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Barrero DJ, Wijeratne SS, Zhao X, Cunningham GF, Rui Y, Nelson CR, Yasuhiro A, Funabiki H, Asbury CL, Yu Z, Subramanian R, Biggins S. Architecture and flexibility of native kinetochores revealed by structural studies utilizing a thermophilic yeast. bioRxiv 2024:2024.02.28.582571. [PMID: 38464254 PMCID: PMC10925344 DOI: 10.1101/2024.02.28.582571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Eukaryotic chromosome segregation requires kinetochores, multi-megadalton protein machines that assemble on the centromeres of chromosomes and mediate attachments to dynamic spindle microtubules. Kinetochores are built from numerous complexes, and understanding how they are arranged is key to understanding how kinetochores perform their multiple functions. However, an integrated understanding of kinetochore architecture has not yet been established. To address this, we purified functional, native kinetochores from Kluyveromyces marxianus and examined them by electron microscopy, cryo-electron tomography and atomic force microscopy. The kinetochores are extremely large, flexible assemblies that exhibit features consistent with prior models. We assigned kinetochore polarity by visualizing their interactions with microtubules and locating the microtubule binder Ndc80c. This work shows that isolated kinetochores are more dynamic and complex than what might be anticipated based on the known structures of recombinant subassemblies, and provides the foundation to study the global architecture and functions of kinetochores at a structural level.
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Affiliation(s)
- Daniel J. Barrero
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA
| | - Sithara S. Wijeratne
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaowei Zhao
- Howard Hughes Medical Institute Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Grace F. Cunningham
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Yan Rui
- Howard Hughes Medical Institute Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Christian R. Nelson
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Arimura Yasuhiro
- The Rockefeller University, 1230 York Ave., New York, NY 10065, USA
| | | | - Charles L. Asbury
- Department of Physiology and Biophysics, 1959 NE Pacific Street, University of Washington, Seattle, WA 98195, USA
| | - Zhiheng Yu
- Howard Hughes Medical Institute Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Radhika Subramanian
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sue Biggins
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
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2
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Leeds BK, Kostello KF, Liu YY, Nelson CR, Biggins S, Asbury CL. Mechanical coupling coordinates microtubule growth. eLife 2023; 12:RP89467. [PMID: 38150374 PMCID: PMC10752587 DOI: 10.7554/elife.89467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023] Open
Abstract
During mitosis, kinetochore-attached microtubules form bundles (k-fibers) in which many filaments grow and shorten in near-perfect unison to align and segregate each chromosome. However, individual microtubules grow at intrinsically variable rates, which must be tightly regulated for a k-fiber to behave as a single unit. This exquisite coordination might be achieved biochemically, via selective binding of polymerases and depolymerases, or mechanically, because k-fiber microtubules are coupled through a shared load that influences their growth. Here, we use a novel dual laser trap assay to show that microtubule pairs growing in vitro are coordinated by mechanical coupling. Kinetic analyses show that microtubule growth is interrupted by stochastic, force-dependent pauses and indicate persistent heterogeneity in growth speed during non-pauses. A simple model incorporating both force-dependent pausing and persistent growth speed heterogeneity explains the measured coordination of microtubule pairs without any free fit parameters. Our findings illustrate how microtubule growth may be synchronized during mitosis and provide a basis for modeling k-fiber bundles with three or more microtubules, as found in many eukaryotes.
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Affiliation(s)
- Bonnibelle K Leeds
- Department of Physiology & Biophysics, University of WashingtonSeattleUnited States
| | - Katelyn F Kostello
- Department of Physiology & Biophysics, University of WashingtonSeattleUnited States
| | - Yuna Y Liu
- Department of Physiology & Biophysics, University of WashingtonSeattleUnited States
| | - Christian R Nelson
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Sue Biggins
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Charles L Asbury
- Department of Physiology & Biophysics, University of WashingtonSeattleUnited States
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3
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Leeds BK, Kostello KF, Liu YY, Nelson CR, Biggins S, Asbury CL. Mechanical coupling coordinates microtubule growth. bioRxiv 2023:2023.06.29.547092. [PMID: 37905093 PMCID: PMC10614740 DOI: 10.1101/2023.06.29.547092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
During mitosis, kinetochore-attached microtubules form bundles (k-fibers) in which many filaments grow and shorten in near-perfect unison to align and segregate each chromosome. However, individual microtubules grow at intrinsically variable rates, which must be tightly regulated for a k-fiber to behave as a single unit. This exquisite coordination might be achieved biochemically, via selective binding of polymerases and depolymerases, or mechanically, because k-fiber microtubules are coupled through a shared load that influences their growth. Here, we use a novel dual laser trap assay to show that microtubule pairs growing in vitro are coordinated by mechanical coupling. Kinetic analyses show that microtubule growth is interrupted by stochastic, force-dependent pauses and indicate persistent heterogeneity in growth speed during non-pauses. A simple model incorporating both force-dependent pausing and persistent growth speed heterogeneity explains the measured coordination of microtubule pairs without any free fit parameters. Our findings illustrate how microtubule growth may be synchronized during mitosis and provide a basis for modeling k-fiber bundles with three or more microtubules, as found in many eukaryotes.
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Affiliation(s)
- Bonnibelle K. Leeds
- Physiology & Biophysics Department, University of Washington School of Medicine, Seattle WA, USA
| | - Katelyn F. Kostello
- Physiology & Biophysics Department, University of Washington School of Medicine, Seattle WA, USA
| | - Yuna Y. Liu
- Physiology & Biophysics Department, University of Washington School of Medicine, Seattle WA, USA
| | | | | | - Charles L. Asbury
- Physiology & Biophysics Department, University of Washington School of Medicine, Seattle WA, USA
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4
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Popchock AR, Larson JD, Dubrulle J, Asbury CL, Biggins S. Direct observation of coordinated assembly of individual native centromeric nucleosomes. EMBO J 2023; 42:e114534. [PMID: 37469281 PMCID: PMC10476280 DOI: 10.15252/embj.2023114534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 07/21/2023] Open
Abstract
Eukaryotic chromosome segregation requires the kinetochore, a megadalton-sized machine that forms on specialized centromeric chromatin containing CENP-A, a histone H3 variant. CENP-A deposition requires a chaperone protein HJURP that targets it to the centromere, but it has remained unclear whether HJURP has additional functions beyond CENP-A targeting and why high AT DNA content, which disfavors nucleosome assembly, is widely conserved at centromeres. To overcome the difficulties of studying nucleosome formation in vivo, we developed a microscopy assay that enables direct observation of de novo centromeric nucleosome recruitment and maintenance with single molecule resolution. Using this assay, we discover that CENP-A can arrive at centromeres without its dedicated centromere-specific chaperone HJURP, but stable incorporation depends on HJURP and additional DNA-binding proteins of the inner kinetochore. We also show that homopolymer AT runs in the yeast centromeres are essential for efficient CENP-A deposition. Together, our findings reveal requirements for stable nucleosome formation and provide a foundation for further studies of the assembly and dynamics of native kinetochore complexes.
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Affiliation(s)
- Andrew R Popchock
- Basic Sciences Division, Howard Hughes Medical InstituteFred Hutchinson Cancer CenterSeattleWAUSA
| | - Joshua D Larson
- Department of Physiology and BiophysicsUniversity of WashingtonSeattleWAUSA
| | | | - Charles L Asbury
- Department of Physiology and BiophysicsUniversity of WashingtonSeattleWAUSA
| | - Sue Biggins
- Basic Sciences Division, Howard Hughes Medical InstituteFred Hutchinson Cancer CenterSeattleWAUSA
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5
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Popchock AR, Larson JD, Dubrulle J, Asbury CL, Biggins S. Direct observation of coordinated assembly of individual native centromeric nucleosomes. bioRxiv 2023:2023.01.20.524981. [PMID: 36711558 PMCID: PMC9882320 DOI: 10.1101/2023.01.20.524981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Eukaryotic chromosome segregation requires the kinetochore, a megadalton-sized machine that forms on specialized centromeric chromatin containing CENP-A, a histone H3 variant. CENP-A deposition requires a chaperone protein HJURP that targets it to the centromere, but it has remained unclear whether HJURP has additional functions beyond CENP-A targeting and why high AT DNA content, which disfavors nucleosome assembly, is widely conserved at centromeres. To overcome the difficulties of studying nucleosome formation in vivo, we developed a microscopy assay that enables direct observation of de novo centromeric nucleosome recruitment and maintenance with single molecule resolution. Using this assay, we discover that CENP-A can arrive at centromeres without its dedicated centromere-specific chaperone HJURP, but stable incorporation depends on HJURP and additional DNA-binding proteins of the inner kinetochore. We also show that homopolymer AT runs in the yeast centromeres are essential for efficient CENP-A deposition. Together, our findings reveal requirements for stable nucleosome formation and provide a foundation for further studies of the assembly and dynamics of native kinetochore complexes.
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Affiliation(s)
- Andrew R. Popchock
- Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Joshua D. Larson
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Julien Dubrulle
- Shared Resources, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Charles L. Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Sue Biggins
- Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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6
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Haase MAB, Ólafsson G, Flores RL, Boakye‐Ansah E, Zelter A, Dickinson MS, Lazar‐Stefanita L, Truong DM, Asbury CL, Davis TN, Boeke JD. DASH/Dam1 complex mutants stabilize ploidy in histone-humanized yeast by weakening kinetochore-microtubule attachments. EMBO J 2023; 42:e112600. [PMID: 36651597 PMCID: PMC10106983 DOI: 10.15252/embj.2022112600] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 01/19/2023] Open
Abstract
Forcing budding yeast to chromatinize their DNA with human histones manifests an abrupt fitness cost. We previously proposed chromosomal aneuploidy and missense mutations as two potential modes of adaptation to histone humanization. Here, we show that aneuploidy in histone-humanized yeasts is specific to a subset of chromosomes that are defined by their centromeric evolutionary origins but that these aneuploidies are not adaptive. Instead, we find that a set of missense mutations in outer kinetochore proteins drives adaptation to human histones. Furthermore, we characterize the molecular mechanism underlying adaptation in two mutants of the outer kinetochore DASH/Dam1 complex, which reduce aneuploidy by suppression of chromosome instability. Molecular modeling and biochemical experiments show that these two mutants likely disrupt a conserved oligomerization interface thereby weakening microtubule attachments. We propose a model through which weakened microtubule attachments promote increased kinetochore-microtubule turnover and thus suppress chromosome instability. In sum, our data show how a set of point mutations evolved in histone-humanized yeasts to counterbalance human histone-induced chromosomal instability through weakening microtubule interactions, eventually promoting a return to euploidy.
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Affiliation(s)
- Max A B Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular PharmacologyNYU Langone HealthNew YorkNYUSA
- Vilcek Institute of Graduate Biomedical SciencesNYU School of MedicineNew YorkNYUSA
| | - Guðjón Ólafsson
- Institute for Systems Genetics and Department of Biochemistry and Molecular PharmacologyNYU Langone HealthNew YorkNYUSA
| | - Rachel L Flores
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | | | - Alex Zelter
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | | | - Luciana Lazar‐Stefanita
- Institute for Systems Genetics and Department of Biochemistry and Molecular PharmacologyNYU Langone HealthNew YorkNYUSA
| | - David M Truong
- Department of Biomedical EngineeringNYU Tandon School of EngineeringBrooklynNYUSA
- Department of PathologyNYU Langone HealthNew YorkNYUSA
| | - Charles L Asbury
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
- Department of Physiology and BiophysicsUniversity of WashingtonSeattleWAUSA
| | - Trisha N Davis
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular PharmacologyNYU Langone HealthNew YorkNYUSA
- Department of Biomedical EngineeringNYU Tandon School of EngineeringBrooklynNYUSA
- Department of Biochemistry and Molecular PharmacologyNYU Langone HealthNew YorkNYUSA
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7
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Murray LE, Maki-Fern L, Rice L, Asbury CL. Working strokes produced by curling protofilaments at disassembling microtubule tips: Their role in kinetochore motility and microtubule dynamics. Biophys J 2023; 122:125a. [PMID: 36782552 DOI: 10.1016/j.bpj.2022.11.844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Lucas E Murray
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Lucia Maki-Fern
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Luke Rice
- University of Texas Southwestern Medical Center Dallas, Dallas, TX, USA
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
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8
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Murray LE, Kim H, Rice LM, Asbury CL. Working strokes produced by curling protofilaments at disassembling microtubule tips can be biochemically tuned and vary with species. eLife 2022; 11:e83225. [PMID: 36580070 PMCID: PMC9799970 DOI: 10.7554/elife.83225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/25/2022] [Indexed: 12/30/2022] Open
Abstract
The disassembly of microtubules can generate force and drive intracellular motility. During mitosis, for example, chromosomes remain persistently attached via kinetochores to the tips of disassembling microtubules, which pull the sister chromatids apart. According to the conformational wave hypothesis, such force generation requires that protofilaments curl outward from the disassembling tips to exert pulling force directly on kinetochores. Rigorously testing this idea will require modifying the mechanical and energetic properties of curling protofilaments, but no way to do so has yet been described. Here, by direct measurement of working strokes generated in vitro by curling protofilaments, we show that their mechanical energy output can be increased by adding magnesium, and that yeast microtubules generate larger and more energetic working strokes than bovine microtubules. Both the magnesium and species-dependent increases in work output can be explained by lengthening the protofilament curls, without any change in their bending stiffness or intrinsic curvature. These observations demonstrate how work output from curling protofilaments can be tuned and suggest evolutionary conservation of the amount of curvature strain energy stored in the microtubule lattice.
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Affiliation(s)
- Lucas E Murray
- Department of Physiology and Biophysics, University of WashingtonSeattleUnited States
| | - Haein Kim
- Department of Physiology and Biophysics, University of WashingtonSeattleUnited States
| | - Luke M Rice
- Department of Biophysics, UT Southwestern Medical CenterDallasUnited States
- Department of Biochemistry, UT Southwestern Medical CenterDallasUnited States
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of WashingtonSeattleUnited States
- Department of Biochemistry, University of WashingtonSeattleUnited States
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9
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Flores RL, Peterson ZE, Zelter A, Riffle M, Asbury CL, Davis TN. Three interacting regions of the Ndc80 and Dam1 complexes support microtubule tip-coupling under load. J Cell Biol 2022; 221:213102. [PMID: 35353161 DOI: 10.1083/jcb.202107016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 12/20/2021] [Accepted: 03/07/2022] [Indexed: 01/15/2023] Open
Abstract
Accurate mitosis requires kinetochores to make persistent, load-bearing attachments to dynamic microtubule tips, thereby coupling chromosome movements to tip growth and shortening. This tip-coupling behavior depends on the conserved Ndc80 complex and, in budding yeast, on the Dam1 complex, which bind each other directly via three distinct interacting regions. The functional relevance of these multiple interactions was mysterious. Here we show that interactions between two of these regions support the high rupture strengths that occur when applied force is rapidly increased and also support the stability of tip-coupling when force is held constant over longer durations. The contribution of either of these two regions to tip-coupling is reduced by phosphorylation by Aurora B kinase. The third interaction region makes no apparent contribution to rupture strength, but its phosphorylation by Aurora B kinase specifically decreases the long-term stability of tip-coupling. The specific reduction of long-term stability relative to short-term strength might have important implications for mitotic error correction.
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Affiliation(s)
- Rachel L Flores
- Department of Biochemistry, University of Washington, Seattle, WA
| | | | - Alex Zelter
- Department of Biochemistry, University of Washington, Seattle, WA
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, WA
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, WA
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, WA
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10
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de Regt AK, Clark CJ, Asbury CL, Biggins S. Tension can directly suppress Aurora B kinase-triggered release of kinetochore-microtubule attachments. Nat Commun 2022; 13:2152. [PMID: 35443757 PMCID: PMC9021268 DOI: 10.1038/s41467-022-29542-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 03/03/2022] [Indexed: 11/09/2022] Open
Abstract
Chromosome segregation requires sister kinetochores to attach microtubules emanating from opposite spindle poles. Proper attachments come under tension and are stabilized, but defective attachments lacking tension are released, giving another chance for correct attachments to form. This error correction process depends on Aurora B kinase, which phosphorylates kinetochores to destabilize their microtubule attachments. However, the mechanism by which Aurora B distinguishes tense versus relaxed kinetochores remains unclear because it is difficult to detect kinase-triggered detachment and to manipulate kinetochore tension in vivo. To address these challenges, we apply an optical trapping-based assay using soluble Aurora B and reconstituted kinetochore-microtubule attachments. Strikingly, the tension on these attachments suppresses their Aurora B-triggered release, suggesting that tension-dependent changes in the conformation of kinetochores can regulate Aurora B activity or its outcome. Our work uncovers the basis for a key mechano-regulatory event that ensures accurate segregation and may inform studies of other mechanically regulated enzymes.
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Affiliation(s)
- Anna K de Regt
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Cordell J Clark
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA.
| | - Sue Biggins
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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11
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Murray LE, Kim H, Rice L, Asbury CL. Magnesium increases the chemo-mechanical energy released by curling protofilaments during microtubule disassembly. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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12
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Leeds BK, Asbury CL. A model suggesting that mechanical coupling can explain the coordination of microtubules within a k-fiber bundle during mitosis. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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13
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Murray LE, Kim H, Rice LM, Asbury CL. Catching the Conformational Wave: Measuring the Working Strokes of Protofilaments as They Curl Outward from Disassembling Microtubule Tips. Methods Mol Biol 2022; 2478:653-676. [PMID: 36063337 PMCID: PMC9542027 DOI: 10.1007/978-1-0716-2229-2_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Optical traps have enabled foundational studies of how mechanoenzymes such as kinesins and dynein motors walk along microtubules, how myosins move along F-actin, and how nucleic acid enzymes move along DNA or RNA. Often the filamentous substrates serve merely as passive tracks for mechanoenzymes but microtubules and F-actin are themselves dynamic protein polymers, capable of generating movement and force independently of conventional motors. Microtubule-driven forces are particularly important during mitosis, when they align duplicated chromosomes at the metaphase plate and then pull them apart during anaphase. These vital movements depend on specialized protein assemblies called kinetochores that couple the chromosomes to the tips of dynamic microtubule filaments, thereby allowing filament shortening to produce pulling forces. Although great strides have been made toward understanding the structures and functions of many kinetochore subcomplexes, the biophysical basis for their coupling to microtubule tips remains unclear. During tip disassembly, strain energy is released when straight protofilaments in the microtubule lattice curl outward, creating a conformational wave that propagates down the microtubule. A popular viewpoint is that the protofilaments as they curl outward hook elements of the kinetochore and tug on them, transferring some of their curvature strain energy to the kinetochore. As a first step toward testing this idea, we recently developed a laser trap assay to directly measure the working strokes generated by curling protofilaments. Our "wave" assay is based on an earlier pioneering study, with improvements that allow measurement of curl-driven movements as functions of force and quantification of their conformational strain energy. In this chapter, we provide a detailed protocol for our assay and describe briefly our instrument setup and data analysis methods.
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Affiliation(s)
- Lucas E. Murray
- Department of Physiology & Biophysics, University of Washington, Seattle WA 98195, USA
| | - Haein Kim
- Department of Physiology & Biophysics, University of Washington, Seattle WA 98195, USA
| | - Luke M. Rice
- Department of Biophysics, UT Southwestern Medical Center, Dallas TX 75390, USA
| | - Charles L. Asbury
- Department of Physiology & Biophysics, University of Washington, Seattle WA 98195, USA.,address correspondence to:
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14
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Laine LJ, Mäki-Jouppila JHE, Kutvonen E, Tiikkainen P, Nyholm TKM, Tien JF, Umbreit NT, Härmä V, Kallio L, Davis TN, Asbury CL, Poso A, Gorbsky GJ, Kallio MJ. VTT-006, an anti-mitotic compound, binds to the Ndc80 complex and suppresses cancer cell growth in vitro. Oncoscience 2021; 8:134-153. [PMID: 34926718 PMCID: PMC8667816 DOI: 10.18632/oncoscience.549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 12/01/2021] [Indexed: 11/25/2022] Open
Abstract
Hec1 (Highly expressed in cancer 1) resides in the outer kinetochore where it works to facilitate proper kinetochore-microtubule interactions during mitosis. Hec1 is overexpressed in various cancers and its expression shows correlation with high tumour grade and poor patient prognosis. Chemical perturbation of Hec1 is anticipated to impair kinetochore-microtubule binding, activate the spindle assembly checkpoint (spindle checkpoint) and thereby suppress cell proliferation. In this study, we performed high-throughput screen to identify novel small molecules that target the Hec1 calponin homology domain (CHD), which is needed for normal microtubule attachments. 4 million compounds were first virtually fitted against the CHD, and the best hit molecules were evaluated in vitro. These approaches led to the identification of VTT-006, a 1,2-disubstituted-tetrahydro-beta-carboline derivative, which showed binding to recombinant Ndc80 complex and modulated Hec1 association with microtubules in vitro. VTT-006 treatment resulted in chromosome congression defects, reduced chromosome oscillations and induced loss of inter-kinetochore tension. Cells remained arrested in mitosis with an active spindle checkpoint for several hours before undergoing cell death. VTT-006 suppressed the growth of several cancer cell lines and enhanced the sensitivity of HeLa cells to Taxol. Our findings propose that VTT-006 is a potential anti-mitotic compound that disrupts M phase, impairs kinetochore-microtubule interactions, and activates the spindle checkpoint.
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Affiliation(s)
- Leena J Laine
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland.,Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland.,These authors contributed equally to this work
| | - Jenni H E Mäki-Jouppila
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland.,Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland.,Drug Research Doctoral Programme, University of Turku, Finland.,Department of Pharmacology, Drug Development and Therapeutics, University of Turku, Turku, Finland.,These authors contributed equally to this work
| | - Emma Kutvonen
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland.,Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Pekka Tiikkainen
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland
| | | | - Jerry F Tien
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Neil T Umbreit
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Ville Härmä
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland
| | - Lila Kallio
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Gary J Gorbsky
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Marko J Kallio
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland.,Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
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15
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Sarangapani KK, Koch LB, Nelson CR, Asbury CL, Biggins S. Kinetochore-bound Mps1 regulates kinetochore-microtubule attachments via Ndc80 phosphorylation. J Cell Biol 2021; 220:e202106130. [PMID: 34647959 PMCID: PMC8641409 DOI: 10.1083/jcb.202106130] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/03/2021] [Accepted: 09/09/2021] [Indexed: 12/22/2022] Open
Abstract
Dividing cells detect and correct erroneous kinetochore-microtubule attachments during mitosis, thereby avoiding chromosome missegregation. The Aurora B kinase phosphorylates microtubule-binding elements specifically at incorrectly attached kinetochores, promoting their release and providing another chance for proper attachments to form. However, growing evidence suggests that the Mps1 kinase is also required for error correction. Here we directly examine how Mps1 activity affects kinetochore-microtubule attachments using a reconstitution-based approach that allows us to separate its effects from Aurora B activity. When endogenous Mps1 that copurifies with kinetochores is activated in vitro, it weakens their attachments to microtubules via phosphorylation of Ndc80, a major microtubule-binding protein. This phosphorylation contributes to error correction because phospho-deficient Ndc80 mutants exhibit genetic interactions and segregation defects when combined with mutants in other error correction pathways. In addition, Mps1 phosphorylation of Ndc80 is stimulated on kinetochores lacking tension. These data suggest that Mps1 provides an additional mechanism for correcting erroneous kinetochore-microtubule attachments, complementing the well-known activity of Aurora B.
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Affiliation(s)
| | - Lori B. Koch
- Howard Hughes Medical Institute, Chevy Chase, MD
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA
| | - Christian R. Nelson
- Howard Hughes Medical Institute, Chevy Chase, MD
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Charles L. Asbury
- Department of Physiology & Biophysics, University of Washington, Seattle, WA
| | - Sue Biggins
- Howard Hughes Medical Institute, Chevy Chase, MD
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
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16
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Ecklund KH, Bailey ME, Kossen KA, Dietvorst CK, Asbury CL, Markus SM. The microtubule-associated protein She1 coordinates directional spindle positioning by spatially restricting dynein activity. J Cell Sci 2021; 134:273583. [PMID: 34854468 DOI: 10.1242/jcs.258510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 10/27/2021] [Indexed: 11/20/2022] Open
Abstract
Dynein motors move the mitotic spindle to the cell division plane in many cell types, including in budding yeast, in which dynein is assisted by numerous factors including the microtubule-associated protein (MAP) She1. Evidence suggests that She1 plays a role in polarizing dynein-mediated spindle movements toward the daughter cell; however, how She1 performs this function is unknown. We find that She1 assists dynein in maintaining the spindle in close proximity to the bud neck, such that, at anaphase onset, the chromosomes are segregated to mother and daughter cells. She1 does so by attenuating the initiation of dynein-mediated spindle movements within the mother cell, thus ensuring such movements are polarized toward the daughter cell. Our data indicate that this activity relies on She1 binding to the microtubule-bound conformation of the dynein microtubule-binding domain, and to astral microtubules within mother cells. Our findings reveal how an asymmetrically localized MAP directionally tunes dynein activity by attenuating motor activity in a spatially confined manner.
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Affiliation(s)
- Kari H Ecklund
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Megan E Bailey
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195, USA
| | - Kelly A Kossen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Carsten K Dietvorst
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195, USA
| | - Steven M Markus
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
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17
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Fong KK, Davis TN, Asbury CL. Microtubule pivoting enables mitotic spindle assembly in S. cerevisiae. J Cell Biol 2021; 220:211686. [PMID: 33464308 PMCID: PMC7814349 DOI: 10.1083/jcb.202007193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/07/2020] [Accepted: 12/16/2020] [Indexed: 12/17/2022] Open
Abstract
To assemble a bipolar spindle, microtubules emanating from two poles must bundle into an antiparallel midzone, where plus end–directed motors generate outward pushing forces to drive pole separation. Midzone cross-linkers and motors display only modest preferences for antiparallel filaments, and duplicated poles are initially tethered together, an arrangement that instead favors parallel interactions. Pivoting of microtubules around spindle poles might help overcome this geometric bias, but the intrinsic pivoting flexibility of the microtubule–pole interface has not been directly measured, nor has its importance during early spindle assembly been tested. By measuring the pivoting of microtubules around isolated yeast spindle poles, we show that pivoting flexibility can be modified by mutating a microtubule-anchoring pole component, Spc110. By engineering mutants with different flexibilities, we establish the importance of pivoting in vivo for timely pole separation. Our results suggest that passive thermal pivoting can bring microtubules from side-by-side poles into initial contact, but active minus end–directed force generation will be needed to achieve antiparallel alignment.
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Affiliation(s)
- Kimberly K Fong
- Department of Physiology and Biophysics, University of Washington, Seattle, WA
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, WA
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, WA
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18
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Murray L, Kim H, Rice L, Asbury CL. Catching the Conformational Wave: Tuning the Working Strokes of Protofilaments as They Curl Outwards from Disassembling Microtubule Tips. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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19
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Gutierrez A, Kim JO, Umbreit NT, Asbury CL, Davis TN, Miller MP, Biggins S. Cdk1 Phosphorylation of the Dam1 Complex Strengthens Kinetochore-Microtubule Attachments. Curr Biol 2020; 30:4491-4499.e5. [PMID: 32946748 PMCID: PMC7497780 DOI: 10.1016/j.cub.2020.08.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 07/20/2020] [Accepted: 08/14/2020] [Indexed: 12/01/2022]
Abstract
To ensure the faithful inheritance of DNA, a macromolecular protein complex called the kinetochore sustains the connection between chromosomes and force-generating dynamic microtubules during cell division. Defects in this process lead to aneuploidy, a common feature of cancer cells and the cause of many developmental diseases [1, 2, 3, 4]. One of the major microtubule-binding activities in the kinetochore is mediated by the conserved Ndc80 complex (Ndc80c) [5, 6, 7]. In budding yeast, the retention of kinetochores on dynamic microtubule tips also depends on the essential heterodecameric Dam1 complex (Dam1c) [8, 9, 10, 11, 12, 13, 14, 15], which binds to the Ndc80c and is proposed to be a functional ortholog of the metazoan Ska complex [16, 17]. The load-bearing activity of the Dam1c depends on its ability to oligomerize, and the purified complex spontaneously self-assembles into microtubule-encircling oligomeric rings, which are proposed to function as collars that allow kinetochores to processively track the plus-end tips of microtubules and harness the forces generated by disassembling microtubules [10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22]. However, it is unknown whether there are specific regulatory events that promote Dam1c oligomerization to ensure accurate segregation. Here, we used a reconstitution system to discover that Cdk1, the major mitotic kinase that drives the cell cycle, phosphorylates the Ask1 component of the Dam1c to increase its residence time on microtubules and enhance kinetochore-microtubule attachment strength. We propose that Cdk1 activity promotes Dam1c oligomerization to ensure that kinetochore-microtubule attachments are stabilized as kinetochores come under tension in mitosis. Cdk1 phosphorylation of Dam1c strengthens kinetochore-microtubule attachments Ask1 is the key Cdk1 target in Dam1c that enhances for kinetochore-microtubule attachments Dynamic phosphorylation of Dam1c by Cdk1 is important in vivo Cdk1 phosphorylation of Ask1 appears to promote Dam1c oligomerization
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Affiliation(s)
- Abraham Gutierrez
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109, USA; Molecular and Cellular Biology Program, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA
| | - Jae Ook Kim
- Department of Biochemistry, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA
| | - Neil T Umbreit
- Department of Biochemistry, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA
| | - Matthew P Miller
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109, USA
| | - Sue Biggins
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109, USA.
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20
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King BR, Moritz M, Kim H, Agard DA, Asbury CL, Davis TN. XMAP215 and γ-tubulin additively promote microtubule nucleation in purified solutions. Mol Biol Cell 2020; 31:2187-2194. [PMID: 32726183 PMCID: PMC7550701 DOI: 10.1091/mbc.e20-02-0160] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 07/06/2020] [Accepted: 07/24/2020] [Indexed: 12/04/2022] Open
Abstract
Microtubule nucleation is spatiotemporally regulated in cells by several known molecules, including the template γ-tubulin and the polymerase XMAP215. The role of XMAP215 in nucleation is under debate, specifically whether it acts independently as a polymerase or acts dependently with γ-tubulin. We first confirm XMAP215 as a classically defined nucleator that reduces the nucleation lag seen in bulk tubulin assembly. Secondly, using deletion constructs, we probe the domain requirements for XMAP215 to promote microtubule nucleation. We show that its ability to nucleate microtubules in purified solutions correlates with its ability to elongate existing microtubules and does not depend on the number of tumor overexpressed gene (TOG) domains. Finally, we show that XMAP215 and γ-tubulin promote αβ-tubulin assembly in an additive, not synergistic, manner. Thus, their modes of action during microtubule nucleation are distinct. These findings suggest there are at least two independent processes in nucleation, one promoted by γ-tubulin and one promoted by XMAP215. We propose that XMAP215 accelerates the addition of subunits to existing nucleation intermediates formed either spontaneously or by oligomers of γ-tubulin. [Media: see text].
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Affiliation(s)
- Brianna R. King
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Michelle Moritz
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158
| | - Haein Kim
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - David A. Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158
| | - Charles L. Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Trisha N. Davis
- Department of Biochemistry, University of Washington, Seattle, WA 98195
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21
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Hamilton GE, Helgeson LA, Noland CL, Asbury CL, Dimitrova YN, Davis TN. Reconstitution reveals two paths of force transmission through the kinetochore. eLife 2020; 9:56582. [PMID: 32406818 PMCID: PMC7367685 DOI: 10.7554/elife.56582] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/13/2020] [Indexed: 01/23/2023] Open
Abstract
Partitioning duplicated chromosomes equally between daughter cells is a microtubule-mediated process essential to eukaryotic life. A multi-protein machine, the kinetochore, drives chromosome segregation by coupling the chromosomes to dynamic microtubule tips, even as the tips grow and shrink through the gain and loss of subunits. The kinetochore must harness, transmit, and sense mitotic forces, as a lack of tension signals incorrect chromosome-microtubule attachment and precipitates error correction mechanisms. But though the field has arrived at a ‘parts list’ of dozens of kinetochore proteins organized into subcomplexes, the path of force transmission through these components has remained unclear. Here we report reconstitution of functional Saccharomyces cerevisiae kinetochore assemblies from recombinantly expressed proteins. The reconstituted kinetochores are capable of self-assembling in vitro, coupling centromeric nucleosomes to dynamic microtubules, and withstanding mitotically relevant forces. They reveal two distinct pathways of force transmission and Ndc80c recruitment.
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Affiliation(s)
- Grace E Hamilton
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Luke A Helgeson
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Cameron L Noland
- Department of Structural Biology, Genentech Inc, South San Francisco, United States
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Yoana N Dimitrova
- Department of Structural Biology, Genentech Inc, South San Francisco, United States
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, United States
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22
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Miller MP, Evans RK, Zelter A, Geyer EA, MacCoss MJ, Rice LM, Davis TN, Asbury CL, Biggins S. Kinetochore-associated Stu2 promotes chromosome biorientation in vivo. PLoS Genet 2019; 15:e1008423. [PMID: 31584935 PMCID: PMC6795502 DOI: 10.1371/journal.pgen.1008423] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/16/2019] [Accepted: 09/13/2019] [Indexed: 12/31/2022] Open
Abstract
Accurate segregation of chromosomes to daughter cells is a critical aspect of cell division. It requires the kinetochores on duplicated chromosomes to biorient, attaching to microtubules from opposite poles of the cell. Bioriented attachments come under tension, while incorrect attachments lack tension and must be released to allow proper attachments to form. A well-studied error correction pathway is mediated by the Aurora B kinase, which destabilizes low tension-bearing attachments. We recently discovered that in vitro, kinetochores display an additional intrinsic tension-sensing pathway that utilizes Stu2. The contribution of kinetochore-associated Stu2 to error correction in cells, however, was unknown. Here, we identify a Stu2 mutant that abolishes its kinetochore function and show that it causes biorientation defects in vivo. We also show that this Stu2-mediated pathway functions together with the Aurora B-mediated pathway. Altogether, our work indicates that cells employ multiple pathways to ensure biorientation and the accuracy of chromosome segregation. The precise regulation of cell division is critical to processes such as self-renewal, proliferation and development. A key event in the cell cycle is the partitioning of every pair of duplicated chromosomes to daughter cells. Defects in chromosome partitioning lead to aneuploidy, a condition that is a common hallmark of cancer cells and the cause of some birth defects. Chromosomes segregate using their kinetochores, the specialized protein structures that are assembled on centromeric DNA sequences and attach to spindle microtubules. Here, we report that a protein that associates with kinetochores called Stu2 ensures that each kinetochore attaches to the proper microtubules. We identified a Stu2 mutant that does not associate with kinetochores and found that it generates aneuploidy. Together, our work identifies a previously unknown mechanism where cells ensure that chromosomes are accurately inherited during cell division.
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Affiliation(s)
- Matthew P. Miller
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Rena K. Evans
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Alex Zelter
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States of America
| | - Elisabeth A. Geyer
- Departments of Biophysics and Biochemistry, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Luke M. Rice
- Departments of Biophysics and Biochemistry, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Trisha N. Davis
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States of America
| | - Charles L. Asbury
- Department of Physiology & Biophysics, University of Washington, Seattle, Washington, United States of America
| | - Sue Biggins
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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23
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Scarborough EA, Davis TN, Asbury CL. Tight bending of the Ndc80 complex provides intrinsic regulation of its binding to microtubules. eLife 2019; 8:44489. [PMID: 31045495 PMCID: PMC6516834 DOI: 10.7554/elife.44489] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/26/2019] [Indexed: 02/07/2023] Open
Abstract
Regulation of the outer kinetochore complex Ndc80 is essential to ensure correct kinetochore-microtubule attachments during mitosis. Here, we present a novel mechanism of regulation that is intrinsic to its structure; tight bending of the Ndc80 complex inhibits its microtubule binding. Using single molecule Förster resonance energy transfer (FRET), we show that the Saccharomyces cerevisiae Ndc80 complex can fluctuate between straight and bent forms, and that binding of the complex to microtubules selects for straightened forms. The loop region of the complex enables its bent conformation, as deletion of the loop promotes straightening. In addition, the kinetochore complex MIND enhances microtubule binding by opposing the tightly bent, auto-inhibited conformation of the Ndc80 complex. We suggest that prior to its assembly at the kinetochore, the Ndc80 complex interchanges between bent (auto-inhibited) and open conformations. Once assembled, its association with MIND stabilizes the Ndc80 complex in a straightened form for higher affinity microtubule binding.
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Affiliation(s)
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
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24
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Llauró A, Hayashi H, Bailey ME, Wilson A, Ludzia P, Asbury CL, Akiyoshi B. The kinetoplastid kinetochore protein KKT4 is an unconventional microtubule tip-coupling protein. J Cell Biol 2018; 217:3886-3900. [PMID: 30209069 PMCID: PMC6219724 DOI: 10.1083/jcb.201711181] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 07/23/2018] [Accepted: 08/24/2018] [Indexed: 01/08/2023] Open
Abstract
The evolutionarily divergent class of kinetoplastid organisms has a set of unconventional kinetochore proteins that drive chromosome segregation, but it is unclear which components interact with spindle microtubules. Llauró et al. now identify KKT4 as the first microtubule-binding kinetochore protein in Trypanosoma brucei, a major human pathogenic parasite. Kinetochores are multiprotein machines that drive chromosome segregation by maintaining persistent, load-bearing linkages between chromosomes and dynamic microtubule tips. Kinetochores in commonly studied eukaryotes bind microtubules through widely conserved components like the Ndc80 complex. However, in evolutionarily divergent kinetoplastid species such as Trypanosoma brucei, which causes sleeping sickness, the kinetochores assemble from a unique set of proteins lacking homology to any known microtubule-binding domains. Here, we show that the T. brucei kinetochore protein KKT4 binds directly to microtubules and maintains load-bearing attachments to both growing and shortening microtubule tips. The protein localizes both to kinetochores and to spindle microtubules in vivo, and its depletion causes defects in chromosome segregation. We define a microtubule-binding domain within KKT4 and identify several charged residues important for its microtubule-binding activity. Thus, despite its lack of significant similarity to other known microtubule-binding proteins, KKT4 has key functions required for driving chromosome segregation. We propose that it represents a primary element of the kinetochore–microtubule interface in kinetoplastids.
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Affiliation(s)
- Aida Llauró
- Department of Physiology and Biophysics, University of Washington, Seattle, WA
| | - Hanako Hayashi
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Megan E Bailey
- Department of Physiology and Biophysics, University of Washington, Seattle, WA
| | - Alex Wilson
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Patryk Ludzia
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, WA
| | - Bungo Akiyoshi
- Department of Biochemistry, University of Oxford, Oxford, UK
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25
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Kim JO, Zelter A, Johnson R, MacCoss MJ, Asbury CL, Davis TN. Role of the Spc105 Complex in Organization and Microtubule‐Binding Activity of the Budding Yeast Kinetochore. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.533.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jae ook Kim
- BiochemistryUniversity of WashingtonSeattleWA
| | - Alex Zelter
- BiochemistryUniversity of WashingtonSeattleWA
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26
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Jung SR, Deng Y, Kushmerick C, Asbury CL, Hille B, Koh DS. Minimizing ATP Depletion by Oxygen Scavengers for Single-Molecule Fluorescence Imaging in Live Cells. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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27
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Driver JW, Geyer EA, Bailey ME, Rice LM, Asbury CL. Direct measurement of conformational strain energy in protofilaments curling outward from disassembling microtubule tips. eLife 2017. [PMID: 28628007 PMCID: PMC5515574 DOI: 10.7554/elife.28433] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Disassembling microtubules can generate movement independently of motor enzymes, especially at kinetochores where they drive chromosome motility. A popular explanation is the 'conformational wave' model, in which protofilaments pull on the kinetochore as they curl outward from a disassembling tip. But whether protofilaments can work efficiently via this spring-like mechanism has been unclear. By modifying a previous assay to use recombinant tubulin and feedback-controlled laser trapping, we directly demonstrate the spring-like elasticity of curling protofilaments. Measuring their mechanical work output suggests they carry ~25% of the energy of GTP hydrolysis as bending strain, enabling them to drive movement with efficiency similar to conventional motors. Surprisingly, a β-tubulin mutant that dramatically slows disassembly has no effect on work output, indicating an uncoupling of disassembly speed from protofilament strain. These results show the wave mechanism can make a major contribution to kinetochore motility and establish a direct approach for measuring tubulin mechano-chemistry.
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Affiliation(s)
- Jonathan W Driver
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Elisabeth A Geyer
- Department of Biophysics, UT Southwestern Medical Center, Dallas, United States.,Department of Biochemistry, UT Southwestern Medical Center, Dallas, United States
| | - Megan E Bailey
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Luke M Rice
- Department of Biophysics, UT Southwestern Medical Center, Dallas, United States.,Department of Biochemistry, UT Southwestern Medical Center, Dallas, United States
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
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28
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Fong KK, Sarangapani KK, Yusko EC, Riffle M, Llauró A, Graczyk B, Davis TN, Asbury CL. Direct measurement of the strength of microtubule attachment to yeast centrosomes. Mol Biol Cell 2017; 28:1853-1861. [PMID: 28331072 PMCID: PMC5541836 DOI: 10.1091/mbc.e17-01-0034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/13/2017] [Accepted: 03/17/2017] [Indexed: 01/14/2023] Open
Abstract
Laser trapping is used to manipulate single attached microtubules in vitro. Direct mechanical measurement shows that attachment of microtubule minus ends to yeast spindle pole bodies is extraordinarily strong. Centrosomes, or spindle pole bodies (SPBs) in yeast, are vital mechanical hubs that maintain load-bearing attachments to microtubules during mitotic spindle assembly, spindle positioning, and chromosome segregation. However, the strength of microtubule-centrosome attachments is unknown, and the possibility that mechanical force might regulate centrosome function has scarcely been explored. To uncover how centrosomes sustain and regulate force, we purified SPBs from budding yeast and used laser trapping to manipulate single attached microtubules in vitro. Our experiments reveal that SPB–microtubule attachments are extraordinarily strong, rupturing at forces approximately fourfold higher than kinetochore attachments under identical loading conditions. Furthermore, removal of the calmodulin-binding site from the SPB component Spc110 weakens SPB–microtubule attachment in vitro and sensitizes cells to increased SPB stress in vivo. These observations show that calmodulin binding contributes to SPB mechanical integrity and suggest that its removal may cause pole delamination and mitotic failure when spindle forces are elevated. We propose that the very high strength of SPB–microtubule attachments may be important for spindle integrity in mitotic cells so that tensile forces generated at kinetochores do not cause microtubule detachment and delamination at SPBs.
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Affiliation(s)
- Kimberly K Fong
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Krishna K Sarangapani
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Erik C Yusko
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Aida Llauró
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Beth Graczyk
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
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29
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Asbury CL. Anaphase A: Disassembling Microtubules Move Chromosomes toward Spindle Poles. Biology (Basel) 2017; 6:E15. [PMID: 28218660 PMCID: PMC5372008 DOI: 10.3390/biology6010015] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/04/2017] [Accepted: 02/10/2017] [Indexed: 11/16/2022]
Abstract
The separation of sister chromatids during anaphase is the culmination of mitosis and one of the most strikingly beautiful examples of cellular movement. It consists of two distinct processes: Anaphase A, the movement of chromosomes toward spindle poles via shortening of the connecting fibers, and anaphase B, separation of the two poles from one another via spindle elongation. I focus here on anaphase A chromosome-to-pole movement. The chapter begins by summarizing classical observations of chromosome movements, which support the current understanding of anaphase mechanisms. Live cell fluorescence microscopy studies showed that poleward chromosome movement is associated with disassembly of the kinetochore-attached microtubule fibers that link chromosomes to poles. Microtubule-marking techniques established that kinetochore-fiber disassembly often occurs through loss of tubulin subunits from the kinetochore-attached plus ends. In addition, kinetochore-fiber disassembly in many cells occurs partly through 'flux', where the microtubules flow continuously toward the poles and tubulin subunits are lost from minus ends. Molecular mechanistic models for how load-bearing attachments are maintained to disassembling microtubule ends, and how the forces are generated to drive these disassembly-coupled movements, are discussed.
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Affiliation(s)
- Charles L Asbury
- Department of Physiology & Biophysics, University of Washington, Seattle, WA 98195, USA.
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30
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Kim JO, Zelter A, Umbreit NT, Bollozos A, Riffle M, Johnson R, MacCoss MJ, Asbury CL, Davis TN. The Ndc80 complex bridges two Dam1 complex rings. eLife 2017; 6. [PMID: 28191870 PMCID: PMC5354518 DOI: 10.7554/elife.21069] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 02/11/2017] [Indexed: 12/18/2022] Open
Abstract
Strong kinetochore-microtubule attachments are essential for faithful segregation of sister chromatids during mitosis. The Dam1 and Ndc80 complexes are the main microtubule binding components of the Saccharomyces cerevisiae kinetochore. Cooperation between these two complexes enhances kinetochore-microtubule coupling and is regulated by Aurora B kinase. We show that the Ndc80 complex can simultaneously bind and bridge across two Dam1 complex rings through a tripartite interaction, each component of which is regulated by Aurora B kinase. Mutations in any one of the Ndc80p interaction regions abrogates the Ndc80 complex's ability to bind two Dam1 rings in vitro, and results in kinetochore biorientation and microtubule attachment defects in vivo. We also show that an extra-long Ndc80 complex, engineered to space the two Dam1 rings further apart, does not support growth. Taken together, our work suggests that each kinetochore in vivo contains two Dam1 rings and that proper spacing between the rings is vital.
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Affiliation(s)
- Jae Ook Kim
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Alex Zelter
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Neil T Umbreit
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Athena Bollozos
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Richard Johnson
- Department of Genome Sciences, University of Washington, Seattle, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, United States
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, United States
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31
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Opoku KN, Koch L, Biggins S, Asbury CL. What Silences the Spindle Checkpoint? A Single Particle Study. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.2304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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32
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Driver JW, Geyer EA, Bailey ME, Rice LM, Asbury CL. Direct Measurement of the Force-Generating Capacity of Protofilaments Curling Outward from Disassembling Microtubule Tips. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.3043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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33
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Abstract
Kinetochores are large multiprotein complexes that drive mitotic chromosome movements by mechanically coupling them to the growing and shortening tips of spindle microtubules. Kinetochores are also regulatory hubs, somehow sensing when they are erroneously attached and, in response, releasing their incorrect attachments and generating diffusible wait signals to delay anaphase until proper attachments can form. The remarkable ability of a kinetochore to sense and respond to its attachment status might stem from attachment- or tension-dependent changes in the structural arrangement of its core subcomplexes. However, direct tests of the relationship between attachment, tension, and core kinetochore structure have not previously been possible because of the difficulties of applying well-controlled forces and determining unambiguously the attachment status of individual kinetochores in vivo. The recent purification of native yeast kinetochores has enabled in vitro optical trapping-based assays of kinetochore tip-coupling and, in separate experiments, fluorescence imaging of single kinetochore particles. Here we introduce a dual instrument, combining optical trapping with multicolor total internal reflection fluorescence (TIRF) imaging, to allow kinetochore structure to be monitored directly with nanometer precision while mechanical tension is simultaneously applied. Our instrument incorporates differential interference contrast (DIC) imaging as well, to minimize the photo-bleaching of fluorescent tags during preparative bead and microtubule manipulations. A simple modification also allows the trapping laser to be easily converted into a real-time focus detection and correction system. Using this combined instrument, the distance between specific subcomplexes within a single kinetochore particle can be measured with 2-nm precision after 50 s observation time, or with 11-nm precision at 1 s temporal resolution. While our instrument was constructed specifically for studying kinetochores, it should also be useful for studying other filament-binding protein complexes, such as spindle poles, cortical microtubule attachments, focal adhesions, or other motor-cytoskeletal junctions.
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Affiliation(s)
- Yi Deng
- Department of Physiology & Biophysics, University of Washington, 1959 NE Pacific Street, Box 357290, Seattle, WA, 98195, USA
| | - Charles L Asbury
- Department of Physiology & Biophysics, University of Washington, 1959 NE Pacific Street, Box 357290, Seattle, WA, 98195, USA.
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34
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Jung SR, Seo JB, Deng Y, Asbury CL, Hille B, Koh DS. Contributions of protein kinases and β-arrestin to termination of protease-activated receptor 2 signaling. ACTA ACUST UNITED AC 2016; 147:255-71. [PMID: 26927499 PMCID: PMC4772372 DOI: 10.1085/jgp.201511477] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Systematic imaging studies and modeling reveal new details of the regulation of the Gq-coupled GPCR, protease-activated receptor 2, by phosphorylation and β-arrestin. Activated Gq protein–coupled receptors (GqPCRs) can be desensitized by phosphorylation and β-arrestin binding. The kinetics and individual contributions of these two mechanisms to receptor desensitization have not been fully distinguished. Here, we describe the shut off of protease-activated receptor 2 (PAR2). PAR2 activates Gq and phospholipase C (PLC) to hydrolyze phosphatidylinositol 4,5-bisphosphate (PIP2) into diacylglycerol and inositol trisphosphate (IP3). We used fluorescent protein–tagged optical probes to monitor several consequences of PAR2 signaling, including PIP2 depletion and β-arrestin translocation in real time. During continuous activation of PAR2, PIP2 was depleted transiently and then restored within a few minutes, indicating fast receptor activation followed by desensitization. Knockdown of β-arrestin 1 and 2 using siRNA diminished the desensitization, slowing PIP2 restoration significantly and even adding a delayed secondary phase of further PIP2 depletion. These effects of β-arrestin knockdown on PIP2 recovery were prevented when serine/threonine phosphatases that dephosphorylate GPCRs were inhibited. Thus, PAR2 may continuously regain its activity via dephosphorylation when there is insufficient β-arrestin to trap phosphorylated receptors. Similarly, blockers of protein kinase C (PKC) and G protein–coupled receptor kinase potentiated the PIP2 depletion. In contrast, an activator of PKC inhibited receptor activation, presumably by augmenting phosphorylation of PAR2. Our interpretations were strengthened by modeling. Simulations supported the conclusions that phosphorylation of PAR2 by protein kinases initiates receptor desensitization and that recruited β-arrestin traps the phosphorylated state of the receptor, protecting it from phosphatases. Speculative thinking suggested a sequestration of phosphatidylinositol 4-phosphate 5 kinase (PIP5K) to the plasma membrane by β-arrestin to explain why knockdown of β-arrestin led to secondary depletion of PIP2. Indeed, artificial recruitment of PIP5K removed the secondary loss of PIP2 completely. Altogether, our experimental and theoretical approaches demonstrate roles and dynamics of the protein kinases, β-arrestin, and PIP5K in the desensitization of PAR2.
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Affiliation(s)
- Seung-Ryoung Jung
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Jong Bae Seo
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Yi Deng
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Bertil Hille
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Duk-Su Koh
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195 Department of Physics, Pohang University of Science and Technology, Pohang, Kyungbuk, 790-784, Republic of Korea
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35
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Miller MP, Asbury CL, Biggins S. A TOG Protein Confers Tension Sensitivity to Kinetochore-Microtubule Attachments. Cell 2016; 165:1428-1439. [PMID: 27156448 DOI: 10.1016/j.cell.2016.04.030] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/25/2016] [Accepted: 04/07/2016] [Indexed: 01/10/2023]
Abstract
The development and survival of all organisms depends on equal partitioning of their genomes during cell division. Accurate chromosome segregation requires selective stabilization of kinetochore-microtubule attachments that come under tension due to opposing pulling forces exerted on sister kinetochores by dynamic microtubule tips. Here, we show that the XMAP215 family member, Stu2, makes a major contribution to kinetochore-microtubule coupling. Stu2 and its human ortholog, ch-TOG, exhibit a conserved interaction with the Ndc80 kinetochore complex that strengthens its attachment to microtubule tips. Strikingly, Stu2 can either stabilize or destabilize kinetochore attachments, depending on the level of kinetochore tension and whether the microtubule tip is assembling or disassembling. These dichotomous effects of Stu2 are independent of its previously studied regulation of microtubule dynamics. Altogether, our results demonstrate how a kinetochore-associated factor can confer opposing, tension-dependent effects to selectively stabilize tension-bearing attachments, providing mechanistic insight into the basis for accuracy during chromosome segregation.
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Affiliation(s)
- Matthew P Miller
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Charles L Asbury
- Department of Physiology & Biophysics, University of Washington, Seattle, WA 98195, USA.
| | - Sue Biggins
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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36
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Kudalkar EM, Deng Y, Davis TN, Asbury CL. Coverslip Cleaning and Functionalization for Total Internal Reflection Fluorescence Microscopy. Cold Spring Harb Protoc 2016; 2016:2016/5/pdb.prot085548. [PMID: 27140911 DOI: 10.1101/pdb.prot085548] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Total internal reflection fluorescence (TIRF) microscopy allows visualization of biological events at the single-molecule level by restricting excitation to a precise focal plane near the coverslip and eliminating out-of-focus fluorescence. The quality of TIRF imaging relies on a high signal-to-noise ratio and therefore it is imperative to prevent adherence of molecules to the glass coverslip. Nonspecific interactions can make it difficult to distinguish true binding events and may also interfere with accurate quantification of background noise. In addition, nonspecific binding of the fluorescently tagged protein will lower the effective working concentration, thereby altering values used to calculate affinity constants. To prevent spurious interactions, we thoroughly clean the surface of the coverslip and then functionalize the glass either by applying a layer of silane or by coating with a lipid bilayer.
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Affiliation(s)
- Emily M Kudalkar
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Yi Deng
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
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37
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Abstract
In the microscopes we use to analyze total internal reflection fluorescence (TIRF), the emitted fluorescence is split chromatically, using dichroic filters, into either two or three different colors ("channels"). In our two-color instrument, the green emission wavelengths (405-488 nm; for imaging green fluorescent protein [GFP]-tagged proteins) and far-red emission wavelengths (650-800 nm; for imaging Alexa-647-labeled microtubules) are projected onto the upper and lower halves, respectively, of a single camera. A single filter can be swapped to collect near-red wavelengths (561-640 nm; for imaging mCherry, or Alexa-568-labeled microtubules) instead of far-red. Our three-color instrument is very similar except that the green, near-red, and far-red color ranges are projected onto three separate cameras. In either case, the different colors can be imaged simultaneously. Typically, we collect images at 10 frames/sec for ∼200 sec. We have developed a series of semiautomated image analysis programs, written in LabView, to obtain the brightness, residence time, and mobility of individual particles bound to single microtubules. The basic analysis steps are straightforward and could also be implemented using ImageJ or Matlab. For convenience, this protocol describes the analysis of a single microtubule. Data from many microtubules across many experimental trials are needed to obtain robust conclusions that are independent of stochastic and trial-to-trial variability.
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Affiliation(s)
- Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
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38
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Abstract
The advent of total internal reflection fluorescence (TIRF) microscopy has permitted visualization of biological events on an unprecedented scale: the single-molecule level. Using TIRF, it is now possible to view complex biological interactions such as cargo transport by a single molecular motor or DNA replication in real time. TIRF allows for visualization of single molecules by eliminating out-of-focus fluorescence and enhancing the signal-to-noise ratio. TIRF has been instrumental for studying in vitro interactions and has also been successfully implemented in live-cell imaging. Visualization of cytoskeletal structures and dynamics at the plasma membrane, such as endocytosis, exocytosis, and adhesion, has become much clearer using TIRF microscopy. Thanks to recent advances in optics and commercial availability, TIRF microscopy is becoming an increasingly popular and user-friendly technique. In this introduction, we describe the fundamental properties of TIRF microscopy and the advantages of using TIRF for single-molecule investigation.
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Affiliation(s)
- Emily M Kudalkar
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
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39
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Kudalkar EM, Davis TN, Asbury CL. Preparation of Reactions for Imaging with Total Internal Reflection Fluorescence Microscopy. Cold Spring Harb Protoc 2016; 2016:2016/5/pdb.prot085563. [PMID: 27140912 DOI: 10.1101/pdb.prot085563] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Here we present our standard protocol for studying the binding of kinetochore proteins to microtubules as a paradigm for designing single-molecule total internal reflection fluorescence (TIRF) microscopy experiments. Several aspects of this protocol require empirical optimization, including the method for anchoring the polymer or substrate to the coverslip, the type and amount of blocking protein to prevent nonspecific protein adsorption to the glass, the appropriate protein concentration, the laser power, and the duration of imaging. Our method uses bovine serum albumin and κ-casein as blocking agents to coat any imperfections in the coverslip silanization and thereby prevent protein adsorption to the coverslip. Protein concentration and duration of imaging must be optimized for each experiment and protein of interest. Ideally, a range is determined that allows for resolution of single complexes binding to microtubules to ensure proper measurement of kinetic off rates and diffusion along microtubules. Excessively high concentrations may lead to overlapping binding of proteins on microtubules, making it impossible to resolve single binding events. The duration of imaging must be long enough to capture very low off rates (long residence time on microtubules) and we typically image at 10 frames/sec for 200 sec. The laser power can be adjusted to prevent photobleaching, but must be high enough to achieve a sufficient signal/noise ratio.
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Affiliation(s)
- Emily M Kudalkar
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
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40
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Jung SR, Seo JB, Deng Y, Asbury CL, Hille B, Koh DS. Contributions of protein kinases and β-arrestin to termination of protease-activated receptor 2 signaling. J Biophys Biochem Cytol 2016. [DOI: 10.1083/jcb.2127oia60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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41
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Driver JW, Geyer E, Rice LM, Asbury CL. On the Force-Generating Capacity of Disassembling Microtubules. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.1071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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42
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Abstract
Cells sense biochemical, electrical, and mechanical cues in their environment that affect their differentiation and behavior. Unlike biochemical and electrical signals, mechanical signals can propagate without the diffusion of proteins or ions; instead, forces are transmitted through mechanically stiff structures, flowing, for example, through cytoskeletal elements such as microtubules or filamentous actin. The molecular details underlying how cells respond to force are only beginning to be understood. Here we review tools for probing force-sensitive proteins and highlight several examples in which forces are transmitted, routed, and sensed by proteins in cells. We suggest that local unfolding and tension-dependent removal of autoinhibitory domains are common features in force-sensitive proteins and that force-sensitive proteins may be commonplace wherever forces are transmitted between and within cells. Because mechanical forces are inherent in the cellular environment, force is a signal that cells must take advantage of to maintain homeostasis and carry out their functions.
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Affiliation(s)
- Erik C Yusko
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195-7290
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195-7290
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43
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Sarangapani KK, Duro E, Deng Y, Alves FDL, Ye Q, Opoku KN, Ceto S, Rappsilber J, Corbett KD, Biggins S, Marston AL, Asbury CL. Sister kinetochores are mechanically fused during meiosis I in yeast. Science 2014; 346:248-51. [PMID: 25213378 DOI: 10.1126/science.1256729] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Production of healthy gametes requires a reductional meiosis I division in which replicated sister chromatids comigrate, rather than separate as in mitosis or meiosis II. Fusion of sister kinetochores during meiosis I may underlie sister chromatid comigration in diverse organisms, but direct evidence for such fusion has been lacking. We used laser trapping and quantitative fluorescence microscopy to study native kinetochore particles isolated from yeast. Meiosis I kinetochores formed stronger attachments and carried more microtubule-binding elements than kinetochores isolated from cells in mitosis or meiosis II. The meiosis I-specific monopolin complex was both necessary and sufficient to drive these modifications. Thus, kinetochore fusion directs sister chromatid comigration, a conserved feature of meiosis that is fundamental to Mendelian inheritance.
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Affiliation(s)
- Krishna K Sarangapani
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Eris Duro
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Yi Deng
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | | | - Qiaozhen Ye
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA 92093, USA
| | - Kwaku N Opoku
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Steven Ceto
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK. Institute of Bioanalytics, Department of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Kevin D Corbett
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA 92093, USA. Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sue Biggins
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Adèle L Marston
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA.
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44
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Abstract
Many proteins and protein complexes perform sophisticated, regulated functions in vivo. Many of these functions can be recapitulated using in vitro reconstitution, which serves as a means to establish unambiguous cause-effect relationships, for example, between a protein and its phosphorylating kinase. Here, we describe a protocol to purify kinetochores, the protein complexes that attach chromosomes to microtubules during mitosis, and quantitatively assay their microtubule-binding characteristics. Our assays, based on DIC imaging and laser trapping microscopy, are used to measure the attachment of microtubules to kinetochores and the load-bearing capabilities of those attachments. These assays provide a platform for studying kinase disruption of kinetochore-microtubule attachments, which is believed to be critical for correcting erroneous kinetochore-spindle attachments and thereby avoiding chromosome missegregation. The principles of our approach should be extensible to studies of a wide range of force-bearing interactions in biology.
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Affiliation(s)
- Jonathan W Driver
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Andrew F Powers
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Krishna K Sarangapani
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Sue Biggins
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, Washington, USA
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45
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Stumpff J, Wagenbach M, Franck A, Asbury CL, Wordeman L. Kif18A and chromokinesins confine centromere movements via microtubule growth suppression and spatial control of kinetochore tension. Dev Cell 2012; 22:1017-29. [PMID: 22595673 DOI: 10.1016/j.devcel.2012.02.013] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 12/08/2011] [Accepted: 02/28/2012] [Indexed: 10/28/2022]
Abstract
Alignment of chromosomes at the metaphase plate is a signature of cell division in metazoan cells, yet the mechanisms controlling this process remain ambiguous. Here we use a combination of quantitative live-cell imaging and reconstituted dynamic microtubule assays to investigate the molecular control of mitotic centromere movements. We establish that Kif18A (kinesin-8) attenuates centromere movement by directly promoting microtubule pausing in a concentration-dependent manner. This activity provides the dominant mechanism for restricting centromere movement to the spindle midzone. Furthermore, polar ejection forces spatially confine chromosomes via position-dependent regulation of kinetochore tension and centromere switch rates. We demonstrate that polar ejection forces are antagonistically modulated by chromokinesins. These pushing forces depend on Kid (kinesin-10) activity and are antagonized by Kif4A (kinesin-4), which functions to directly suppress microtubule growth. These data support a model in which Kif18A and polar ejection forces synergistically promote centromere alignment via spatial control of kinetochore-microtubule dynamics.
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Affiliation(s)
- Jason Stumpff
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA.
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46
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Asbury CL, Sarangapani KK, Akiyoshi B, Duggan N, Driver JW, Arellano-Santoyo H, Powers AF, Biggins S. How Kinetochores Promote Accuracy in Mitosis: Tension, Phosphoregulation, and the Chinese ‘Finger Trap’ Effect. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.1219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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47
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Stumpff J, Du Y, English CA, Maliga Z, Wagenbach M, Asbury CL, Wordeman L, Ohi R. A tethering mechanism controls the processivity and kinetochore-microtubule plus-end enrichment of the kinesin-8 Kif18A. Mol Cell 2011; 43:764-75. [PMID: 21884977 DOI: 10.1016/j.molcel.2011.07.022] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 06/23/2011] [Accepted: 07/28/2011] [Indexed: 10/17/2022]
Abstract
Metaphase chromosome positioning depends on Kif18A, a kinesin-8 that accumulates at and suppresses the dynamics of K-MT plus ends. By engineering Kif18A mutants that suppress MT dynamics but fail to concentrate at K-MT plus ends, we identify a mechanism that allows Kif18A to accumulate at K-MT plus ends to a level required to suppress chromosome movements. Enrichment of Kif18A at K-MT plus ends depends on its C-terminal tail domain, while the ability of Kif18A to suppress MT growth is conferred by the N-terminal motor domain. The Kif18A tail contains a second MT-binding domain that diffuses along the MT lattice, suggesting that it tethers the motor to the MT track. Consistently, the tail enhances Kif18A processivity and is crucial for it to accumulate at K-MT plus ends. The heightened processivity of Kif18A, conferred by its tail domain, thus promotes concentration of Kif18A at K-MT plus ends, where it suppresses their dynamics to control chromosome movements.
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Affiliation(s)
- Jason Stumpff
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, WA 98195, USA
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Wargacki MM, Tay JC, Muller EG, Asbury CL, Davis TN. Kip3, the yeast kinesin-8, is required for clustering of kinetochores at metaphase. Cell Cycle 2011; 9:2581-8. [PMID: 20603597 DOI: 10.4161/cc.9.13.12076] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In Saccharomyces cerevisiae, chromosome congression clusters kinetochores on either side of the spindle equator at metaphase. Many organisms require one or more kinesin-8 molecular motors to achieve chromosome alignment. The yeast kinesin-8, Kip3, has been well studied in vitro but a role in chromosome congression has not been reported. We investigated Kip3's role in this process using semi-automated, quantitative fluorescence microscopy and time-lapse imaging and found that Kip3 is required for congression. Deletion of KIP3 increases inter-kinetochore distances and increases the variability in the position of sister kinetochores along the spindle axis during metaphase. Kip3 does not regulate spindle length and is not required for kinetochore-microtubule attachment. Instead, Kip3 clusters kinetochores on the metaphase spindle by tightly regulating kinetochore microtubule lengths.
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Affiliation(s)
- Megan M Wargacki
- Department of Biochemistry, University of Washington, Seattle, WA, USA
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Asbury CL, Akiyoshi B, Sarangapani KK, Powers AF, Nelson CR, Reichow SL, Gonen T, Ranish JA, Biggins S. Tension Directly Stabilizes Reconstituted Kinetochore-Microtubule Attachments. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.3099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Asbury CL, Tien JF, Davis TN. Kinetochores' gripping feat: conformational wave or biased diffusion? Trends Cell Biol 2010; 21:38-46. [PMID: 20951587 DOI: 10.1016/j.tcb.2010.09.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 09/01/2010] [Accepted: 09/07/2010] [Indexed: 12/30/2022]
Abstract
Climbing up a cliff while the rope unravels underneath your fingers does not sound like a well-planned adventure. Yet chromosomes face a similar challenge during each cell division. Their alignment and accurate segregation depends on staying attached to the assembling and disassembling tips of microtubule fibers. This coupling is mediated by kinetochores, intricate machines that attach chromosomes to an ever-changing microtubule substrate. Two models for kinetochore-microtubule coupling were proposed a quarter century ago: conformational wave and biased diffusion. These models differ in their predictions for how coupling is performed and regulated. The availability of purified kinetochore proteins has enabled biochemical and biophysical analyses of the kinetochore-microtubule interface. Here, we discuss what these studies reveal about the contributions of each model.
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Affiliation(s)
- Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA.
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