUKARYOTIC CELL 2010; 9:1825-34. [PMID: 20870876 DOI: 10.1128/ec.00140-10] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Plant and protozoan microtubules are selectively sensitive to dinitroanilines, which do not disrupt vertebrate or fungal microtubules. Tetrahymena thermophila is an abundant source of dinitroaniline-sensitive tubulin, and we have modified the single T. thermophila α-tubulin gene to create strains that solely express mutant α-tubulin in functional dimers. Previous research identified multiple α-tubulin mutations that confer dinitroaniline resistance in the human parasite Toxoplasma gondii, and when two of these mutations (L136F and I252L) were introduced into T. thermophila, they conferred resistance in these free-living ciliates. Purified tubulin heterodimers composed of L136F or I252L α-tubulin display decreased affinity for the dinitroaniline oryzalin relative to wild-type T. thermophila tubulin. Moreover, the L136F substitution dramatically reduces the critical concentration for microtubule assembly relative to the properties of wild-type T. thermophila tubulin. Our data provide additional support for the proposed dinitroaniline binding site on α-tubulin and validate the use of T. thermophila for expression of genetically homogeneous populations of mutant tubulins for biochemical characterization.
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18
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Abstract
We developed tubulin purification strategies that allowed sufficient material to be produced for compound-screening projects. Tubulins were polymerized in the presence of compounds using either turbidometric or fluorescence polymerization assays. IC50 and EC50 values were calculated and used to determine ratios between host and target tubulin (TT) (e.g., IC50-neuronal tubulin/IC50-TT). This ratio can be compared between compounds to identify the ones which are most selective for a particular TT. We found ratios for different compounds ranged from 0.16 to 4.0 between neuronal and cancer cell tubulin indicating that the sequence and posttranslational heterogeneity between these tubulins are sufficient to identify selective ligands for the TT. Likewise, compounds compared between neuronal and fungal tubulin had ratios ranging from 0.03 to 0.60, and compounds compared between neuronal to plant tubulin had ratios ranging from 0.03 to 52. Considering these data, we believe cancer cell tubulin-targeted drugs could be obtained with ratios in excess of 20, herbicides with ratios in excess of 200, and fungicides in excess of 200.
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19
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Lacroix B, van Dijk J, Gold ND, Guizetti J, Aldrian-Herrada G, Rogowski K, Gerlich DW, Janke C. Tubulin polyglutamylation stimulates spastin-mediated microtubule severing. ACTA ACUST UNITED AC 2010; 189:945-54. [PMID: 20530212 PMCID: PMC2886356 DOI: 10.1083/jcb.201001024] [Citation(s) in RCA: 208] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microtubules with long polyglutamylated C-terminal tails are more prone to severing by spastin, establishing the importance of tubulin posttranslational modifications. Posttranslational glutamylation of tubulin is present on selected subsets of microtubules in cells. Although the modification is expected to contribute to the spatial and temporal organization of the cytoskeleton, hardly anything is known about its functional relevance. Here we demonstrate that glutamylation, and in particular the generation of long glutamate side chains, promotes the severing of microtubules. In human cells, the generation of long side chains induces spastin-dependent microtubule disassembly and, consistently, only microtubules modified by long glutamate side chains are efficiently severed by spastin in vitro. Our study reveals a novel control mechanism for microtubule mass and stability, which is of fundamental importance to cellular physiology and might have implications for diseases related to microtubule severing.
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Affiliation(s)
- Benjamin Lacroix
- Centre de Recherche de Biochimie Macromoléculaire, Université Montpellier 2 and 1, Centre National de la Recherche Scientifique UMR 5237, Montpellier, France
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20
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Abstract
Tubulin is a highly conserved, negatively charged protein that is found in essentially all eukaryotic cells. These properties ensure that isolation protocols successful in one system will likely work, with a few modifications, in most systems. Tubulin has been isolated most frequently from mammalian brain, and the main difference encountered in other systems versus brain is that tubulin is much less abundant in nearly all other sources than it is in brain. This means that attempting to purify tubulin by direct polymerization from a homogenate will often fail or be quite inefficient. However, the conservation of negative charge on tubulin means that an initial ion exchange step can be used to both purify and concentrate the protein from most systems. Polymerization-competent tubulin can usually be obtained by inducing polymerization in the salt eluate from the ion exchange step. We describe protocols for this procedure and describe its application to a number of vertebrate, fungal, protozoal, and plant sources.
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Affiliation(s)
- Dan L Sackett
- Laboratory of Integrative and Medical Biophysics, Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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21
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Braun M, Drummond DR, Cross RA, McAinsh AD. The kinesin-14 Klp2 organizes microtubules into parallel bundles by an ATP-dependent sorting mechanism. Nat Cell Biol 2009; 11:724-30. [PMID: 19430466 DOI: 10.1038/ncb1878] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 02/24/2009] [Indexed: 11/08/2022]
Abstract
The dynamic organization of microtubules into parallel arrays allows interphase cells to set up multi-lane highways for intracellular transport and M-phase cells to build the mitotic and meiotic spindles. Here we show that a minimally reconstituted system composed of Klp2, a kinesin-14 from the fission yeast Schizosaccharomyces pombe, together with microtubules assembled from purified S. pombe tubulin, autonomously assembles bundles of parallel microtubules. Bundles form by an ATP-dependent sorting mechanism that requires the full-length Klp2 motor. By this mechanism, antiparallel-overlapped microtubules slide over one another until they dissociate from the bundles, whereas parallel-overlapped microtubules are selectively trapped by an energy-dissipating force-balance mechanism. Klp2-driven microtubule sorting provides a robust pathway for the organization of microtubules into parallel arrays. In vivo evidence indicates that Klp2 is required for the proper organization of S. pombe interphase microtubules into bipolar arrays of parallel-overlapped microtubules, suggesting that kinesin-14-dependent microtubule sorting may have wide biological importance.
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Affiliation(s)
- Marcus Braun
- Chromosome Segregation Laboratory, Marie Curie Research Institute, The Chart, Oxted, RH8 0TL, Surrey, UK
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22
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Koo BS, Park H, Kalme S, Park HY, Han JW, Yeo YS, Yoon SH, Kim SJ, Lee CM, Yoon MY. α- and β-tubulin from Phytophthora capsici KACC 40483: molecular cloning, biochemical characterization, and antimicrotubule screening. Appl Microbiol Biotechnol 2009; 82:513-24. [DOI: 10.1007/s00253-008-1821-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 11/24/2008] [Accepted: 12/08/2008] [Indexed: 10/21/2022]
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23
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Characterization of Capsicum annuum Recombinant α- and β-Tubulin. Appl Biochem Biotechnol 2009; 160:122-8. [DOI: 10.1007/s12010-008-8489-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2008] [Accepted: 12/11/2008] [Indexed: 11/25/2022]
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24
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des Georges A, Katsuki M, Drummond DR, Osei M, Cross RA, Amos LA. Mal3, the Schizosaccharomyces pombe homolog of EB1, changes the microtubule lattice. Nat Struct Mol Biol 2008; 15:1102-8. [PMID: 18794845 DOI: 10.1038/nsmb.1482] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 07/29/2008] [Indexed: 11/09/2022]
Abstract
In vitro studies of pure tubulin have suggested that tubulin heterodimers in cells assemble into B-lattice microtubules, where the 8-nm dimers in adjacent protofilaments are staggered by 0.9 nm. This arrangement requires the tube to close by forming a seam with an A-lattice, in which the protofilaments are staggered by 4.9 nm. Here we show that Mal3, an EB1 family tip-tracking protein, drives tubulin to assemble in vitro into exclusively 13-protofilament microtubules with a high proportion of A-lattice protofilament contacts. We present a three-dimensional cryo-EM reconstruction of a purely A-lattice microtubule decorated with Mal3, in which Mal3 occupies the groove between protofilaments and associates closely with one tubulin monomer. We propose that Mal3 promotes assembly by binding to freshly formed tubulin polymer and particularly favors any with A-lattice arrangement. These results reopen the question of microtubule structure in cells.
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25
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Andreu JM. Large scale purification of brain tubulin with the modified Weisenberg procedure. METHODS IN MOLECULAR MEDICINE 2007; 137:17-28. [PMID: 18085219 DOI: 10.1007/978-1-59745-442-1_2] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This method is a modification of the initial procedure employed to purify tubulin from mammalian brain. It consists of tissue homogenization, elimination of cell membranes, ammonium sulfate fractionation, and batch anion exchange, followed by selective precipitation with magnesium chloride. Half gram of electrophoretically homogenous, active, concentrated calf brain tubulin is typically purified in 9 h, dialyzed overnight, and stored under liquid nitrogen. Prior to use the protein is equilibrated in the experimental buffer and its concentration measured. This tubulin preparation has been very extensively characterized. Frozen aliquots have been found to retain microtubule assembly activity after 10 yr of storage.
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26
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Uchimura S, Oguchi Y, Katsuki M, Usui T, Osada H, Nikawa JI, Ishiwata S, Muto E. Identification of a strong binding site for kinesin on the microtubule using mutant analysis of tubulin. EMBO J 2006; 25:5932-41. [PMID: 17124495 PMCID: PMC1698889 DOI: 10.1038/sj.emboj.7601442] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Accepted: 10/23/2006] [Indexed: 11/09/2022] Open
Abstract
The kinesin-binding site on the microtubule has not been identified because of the technical difficulties involved in the mutant analyses of tubulin. Exploiting the budding yeast expression system, we succeeded in replacing the negatively charged residues in the alpha-helix 12 of beta-tubulin with alanine and analyzed their effect on kinesin-microtubule interaction in vitro. The microtubule gliding assay showed that the affinity of the microtubules for kinesin was significantly reduced in E410A, D417A, and E421A, but not in E412A mutant. The unbinding force measurement revealed that in the former three mutants, the kinesin-microtubule interaction in the adenosine 5'-[beta,gamma-imido]triphosphate state (AMP-PNP state) became less stable when a load was imposed towards the microtubule minus end. In parallel with this decreased stability, the stall force of kinesin was reduced. Our results implicate residues E410, D417, and E421 as crucial for the kinesin-microtubule interaction in the strong binding state, thereby governing the size of kinesin stall force.
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Affiliation(s)
- Seiichi Uchimura
- Brain Development Research Group, Brain Science Institute, RIKEN, Wako, Saitama, Japan
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka, Japan
| | - Yusuke Oguchi
- Department of Physics, School of Science and Engineering, Waseda University, Tokyo, Japan
| | - Miho Katsuki
- Brain Development Research Group, Brain Science Institute, RIKEN, Wako, Saitama, Japan
| | - Takeo Usui
- Antibiotics Laboratory, Discovery Research Institute, RIKEN, Wako, Saitama, Japan
| | - Hiroyuki Osada
- Antibiotics Laboratory, Discovery Research Institute, RIKEN, Wako, Saitama, Japan
| | - Jun-ichi Nikawa
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka, Japan
| | - Shin'ichi Ishiwata
- Department of Physics, School of Science and Engineering, Waseda University, Tokyo, Japan
- Advanced Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Etsuko Muto
- Brain Development Research Group, Brain Science Institute, RIKEN, Wako, Saitama, Japan
- Brain Development Research Group, Brain Science Institute, RIKEN, Hirosawa 2-1, Wako, Saitama 351-0198, Japan. Tel.: +81 48 467 6959; Fax: +81 48 467 7145; E-mail:
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27
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Affiliation(s)
- R G Burns
- Biophysics Section, Blackett Laboratory, Imperial College of Science, Technology and Medicine, London, UK SW7 2BZ
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28
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Tirnauer JS, Grego S, Salmon ED, Mitchison TJ. EB1-microtubule interactions in Xenopus egg extracts: role of EB1 in microtubule stabilization and mechanisms of targeting to microtubules. Mol Biol Cell 2003. [PMID: 12388761 DOI: 10.1091/mbc.e02-04-0210] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
EB1 targets to polymerizing microtubule ends, where it is favorably positioned to regulate microtubule polymerization and confer molecular recognition of the microtubule end. In this study, we focus on two aspects of the EB1-microtubule interaction: regulation of microtubule dynamics by EB1 and the mechanism of EB1 association with microtubules. Immunodepletion of EB1 from cytostatic factor-arrested M-phase Xenopus egg extracts dramatically reduced microtubule length; this was complemented by readdition of EB1. By time-lapse microscopy, EB1 increased the frequency of microtubule rescues and decreased catastrophes, resulting in increased polymerization and decreased depolymerization and pausing. Imaging of EB1 fluorescence revealed a novel structure: filamentous extensions on microtubule plus ends that appeared during microtubule pauses; loss of these extensions correlated with the abrupt onset of polymerization. Fluorescent EB1 localized to comets at the polymerizing plus ends of microtubules in cytostatic factor extracts and uniformly along the lengths of microtubules in interphase extracts. The temporal decay of EB1 fluorescence from polymerizing microtubule plus ends predicted a dissociation half-life of seconds. Fluorescence recovery after photobleaching also revealed dissociation and rebinding of EB1 to the microtubule wall with a similar half-life. EB1 targeting to microtubules is thus described by a combination of higher affinity binding to polymerizing ends and lower affinity binding along the wall, with continuous dissociation. The latter is likely to be attenuated in interphase. The highly conserved effect of EB1 on microtubule dynamics suggests it belongs to a core set of regulatory factors conserved in higher organisms, and the complex pattern of EB1 targeting to microtubules could be exploited by the cell for coordinating microtubule behaviors.
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Affiliation(s)
- Jennifer S Tirnauer
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
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29
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Lila T, Renau TE, Wilson L, Philips J, Natsoulis G, Cope MJ, Watkins WJ, Buysse J. Molecular basis for fungal selectivity of novel antimitotic compounds. Antimicrob Agents Chemother 2003; 47:2273-82. [PMID: 12821479 PMCID: PMC161869 DOI: 10.1128/aac.47.7.2273-2282.2003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Compounds that selectively disrupt fungal mitosis have proven to be effective in controlling agricultural pests, but no specific mitotic inhibitor is available for the treatment of systemic mycoses in mammalian hosts. In an effort to identify novel mitotic inhibitors, we used a cell-based screening strategy that exploited the hypersensitivity of a yeast alpha-tubulin mutant strain to growth inhibition by antimitotic agents. The compounds identified inhibited yeast nuclear division and included one structural class of compounds shown to be fungus specific. MC-305904 and structural analogs inhibited fungal cell mitosis and inhibited the in vitro polymerization of fungal tubulin but did not block mammalian cell microtubule function or mammalian tubulin polymerization. Extensive analysis of yeast mutations that specifically alter sensitivity to MC-305904 structural analogs suggested that compounds in the series bind to a site on fungal beta-tubulin near amino acid 198. Features of the proposed binding site explain the observed fungal tubulin specificity of the series and are consistent with structure-activity relationships among a library of related compounds.
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Affiliation(s)
- Thomas Lila
- Essential Therapeutics, Mountain View, California 94043, USA.
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30
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Gupta ML, Bode CJ, Georg GI, Himes RH. Understanding tubulin-Taxol interactions: mutations that impart Taxol binding to yeast tubulin. Proc Natl Acad Sci U S A 2003; 100:6394-7. [PMID: 12740436 PMCID: PMC164457 DOI: 10.1073/pnas.1131967100] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have successfully used mutagenesis to engineer Taxol (paclitaxel) binding activity in Saccharomyces cerevisiae tubulin. Taxol, a successful antitumor agent, acts by promoting tubulin assembly and stabilizing microtubules. Several structurally diverse antimitotic compounds, including the epothilones, compete with Taxol for binding to mammalian microtubules, suggesting that Taxol and these compounds share an overlapping binding site. However, Taxol has no effect on tubulin or microtubules from S. cerevisiae, whereas epothilone does. After considering data on Taxol binding to mammalian tubulin and recent modeling studies, we have hypothesized that differences in five key amino acids are responsible for the lack of Taxol binding to yeast tubulin. After changing these amino acids to those found in mammalian brain tubulin, we observed Taxol-related activity in yeast tubulin comparable to that in mammalian tubulin. Importantly, this experimental system can be used to reveal tubulin interactions with Taxol, the epothilones, and other Taxol-like compounds.
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Affiliation(s)
- Mohan L Gupta
- Department of Molecular Biosciences, University of Kansas, Lawrence 66045, USA
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31
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Bode CJ, Gupta ML, Suprenant KA, Himes RH. The two alpha-tubulin isotypes in budding yeast have opposing effects on microtubule dynamics in vitro. EMBO Rep 2003; 4:94-9. [PMID: 12524528 PMCID: PMC1315816 DOI: 10.1038/sj.embor.embor716] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2002] [Revised: 10/25/2002] [Accepted: 11/08/2002] [Indexed: 11/08/2022] Open
Abstract
The yeast Saccharomyces cerevisiae has two genes for alpha-tubulin, TUB1 and TUB3, and one beta-tubulin gene, TUB2. The gene product of TUB3, Tub3, represents approximately 10% of alpha-tubulin in the cell. We determined the effects of the two alpha-tubulin isotypes on microtubule dynamics in vitro. Tubulin was purified from wild-type and deletion strains lacking either Tub1 or Tub3, and parameters of microtubule dynamics were examined. Microtubules containing Tub3 as the only alpha-tubulin isotype were less dynamic than wild-type microtubules, as shown by a shrinkage rate and catastrophe frequency that were about one-third of that for wild-type microtubules. Conversely, microtubules containing Tub1 as the only alpha-tubulin isotype were more dynamic than wild-type microtubules, as shown by a shrinkage rate that was 50% higher and a catastrophe frequency that was 30% higher than those of wild-type microtubules. The results suggest that a role of Tub3 in budding yeast is to control microtubule dynamics.
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Affiliation(s)
- Claudia J. Bode
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Mohan L. Gupta
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Kathy A. Suprenant
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Richard H. Himes
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
- Tel: +1 785 864 3813; Fax: +1 785 864 5321;
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32
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Newton CN, DeLuca JG, Himes RH, Miller HP, Jordan MA, Wilson L. Intrinsically slow dynamic instability of HeLa cell microtubules in vitro. J Biol Chem 2002; 277:42456-62. [PMID: 12207023 DOI: 10.1074/jbc.m207134200] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The dynamic behavior of mammalian microtubules has been extensively studied, both in living cells and with microtubules assembled from purified brain tubulin. To understand the intrinsic dynamic behavior of mammalian nonneural microtubules, we purified tubulin from cultured HeLa cells. We find that HeLa cell microtubules exhibit remarkably slow dynamic instability, spending most of their time in an attenuated state. The tempered dynamics contrast sharply with the dynamics of microtubules prepared from purified bovine brain tubulin under similar conditions. In accord with their minimal dynamic instability, assembled HeLa cell microtubules displayed a slow treadmilling rate and a low guanosine-5'-triphosphate hydrolysis rate at steady state. We find that unlike brain tubulin, which consists of a heterogeneous mixture of beta-tubulin isotypes (beta(II), beta(III), and beta(IV) and a low level of beta(I)), HeLa cell tubulin consists of beta(I) tubulin ( approximately 80%) and a minor amount of beta(IV) tubulin ( approximately 20%). The slow dynamic behavior of HeLa cell microtubules in vitro differs strikingly from the dynamic behavior of microtubules in living cultured mammalian cells, supporting the idea that accessory factors create the robust dynamics that occur in cells.
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Affiliation(s)
- Cori N Newton
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106, USA.
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33
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Tirnauer JS, Grego S, Salmon ED, Mitchison TJ. EB1-microtubule interactions in Xenopus egg extracts: role of EB1 in microtubule stabilization and mechanisms of targeting to microtubules. Mol Biol Cell 2002; 13:3614-26. [PMID: 12388761 PMCID: PMC129970 DOI: 10.1091/mbc.02-04-0210] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
EB1 targets to polymerizing microtubule ends, where it is favorably positioned to regulate microtubule polymerization and confer molecular recognition of the microtubule end. In this study, we focus on two aspects of the EB1-microtubule interaction: regulation of microtubule dynamics by EB1 and the mechanism of EB1 association with microtubules. Immunodepletion of EB1 from cytostatic factor-arrested M-phase Xenopus egg extracts dramatically reduced microtubule length; this was complemented by readdition of EB1. By time-lapse microscopy, EB1 increased the frequency of microtubule rescues and decreased catastrophes, resulting in increased polymerization and decreased depolymerization and pausing. Imaging of EB1 fluorescence revealed a novel structure: filamentous extensions on microtubule plus ends that appeared during microtubule pauses; loss of these extensions correlated with the abrupt onset of polymerization. Fluorescent EB1 localized to comets at the polymerizing plus ends of microtubules in cytostatic factor extracts and uniformly along the lengths of microtubules in interphase extracts. The temporal decay of EB1 fluorescence from polymerizing microtubule plus ends predicted a dissociation half-life of seconds. Fluorescence recovery after photobleaching also revealed dissociation and rebinding of EB1 to the microtubule wall with a similar half-life. EB1 targeting to microtubules is thus described by a combination of higher affinity binding to polymerizing ends and lower affinity binding along the wall, with continuous dissociation. The latter is likely to be attenuated in interphase. The highly conserved effect of EB1 on microtubule dynamics suggests it belongs to a core set of regulatory factors conserved in higher organisms, and the complex pattern of EB1 targeting to microtubules could be exploited by the cell for coordinating microtubule behaviors.
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Affiliation(s)
- Jennifer S Tirnauer
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
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34
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Gupta ML, Bode CJ, Thrower DA, Pearson CG, Suprenant KA, Bloom KS, Himes RH. beta-Tubulin C354 mutations that severely decrease microtubule dynamics do not prevent nuclear migration in yeast. Mol Biol Cell 2002; 13:2919-32. [PMID: 12181356 PMCID: PMC117952 DOI: 10.1091/mbc.e02-01-0003] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Microtubule dynamics are influenced by interactions of microtubules with cellular factors and by changes in the primary sequence of the tubulin molecule. Mutations of yeast beta-tubulin C354, which is located near the binding site of some antimitotic compounds, reduce microtubule dynamicity greater than 90% in vivo and in vitro. The resulting intrinsically stable microtubules allowed us to determine which, if any, cellular processes are dependent on dynamic microtubules. The average number of cytoplasmic microtubules decreased from 3 in wild-type to 1 in mutant cells. The single microtubule effectively located the bud site before bud emergence. Although spindles were positioned near the bud neck at the onset of anaphase, the mutant cells were deficient in preanaphase spindle alignment along the mother-bud axis. Spindle microtubule dynamics and spindle elongation rates were also severely depressed in the mutants. The pattern and extent of cytoplasmic microtubule dynamics modulation through the cell cycle may reveal the minimum dynamic properties required to support growth. The ability to alter intrinsic microtubule dynamics and determine the in vivo phenotype of cells expressing the mutant tubulin provides a critical advance in assessing the dynamic requirements of an essential gene function.
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Affiliation(s)
- Mohan L Gupta
- Department of Molecular Biosciences, University of Kansas, Lawrence 66045, USA
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35
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Bode CJ, Gupta ML, Reiff EA, Suprenant KA, Georg GI, Himes RH. Epothilone and paclitaxel: unexpected differences in promoting the assembly and stabilization of yeast microtubules. Biochemistry 2002; 41:3870-4. [PMID: 11900528 DOI: 10.1021/bi0121611] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Paclitaxel (Taxol) and the epothilones are antimitotic agents that promote the assembly of mammalian tubulin and stabilization of microtubules. The epothilones competitively inhibit the binding of paclitaxel to mammalian brain tubulin, suggesting that the two types of compounds share a common binding site in tubulin, despite the lack of structural similarities. It is known that paclitaxel does not stabilize microtubules formed in vitro from Saccharomyces cerevisiae tubulin; thus, it would be expected that the epothilones would not affect yeast microtubules. However, we found that epothilone A and B do stimulate the formation of microtubules from purified yeast tubulin. In addition, epothilone B severely dampens the dynamics of yeast microtubules in vitro in a manner similar to the effect of paclitaxel on mammalian microtubules. We used current models describing paclitaxel and epothilone binding to mammalian beta-tubulin to explain why paclitaxel apparently fails to bind to yeast tubulin. We propose that three amino acid substitutions in the N-terminal region and at position 227 in yeast beta-tubulin weaken the interaction of the 3'-benzamido group of paclitaxel with the protein. These results also indicate that mutagenesis of yeast tubulin could help define the sites of interaction with paclitaxel and the epothilones.
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Affiliation(s)
- Claudia J Bode
- Department of Molecular Biosciences and the Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
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36
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Dougherty CA, Sage CR, Davis A, Farrell KW. Mutation in the beta-tubulin signature motif suppresses microtubule GTPase activity and dynamics, and slows mitosis. Biochemistry 2001; 40:15725-32. [PMID: 11747449 DOI: 10.1021/bi010070y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We introduced a threonine-to-glycine point mutation at position 143 in the "tubulin signature motif" 140Gly-Gly-Gly-Thr-Gly-Ser-Gly146 of Saccharomyces cerevisiae beta-tubulin. In an electron diffraction model of the tubulin dimer, this sequence comes close to the phosphates of a guanine nucleotide bound in the beta-tubulin exchangeable E site. Both the GTP-binding affinity and the microtubule (MT)-dependent GTPase activity of tubulin isolated from haploid tub2-T143G mutant cells were reduced by at least 15-fold, compared to tubulin isolated from control wild-type cells. The growing and shortening dynamics of MTs assembled from alphabeta:Thr143Gly-mutated dimers were also strongly suppressed, compared to control MTs. The in vitro properties of the mutated MTs (slower growing and more stable) are consistent with the effects of the tub2-T143G mutation in haploid cells. The average length of MT spindles in large-budded mutant cells was only 3.7 +/- 0.2 microm, approximately half of the size of MT arrays in large-budded wild-type cells (average length = 7.1 +/- 0.4 microm), suggesting that there is a delay in mitosis in the mutant cells. There was also a higher proportion of large-budded cells with unsegregated nuclei in mutant cultures (30% versus 12% for wild-type cells), again suggesting such a delay. The results show that beta:Thr143 of the tubulin signature motif plays an important role in GTP binding and hydrolysis by the beta-tubulin E site and support the idea that tubulins belong to a family of proteins within the GTPase superfamily that are structurally distinct from the classic GTPases, such as EF-Tu and p21(ras). The data also suggest that MT dynamics are critical for MT function in yeast cells and that spindle MT assembly and disassembly could be coordinated with other cell-cycle events by regulating beta-tubulin GTPase activity.
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Affiliation(s)
- C A Dougherty
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, USA
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37
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Kosco KA, Pearson CG, Maddox PS, Wang PJ, Adams IR, Salmon ED, Bloom K, Huffaker TC. Control of microtubule dynamics by Stu2p is essential for spindle orientation and metaphase chromosome alignment in yeast. Mol Biol Cell 2001; 12:2870-80. [PMID: 11553724 PMCID: PMC59720 DOI: 10.1091/mbc.12.9.2870] [Citation(s) in RCA: 139] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Stu2p is a member of a conserved family of microtubule-binding proteins and an essential protein in yeast. Here, we report the first in vivo analysis of microtubule dynamics in cells lacking a member of this protein family. For these studies, we have used a conditional Stu2p depletion strain expressing alpha-tubulin fused to green fluorescent protein. Depletion of Stu2p leads to fewer and less dynamic cytoplasmic microtubules in both G1 and preanaphase cells. The reduction in cytoplasmic microtubule dynamics is due primarily to decreases in both the catastrophe and rescue frequencies and an increase in the fraction of time microtubules spend pausing. These changes have significant consequences for the cell because they impede the ability of cytoplasmic microtubules to orient the spindle. In addition, recovery of fluorescence after photobleaching indicates that kinetochore microtubules are no longer dynamic in the absence of Stu2p. This deficiency is correlated with a failure to properly align chromosomes at metaphase. Overall, we provide evidence that Stu2p promotes the dynamics of microtubule plus-ends in vivo and that these dynamics are critical for microtubule interactions with kinetochores and cortical sites in the cytoplasm.
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Affiliation(s)
- K A Kosco
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
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38
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Shah C, Xu CZ, Vickers J, Williams R. Properties of microtubules assembled from mammalian tubulin synthesized in Escherichia coli. Biochemistry 2001; 40:4844-52. [PMID: 11294652 DOI: 10.1021/bi002446y] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
When isolated from tissues, the alpha beta-dimeric protein tubulin consists of multiple isoforms which originate from the expression and subsequent posttranslational modification of multiple polypeptide sequences. Microtubules studied in vitro consist of mixtures of these isoforms. It is therefore not known whether dimers composed of single sequences of alpha- and beta-tubulin can polymerize to form microtubules, or whether posttranslational modifications may be necessary for microtubule assembly. To initiate investigation of these questions, rabbit reticulocyte lysate, which contains the cytoplasmic chaperonin CCT and its cofactors, was employed to prepare substantial quantities (tens of micrograms) of active tubulin by in vitro folding of mouse alpha- and beta-tubulins recombinantly synthesized in E. coli. This recombinant tubulin is composed of only a single alpha-chain and a single beta-chain. When analyzed after folding by isoelectric focusing, each chain yielded only one band, indicating that neither was detectably posttranslationally modified in the course of the folding reaction. When subjected to assembly-promoting conditions, this tubulin formed microtubules without the addition of any exogenous protein. Electron microscopy showed them to be of normal morphology. Analysis of their protein composition showed that they are composed nearly entirely of recombinant tubulin. These results demonstrate that the naturally occurring mixtures of isoforms are not strictly required for the formation of microtubules. They also open a route to other studies, both biomedical and structural, of fully defined tubulin in vitro.
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Affiliation(s)
- C Shah
- Department of Biological Sciences, VU Station B 351634, Vanderbilt University, Nashville, Tennessee 37235-1634, USA
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39
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Sossong TM, Brigham-Burke MR, Hensley P, Pearce KH. Self-activation of guanosine triphosphatase activity by oligomerization of the bacterial cell division protein FtsZ. Biochemistry 1999; 38:14843-50. [PMID: 10555966 DOI: 10.1021/bi990917e] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The essential bacterial cell division protein FtsZ (filamentation temperature-sensitive protein Z) is a distant homologue to the eukaryotic cytoskeletal protein tubulin. We have examined the GTP hydrolytic activity of Escherichia coli FtsZ using a real-time fluorescence assay that monitors phosphate production. The GTPase activity shows a dramatic, nonlinear dependence on FtsZ concentration, with activity only observed at enzyme concentrations greater than 1 microM. At 5 microM FtsZ, we have determined a K(m) of 82 microM GTP and a V(max) of 490 nmol of P(i) min(-1) (mg of protein)(-1). Hydrolysis of GTP requires Mg(2+) and other divalent cations substitute only poorly for this requirement. We have compared the concentration dependence of FtsZ GTPase activity with the oligomeric state by use of analytical ultracentrifugation and chemical cross-linking. Equilibrium analytical ultracentrifugation experiments show that FtsZ exists as 68% dimer and 13% trimer at 2 microM total protein concentration. Chemical cross-linking of FtsZ also shows that monomer, dimer, trimer, and tetramer species are present at higher (>2 microM) FtsZ concentrations. However, as shown by analytical centrifugation, GDP-bound FtsZ is significantly shifted to the monomeric state, which suggests that GTP hydrolysis regulates polymer destabilization. We also monitored the effect of nucleotide and metal ion on the secondary structure of FtsZ; nucleotide yielded no evidence of structural changes in FtsZ, but both Mg(2+) and Ca(2+) had significant effects on secondary structure. Taken together, our results support the hypothesis that Mg(2+)-dependent GTP hydrolysis by FtsZ requires oligomerization of FtsZ. On the basis of these results and structural comparisons with the alpha-beta tubulin dimer, GTP is likely hydrolyzed in a shared active site formed between two monomer subunits.
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Affiliation(s)
- T M Sossong
- Department of Anti-Infectives Research, SmithKline Beecham Pharmaceuticals, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, USA.
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Tirnauer JS, O'Toole E, Berrueta L, Bierer BE, Pellman D. Yeast Bim1p promotes the G1-specific dynamics of microtubules. J Biophys Biochem Cytol 1999; 145:993-1007. [PMID: 10352017 PMCID: PMC2133138 DOI: 10.1083/jcb.145.5.993] [Citation(s) in RCA: 210] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Microtubule dynamics vary during the cell cycle, and microtubules appear to be more dynamic in vivo than in vitro. Proteins that promote dynamic instability are therefore central to microtubule behavior in living cells. Here, we report that a yeast protein of the highly conserved EB1 family, Bim1p, promotes cytoplasmic microtubule dynamics specifically during G1. During G1, microtubules in cells lacking BIM1 showed reduced dynamicity due to a slower shrinkage rate, fewer rescues and catastrophes, and more time spent in an attenuated/paused state. Human EB1 was identified as an interacting partner for the adenomatous polyposis coli (APC) tumor suppressor protein. Like human EB1, Bim1p localizes to dots at the distal ends of cytoplasmic microtubules. This localization, together with data from electron microscopy and a synthetic interaction with the gene encoding the kinesin Kar3p, suggests that Bim1p acts at the microtubule plus end. Our in vivo data provide evidence of a cell cycle-specific microtubule-binding protein that promotes microtubule dynamicity.
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Affiliation(s)
- J S Tirnauer
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
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41
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Mukherjee A, Lutkenhaus J. Analysis of FtsZ assembly by light scattering and determination of the role of divalent metal cations. J Bacteriol 1999; 181:823-32. [PMID: 9922245 PMCID: PMC93448 DOI: 10.1128/jb.181.3.823-832.1999] [Citation(s) in RCA: 219] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
FtsZ is an ancestral homologue of tubulin that polymerizes in a GTP-dependent manner. In this study, we used 90 degrees angle light scattering to investigate FtsZ polymerization. The critical concentration for polymerization obtained by this method is similar to that obtained by centrifugation, confirming that the light scattering is proportional to polymer mass. Furthermore, the dynamics of FtsZ polymerization could be readily monitored by light scattering. Polymerization was very rapid, reaching steady state within 30 s. The length of the steady-state phase was proportional to the GTP concentration and was followed by a rapid decrease in light scattering. This decrease indicated net depolymerization that always occurred as the GTP in the reaction was consumed. FtsZ polymerization was observed over the pH range 6.5 to 7.9. Importantly, Mg2+ was not required for polymerization although it was required for the dynamic behavior of the polymers. It was reported that 7 to 25 mM Ca2+ mediated dynamic assembly of FtsZ (X. -C. Yu and W. Margolin, EMBO J. 16:5455-5463, 1997). However, we found that Ca2+ was not required for FtsZ assembly and that this concentration of Ca2+ reduced the dynamic behavior of FtsZ assembly.
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Affiliation(s)
- A Mukherjee
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
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Dougherty CA, Himes RH, Wilson L, Farrell KW. Detection of GTP and Pi in wild-type and mutated yeast microtubules: implications for the role of the GTP/GDP-Pi cap in microtubule dynamics. Biochemistry 1998; 37:10861-5. [PMID: 9692978 DOI: 10.1021/bi980677n] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Microtubule dynamics are believed to be controlled by a stabilizing cap of tubulin dimers at microtubule ends that contain either GTP or GDP and Pi in the exchangeable nucleotide site (E-site) of the beta-subunit. However, it has been difficult to obtain convincing evidence to support this hypothesis because the quantity of GTP and Pi in the E-site of assembled brain tubulin (the tubulin used in most studies thus far) is extremely low. In this study, we have measured the amount of GTP and Pi in the E-site of wild-type and mutated yeast assembled tubulins. In contrast to brain microtubules, 6% of the tubulin in a wild-type yeast microtubule contains a combination of E-site GTP and Pi. This result indicates that GTP hydrolysis and Pi release are not coupled to dimer addition to the end of the microtubule and supports the hypothesis that microtubules contain a cap of tubulin dimers with GTP or Pi in their E-sites. In addition, we have measured the E-site content of GTP and Pi in microtubules assembled from two yeast tubulins that had been mutated at residues T107 and T143 in beta-tubulin, sites thought to interact with the nucleotide bound in the E-site. Previous studies have shown that microtubules containing these mutated tubulins have modified dynamic behavior in vitro. The results from these experiments indicate that the GTP or GDP-Pi cap model does not adequately explain yeast microtubule dynamic behavior.
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Affiliation(s)
- C A Dougherty
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara 93106, USA.
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Affiliation(s)
- T I Lee
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA.
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Mick GJ, Chun KY, VanderBloomer TL, Fu CL, McCormick KL. Inhibition of acetyl CoA carboxylase by GTP gamma S. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1384:130-40. [PMID: 9602094 DOI: 10.1016/s0167-4838(98)00007-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The effect of nonhydrolyzable guanine nucleotides on mammalian acetyl CoA carboxylase (ACC) activity was examined. Using porous rat adipocytes and crude fat cell homogenates to study metabolic pathway flux, GMPPNP and/or GTP gamma S inhibited [14C]fatty acid formation by up to 95% when either [6-14C]glucose-6-phosphate or [1-14C]acetyl CoA was used as substrate. If [2-14C]malonyl CoA initiated flux, however, no inhibition was apparent. These pathway flux studies suggested that ACC was the locus of inhibition, and that the mechanism might involve a disruption of guanine nucleotide hydrolysis by the nonhydrolyzable analogues. Using partially and avidin-sepharose-purified ACC preparations from rat fat, liver and mammary tissue, citrate-stimulated ACC activity was inhibited by 25-75% with 50 microM GTP gamma S. Related compounds and nucleotides had absent-to-minimal effects on ACC. ATP gamma S was inhibitory (10-30% at 5-15 microM), but always to a lesser degree than equimolar GTP gamma S. Filter binding assays with [alpha-32P]GTP or [35S]GTP gamma S were negative, but low-level GTPase activity was detected. Using photoaffinity labelling techniques, [alpha-32P]GTP was found to bind ACC and not pyruvate carboxylase. The hypothesis that citrate-responsive ACC activity may be modulated by an intrinsic or associated GTP binding site is explored. Since ACC forms polymers, as does the cytoskeletal protein beta-tubulin, amino acid sequence comparisons between ACC and atypical GTP binding domain of beta tubulin are presented.
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Affiliation(s)
- G J Mick
- Dept of Pediatrics, Medical College of Wisconsin, Milwaukee 53226, USA.
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Xu S, Gaskin F. Probing the ATP binding site of tubulin with thiotriphosphate analogues of ATP. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1383:111-22. [PMID: 9546052 DOI: 10.1016/s0167-4838(97)00193-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Tubulin assembly studies with GTP alpha S diastereoisomers have shown that there is stereoselectivity at the alpha-phosphate binding region of tubulin. GTP alpha S(Sp) bound tighter than GTP alpha S(Rp) and promoted nucleation and assembly better than GTP and GTP alpha S(Rp). ATP and dATP have been reported to bind weakly to tubulin and to be less effective than GTP and dGTP in promoting tubulin assembly. This study was done to learn if ATP alpha S(Sp) and dATP alpha S(Sp) are good promoters of tubulin assembly and to compare these ATP thiotriphosphate analogues to the corresponding GTP analogues in tubulin assembly. Studies were also done with ATP alpha S(Rp), GTP, ATP beta S(Sp) and ATP gamma S. At least three cycles of tubulin (25 microM) assembly-disassembly were found with 1 mM ATP alpha S(Sp) and dATP alpha S(Sp) and both nucleotides were incorporated and hydrolyzed in the polymers. Less dATP alpha S(Sp) (25 microM) than ATP alpha S(Sp) (100 microM) promoted assembly to 50% of the maximum value. The critical concentrations (Cc) for assembly with 1 mM nucleotide were low for ATP alpha S(Sp) (3 microM) and dATP alpha S(Sp) (2 microM) and compared favorably with GTP (5 microM), GTP alpha S(Sp) (2 microM) and dGTP alpha S(Sp) (1 microM). Both 1 mM ATP and dATP were poor promoters of tubulin assembly and were not detected in the polymers. The predominant structures induced by 1 mM (ATP alpha S(Sp) and dATP alpha S(Sp) were bundles of sheets and microtubules, which were more stable to the cold and to Ca(II) than microtubules assembled with GTP, ATP or dATP. ATP alpha S(Rp) (1 mM) did not promote assembly suggesting that there is stereoselectivity at the ATP alpha S alpha-phosphate binding region of tubulin as there is with GTP alpha S diastereoisomers. ATP alpha S(Sp) and dATP alpha S(Sp) mimic GTP alpha S(Sp) and dGTP alpha S(Sp) in tubulin assembly since all four nucleotides promote bundles of tubulin in buffer with glycerol, and the deoxy nucleotides have lower Cc, shorter lags and faster rates for tubulin assembly.
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Affiliation(s)
- S Xu
- Department of Psychiatric Medicine, University of Virginia School of Medicine, Charlottesville 22908, USA
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46
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Abstract
FtsZ forms a cytokinetic ring, designated the Z ring, that directs cytokinesis in prokaryotes. It has limited sequence similarity to eukaryotic tubulins and, like tubulin, it has GTPase activity and the ability to assemble into various structures including protofilaments, bundles and minirings. By using both electron microscopy and sedimentation, we demonstrate that FtsZ from Escherichia coli undergoes a strictly GTP-dependent polymerization and the polymers disappear as the GTP is consumed. Thus, FtsZ polymerization, like that of tubulin, is dynamic and regulated by GTP hydrolysis. These results provide the basis for the dynamics of the Z ring and favor a model in which the Z ring is formed by a nucleation event.
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Affiliation(s)
- A Mukherjee
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City 66160, USA
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Linder S, Schliwa M, Kube-Granderath E. Expression of Reticulomyxa filosa tubulins in Pichia pastoris: regulation of tubulin pools. FEBS Lett 1997; 417:33-7. [PMID: 9395069 DOI: 10.1016/s0014-5793(97)01250-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We expressed the alpha2- and beta2-tubulin isoforms of the giant freshwater amoeba Reticulomyxa filosa in the methylotrophic yeast Pichia pastoris. Single expression lead to little or no detectable material. Coexpression of both tubulins, however, resulted in a significant increase of expressed proteins. At the same time, the detectable internal tubulins of the host yeast cell were downregulated. This finding indicates the functionality of the expressed amoeba tubulins. Further regulation phenomena were observed on the level of equilibrium between the two R. filosa tubulin isoforms and on the level of the total tubulin pool. The P. pastoris/R. filosa system therefore seems to be an accessible system for the simultaneous study of the various mechanisms involved in tubulin regulation.
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Affiliation(s)
- S Linder
- Adolf-Butenandt-Institut für Zellbiologie, München, Germany.
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48
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Carminati JL, Stearns T. Microtubules orient the mitotic spindle in yeast through dynein-dependent interactions with the cell cortex. J Biophys Biochem Cytol 1997; 138:629-41. [PMID: 9245791 PMCID: PMC2141630 DOI: 10.1083/jcb.138.3.629] [Citation(s) in RCA: 409] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Proper orientation of the mitotic spindle is critical for successful cell division in budding yeast. To investigate the mechanism of spindle orientation, we used a green fluorescent protein (GFP)-tubulin fusion protein to observe microtubules in living yeast cells. GFP-tubulin is incorporated into microtubules, allowing visualization of both cytoplasmic and spindle microtubules, and does not interfere with normal microtubule function. Microtubules in yeast cells exhibit dynamic instability, although they grow and shrink more slowly than microtubules in animal cells. The dynamic properties of yeast microtubules are modulated during the cell cycle. The behavior of cytoplasmic microtubules revealed distinct interactions with the cell cortex that result in associated spindle movement and orientation. Dynein-mutant cells had defects in these cortical interactions, resulting in misoriented spindles. In addition, microtubule dynamics were altered in the absence of dynein. These results indicate that microtubules and dynein interact to produce dynamic cortical interactions, and that these interactions result in the force driving spindle orientation.
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Affiliation(s)
- J L Carminati
- Department of Biological Sciences, Stanford University, Stanford, California 94305-5020, USA
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Goode BL, Denis PE, Panda D, Radeke MJ, Miller HP, Wilson L, Feinstein SC. Functional interactions between the proline-rich and repeat regions of tau enhance microtubule binding and assembly. Mol Biol Cell 1997; 8:353-65. [PMID: 9190213 PMCID: PMC276085 DOI: 10.1091/mbc.8.2.353] [Citation(s) in RCA: 210] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Tau is a neuronal microtubule-associated protein that promotes microtubule assembly, stability, and bundling in axons. Two distinct regions of tau are important for the tau-microtubule interaction, a relatively well-characterized "repeat region" in the carboxyl terminus (containing either three or four imperfect 18-amino acid repeats separated by 13- or 14-amino acid long inter-repeats) and a more centrally located, relatively poorly characterized proline-rich region. By using amino-terminal truncation analyses of tau, we have localized the microtubule binding activity of the proline-rich region to Lys215-Asn246 and identified a small sequence within this region, 215KKVAVVR221, that exerts a strong influence on microtubule binding and assembly in both three- and four-repeat tau isoforms. Site-directed mutagenesis experiments indicate that these capabilities are derived largely from Lys215/Lys216 and Arg221. In marked contrast to synthetic peptides corresponding to the repeat region, peptides corresponding to Lys215-Asn246 and Lys215-Thr222 alone possess little or no ability to promote microtubule assembly, and the peptide Lys215-Thr222 does not effectively suppress in vitro microtubule dynamics. However, combining the proline-rich region sequences (Lys215-Asn246) with their adjacent repeat region sequences within a single peptide (Lys215-Lys272) enhances microtubule assembly by 10-fold, suggesting intramolecular interactions between the proline-rich and repeat regions. Structural complexity in this region of tau also is suggested by sequential amino-terminal deletions through the proline-rich and repeat regions, which reveal an unusual pattern of loss and gain of function. Thus, these data lead to a model in which efficient microtubule binding and assembly activities by tau require intramolecular interactions between its repeat and proline-rich regions. This model, invoking structural complexity for the microtubule-bound conformation of tau, is fundamentally different from previous models of tau structure and function, which viewed tau as a simple linear array of independently acting tubulin-binding sites.
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Affiliation(s)
- B L Goode
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara 93106, USA
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50
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Machin NA, Lee JM, Chamany K, Barnes G. Dosage suppressors of a benomyl-dependent tubulin mutant: evidence for a link between microtubule stability and cellular metabolism. Genetics 1996; 144:1363-73. [PMID: 8978026 PMCID: PMC1207690 DOI: 10.1093/genetics/144.4.1363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
To identify factors important for the regulation of microtubule stability in yeast, dosage suppressors of the hyperstable microtubule phenotype of the budding yeast tub2-150 beta-tubulin mutation were isolated. Of the two suppressors reported here, one (JSN2) encodes a tRNAVal, and the other (JSN3) is an antimorphic allele of the methionine biosynthesis transcription factor Met4p. Furthermore, growth of tub2-150 mutants and suppression of tub2-150 mutants by JSN3 are sensitive to levels of methionine in the growth medium. We explore several possible explanations for these findings, including the potential involvement of the general amino acid control and the involvement of Cbflp, a component of yeast kinetochores that is also necessary for Met4p-mediated transcription.
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Affiliation(s)
- N A Machin
- Department of Molecular and Cell Biology, University of California, Berkeley, USA
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