1
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Marunaka Y. Physiological roles of chloride ions in bodily and cellular functions. J Physiol Sci 2023; 73:31. [PMID: 37968609 PMCID: PMC10717538 DOI: 10.1186/s12576-023-00889-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/31/2023] [Indexed: 11/17/2023]
Abstract
Physiological roles of Cl-, a major anion in the body, are not well known compared with those of cations. This review article introduces: (1) roles of Cl- in bodily and cellular functions; (2) the range of cytosolic Cl- concentration ([Cl-]c); (3) whether [Cl-]c could change with cell volume change under an isosmotic condition; (4) whether [Cl-]c could change under conditions where multiple Cl- transporters and channels contribute to Cl- influx and efflux in an isosmotic state; (5) whether the change in [Cl-]c could be large enough to act as signals; (6) effects of Cl- on cytoskeletal tubulin polymerization through inhibition of GTPase activity and tubulin polymerization-dependent biological activity; (7) roles of cytosolic Cl- in cell proliferation; (8) Cl--regulatory mechanisms of ciliary motility; (9) roles of Cl- in sweet/umami taste receptors; (10) Cl--regulatory mechanisms of with-no-lysine kinase (WNK); (11) roles of Cl- in regulation of epithelial Na+ transport; (12) relationship between roles of Cl- and H+ in body functions.
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Affiliation(s)
- Yoshinori Marunaka
- Medical Research Institute, Kyoto Industrial Health Association, General Incorporated Foundation, 67 Kitatsuboi-Cho, Nishinokyo, Nakagyo-Ku, Kyoto, 604-8472, Japan.
- Research Organization of Science and Technology, Ritsumeikan University, Kusatsu, 525-8577, Japan.
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-Ku, Kyoto, 602-8566, Japan.
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2
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Beckett D, Voth GA. Unveiling the Catalytic Mechanism of GTP Hydrolysis in Microtubules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.01.538927. [PMID: 37205601 PMCID: PMC10187240 DOI: 10.1101/2023.05.01.538927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Microtubules (MTs) are large cytoskeletal polymers, composed of αβ-tubulin heterodimers, capable of stochastically converting from polymerizing to depolymerizing states and vice-versa. Depolymerization is coupled with hydrolysis of GTP within β-tubulin. Hydrolysis is favored in the MT lattice compared to free heterodimer with an experimentally observed rate increase of 500 to 700 fold, corresponding to an energetic barrier lowering of 3.8 to 4.0 kcal/mol. Mutagenesis studies have implicated α-tubulin residues, α:E254 and α:D251, as catalytic residues completing the β-tubulin active site of the lower heterodimer in the MT lattice. The mechanism for GTP hydrolysis in the free heterodimer, however, is not understood. Additionally, there has been debate concerning whether the GTP-state lattice is expanded or compacted relative to the GDP-state and whether a "compacted" GDP-state lattice is required for hydrolysis. In this work, extensive QM/MM simulations with transition-tempered metadynamics free energy sampling of compacted and expanded inter-dimer complexes, as well as free heterodimer, have been carried out to provide clear insight into the GTP hydrolysis mechanism. α:E254 was found to be the catalytic residue in a compacted lattice, while in the expanded lattice disruption of a key salt bridge interaction renders α:E254 less effective. The simulations reveal a barrier decrease of 3.8 ± 0.5 kcal/mol for the compacted lattice compared to free heterodimer, in good agreement with experimental kinetic measurements. Additionally, the expanded lattice barrier was found to be 6.3 ± 0.5 kcal/mol higher than compacted, demonstrating that GTP hydrolysis is variable with lattice state and slower at the MT tip. Significance Statement Microtubules (MTs) are large and dynamic components of the eukaryotic cytoskeleton with the ability to stochastically convert from a polymerizing to a depolymerizing state and vice-versa. Depolymerization is coupled to the hydrolysis of guanosine-5'-triphosphate (GTP), which is orders of magnitude faster in the MT lattice than in free tubulin heterodimers. Our results computationally ascertain the catalytic residue contacts in the MT lattice that accelerate GTP hydrolysis compared to the free heterodimer as well as confirm that a compacted MT lattice is necessary for hydrolysis while a more expanded lattice is unable to form the necessary contacts and thereby hydrolyze GTP.
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3
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Morrissette N, Abbaali I, Ramakrishnan C, Hehl AB. The Tubulin Superfamily in Apicomplexan Parasites. Microorganisms 2023; 11:microorganisms11030706. [PMID: 36985278 PMCID: PMC10056924 DOI: 10.3390/microorganisms11030706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
Microtubules and specialized microtubule-containing structures are assembled from tubulins, an ancient superfamily of essential eukaryotic proteins. Here, we use bioinformatic approaches to analyze features of tubulins in organisms from the phylum Apicomplexa. Apicomplexans are protozoan parasites that cause a variety of human and animal infectious diseases. Individual species harbor one to four genes each for α- and β-tubulin isotypes. These may specify highly similar proteins, suggesting functional redundancy, or exhibit key differences, consistent with specialized roles. Some, but not all apicomplexans harbor genes for δ- and ε-tubulins, which are found in organisms that construct appendage-containing basal bodies. Critical roles for apicomplexan δ- and ε-tubulin are likely to be limited to microgametes, consistent with a restricted requirement for flagella in a single developmental stage. Sequence divergence or the loss of δ- and ε-tubulin genes in other apicomplexans appears to be associated with diminished requirements for centrioles, basal bodies, and axonemes. Finally, because spindle microtubules and flagellar structures have been proposed as targets for anti-parasitic therapies and transmission-blocking strategies, we discuss these ideas in the context of tubulin-based structures and tubulin superfamily properties.
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Affiliation(s)
- Naomi Morrissette
- Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA
- Correspondence: ; Tel.: +1-949-824-9243
| | - Izra Abbaali
- Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Chandra Ramakrishnan
- Institute for Parasitology, University of Zurich, Winterthurerstrasse 266a, 8057 Zürich, Switzerland
| | - Adrian B. Hehl
- Institute for Parasitology, University of Zurich, Winterthurerstrasse 266a, 8057 Zürich, Switzerland
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4
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Wethekam LC, Moore JK. Tubulin isotype regulation maintains asymmetric requirement for α-tubulin over β-tubulin. J Cell Biol 2023; 222:e202202102. [PMID: 36719400 PMCID: PMC9930134 DOI: 10.1083/jcb.202202102] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 07/19/2022] [Accepted: 11/14/2022] [Indexed: 02/01/2023] Open
Abstract
How cells regulate α- and β-tubulin to meet the demand for αβ-heterodimers and avoid consequences of monomer imbalance is not understood. We investigate the role of gene copy number and how shifting expression of α- or β-tubulin genes impacts tubulin proteostasis and microtubule function in Saccharomyces cerevisiae. We find that α-tubulin gene copy number is important for maintaining excess α-tubulin protein compared to β-tubulin protein. Excess α-tubulin prevents accumulation of super-stoichiometric β-tubulin, which leads to loss of microtubules, formation of non-microtubule assemblies of tubulin, and disrupts cell proliferation. In contrast, sub-stoichiometric β-tubulin or overexpression of α-tubulin has minor effects. We provide evidence that yeast cells equilibrate α-tubulin protein concentration when α-tubulin isotype expression is increased. We propose an asymmetric relationship between α- and β-tubulins, in which α-tubulins are maintained in excess to supply αβ-heterodimers and limit the accumulation of β-tubulin monomers.
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Affiliation(s)
- Linnea C. Wethekam
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jeffrey K. Moore
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO, USA
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5
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Buscaglia G, Northington KR, Aiken J, Hoff KJ, Bates EA. Bridging the Gap: The Importance of TUBA1A α-Tubulin in Forming Midline Commissures. Front Cell Dev Biol 2022; 9:789438. [PMID: 35127710 PMCID: PMC8807549 DOI: 10.3389/fcell.2021.789438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Developing neurons undergo dramatic morphological changes to appropriately migrate and extend axons to make synaptic connections. The microtubule cytoskeleton, made of α/β-tubulin dimers, drives neurite outgrowth, promotes neuronal growth cone responses, and facilitates intracellular transport of critical cargoes during neurodevelopment. TUBA1A constitutes the majority of α-tubulin in the developing brain and mutations to TUBA1A in humans cause severe brain malformations accompanied by varying neurological defects, collectively termed tubulinopathies. Studies of TUBA1A function in mammalian cells have been limited by the presence of multiple genes encoding highly similar tubulin proteins, which leads to α-tubulin antibody promiscuity and makes genetic manipulation challenging. Here, we test mutant tubulin levels and assembly activity and analyze the impact of TUBA1A reduction on growth cone composition, neurite extension, and commissural axon architecture during brain development. We present a novel tagging method for studying and manipulating TUBA1A in cells without impairing tubulin function. Using this tool, we show that a TUBA1A loss-of-function mutation TUBA1A N102D (TUBA1A ND ), reduces TUBA1A protein levels and prevents incorporation of TUBA1A into microtubule polymers. Reduced Tuba1a α-tubulin in heterozygous Tuba1a ND/+ mice leads to grossly normal brain formation except a significant impact on axon extension and impaired formation of forebrain commissures. Neurons with reduced Tuba1a as a result of the Tuba1a ND mutation exhibit slower neuron outgrowth compared to controls. Neurons deficient in Tuba1a failed to localize microtubule associated protein-1b (Map1b) to the developing growth cone, likely impacting stabilization of microtubules. Overall, we show that reduced Tuba1a is sufficient to support neuronal migration and cortex development but not commissure formation, and provide mechanistic insight as to how TUBA1A tunes microtubule function to support neurodevelopment.
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Affiliation(s)
- Georgia Buscaglia
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Kyle R. Northington
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jayne Aiken
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Katelyn J. Hoff
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Emily A. Bates
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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6
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Abstract
Members of the tubulin superfamily are GTPases; the activities of GTPases are necessary for life. The members of the tubulin superfamily are the constituents of the microtubules and the γ-tubulin meshwork. Mutations in members of the tubulin superfamily are involved in developmental brain disorders, and tubulin activities are the target for various chemotherapies. The intricate functions (game) of tubulins depend on the activities of the GTP-binding domain of α-, β-, and γ-tubulin. This review compares the GTP-binding domains of γ-tubulin, α-tubulin, and β-tubulin and, based on their similarities, recapitulates the known functions and the impact of the γ-tubulin GTP-binding domain in the regulation of the γ-tubulin meshwork and cellular homeostasis.
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Affiliation(s)
- Maria Alvarado Kristensson
- Molecular Pathology, Department of Translational Medicine, Lund University, Skåne University Hospital, 20502 Malmö, Sweden
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7
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Roostalu J, Thomas C, Cade NI, Kunzelmann S, Taylor IA, Surrey T. The speed of GTP hydrolysis determines GTP cap size and controls microtubule stability. eLife 2020; 9:e51992. [PMID: 32053491 PMCID: PMC7018511 DOI: 10.7554/elife.51992] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/25/2020] [Indexed: 11/30/2022] Open
Abstract
Microtubules are cytoskeletal polymers whose function depends on their property to switch between states of growth and shrinkage. Growing microtubules are thought to be stabilized by a GTP cap at their ends. The nature of this cap, however, is still poorly understood. End Binding proteins (EBs) recruit a diverse range of regulators of microtubule function to growing microtubule ends. Whether the EB binding region is identical to the GTP cap is unclear. Using mutated human tubulin with blocked GTP hydrolysis, we demonstrate that EBs bind with high affinity to the GTP conformation of microtubules. Slowing-down GTP hydrolysis leads to extended GTP caps. We find that cap length determines microtubule stability and that the microtubule conformation changes gradually in the cap as GTP is hydrolyzed. These results demonstrate the critical importance of the kinetics of GTP hydrolysis for microtubule stability and establish that the GTP cap coincides with the EB-binding region.
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Affiliation(s)
| | | | | | | | | | - Thomas Surrey
- The Francis Crick InstituteLondonUnited Kingdom
- Centre for Genomic RegulationBarcelona Institute of Science and TechnologyBarcelonaSpain
- ICREABarcelonaSpain
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8
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Tubulin response to intense nanosecond-scale electric field in molecular dynamics simulation. Sci Rep 2019; 9:10477. [PMID: 31324834 PMCID: PMC6642143 DOI: 10.1038/s41598-019-46636-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/18/2019] [Indexed: 12/12/2022] Open
Abstract
Intense pulsed electric fields are known to act at the cell membrane level and are already being exploited in biomedical and biotechnological applications. However, it is not clear if electric pulses within biomedically-attainable parameters could directly influence intra-cellular components such as cytoskeletal proteins. If so, a molecular mechanism of action could be uncovered for therapeutic applications of such electric fields. To help clarify this question, we first identified that a tubulin heterodimer is a natural biological target for intense electric fields due to its exceptional electric properties and crucial roles played in cell division. Using molecular dynamics simulations, we then demonstrated that an intense - yet experimentally attainable - electric field of nanosecond duration can affect the bβ-tubulin’s C-terminus conformations and also influence local electrostatic properties at the GTPase as well as the binding sites of major tubulin drugs site. Our results suggest that intense nanosecond electric pulses could be used for physical modulation of microtubule dynamics. Since a nanosecond pulsed electric field can penetrate the tissues and cellular membranes due to its broadband spectrum, our results are also potentially significant for the development of new therapeutic protocols.
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9
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Manandhar A, Kang M, Chakraborty K, Loverde SM. Effect of Nucleotide State on the Protofilament Conformation of Tubulin Octamers. J Phys Chem B 2018; 122:6164-6178. [PMID: 29768004 DOI: 10.1021/acs.jpcb.8b02193] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
At the molecular level, the dynamic instability (random growth and shrinkage) of the microtubule (MT) is driven by the nucleotide state (GTP vs GDP) in the β subunit of the tubulin dimers at the MT cap. Here, we use large-scale molecular dynamics (MD) simulations and normal-mode analysis (NMA) to characterize the effect of a single GTP cap layer on tubulin octamers composed of two neighboring protofilaments (PFs). We utilize recently reported high-resolution structures of dynamic MTs to simulate a GDP octamer both with and without a single GTP cap layer. We perform multiple replicas of long-time atomistic MD simulations (3 replicas, 0.3 μs for each replica, 0.9 μs for each octamer system, and 1.8 μs total) of both octamers. We observe that a single GTP cap layer induces structural differences in neighboring PFs, finding that one PF possesses a gradual curvature, compared to the second PF which possesses a kinked conformation. This results in either curling or splaying between these PFs. We suggest that this is due to asymmetric strengths of longitudinal contacts between the two PFs. Furthermore, using NMA, we calculate mechanical properties of these octamer systems and find that octamer system with a single GTP cap layer possesses a lower flexural rigidity.
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Affiliation(s)
- Anjela Manandhar
- Department of Chemistry, College of Staten Island , City University of New York , 2800 Victory Boulevard , Staten Island , New York 10314 , United States.,Ph.D. Program in Biochemistry , The Graduate Center of the City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Myungshim Kang
- Department of Chemistry, College of Staten Island , City University of New York , 2800 Victory Boulevard , Staten Island , New York 10314 , United States
| | - Kaushik Chakraborty
- Department of Chemistry, College of Staten Island , City University of New York , 2800 Victory Boulevard , Staten Island , New York 10314 , United States
| | - Sharon M Loverde
- Department of Chemistry, College of Staten Island , City University of New York , 2800 Victory Boulevard , Staten Island , New York 10314 , United States.,Ph.D. Program in Biochemistry , The Graduate Center of the City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
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10
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Pesce CG, Zdraljevic S, Peria WJ, Bush A, Repetto MV, Rockwell D, Yu RC, Colman-Lerner A, Brent R. Single-cell profiling screen identifies microtubule-dependent reduction of variability in signaling. Mol Syst Biol 2018; 14:e7390. [PMID: 29618636 PMCID: PMC5884679 DOI: 10.15252/msb.20167390] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/25/2018] [Accepted: 02/06/2018] [Indexed: 01/01/2023] Open
Abstract
Populations of isogenic cells often respond coherently to signals, despite differences in protein abundance and cell state. Previously, we uncovered processes in the Saccharomyces cerevisiae pheromone response system (PRS) that reduced cell-to-cell variability in signal strength and cellular response. Here, we screened 1,141 non-essential genes to identify 50 "variability genes". Most had distinct, separable effects on strength and variability of the PRS, defining these quantities as genetically distinct "axes" of system behavior. Three genes affected cytoplasmic microtubule function: BIM1, GIM2, and GIM4 We used genetic and chemical perturbations to show that, without microtubules, PRS output is reduced but variability is unaffected, while, when microtubules are present but their function is perturbed, output is sometimes lowered, but its variability is always high. The increased variability caused by microtubule perturbations required the PRS MAP kinase Fus3 and a process at or upstream of Ste5, the membrane-localized scaffold to which Fus3 must bind to be activated. Visualization of Ste5 localization dynamics demonstrated that perturbing microtubules destabilized Ste5 at the membrane signaling site. The fact that such microtubule perturbations cause aberrant fate and polarity decisions in mammals suggests that microtubule-dependent signal stabilization might also operate throughout metazoans.
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Affiliation(s)
| | - Stefan Zdraljevic
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | | | - Alan Bush
- IFIBYNE-UBA-CONICET and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Victoria Repetto
- IFIBYNE-UBA-CONICET and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | | | - Alejandro Colman-Lerner
- IFIBYNE-UBA-CONICET and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Roger Brent
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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11
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Wang W, Zhang H, Wang X, Patterson J, Winter P, Graham K, Ghosh S, Lee JC, Katsetos CD, Mackey JR, Tuszynski JA, Wong GKS, Ludueña RF. Novel mutations involving βI-, βIIA-, or βIVB-tubulin isotypes with functional resemblance to βIII-tubulin in breast cancer. PROTOPLASMA 2017; 254:1163-1173. [PMID: 27943021 DOI: 10.1007/s00709-016-1060-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/02/2016] [Indexed: 06/06/2023]
Abstract
Tubulin is the target for very widely used anti-tumor drugs, including Vinca alkaloids, taxanes, and epothilones, which are an important component of chemotherapy in breast cancer and other malignancies. Paclitaxel and other tubulin-targeting drugs bind to the β subunit of tubulin, which is a heterodimer of α and β subunits. β-Tubulin exists in the form of multiple isotypes, which are differentially expressed in normal and neoplastic cells and differ in their ability to bind to drugs. Among them, the βIII isotype is overexpressed in many aggressive and metastatic cancers and may serve as a prognostic marker in certain types of cancer. The underpinning mechanisms accounting for the overexpression of this isotype in cancer cells are unclear. To better understand the role of β-tubulin isotypes in cancer, we analyzed over 1000 clones from 90 breast cancer patients, sequencing their β-tubulin isotypes, in search of novel mutations. We have elucidated two putative emerging molecular subgroups of invasive breast cancer, each of which involve mutations in the βI-, βIIA-, or βIVB isotypes of tubulin that increase their structural, and possibly functional, resemblance to the βIII isotype. A unifying feature of the first of the two subgroups is the mutation of the highly reactive C239 residue of βI- or βIVB-tubulin to L239, R239, Y239, or P239, culminating in probable conversion of these isotypes from ROS-sensitive to ROS-resistant species. In the second subgroup, βI, βIIA, and βIVB have up to seven mutations to the corresponding residues in βIII-tubulin. Given that βIII-tubulin has emerged as a pro-survival factor, overexpression of this isotype may confer survival advantages to certain cancer cell types. In this mini-review, we bring attention to a novel mechanism by which cancer cells may undergo adaptive mutational changes involving alternate β-tubulin isotypes to make them acquire some of the pro-survival properties of βIII-tubulin. These "hybrid" tubulins, combining the sequences and/or properties of two wild-type tubulins (βIII and either βI, βIIA, or βIVB), are novel isotypes expressed solely in cancer cells and may contribute to the molecular understanding and stratification of invasive breast cancer and provide novel molecular targets for rational drug development.
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Affiliation(s)
- Weiwei Wang
- Department of Medicine, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Hangxiao Zhang
- Beijing Institute of Genomics, Key Laboratory of Genome Sciences and Information, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xumin Wang
- Beijing Institute of Genomics, Key Laboratory of Genome Sciences and Information, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jordan Patterson
- Department of Medicine, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Philip Winter
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada
| | - Kathryn Graham
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada
| | - Sunita Ghosh
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada
| | - John C Lee
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Christos D Katsetos
- Department of Pediatrics, St. Christopher's Hospital for Children, Drexel University College of Medicine, Philadelphia, PA, 19134, USA
- Department of Pathology and Laboratory Medicine, St. Christopher's Hospital for Children, Drexel University College of Medicine, Philadelphia, PA, 19134, USA
| | - John R Mackey
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada
| | - Jack A Tuszynski
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada
| | - Gane Ka-Shu Wong
- Department of Medicine, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Richard F Ludueña
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
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12
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Lyu Z, Coltharp C, Yang X, Xiao J. Influence of FtsZ GTPase activity and concentration on nanoscale Z-ring structure in vivo revealed by three-dimensional Superresolution imaging. Biopolymers 2016; 105:725-34. [PMID: 27310678 PMCID: PMC4958570 DOI: 10.1002/bip.22895] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 06/10/2016] [Accepted: 06/13/2016] [Indexed: 12/18/2022]
Abstract
FtsZ is an essential bacterial cytoskeletal protein that assembles into a ring-like structure (Z-ring) at midcell to carry out cytokinesis. In vitro, FtsZ exhibits polymorphism in polymerizing into different forms of filaments based on its GTPase activity, concentration, and buffer condition. In vivo, the Z-ring appeared to be punctate and heterogeneously organized, although continuous, homogenous Z-ring structures have also been observed. Understanding how the Z-ring is organized in vivo is important because it provides a structural basis for the functional role of the Z-ring in cytokinesis. Here, we assess the effects of both GTPase activity and FtsZ concentration on the organization of the Z-ring in vivo using three-dimensional (3D) superresolution microscopy. We found that the Z-ring became more homogenous when assembled in the presence of a GTPase-deficient mutant, and upon overexpression of either wt or mutant FtsZ. These results suggest that the in vivo organization of the Z-ring is largely dependent on the intrinsic polymerization properties of FtsZ, which are significantly influenced by the GTPase activity and concentration of FtsZ. Our work provides a unifying theme to reconcile previous observations of different Z-ring structures, and supports a model in which the wt Z-ring comprises loosely associated, heterogeneously distributed FtsZ clusters. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 725-734, 2016.
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Affiliation(s)
- Zhixin Lyu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD
| | - Carla Coltharp
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD
| | - Xinxing Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD
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13
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Zhang R, Nogales E. A new protocol to accurately determine microtubule lattice seam location. J Struct Biol 2015; 192:245-54. [PMID: 26424086 DOI: 10.1016/j.jsb.2015.09.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 09/18/2015] [Accepted: 09/25/2015] [Indexed: 01/27/2023]
Abstract
Microtubules (MTs) are cylindrical polymers of αβ-tubulin that display pseudo-helical symmetry due to the presence of a lattice seam of heterologous lateral contacts. The structural similarity between α- and β-tubulin makes it difficult to computationally distinguish them in the noisy cryo-EM images, unless a marker protein for the tubulin dimer, such as kinesin motor domain, is present. We have developed a new data processing protocol that can accurately determine αβ-tubulin register and seam location for MT segments. Our strategy can deal with difficult situations, where the marker protein is relatively small or the decoration of marker protein is sparse. Using this new seam-search protocol, combined with movie processing for data from a direct electron detection camera, we were able to determine the cryo-EM structures of MT at 3.5 Å resolution in different functional states. The successful distinction of α- and β-tubulin allowed us to visualize the nucleotide state at the E-site and the configuration of lateral contacts at the seam.
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Affiliation(s)
- Rui Zhang
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
| | - Eva Nogales
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
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14
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Mechanistic Origin of Microtubule Dynamic Instability and Its Modulation by EB Proteins. Cell 2015; 162:849-59. [PMID: 26234155 DOI: 10.1016/j.cell.2015.07.012] [Citation(s) in RCA: 293] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 05/05/2015] [Accepted: 06/23/2015] [Indexed: 11/22/2022]
Abstract
Microtubule (MT) dynamic instability is driven by GTP hydrolysis and regulated by microtubule-associated proteins, including the plus-end tracking end-binding protein (EB) family. We report six cryo-electron microscopy (cryo-EM) structures of MTs, at 3.5 Å or better resolution, bound to GMPCPP, GTPγS, or GDP, either decorated with kinesin motor domain after polymerization or copolymerized with EB3. Subtle changes around the E-site nucleotide during hydrolysis trigger conformational changes in α-tubulin around an "anchor point," leading to global lattice rearrangements and strain generation. Unlike the extended lattice of the GMPCPP-MT, the EB3-bound GTPγS-MT has a compacted lattice that differs in lattice twist from that of the also compacted GDP-MT. These results and the observation that EB3 promotes rapid hydrolysis of GMPCPP suggest that EB proteins modulate structural transitions at growing MT ends by recognizing and promoting an intermediate state generated during GTP hydrolysis. Our findings explain both EBs end-tracking behavior and their effect on microtubule dynamics.
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15
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Gombos L, Neuner A, Berynskyy M, Fava LL, Wade RC, Sachse C, Schiebel E. GTP regulates the microtubule nucleation activity of γ-tubulin. Nat Cell Biol 2013; 15:1317-27. [PMID: 24161932 DOI: 10.1038/ncb2863] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 09/19/2013] [Indexed: 12/25/2022]
Abstract
Both subunits of αβ-tubulin that comprise the core components of microtubules bind GTP. GTP binding to α-tubulin has a structural role, whereas β-tubulin binds and hydrolyses GTP to regulate microtubule dynamics. γ-tubulin, another member of the tubulin superfamily that seeds microtubule nucleation at microtubule-organizing centres, also binds GTP; however, the importance of this association remains elusive. To address the role of GTP binding to γ-tubulin, we systematically mutagenized the GTP contact residues in the yeast γ-tubulin Tub4. Tub4(GTP)-mutant proteins that exhibited greatly reduced GTP affinity still assembled into the small γ-tubulin complex. However, tub4(GTP) mutants were no longer viable, and had defects in interaction between γ-tubulin and αβ-tubulin, decreased microtubule nucleation and defects in microtubule organization. In vitro and in vivo data show that only γ-tubulin loaded with GTP nucleates microtubules. Our results suggest that GTP recruitment to γ-tubulin enhances its interaction with αβ-tubulin similarly to GTP recruitment to β-tubulin.
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Affiliation(s)
- Linda Gombos
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), ZMBH-DKFZ Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
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16
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Grafmüller A, Noya EG, Voth GA. Nucleotide-dependent lateral and longitudinal interactions in microtubules. J Mol Biol 2013; 425:2232-46. [PMID: 23541590 DOI: 10.1016/j.jmb.2013.03.029] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 03/11/2013] [Accepted: 03/16/2013] [Indexed: 01/31/2023]
Abstract
Microtubule (MT) stability is related to the hydrolysis of the guanosine triphosphate nucleotide (NT) bound to β-tubulin. However, the molecular mechanism by which the NT state influences the stability of the contacts in the MT lattice remains elusive. Here, we present large-scale atomistic simulations of different tubulin aggregates, including individual dimers, short protofilaments, a small lattice patch, and a piece of the MT lattice with two infinite protofilaments in both NT states. Together with a coarse-grained (CG) analysis of the fluctuations, these simulations highlight several regions of the protein where local changes are induced by the NT state or by the lateral and longitudinal contacts in the aggregates. Additionally, the CG analysis provides an indication of how the structural changes affect the bonds between the proteins. The results suggest a consistent picture of a possible molecular mechanism by which the NT state induces changes in the H1-S2 loop and more stable longitudinal bonds, both of which locate the H1-S2 and M-loop in more favorable positions to form lateral contacts.
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Affiliation(s)
- Andrea Grafmüller
- Theory and Biosystems, Max Planck Institute for Colloids and Interfaces, 14424 Potsdam, Germany.
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17
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Hashimoto T. Dissecting the cellular functions of plant microtubules using mutant tubulins. Cytoskeleton (Hoboken) 2013; 70:191-200. [PMID: 23585382 DOI: 10.1002/cm.21099] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/07/2013] [Accepted: 01/15/2013] [Indexed: 12/22/2022]
Abstract
α- and β-tubulins, the building blocks of the microtubule (MT) polymer, are encoded by multiple genes that are largely functionally redundant in plants. Null tubulin mutants are thus phenotypically indistinguishable from the wild type, but miss-sense or deletion mutations of critical amino acid residues that are important for the assembly, stability, or dynamics of the polymer disrupt the proper organization and function of the resultant MT arrays. Mutant tubulins co-assemble with wild-type tubulins into mutant MTs with compromised functions, and thus mechanistically act as dominant-negative MT poisons. Cortical MT arrays in interphase plant cells are most sensitive to tubulin mutations, and are transformed into helical structures or random orientation, which produce twisted or radially swollen cells. Mutant plants resistant to MT-targeted herbicides may possess tubulin mutations at the binding sites of the herbicides. Tubulin mutants are valuable tools for investigating how individual MTs are organized into particular patterns in cortical arrays, and for defining the functional contribution of MTs to various MT-dependent or -assisted cellular processes in plant cells.
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Affiliation(s)
- Takashi Hashimoto
- Graduate School of Biological Sciences, Nara Institute for Science and Technology, Ikoma, Nara, 630-0192, Japan.
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18
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Abstract
Microtubules play essential roles in a wide variety of cellular processes including cell division, motility, and vesicular transport. Microtubule function depends on the polymerization dynamics of tubulin and specific interactions between tubulin and diverse microtubule-associated proteins. To date, investigation of the structural and functional properties of tubulin and tubulin mutants has been limited by the inability to obtain functional protein from overexpression systems, and by the heterogeneous mixture of tubulin isotypes typically isolated from higher eukaryotes. The budding yeast, Saccharomyces cerevisiae, has emerged as a leading system for tubulin structure-function analysis. Yeast cells encode a single beta-tubulin gene and can be engineered to express just one of two alpha isotypes. Moreover, yeast allows site-directed modification of tubulin genes at the endogenous loci expressed under the native promoter and regulatory elements. These advantageous features provide a homogeneous and controlled environment for analysis of the functional consequences of specific mutations. Here, we present the techniques to generate site-specific tubulin mutations in diploid and haploid cells, assess the ability of the mutated protein to support cell viability, measure overall microtubule stability, and define changes in the specific parameters of microtubule dynamic instability. We also outline strategies to determine whether mutations disrupt interactions with microtubule-associated proteins. Microtubule-based functions in yeast are well defined, which allows the observed changes in microtubule properties to be related to the role of microtubules in specific cellular processes.
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Affiliation(s)
- Anna Luchniak
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Yusuke Fukuda
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, USA
| | - Mohan L. Gupta
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, USA
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19
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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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20
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Rendine S, Pieraccini S, Sironi M. Vinblastine perturbation of tubulin protofilament structure: a computational insight. Phys Chem Chem Phys 2010; 12:15530-6. [PMID: 20978652 DOI: 10.1039/c0cp00594k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Tubulin is a heterodimeric protein whose self assembly leads to the formation of protofilaments and of more complex structures called microtubules, key components of the cytoskeleton which have a fundamental role in the cell division process. Due to its biological function, tubulin is the target of many antitumoral molecules that exert their action on proliferating tumoral cells. Among these drugs, vinblastine has been widely used in therapy for a long time, albeit its mechanism of interaction with tubulin has remained elusive until recently. Vinblastine acts as a microtubule destabilizing agent and induces the formation of curved or ring-shaped tubulin polymers instead of linear protofilaments in vitro. In this paper we compare, using molecular dynamics simulations and free energy calculations, the network of interactions that allow the assembly of model linear protofilaments with those present in curved tubulin polymers complexed with vinblastine. It is shown that vinblastine, wedging between tubulin heterodimers, actually mediates part of the interactions between them and acts by crosslinking the two proteins, leading to the observed curved polymers rather than to their disassembly.
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Affiliation(s)
- Stefano Rendine
- Dipartimento di Chimica Fisica ed Elettrochimica, Università degli Studi di Milano, Via Golgi 19, 20133, Milano, Italy
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21
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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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22
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Khrapunovich-Baine M, Menon V, Verdier-Pinard P, Smith AB, Angeletti RH, Fiser A, Horwitz SB, Xiao H. Distinct pose of discodermolide in taxol binding pocket drives a complementary mode of microtubule stabilization. Biochemistry 2010; 48:11664-77. [PMID: 19863156 DOI: 10.1021/bi901351q] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The microtubule cytoskeleton has proven to be an effective target for cancer therapeutics. One class of drugs, known as microtubule stabilizing agents (MSAs), binds to microtubule polymers and stabilizes them against depolymerization. The prototype of this group of drugs, Taxol, is an effective chemotherapeutic agent used extensively in the treatment of human ovarian, breast, and lung carcinomas. Although electron crystallography and photoaffinity labeling experiments determined that the binding site for Taxol is in a hydrophobic pocket in beta-tubulin, little was known about the effects of this drug on the conformation of the entire microtubule. A recent study from our laboratory utilizing hydrogen-deuterium exchange (HDX) in concert with various mass spectrometry (MS) techniques has provided new information on the structure of microtubules upon Taxol binding. In the current study we apply this technique to determine the binding mode and the conformational effects on chicken erythrocyte tubulin (CET) of another MSA, discodermolide, whose synthetic analogues may have potential use in the clinic. We confirmed that, like Taxol, discodermolide binds to the taxane binding pocket in beta-tubulin. However, as opposed to Taxol, which has major interactions with the M-loop, discodermolide orients itself away from this loop and toward the N-terminal H1-S2 loop. Additionally, discodermolide stabilizes microtubules mainly via its effects on interdimer contacts, specifically on the alpha-tubulin side, and to a lesser extent on interprotofilament contacts between adjacent beta-tubulin subunits. Also, our results indicate complementary stabilizing effects of Taxol and discodermolide on the microtubules, which may explain the synergy observed between the two drugs in vivo.
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Affiliation(s)
- Marina Khrapunovich-Baine
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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23
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Pieraccini S, Saladino G, Cappelletti G, Cartelli D, Francescato P, Speranza G, Manitto P, Sironi M. In silico design of tubulin-targeted antimitotic peptides. Nat Chem 2009; 1:642-8. [DOI: 10.1038/nchem.401] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Accepted: 09/08/2009] [Indexed: 11/09/2022]
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24
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Thaler DS. The cytoplasmic structure hypothesis for ribosome assembly, vertical inheritance, and phylogeny. Bioessays 2009; 31:774-83. [DOI: 10.1002/bies.200800190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Buschmann H, Hauptmann M, Niessing D, Lloyd CW, Schäffner AR. Helical growth of the Arabidopsis mutant tortifolia2 does not depend on cell division patterns but involves handed twisting of isolated cells. THE PLANT CELL 2009; 21:2090-106. [PMID: 19638477 PMCID: PMC2729594 DOI: 10.1105/tpc.108.061242] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Revised: 06/17/2009] [Accepted: 07/10/2009] [Indexed: 05/19/2023]
Abstract
Several factors regulate plant organ growth polarity. tortifolia2 (tor2), a right-handed helical growth mutant, has a conservative replacement of Arg-2 with Lys in the alpha-tubulin 4 protein. Based on a published high-resolution (2.89 A) tubulin structure, we predict that Arg-2 of alpha-tubulin forms hydrogen bonds with the GTPase domain of beta-tubulin, and structural modeling suggests that these contacts are interrupted in tor2. Consistent with this, we found that microtubule dynamicity is reduced in the tor2 background. We investigated the developmental origin of the helical growth phenotype using tor2. One hypothesis predicts that cell division patterns cause helical organ growth in Arabidopsis thaliana mutants. However, cell division patterns of tor2 root tips appear normal. Experimental uncoupling of cell division and expansion suggests that helical organ growth is based on cell elongation defects only. Another hypothesis is that twisting is due to inequalities in expansion of epidermal and cortical tissues. However, freely growing leaf trichomes of tor2 mutants show right-handed twisting and cortical microtubules form left-handed helices as early as the unbranched stage of trichome development. Trichome twisting is inverted in double mutants with tor3, a left-handed mutant. Single tor2 suspension cells also exhibit handed twisting. Thus, twisting of tor2 mutant organs appears to be a higher-order expression of the helical expansion of individual cells.
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Affiliation(s)
- Henrik Buschmann
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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26
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Secondary mutations correct fitness defects in Toxoplasma gondii with dinitroaniline resistance mutations. Genetics 2008; 180:845-56. [PMID: 18780736 DOI: 10.1534/genetics.108.092494] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dinitroanilines (oryzalin, trifluralin, ethafluralin) disrupt microtubules in protozoa but not in vertebrate cells, causing selective death of intracellular Toxoplasma gondii parasites without affecting host cells. Parasites containing alpha1-tubulin point mutations are dinitroaniline resistant but show increased rates of aberrant replication relative to wild-type parasites. T. gondii parasites bearing the F52Y mutation were previously demonstrated to spontaneously acquire two intragenic mutations that decrease both resistance levels and replication defects. Parasites bearing the G142S mutation are largely dependent on oryzalin for viable growth in culture. We isolated 46 T. gondii lines that have suppressed microtubule defects associated with the G142S or the F52Y mutations by acquiring secondary mutations. These compensatory mutations were alpha1-tubulin pseudorevertants or extragenic suppressors (the majority alter the beta1-tubulin gene). Many secondary mutations were located in tubulin domains that suggest that they function by destabilizing microtubules. Most strikingly, we identified seven novel mutations that localize to an eight-amino-acid insert that stabilizes the alpha1-tubulin M loop, including one (P364R) that acts as a compensatory mutation in both F52Y and G142S lines. These lines have reduced dinitroaniline resistance but most perform better than parental lines in competition assays, indicating that there is a trade-off between resistance and replication fitness.
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27
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Ma C, Li C, Ganesan L, Oak J, Tsai S, Sept D, Morrissette NS. Mutations in alpha-tubulin confer dinitroaniline resistance at a cost to microtubule function. Mol Biol Cell 2007; 18:4711-20. [PMID: 17881728 PMCID: PMC2096588 DOI: 10.1091/mbc.e07-04-0379] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Protozoan microtubules are sensitive to disruption by dinitroanilines, compounds that kill intracellular Toxoplasma gondii parasites without affecting microtubules in vertebrate host cells. We previously isolated a number of resistant Toxoplasma lines that harbor mutations to the alpha1-tubulin gene. Some of the mutations are localized in or near the M and N loops, domains that coordinate lateral interactions between protofilaments. Other resistance mutations map to a computationally identified binding site beneath the N loop. Allelic replacement of wild-type alpha1-tubulin with the individual mutations is sufficient to confer dinitroaniline resistance. Some mutations seem to increase microtubule length, suggesting that they increase subunit affinity. All mutations are associated with replication defects that decrease parasite viability. When parasites bearing the N loop mutation Phe52Tyr are grown without dinitroaniline selection, they spontaneously acquired secondary mutations in the M loop (Ala273Val) or in an alpha-tubulin-specific insert that stabilizes the M loop (Asp367Val). Parasites with the double mutations have both reduced resistance and diminished incidence of replication defects, suggesting that the secondary mutations decrease protofilament affinity to increase parasite fitness.
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Affiliation(s)
- Christopher Ma
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
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28
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Ishida T, Kaneko Y, Iwano M, Hashimoto T. Helical microtubule arrays in a collection of twisting tubulin mutants of Arabidopsis thaliana. Proc Natl Acad Sci U S A 2007; 104:8544-9. [PMID: 17488810 PMCID: PMC1895986 DOI: 10.1073/pnas.0701224104] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Indexed: 12/23/2022] Open
Abstract
Anisotropic expansion of plant cells requires organized arrays of cortical microtubules. Mutations in microtubule-associated proteins and a particular mutation in alpha-tubulins were reported to cause abnormal microtubule arrays and result in helical growth in Arabidopsis thaliana. However, the way in which these mutations affect the organization of microtubules remains unknown. We here identified 32 Arabidopsis twisting mutants that have either missense or amino acid deletion mutations in alpha- or beta-tubulins. Mutations were mapped to the GTPase-activating region in alpha-tubulin, intra- and interdimer interfaces of tubulin heterodimers, and lateral contact regions among adjacent protofilaments. These dominant-negative tubulin mutants were incorporated into the microtubule polymer and formed shallow helical arrays of distinct handedness along the long axis of the root epidermal cells. A striking correlation exists between the direction in which cortical helical arrays are skewed and the growth direction of elongating roots. The GTPase-activating-region mutant had left-handed helical arrays composed of highly stabilized microtubules, which could be decorated along the entire microtubule lattices with the otherwise tip-localized End Binding 1 protein. A mutation at the intradimer interface, on the other hand, generated highly dynamic microtubules and right-handed helical arrays. Cortical microtubules in wild type and these two tubulin mutants were composed mainly of 13 protofilaments. This comprehensive analysis of tubulin mutations provides insights into the mechanism by which tubulin structures influence microtubule dynamics and organization.
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Affiliation(s)
- Takashi Ishida
- Nara Institute of Science and Technology, Graduate School of Biological Sciences, Ikoma, Nara 630-0192, Japan
| | - Yayoi Kaneko
- Nara Institute of Science and Technology, Graduate School of Biological Sciences, Ikoma, Nara 630-0192, Japan
| | - Megumi Iwano
- Nara Institute of Science and Technology, Graduate School of Biological Sciences, Ikoma, Nara 630-0192, Japan
| | - Takashi Hashimoto
- Nara Institute of Science and Technology, Graduate School of Biological Sciences, Ikoma, Nara 630-0192, Japan
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29
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Xiao H, Verdier-Pinard P, Fernandez-Fuentes N, Burd B, Angeletti R, Fiser A, Horwitz SB, Orr GA. Insights into the mechanism of microtubule stabilization by Taxol. Proc Natl Acad Sci U S A 2006; 103:10166-10173. [PMID: 16801540 PMCID: PMC1502429 DOI: 10.1073/pnas.0603704103] [Citation(s) in RCA: 234] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The antitumor drug Taxol stabilizes microtubules and reduces their dynamicity, promoting mitotic arrest and cell death. Upon assembly of the alpha/beta-tubulin heterodimer, GTP bound to beta-tubulin is hydrolyzed to GDP reaching a steady-state equilibrium between free tubulin dimers and microtubules. The binding of Taxol to beta-tubulin in the polymer results in cold-stable microtubules at the expense of tubulin dimers, even in the absence of exogenous GTP. However, there is little biochemical insight into the mechanism(s) by which Taxol stabilizes microtubules. Here, we analyze the structural changes occurring in both beta- and alpha-tubulin upon microtubule stabilization by Taxol. Hydrogen/deuterium exchange (HDX) coupled to liquid chromatography-electrospray ionization MS demonstrated a marked reduction in deuterium incorporation in both beta-and alpha-tubulin when Taxol was present. Decreased local HDX in peptic peptides was mapped on the tubulin structure and revealed both expected and new dimer-dimer interactions. The increased rigidity in Taxol microtubules was distinct from and complementary to that due to GTP-induced polymerization. The Taxol-induced changes in tubulin conformation act against microtubule depolymerization in a precise directional way. These results demonstrate that HDX coupled to liquid chromatography-electrospray ionization MS can be effectively used to study conformational effects induced by small ligands on microtubules. The present study also opens avenues for locating drug and protein binding sites and for deciphering the mechanisms by which their interactions alter the conformation of microtubules and tubulin dimers.
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Affiliation(s)
- Hui Xiao
- *Laboratory of Macromolecular Analysis and Proteomics, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Pascal Verdier-Pinard
- Departments of Molecular Pharmacology
- Obstetrics & Gynecology and Women's Health, and
| | | | | | - Ruth Angeletti
- *Laboratory of Macromolecular Analysis and Proteomics, Albert Einstein College of Medicine, Bronx, NY 10461
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30
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Redick SD, Stricker J, Briscoe G, Erickson HP. Mutants of FtsZ targeting the protofilament interface: effects on cell division and GTPase activity. J Bacteriol 2005; 187:2727-36. [PMID: 15805519 PMCID: PMC1070378 DOI: 10.1128/jb.187.8.2727-2736.2005] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterial cell division protein FtsZ assembles into straight protofilaments, one subunit thick, in which subunits appear to be connected by identical bonds or interfaces. These bonds involve the top surface of one subunit making extensive contact with the bottom surface of the subunit above it. We have investigated this interface by site-directed mutagenesis. We found nine bottom and eight top mutants that were unable to function for cell division. We had expected that some of the mutants might poison cell division substoichiometrically, but this was not found for any mutant. Eight of the bottom mutants exhibited dominant negative effects (reduced colony size) and four completely blocked colony formation, but this required expression of the mutant protein at four to five times the wild-type FtsZ level. Remarkably, the top mutants were even weaker, most showing no effect at the highest expression level. This suggests a directional assembly or treadmilling, where subunit addition is primarily to the bottom end of the protofilament. Selected pairs of top and bottom mutants showed no GTPase activity up to 10 to 20 microM, in contrast to the high GTPase activity of wild-type FtsZ above 1 muM. Overall, these results suggest that in order for a subunit to bind a protofilament at the 1 microM K(d) for elongation, it must have functional interfaces at both the top and bottom. This is inconsistent with the present model of the protofilament, as a simple stack of subunits one on top of the other, and may require a new structural model.
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Affiliation(s)
- Sambra D Redick
- Department of Cell Biology, Duke University, 3709 Duke University Medical Center, Durham, NC 27710, USA
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31
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Abe T, Hashimoto T. Altered microtubule dynamics by expression of modified alpha-tubulin protein causes right-handed helical growth in transgenic Arabidopsis plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 43:191-204. [PMID: 15998306 DOI: 10.1111/j.1365-313x.2005.02442.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The proper organization of cortical microtubule arrays is essential for anisotropic growth in plants but how distinct array patterns are formed is not understood. Here, we report a relationship between microtubule dynamics and array organization using transgenic plants expressing modified tubulins. When green fluorescent protein (GFP) or a hemaglutinin epitope tag was fused to the N-terminus of tubulins and expressed in Arabidopsis plants, these tubulins were incorporated into microtubules along with endogenous tubulins. Plants expressing the modified beta-tubulins were phenotypically normal and possessed transversely oriented cortical arrays in the epidermal cells of the root elongation zone; however, the expression of modified alpha-tubulins caused right-handed helical growth, increased trichome branching, and a shallow left-handed (S-form) helical array organization. In cells expressing the modified alpha-tubulins, microtubule dynamicity was suppressed and polymerization was promoted, and GFP-EB1 (End Binding 1) labeled larger regions of the microtubule end more frequently, when compared with control cells. We propose that the N-terminal appendage introduced into alpha-tubulin inhibits GTP hydrolysis, thus producing polymerization-prone microtubules with an extended GTP cap. Consistent with this interpretation, plants expressing an alpha-tubulin mutated in the GTPase-activating domain exhibited similar microtubule properties, with regard to dynamics and the localization of GFP-EB1, and showed right-handed helical growth.
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Affiliation(s)
- Tatsuya Abe
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara 630-0192, Japan
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Sontag CA, Staley JT, Erickson HP. In vitro assembly and GTP hydrolysis by bacterial tubulins BtubA and BtubB. ACTA ACUST UNITED AC 2005; 169:233-8. [PMID: 15851515 PMCID: PMC2171859 DOI: 10.1083/jcb.200410027] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Arecent study identified genuine tubulin proteins, BtubA and BtubB, in the bacterial genus Prosthecobacter. We have expressed BtubA and BtubB in Escherichia coli and studied their in vitro assembly. BtubB by itself formed rings with an outer diameter of 35–36 nm in the presence of GTP or GDP. Mixtures of BtubB and BtubA formed long protofilament bundles, 4–7 protofilaments wide (20–30 protofilaments in the three-dimensional bundle). Regardless of the starting stoichiometry, the polymers always contained equal concentrations of BtubA and BtubB, suggesting that BtubA and B alternate along the protofilament. BtubA showed negligible GTP hydrolysis, whereas BtubB hydrolyzed 0.40 mol GTP per min per mol BtubB. This GTPase activity increased to 1.37 per min when mixed 1:1 with BtubA. A critical concentration of 0.4–1.0 μM was indicated by light scattering experiments and extrapolation of GTPase versus concentration, thus suggesting a cooperative assembly mechanism.
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Affiliation(s)
- Christopher A Sontag
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
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Lu C, Mains PE. Mutations of a redundant alpha-tubulin gene affect Caenorhabditis elegans early embryonic cleavage via MEI-1/katanin-dependent and -independent pathways. Genetics 2005; 170:115-26. [PMID: 15781712 PMCID: PMC1449697 DOI: 10.1534/genetics.104.030106] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The C. elegans zygote supports both meiosis and mitosis within a common cytoplasm. The meiotic spindle is small and is located anteriorly, whereas the first mitotic spindle fills the zygote. The C. elegans microtubule-severing complex, katanin, is encoded by the mei-1 and mei-2 genes and is solely required for oocyte meiotic spindle formation; ectopic mitotic katanin activity disrupts mitotic spindles. Here we characterize two mutations that rescue the lethality caused by ectopic MEI-1/MEI-2. Both mutations are gain-of-function alleles of tba-2 alpha-tubulin. These tba-2 alleles do not prevent MEI-1/MEI-2 microtubule localization but do interfere with its activity. TBA-1 and TBA-2 are redundant for viability, but when katanin activity is limiting, TBA-2 is preferred over TBA-1 by katanin. This is similar to what we previously reported for the beta-tubulins. Removing both preferred alpha- and beta-isoforms results in normal development, suggesting that the katanin isoform preferences are not absolute. We conclude that while the C. elegans embryo expresses redundant alpha- and beta-tubulin isoforms, they nevertheless have subtle functional specializations. Finally, we identified a dominant tba-2 allele that disrupts both meiotic and mitotic spindle formation independently of MEI-1/MEI-2 activity. Genetic studies suggest that this tba-2 mutation has a "poisonous" effect on microtubule function.
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Affiliation(s)
- Chenggang Lu
- Genes and Development Research Group, Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada
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Phillips JB, Lyczak R, Ellis GC, Bowerman B. Roles for two partially redundant alpha-tubulins during mitosis in early Caenorhabditis elegans embryos. ACTA ACUST UNITED AC 2005; 58:112-26. [PMID: 15083533 DOI: 10.1002/cm.20003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The Caenorhabditis elegans genome encodes multiple isotypes of alpha-tubulin and beta-tubulin. Roles for a number of these tubulins in neuronal development have been described, but less is known about the isoforms that function during early embryonic development. Microtubules are required for multiple events after fertilization produces a one-cell zygote in C. elegans, including pronuclear migration, mitotic spindle assembly and function, and proper spindle positioning. Here we describe a conditional and dominant mis-sense mutation in the C. elegans alpha-tubulin gene tba-1 that disrupts pronuclear migration and positioning of the first mitotic spindle, and results in a highly penetrant embryonic lethality, at the restrictive temperature of 26 degrees C. Our analysis of the dominant tba-1 (or346ts) allele suggests that TBA-1 assembles into microtubules in early embryonic cells. However, we also show that reduction of tba-1 function using RNA interference results in defects much less severe than those caused by the dominant or346ts mutation, due to partial redundancy of TBA-1 and another alpha-tubulin called TBA-2. Reducing the function of both TBA-1 and TBA-2 results in severe defects in microtubule-dependent processes. We conclude that microtubules in the early C. elegans embryo are composed of both TBA-1 and TBA-2, and that the dominant tba-1(or346ts) mutation disrupts MT assembly or stability. Cell Motil.
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Usui T, Watanabe H, Nakayama H, Tada Y, Kanoh N, Kondoh M, Asao T, Takio K, Watanabe H, Nishikawa K, Kitahara T, Osada H. The Anticancer Natural Product Pironetin Selectively Targets Lys352 of α-Tubulin. ACTA ACUST UNITED AC 2004; 11:799-806. [PMID: 15217613 DOI: 10.1016/j.chembiol.2004.03.028] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2004] [Revised: 03/01/2004] [Accepted: 03/24/2004] [Indexed: 01/09/2023]
Abstract
Pironetin is a potent inhibitor of tubulin assembly and arrests cell cycle progression in M phase. Analyses of its structure-activity relationships suggested that pironetin covalently binds tubulin. To determine the binding site of pironetin, we synthesized biotinylated pironetin, which inhibited tubulin assembly both in vitro and in situ. The biotinylated pironetin selectively and covalently bound with tubulin. Partial digestion of biotinylated pironetin-treated tubulin by several proteases revealed that the binding site is the C-terminal portion of alpha-tubulin. By systematic alanine scanning, the pironetin binding site was determined to be Lys352 of alpha-tubulin. Lys352 is located at the entrance of a small pocket of alpha-tubulin, and this pocket faces the beta-tubulin of the next dimer. This is the first compound that covalently binds to the alpha subunit of tubulin and Lys352 of alpha-tubulin and inhibits the interaction of tubulin heterodimers.
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Affiliation(s)
- Takeo Usui
- Antibiotics Laboratory, RIKEN Discovery Research Institute, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
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Abstract
New evidence that cortical actin patches and the endocytic machinery share components supports the idea that actin patches are in fact transient membrane coats at the initial stage of endocytosis. Recent studies of actin cables have identified formins as the core of a novel actin-filament-assembling machine. Meanwhile, microtubule-binding proteins have been found in the kinetochore, and factors affecting microtubule dynamic instability have been identified.
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Affiliation(s)
- Daniel Schott
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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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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Current awareness on yeast. Yeast 2002; 19:651-8. [PMID: 11967835 DOI: 10.1002/yea.824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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39
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Current awareness on yeast. Yeast 2002; 19:565-72. [PMID: 11921105 DOI: 10.1002/yea.823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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