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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] [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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2
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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] [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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3
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Pajpach F, Wu T, Shearwin-Whyatt L, Jones K, Grützner F. Flavors of Non-Random Meiotic Segregation of Autosomes and Sex Chromosomes. Genes (Basel) 2021; 12:genes12091338. [PMID: 34573322 PMCID: PMC8471020 DOI: 10.3390/genes12091338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022] Open
Abstract
Segregation of chromosomes is a multistep process occurring both at mitosis and meiosis to ensure that daughter cells receive a complete set of genetic information. Critical components in the chromosome segregation include centromeres, kinetochores, components of sister chromatid and homologous chromosomes cohesion, microtubule organizing centres, and spindles. Based on the cytological work in the grasshopper Brachystola, it has been accepted for decades that segregation of homologs at meiosis is fundamentally random. This ensures that alleles on chromosomes have equal chance to be transmitted to progeny. At the same time mechanisms of meiotic drive and an increasing number of other examples of non-random segregation of autosomes and sex chromosomes provide insights into the underlying mechanisms of chromosome segregation but also question the textbook dogma of random chromosome segregation. Recent advances provide a better understanding of meiotic drive as a prominent force where cellular and chromosomal changes allow autosomes to bias their segregation. Less understood are mechanisms explaining observations that autosomal heteromorphism may cause biased segregation and regulate alternating segregation of multiple sex chromosome systems or translocation heterozygotes as an extreme case of non-random segregation. We speculate that molecular and cytological mechanisms of non-random segregation might be common in these cases and that there might be a continuous transition between random and non-random segregation which may play a role in the evolution of sexually antagonistic genes and sex chromosome evolution.
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Affiliation(s)
- Filip Pajpach
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (F.P.); (L.S.-W.)
| | - Tianyu Wu
- Department of Central Laboratory, Clinical Laboratory, Jing’an District Centre Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China;
| | - Linda Shearwin-Whyatt
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (F.P.); (L.S.-W.)
| | - Keith Jones
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK;
| | - Frank Grützner
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (F.P.); (L.S.-W.)
- Correspondence:
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4
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Mechanical Mechanisms of Chromosome Segregation. Cells 2021; 10:cells10020465. [PMID: 33671543 PMCID: PMC7926803 DOI: 10.3390/cells10020465] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/11/2022] Open
Abstract
Chromosome segregation—the partitioning of genetic material into two daughter cells—is one of the most crucial processes in cell division. In all Eukaryotes, chromosome segregation is driven by the spindle, a microtubule-based, self-organizing subcellular structure. Extensive research performed over the past 150 years has identified numerous commonalities and contrasts between spindles in different systems. In this review, we use simple coarse-grained models to organize and integrate previous studies of chromosome segregation. We discuss sites of force generation in spindles and fundamental mechanical principles that any understanding of chromosome segregation must be based upon. We argue that conserved sites of force generation may interact differently in different spindles, leading to distinct mechanical mechanisms of chromosome segregation. We suggest experiments to determine which mechanical mechanism is operative in a particular spindle under study. Finally, we propose that combining biophysical experiments, coarse-grained theories, and evolutionary genetics will be a productive approach to enhance our understanding of chromosome segregation in the future.
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5
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Ulyanov EV, Vinogradov DS, McIntosh JR, Gudimchuk NB. Brownian dynamics simulation of protofilament relaxation during rapid freezing. PLoS One 2021; 16:e0247022. [PMID: 33577570 PMCID: PMC7880439 DOI: 10.1371/journal.pone.0247022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/31/2021] [Indexed: 11/18/2022] Open
Abstract
Electron cryo-microscopy (Cryo-EM) is a powerful method for visualizing biological objects with up to near-angstrom resolution. Instead of chemical fixation, the method relies on very rapid freezing to immobilize the sample. Under these conditions, crystalline ice does not have time to form and distort structure. For many practical applications, the rate of cooling is fast enough to consider sample immobilization instantaneous, but in some cases, a more rigorous analysis of structure relaxation during freezing could be essential. This difficult yet important problem has been significantly under-reported in the literature, despite spectacular recent developments in Cryo-EM. Here we use Brownian dynamics modeling to examine theoretically the possible effects of cryo-immobilization on the apparent shapes of biological polymers. The main focus of our study is on tubulin protofilaments. These structures are integral parts of microtubules, which in turn are key elements of the cellular skeleton, essential for intracellular transport, maintenance of cell shape, cell division and migration. We theoretically examine the extent of protofilament relaxation within the freezing time as a function of the cooling rate, the filament's flexural rigidity, and the effect of cooling on water's viscosity. Our modeling suggests that practically achievable cooling rates are not rapid enough to capture tubulin protofilaments in conformations that are incompletely relaxed, suggesting that structures seen by cryo-EM are good approximations to physiological shapes. This prediction is confirmed by our analysis of curvatures of tubulin protofilaments, using samples, prepared and visualized with a variety of methods. We find, however, that cryofixation may capture incompletely relaxed shapes of more flexible polymers, and it may affect Cryo-EM-based measurements of their persistence lengths. This analysis will be valuable for understanding of structures of different types of biopolymers, observed with Cryo-EM.
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Affiliation(s)
- Evgeniy V. Ulyanov
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
| | | | - J. Richard McIntosh
- Department of MCD Biology, University of Colorado, Boulder, CO, United States of America
| | - Nikita B. Gudimchuk
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
- Department of MCD Biology, University of Colorado, Boulder, CO, United States of America
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
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6
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Microtubules pull the strings: disordered sequences as efficient couplers of microtubule-generated force. Essays Biochem 2020; 64:371-382. [PMID: 32502246 DOI: 10.1042/ebc20190078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/01/2020] [Accepted: 05/14/2020] [Indexed: 11/17/2022]
Abstract
Microtubules are dynamic polymers that grow and shrink through addition or loss of tubulin subunits at their ends. Microtubule ends generate mechanical force that moves chromosomes and cellular organelles, and provides mechanical tension. Recent literature describes a number of proteins and protein complexes that couple dynamics of microtubule ends to movements of their cellular cargoes. These 'couplers' are quite diverse in their microtubule-binding domains (MTBDs), while sharing similarity in function, but a systematic understanding of the principles underlying their activity is missing. Here, I review various types of microtubule couplers, focusing on their essential activities: ability to follow microtubule ends and capture microtubule-generated force. Most of the couplers require presence of unstructured positively charged sequences and multivalency in their microtubule-binding sites to efficiently convert the microtubule-generated force into useful connection to a cargo. An overview of the microtubule features supporting end-tracking and force-coupling, and the experimental methods to assess force-coupling properties is also provided.
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7
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Chowdhury D, Ghanti D. Soft mechano-chemistry of molecular hubs in mitotic spindle: biomechanics and mechanical proofreading at microtubule ends. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:284001. [PMID: 32133984 DOI: 10.1088/1361-648x/ab7cc5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A microtubule (MT) is a long stiff tube-shaped filament formed by a hierarchical organization of a large number of tubulin protein molecules. These filaments constitute a major structural component of the scaffold of a multi-component macromolecular machine called mitotic spindle. The plus ends of the MTs are tethered to some specific binding partners by molecular tethers while those of some others are crosslinked by crosslinking molecules. Because of the non-covalent binding involved in the tethering and crosslinking, the attachments formed are intrinsically 'soft'. These attachments are transient because these can get ruptured spontaneously by thermal fluctuations. By implementing in silico the standard protocols of in vitro molecular force spectroscopy, we compute the lifetimes of simple theoretical models of these attachments. The mean lifetime is essentially a mean first-passage time. The stability of cross-linked antiparallel MTs is shown to decrease monotonically with increasing tension, a characteristic of all 'slip-bonds'. This is in sharp contrast to the nonmonotonic variation of the mean lifetime with tension, a mechanical fingerprint of 'catch-bonds', displayed by the MTs tethered to two distinct binding partners. We mention plausible functional implications of these observations in the context of mechanical proofreading.
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8
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Lee CT, Terentjev EM. Structural effects of cap, crack, and intrinsic curvature on the microtubule catastrophe kinetics. J Chem Phys 2019; 151:135101. [PMID: 31594313 DOI: 10.1063/1.5122304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Microtubules (MTs) experience an effect called "catastrophe," which is the transition from the MT growth to a sudden dramatic shrinkage in length. The straight guanosine triphosphate (GTP)-tubulin cap at the filament tip and the intrinsic curvature of guanosine diphosphate (GDP)-tubulins are known to be the key thermodynamic factors that determine MT catastrophe, while the hydrolysis of this GTP-cap acts as the kinetic control of the process. Although several theoretical models have been developed, assuming the catastrophe occurs when the GTP-cap shrinks to a minimal stabilizing size, the structural effect of the GTP-cap and GDP-curvature is not explicitly included; thus, their influence on catastrophe kinetics remains less understood. To investigate this structural effect, we apply a single-protofilament model with one GTP-cap while assuming a random hydrolysis mechanism and take the occurrence of a crack in the lateral bonds between neighboring protofilaments as the onset of the catastrophe. Therein, we find the effective potential of the tip along the peel-off direction and formulate the catastrophe kinetics as a mean first-passage time problem, subject to thermal fluctuations. We consider cases with and without a compressive force on the MT tip, both of which give a quadratic effective potential, making MT catastrophe an Ornstein-Uhlenbeck process in our formalism. In the free-standing case, the mean catastrophe time has a sensitive tubulin-concentration dependence, similar to a double-exponential function, and agrees well with the experiment. For a compressed MT, we find a modified exponential function of force that shortens the catastrophe time.
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Affiliation(s)
- Cheng-Tai Lee
- Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Eugene M Terentjev
- Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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9
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Elting MW, Suresh P, Dumont S. The Spindle: Integrating Architecture and Mechanics across Scales. Trends Cell Biol 2018; 28:896-910. [PMID: 30093097 PMCID: PMC6197898 DOI: 10.1016/j.tcb.2018.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/02/2018] [Accepted: 07/09/2018] [Indexed: 01/28/2023]
Abstract
The spindle segregates chromosomes at cell division, and its task is a mechanical one. While we have a nearly complete list of spindle components, how their molecular-scale mechanics give rise to cellular-scale spindle architecture, mechanics, and function is not yet clear. Recent in vitro and in vivo measurements bring new levels of molecular and physical control and shed light on this question. Highlighting recent findings and open questions, we introduce the molecular force generators of the spindle, and discuss how they organize microtubules into diverse architectural modules and give rise to the emergent mechanics of the mammalian spindle. Throughout, we emphasize the breadth of space and time scales at play, and the feedback between spindle architecture, dynamics, and mechanics that drives robust function.
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Affiliation(s)
- Mary Williard Elting
- Department of Cell & Tissue Biology, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA; Department of Physics, Riddick Hall 258A, Box 8202, North Carolina State University, Raleigh, NC 27695, USA; These authors contributed equally
| | - Pooja Suresh
- Department of Cell & Tissue Biology, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA; Biophysics Graduate Program, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA; These authors contributed equally
| | - Sophie Dumont
- Department of Cell & Tissue Biology, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA; Biophysics Graduate Program, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA; Department of Cellular & Molecular Pharmacology, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA.
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10
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Jenni S, Harrison SC. Structure of the DASH/Dam1 complex shows its role at the yeast kinetochore-microtubule interface. Science 2018; 360:552-558. [PMID: 29724956 DOI: 10.1126/science.aar6436] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/15/2018] [Indexed: 12/13/2022]
Abstract
Kinetochores connect mitotic-spindle microtubules with chromosomes, allowing microtubule depolymerization to pull chromosomes apart during anaphase while resisting detachment as the microtubule shortens. The heterodecameric DASH/Dam1 complex (DASH/Dam1c), an essential component of yeast kinetochores, assembles into a microtubule-encircling ring. The ring associates with rodlike Ndc80 complexes to organize the kinetochore-microtubule interface. We report the cryo-electron microscopy structure (at ~4.5-angstrom resolution) of a DASH/Dam1c ring and a molecular model of its ordered components, validated by evolutionary direct-coupling analysis. Integrating this structure with that of the Ndc80 complex and with published interaction data yields a molecular picture of kinetochore-microtubule attachment, including how flexible, C-terminal extensions of DASH/Dam1c subunits project and contact widely separated sites on the Ndc80 complex rod and how phosphorylation at previously identified sites might regulate kinetochore assembly.
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Affiliation(s)
- Simon Jenni
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Stephen C Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA. .,Howard Hughes Medical Institute, Harvard University, 250 Longwood Avenue, Boston, MA 02115, USA
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11
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Abstract
Chromosome segregation relies on forces generated by spindle microtubules that are translated into chromosome movement through interactions with kinetochores, highly conserved macromolecular machines that assemble on a specialized centromeric chromatin structure. Kinetochores not only have to stably attach to growing and shrinking microtubules, but they also need to recruit spindle assembly checkpoint proteins to halt cell cycle progression when there are attachment defects. Even the simplest kinetochore in budding yeast contains more than 50 unique components that are present in multiple copies, totaling more than 250 proteins in a single kinetochore. The complex nature of kinetochores makes it challenging to elucidate the contributions of individual components to its various functions. In addition, it is difficult to manipulate forces in vivo to understand how they regulate kinetochore-microtubule attachments and the checkpoint. To address these issues, we developed a technique to purify kinetochores from budding yeast that can be used to analyze kinetochore functions and composition as well as to reconstitute kinetochore-microtubule attachments in vitro.
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12
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Ghanti D, Patra S, Chowdhury D. Molecular force spectroscopy of kinetochore-microtubule attachment in silico: Mechanical signatures of an unusual catch bond and collective effects. Phys Rev E 2018; 97:052414. [PMID: 29906871 DOI: 10.1103/physreve.97.052414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Indexed: 06/08/2023]
Abstract
Measurement of the lifetime of attachments formed by a single microtubule (MT) with a single kinetochore (kt) in vitro under force-clamp conditions had earlier revealed a catch-bond-like behavior. In the past, the physical origin of this apparently counterintuitive phenomenon was traced to the nature of the force dependence of the (de)polymerization kinetics of the MTs. Here, first the same model MT-kt attachment is subjected to external tension that increases linearly with time until rupture occurs. In our force-ramp experiments in silico, the model displays the well known "mechanical signatures" of a catch bond probed by molecular force spectroscopy. Exploiting this evidence, we have further strengthened the analogy between MT-kt attachments and common ligand-receptor bonds in spite of the crucial differences in their underlying physical mechanisms. We then extend the formalism to model the stochastic kinetics of an attachment formed by a bundle of multiple parallel microtubules with a single kt considering the effect of rebinding under force-clamp and force-ramp conditions. From numerical studies of the model we predict the trends of variation of the mean lifetime and mean rupture force with the increasing number of MTs in the bundle. Both the mean lifetime and the mean rupture force display nontrivial nonlinear dependence on the maximum number of MTs that can attach simultaneously to the same kt.
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Affiliation(s)
- Dipanwita Ghanti
- Department of Physics, Indian Institute of Technology Kanpur, 208016, India
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13
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Volkov VA, Huis In 't Veld PJ, Dogterom M, Musacchio A. Multivalency of NDC80 in the outer kinetochore is essential to track shortening microtubules and generate forces. eLife 2018; 7:36764. [PMID: 29629870 PMCID: PMC5940359 DOI: 10.7554/elife.36764] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 03/31/2018] [Indexed: 12/31/2022] Open
Abstract
Presence of multiple copies of the microtubule-binding NDC80 complex is an evolutionary conserved feature of kinetochores, points of attachment of chromosomes to spindle microtubules. This may enable multivalent attachments to microtubules, with implications that remain unexplored. Using recombinant human kinetochore components, we show that while single NDC80 complexes do not track depolymerizing microtubules, reconstituted particles containing the NDC80 receptor CENP-T bound to three or more NDC80 complexes do so effectively, as expected for a kinetochore force coupler. To study multivalency systematically, we engineered modules allowing incremental addition of NDC80 complexes. The modules’ residence time on microtubules increased exponentially with the number of NDC80 complexes. Modules with two or more complexes tracked depolymerizing microtubules with increasing efficiencies, and stalled and rescued microtubule depolymerization in a force-dependent manner when conjugated to cargo. Our observations indicate that NDC80, rather than through biased diffusion, tracks depolymerizing microtubules by harnessing force generated during microtubule disassembly. Before a cell divides, its genome duplicates so that each copy can be given to the daughter cells. In a dividing cell, the chromosomes – the structures that store genetic information – look like an ‘X’. This is because each chromosome is formed of two identical, rod-like, ‘sister chromatids’ which are attached by their middle. Each daughter cell should inherit one of the chromatids. As division progresses, both sister chromatids in a pair fasten to ‘microtubules’, string-like structures made of a large number of identical proteins stacked together. These strings attach each chromatids to opposite sides of the cell. Then, the ends of the microtubules that bind to a chromatid start to peel off and disassemble. The microtubules get shorter and shorter, which creates a force that pulls the chromatids apart. Microtubules latch on a chromatid via a large structure known as the kinetochore, which has tether-like protein complexes called NDC80 at its surface. NDC80 links the kinetochore with the microtubules, yet little is known about this connection. In particular, it is unclear how this complex relays the forces from the shortening microtubules to the chromatids, and how many NDC80 complexes are required for this process. To study how these proteins interact without any molecular background ‘noise’ from the cell, Volkov, Huis in ‘t Veld et al. engineered simplified versions of the microtubule-kinetochore-NDC80 connection using components of human kinetochores. These versions, named ‘modules’, contained different numbers of NDC80 complexes, from one to four copies. Volkov, Huis in ‘t Veld et al. found that single NDC80 complexes did not follow the microtubules as they shortened, while the connections with two or more NDC80 complexes did. When a few modules, each with two or three NDC80s, were closeby, they also bound to the end of the same shortening microtubule, and captured more force as a team. NDC80 complexes therefore work together to connect to microtubule ends and harness their energy. The artificial kinetochore-microtubule-NDC80 connections developed by Volkov, Huis in ‘t Veld et al. provides a new method to study how cells divide, and it could reveal how other proteins and biological processes participate in this mechanism. It could also help understand how chromatids are kept from separating incorrectly during division, which is an error that could be fatal for the cell.
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Affiliation(s)
- Vladimir A Volkov
- Department of Bionanoscience, Faculty of Applied Sciences, Delft University of Technology, Delft, Netherlands
| | - Pim J Huis In 't Veld
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Marileen Dogterom
- Department of Bionanoscience, Faculty of Applied Sciences, Delft University of Technology, Delft, Netherlands
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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14
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Barsegov V, Ross JL, Dima RI. Dynamics of microtubules: highlights of recent computational and experimental investigations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:433003. [PMID: 28812545 DOI: 10.1088/1361-648x/aa8670] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Microtubules are found in most eukaryotic cells, with homologs in eubacteria and archea, and they have functional roles in mitosis, cell motility, intracellular transport, and the maintenance of cell shape. Numerous efforts have been expended over the last two decades to characterize the interactions between microtubules and the wide variety of microtubule associated proteins that control their dynamic behavior in cells resulting in microtubules being assembled and disassembled where and when they are required by the cell. We present the main findings regarding microtubule polymerization and depolymerization and review recent work about the molecular motors that modulate microtubule dynamics by inducing either microtubule depolymerization or severing. We also discuss the main experimental and computational approaches used to quantify the thermodynamics and mechanics of microtubule filaments.
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Affiliation(s)
- Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, United States of America
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15
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Dhatchinamoorthy K, Shivaraju M, Lange JJ, Rubinstein B, Unruh JR, Slaughter BD, Gerton JL. Structural plasticity of the living kinetochore. J Cell Biol 2017; 216:3551-3570. [PMID: 28939613 PMCID: PMC5674893 DOI: 10.1083/jcb.201703152] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/17/2017] [Accepted: 08/21/2017] [Indexed: 11/30/2022] Open
Abstract
Dhatchinamoorthy et al. use calibrated imaging, FRAP, and photoconversion to study the changes in kinetochore component copy numbers from G1 to anaphase and find that the Dam1 submodule is unchanged during anaphase, whereas MIND and Ndc80 submodules add copies, providing insight into the dynamics and plasticity of the kinetochore structure during chromosome segregation. The kinetochore is a large, evolutionarily conserved protein structure that connects chromosomes with microtubules. During chromosome segregation, outer kinetochore components track depolymerizing ends of microtubules to facilitate the separation of chromosomes into two cells. In budding yeast, each chromosome has a point centromere upon which a single kinetochore is built, which attaches to a single microtubule. This defined architecture facilitates quantitative examination of kinetochores during the cell cycle. Using three independent measures—calibrated imaging, FRAP, and photoconversion—we find that the Dam1 submodule is unchanged during anaphase, whereas MIND and Ndc80 submodules add copies to form an “anaphase configuration” kinetochore. Microtubule depolymerization and kinesin-related motors contribute to copy addition. Mathematical simulations indicate that the addition of microtubule attachments could facilitate tracking during rapid microtubule depolymerization. We speculate that the minimal kinetochore configuration, which exists from G1 through metaphase, allows for correction of misattachments. Our study provides insight into dynamics and plasticity of the kinetochore structure during chromosome segregation in living cells.
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Affiliation(s)
- Karthik Dhatchinamoorthy
- Stowers Institute for Medical Research, Kansas City, MO.,The Open University, Milton Keynes, England, UK
| | | | | | | | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO
| | | | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO .,Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS
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16
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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] [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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17
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Asbury CL. Anaphase A: Disassembling Microtubules Move Chromosomes toward Spindle Poles. BIOLOGY 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] [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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18
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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: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [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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19
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Grishchuk EL. Biophysics of Microtubule End Coupling at the Kinetochore. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2017; 56:397-428. [PMID: 28840247 DOI: 10.1007/978-3-319-58592-5_17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The main physiological function of mitotic kinetochores is to provide durable attachment to spindle microtubules, which segregate chromosomes in order to partition them equally between the two daughter cells. Numerous kinetochore components that can bind directly to microtubules have been identified, including ATP-dependent motors and various microtubule-associated proteins with no motor activity. A major challenge facing the field is to explain chromosome motions based on the biochemical and structural properties of these individual kinetochore components and their assemblies. This chapter reviews the molecular mechanisms responsible for the motions associated with dynamic microtubule tips at the single-molecule level, as well as the activities of multimolecular ensembles called couplers. These couplers enable persistent kinetochore motion even under load, but their exact composition and structure remain unknown. Because no natural or artificial macro-machines function in an analogous manner to these molecular nano-devices, understanding their underlying biophysical mechanisms will require conceptual advances.
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Affiliation(s)
- Ekaterina L Grishchuk
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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20
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Legal T, Zou J, Sochaj A, Rappsilber J, Welburn JPI. Molecular architecture of the Dam1 complex-microtubule interaction. Open Biol 2016; 6:rsob.150237. [PMID: 26962051 PMCID: PMC4821239 DOI: 10.1098/rsob.150237] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mitosis is a highly regulated process that allows the equal distribution of the genetic material to the daughter cells. Chromosome segregation requires the formation of a bipolar mitotic spindle and assembly of a multi-protein structure termed the kinetochore to mediate attachments between condensed chromosomes and spindle microtubules. In budding yeast, a single microtubule attaches to each kinetochore, necessitating robustness and processivity of this kinetochore-microtubule attachment. The yeast kinetochore-localized Dam1 complex forms a direct interaction with the spindle microtubule. In vitro, the Dam1 complex assembles as a ring around microtubules and couples microtubule depolymerization with cargo movement. However, the subunit organization within the Dam1 complex, its higher-order oligomerization and how it interacts with microtubules remain under debate. Here, we used chemical cross-linking and mass spectrometry to define the architecture and subunit organization of the Dam1 complex. This work reveals that both the C termini of Duo1 and Dam1 subunits interact with the microtubule and are critical for microtubule binding of the Dam1 complex, placing Duo1 and Dam1 on the inside of the ring structure. Integrating this information with available structural data, we provide a coherent model for how the Dam1 complex self-assembles around microtubules.
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Affiliation(s)
- Thibault Legal
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Juan Zou
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Alicja Sochaj
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Julie P I Welburn
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
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21
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Kent IA, Lele TP. Microtubule-based force generation. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2016; 9. [PMID: 27562344 DOI: 10.1002/wnan.1428] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/20/2016] [Accepted: 07/30/2016] [Indexed: 11/11/2022]
Abstract
Microtubules are vital to many important cell processes, such as cell division, transport of cellular cargo, organelle positioning, and cell migration. Owing to their diverse functions, understanding microtubule function is an important part of cell biological research that can help in combating various diseases. For example, microtubules are an important target of chemotherapeutic drugs such as paclitaxel because of their pivotal role in cell division. Many functions of microtubules relate to the generation of mechanical forces. These forces are generally either a direct result of microtubule polymerization/depolymerization or generated by motor proteins that move processively along microtubules. In this review, we summarize recent efforts to quantify and model force generation by microtubules in the context of microtubule function. WIREs Nanomed Nanobiotechnol 2017, 9:e1428. doi: 10.1002/wnan.1428 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Ian A Kent
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
| | - Tanmay P Lele
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
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22
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Zelter A, Bonomi M, Kim JO, Umbreit NT, Hoopmann MR, Johnson R, Riffle M, Jaschob D, MacCoss MJ, Moritz RL, Davis TN. The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling. Nat Commun 2015; 6:8673. [PMID: 26560693 PMCID: PMC4660060 DOI: 10.1038/ncomms9673] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 09/18/2015] [Indexed: 12/28/2022] Open
Abstract
Accurate segregation of chromosomes during cell division is essential. The Dam1 complex binds kinetochores to microtubules and its oligomerization is required to form strong attachments. It is a key target of Aurora B kinase, which destabilizes erroneous attachments allowing subsequent correction. Understanding the roles and regulation of the Dam1 complex requires structural information. Here we apply cross-linking/mass spectrometry and structural modelling to determine the molecular architecture of the Dam1 complex. We find microtubule attachment is accompanied by substantial conformational changes, with direct binding mediated by the carboxy termini of Dam1p and Duo1p. Aurora B phosphorylation of Dam1p C terminus weakens direct interaction with the microtubule. Furthermore, the Dam1p amino terminus forms an interaction interface between Dam1 complexes, which is also disrupted by phosphorylation. Our results demonstrate that Aurora B inhibits both direct interaction with the microtubule and oligomerization of the Dam1 complex to drive error correction during mitosis.
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Affiliation(s)
- Alex Zelter
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | | | - Jae Ook Kim
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Neil T Umbreit
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | | | - Richard Johnson
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Daniel Jaschob
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, USA
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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23
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Abstract
During eukaryotic cell division, chromosomes must be precisely partitioned to daughter cells. This relies on a mechanism to move chromosomes in defined directions within the parental cell. While sister chromatids are segregated from one another in mitosis and meiosis II, specific adaptations enable the segregation of homologous chromosomes during meiosis I to reduce ploidy for gamete production. Many of the factors that drive these directed chromosome movements are known, and their molecular mechanism has started to be uncovered. Here we review the mechanisms of eukaryotic chromosome segregation, with a particular emphasis on the modifications that ensure the segregation of homologous chromosomes during meiosis I.
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Affiliation(s)
- Eris Duro
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Adèle L Marston
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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24
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Kononova O, Kholodov Y, Theisen KE, Marx KA, Dima RI, Ataullakhanov FI, Grishchuk EL, Barsegov V. Tubulin bond energies and microtubule biomechanics determined from nanoindentation in silico. J Am Chem Soc 2014; 136:17036-45. [PMID: 25389565 PMCID: PMC4277772 DOI: 10.1021/ja506385p] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Microtubules,
the primary components of the chromosome segregation
machinery, are stabilized by longitudinal and lateral noncovalent
bonds between the tubulin subunits. However, the thermodynamics of
these bonds and the microtubule physicochemical properties are poorly
understood. Here, we explore the biomechanics of microtubule polymers
using multiscale computational modeling and nanoindentations in silico of a contiguous microtubule fragment. A close
match between the simulated and experimental force–deformation
spectra enabled us to correlate the microtubule biomechanics with
dynamic structural transitions at the nanoscale. Our mechanical testing
revealed that the compressed MT behaves as a system of rigid elements
interconnected through a network of lateral and longitudinal elastic
bonds. The initial regime of continuous elastic deformation of the
microtubule is followed by the transition regime, during which the
microtubule lattice undergoes discrete structural changes, which include
first the reversible dissociation of lateral bonds followed by irreversible
dissociation of the longitudinal bonds. We have determined the free
energies of dissociation of the lateral (6.9 ± 0.4 kcal/mol)
and longitudinal (14.9 ± 1.5 kcal/mol) tubulin–tubulin
bonds. These values in conjunction with the large flexural rigidity
of tubulin protofilaments obtained (18,000–26,000 pN·nm2) support the idea that the disassembling microtubule is capable
of generating a large mechanical force to move chromosomes during
cell division. Our computational modeling offers a comprehensive quantitative
platform to link molecular tubulin characteristics with the physiological
behavior of microtubules. The developed in silico nanoindentation method provides a powerful tool for the exploration
of biomechanical properties of other cytoskeletal and multiprotein
assemblies.
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Affiliation(s)
- Olga Kononova
- Department of Chemistry, University of Massachusetts , Lowell, Massachusetts 01854, United States
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25
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A mathematical model of force generation by flexible kinetochore-microtubule attachments. Biophys J 2014; 106:998-1007. [PMID: 24606925 DOI: 10.1016/j.bpj.2014.01.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 12/26/2013] [Accepted: 01/07/2014] [Indexed: 01/26/2023] Open
Abstract
Important mechanical events during mitosis are facilitated by the generation of force by chromosomal kinetochore sites that attach to dynamic microtubule tips. Several theoretical models have been proposed for how these sites generate force, and molecular diffusion of kinetochore components has been proposed as a key component that facilitates kinetochore function. However, these models do not explicitly take into account the recently observed flexibility of kinetochore components and variations in microtubule shape under load. In this paper, we develop a mathematical model for kinetochore-microtubule connections that directly incorporates these two important components, namely, flexible kinetochore binder elements, and the effects of tension load on the shape of shortening microtubule tips. We compare our results with existing biased diffusion models and explore the role of protein flexibility inforce generation at the kinetochore-microtubule junctions. Our model results suggest that kinetochore component flexibility and microtubule shape variation under load significantly diminish the need for high diffusivity (or weak specific binding) of kinetochore components; optimal kinetochore binder stiffness regimes are predicted by our model. Based on our model results, we suggest that the underlying principles of biased diffusion paradigm need to be reinterpreted.
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26
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London N, Biggins S. Signalling dynamics in the spindle checkpoint response. Nat Rev Mol Cell Biol 2014; 15:736-47. [PMID: 25303117 DOI: 10.1038/nrm3888] [Citation(s) in RCA: 227] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The spindle checkpoint ensures proper chromosome segregation during cell division. Unravelling checkpoint signalling has been a long-standing challenge owing to the complexity of the structures and forces that regulate chromosome segregation. New reports have now substantially advanced our understanding of checkpoint signalling mechanisms at the kinetochore, the structure that connects microtubules and chromatin. In contrast to the traditional view of a binary checkpoint response - either completely on or off - new findings indicate that the checkpoint response strength is variable. This revised perspective provides insight into how checkpoint bypass can lead to aneuploidy and informs strategies to exploit these errors for cancer treatments.
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Affiliation(s)
- Nitobe London
- 1] Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., PO Box 19024, Seattle, Washington 98109, USA. [2] Molecular and Cellular Biology Program, University of Washington/Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Sue Biggins
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., PO Box 19024, Seattle, Washington 98109, USA
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27
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Sharma AK, Shtylla B, Chowdhury D. Distribution of lifetimes of kinetochore–microtubule attachments: interplay of energy landscape, molecular motors and microtubule (de-)polymerization. Phys Biol 2014; 11:036004. [DOI: 10.1088/1478-3975/11/3/036004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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28
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Volkov VA, Zaytsev AV, Grishchuk EL. Preparation of segmented microtubules to study motions driven by the disassembling microtubule ends. J Vis Exp 2014. [PMID: 24686554 DOI: 10.3791/51150] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Microtubule depolymerization can provide force to transport different protein complexes and protein-coated beads in vitro. The underlying mechanisms are thought to play a vital role in the microtubule-dependent chromosome motions during cell division, but the relevant proteins and their exact roles are ill-defined. Thus, there is a growing need to develop assays with which to study such motility in vitro using purified components and defined biochemical milieu. Microtubules, however, are inherently unstable polymers; their switching between growth and shortening is stochastic and difficult to control. The protocols we describe here take advantage of the segmented microtubules that are made with the photoablatable stabilizing caps. Depolymerization of such segmented microtubules can be triggered with high temporal and spatial resolution, thereby assisting studies of motility at the disassembling microtubule ends. This technique can be used to carry out a quantitative analysis of the number of molecules in the fluorescently-labeled protein complexes, which move processively with dynamic microtubule ends. To optimize a signal-to-noise ratio in this and other quantitative fluorescent assays, coverslips should be treated to reduce nonspecific absorption of soluble fluorescently-labeled proteins. Detailed protocols are provided to take into account the unevenness of fluorescent illumination, and determine the intensity of a single fluorophore using equidistant Gaussian fit. Finally, we describe the use of segmented microtubules to study microtubule-dependent motions of the protein-coated microbeads, providing insights into the ability of different motor and nonmotor proteins to couple microtubule depolymerization to processive cargo motion.
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Affiliation(s)
- Vladimir A Volkov
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences; Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Anatoly V Zaytsev
- Physiology Department, Perelman School of Medicine, University of Pennsylvania
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29
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Abstract
The propagation of all organisms depends on the accurate and orderly segregation of chromosomes in mitosis and meiosis. Budding yeast has long served as an outstanding model organism to identify the components and underlying mechanisms that regulate chromosome segregation. This review focuses on the kinetochore, the macromolecular protein complex that assembles on centromeric chromatin and maintains persistent load-bearing attachments to the dynamic tips of spindle microtubules. The kinetochore also serves as a regulatory hub for the spindle checkpoint, ensuring that cell cycle progression is coupled to the achievement of proper microtubule-kinetochore attachments. Progress in understanding the composition and overall architecture of the kinetochore, as well as its properties in making and regulating microtubule attachments and the spindle checkpoint, is discussed.
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30
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Civelekoglu-Scholey G, He B, Shen M, Wan X, Roscioli E, Bowden B, Cimini D. Dynamic bonds and polar ejection force distribution explain kinetochore oscillations in PtK1 cells. ACTA ACUST UNITED AC 2013; 201:577-93. [PMID: 23671311 PMCID: PMC3653364 DOI: 10.1083/jcb.201301022] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A computational model of kinetochore dynamics suggests that differences in the distribution of polar ejection forces at the periphery and in the middle of PtK1 cell spindles underlie the observed position-dependence of metaphase chromosome behavior. Duplicated mitotic chromosomes aligned at the metaphase plate maintain dynamic attachments to spindle microtubules via their kinetochores, and multiple motor and nonmotor proteins cooperate to regulate their behavior. Depending on the system, sister chromatids may display either of two distinct behaviors, namely (1) the presence or (2) the absence of oscillations about the metaphase plate. Significantly, in PtK1 cells, in which chromosome behavior appears to be dependent on the position along the metaphase plate, both types of behavior are observed within the same spindle, but how and why these distinct behaviors are manifested is unclear. Here, we developed a new quantitative model to describe metaphase chromosome dynamics via kinetochore–microtubule interactions mediated by nonmotor viscoelastic linkages. Our model reproduces all the key features of metaphase sister kinetochore dynamics in PtK1 cells and suggests that differences in the distribution of polar ejection forces at the periphery and in the middle of PtK1 cell spindles underlie the observed dichotomy of chromosome behavior.
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Affiliation(s)
- Gul Civelekoglu-Scholey
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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31
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A Sensitized Emission Based Calibration of FRET Efficiency for Probing the Architecture of Macromolecular Machines. Cell Mol Bioeng 2013; 6:369-382. [PMID: 24319499 PMCID: PMC3843746 DOI: 10.1007/s12195-013-0290-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 07/02/2013] [Indexed: 01/24/2023] Open
Abstract
Macromolecular machines participate in almost every cell biological function. These machines can take the form of well-defined protein structures such as the kinetochore, or more loosely organized protein assemblies like the endocytic coat. The protein architecture of these machines—the arrangement of multiple copies of protein subunits at the nanoscale, is necessary for understanding their cell biological function and biophysical mechanism. Defining this architecture in vivo presents a major challenge. High density of protein molecules within macromolecular machines severely limits the effectiveness of super-resolution microscopy. However, this density is ideal for Forster Resonance Energy Transfer (FRET), which can determine the proximity between neighboring molecules. Here, we present a simple FRET quantitation scheme that calibrates a standard epifluorescence microscope for measuring donor–acceptor separations. This calibration can be used to deduce FRET efficiency fluorescence intensity measurements. This method will allow accurate determination of FRET efficiency over a wide range of values and FRET pair number. It will also allow dynamic FRET measurements with high spatiotemporal resolution under cell biological conditions. Although the poor maturation efficiency of genetically encoded fluorescent proteins presents a challenge, we show that its effects can be alleviated. To demonstrate this methodology, we probe the in vivo architecture of the γ-Tubulin Ring. Our technique can be applied to study the architecture and dynamics of a wide range of macromolecular machines.
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Volkov VA, Zaytsev AV, Gudimchuk N, Grissom PM, Gintsburg AL, Ataullakhanov FI, McIntosh JR, Grishchuk EL. Long tethers provide high-force coupling of the Dam1 ring to shortening microtubules. Proc Natl Acad Sci U S A 2013; 110:7708-13. [PMID: 23610433 PMCID: PMC3651439 DOI: 10.1073/pnas.1305821110] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Microtubule kinetochore attachments are essential for accurate mitosis, but how these force-generating connections move chromosomes remains poorly understood. Processive motion at shortening microtubule ends can be reconstituted in vitro using microbeads conjugated to the budding yeast kinetochore protein Dam1, which forms microtubule-encircling rings. Here, we report that, when Dam1 is linked to a bead cargo by elongated protein tethers, the maximum force transmitted from a disassembling microtubule increases sixfold compared with a short tether. We interpret this significant improvement with a theory that considers the geometry and mechanics of the microtubule-ring-bead system. Our results show the importance of fibrillar links in tethering microtubule ends to cargo: fibrils enable the cargo to align coaxially with the microtubule, thereby increasing the stability of attachment and the mechanical work that it can do. The force-transducing characteristics of fibril-tethered Dam1 are similar to the analogous properties of purified yeast kinetochores, suggesting that a tethered Dam1 ring comprises the main force-bearing unit of the native attachment.
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Affiliation(s)
- Vladimir A. Volkov
- Laboratory of Biophysics, Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow 117198, Russia
| | - Anatoly V. Zaytsev
- Physiology Department, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Nikita Gudimchuk
- Physiology Department, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Paula M. Grissom
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
| | | | - Fazly I. Ataullakhanov
- Laboratory of Biophysics, Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow 117198, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow 119991, Russia; and
- Physics Department, Moscow State University, Moscow 119991, Russia
| | - J. Richard McIntosh
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
| | - Ekaterina L. Grishchuk
- Physiology Department, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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Gonen S, Akiyoshi B, Iadanza MG, Shi D, Duggan N, Biggins S, Gonen T. The structure of purified kinetochores reveals multiple microtubule-attachment sites. Nat Struct Mol Biol 2012; 19:925-9. [PMID: 22885327 PMCID: PMC3443262 DOI: 10.1038/nsmb.2358] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 07/09/2012] [Indexed: 01/21/2023]
Abstract
Chromosomes must be accurately partitioned to daughter cells to prevent aneuploidy, a hallmark of many tumors and birth defects. Kinetochores are the macromolecular machines that segregate chromosomes by maintaining load-bearing attachments to the dynamic tips of microtubules. Here, we present the structure of isolated budding yeast kinetochore particles as visualized by electron microscopy (EM) and electron tomography of negatively stained preparations. The kinetochore appears as a ~126 nm particle containing a large central hub surrounded by multiple outer globular domains. In the presence of microtubules, some particles also have a ring that encircles the microtubule. Our data show that kinetochores bind to microtubules via multivalent attachments and lay the foundation to uncover the key mechanical and regulatory mechanisms by which kinetochores control chromosome segregation and cell division.
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Affiliation(s)
- Shane Gonen
- Howard Hughes Medical Institute, Department of Biochemistry, University of Washington, Seattle, Washington, USA
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Dumont S, Salmon ED, Mitchison TJ. Deformations within moving kinetochores reveal different sites of active and passive force generation. Science 2012; 337:355-8. [PMID: 22722252 DOI: 10.1126/science.1221886] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Kinetochores mediate chromosome segregation at mitosis. They are thought to contain both active, force-producing and passive, frictional interfaces with microtubules whose relative locations have been unclear. We inferred mechanical deformation within single kinetochores during metaphase oscillations by measuring average separations between fluorescently labeled kinetochore subunits in living cells undergoing mitosis. Inter-subunit distances were shorter in kinetochores moving toward poles than in those moving away. Inter-subunit separation decreased abruptly when kinetochores switched to poleward movement and decreased further when pulling force increased, suggesting that active force generation during poleward movement compresses kinetochores. The data revealed an active force-generating interface within kinetochores and a separate passive frictional interface located at least 20 nanometers away poleward. Together, these interfaces allow persistent attachment with intermittent active force generation.
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Affiliation(s)
- Sophie Dumont
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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Dorn JF, Maddox PS. Kinetochore dynamics: how protein dynamics affect chromosome segregation. Curr Opin Cell Biol 2011; 24:57-63. [PMID: 22209729 DOI: 10.1016/j.ceb.2011.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 11/29/2011] [Accepted: 12/04/2011] [Indexed: 11/19/2022]
Abstract
Protein dynamics generate adaptive cellular architecture. This concept is exemplified by kinetochores, organelles that orchestrate chromosome segregation during mitosis. In this review, we will focus on protein dynamics at kinetochores and discuss how these dynamics impact chromosome motility during mitosis.
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Affiliation(s)
- Jonas F Dorn
- Institute for Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal, P.O. Box 6128, Station Centre-Ville, Montréal, QC, H3C 3J7, Canada
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36
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Ji XY, Feng XQ. Mechanochemical modeling of dynamic microtubule growth involving sheet-to-tube transition. PLoS One 2011; 6:e29049. [PMID: 22205994 PMCID: PMC3243706 DOI: 10.1371/journal.pone.0029049] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 11/18/2011] [Indexed: 01/12/2023] Open
Abstract
Microtubule dynamics is largely influenced by nucleotide hydrolysis and the resultant tubulin configuration changes. The GTP cap model has been proposed to interpret the stabilizing mechanisms of microtubule growth from the view of hydrolysis effects. Besides, the growth of a microtubule involves the closure of a curved sheet at its growing end. The curvature conversion from the longitudinal direction to the circumferential direction also helps to stabilize the successive growth, and the curved sheet is referred to as the conformational cap. However, there still lacks theoretical investigation on the mechanical–chemical coupling growth process of microtubules. In this paper, we study the growth mechanisms of microtubules by using a coarse-grained molecular method. First, the closure process involving a sheet-to-tube transition is simulated. The results verify the stabilizing effect of the sheet structure and predict that the minimum conformational cap length that can stabilize the growth is two dimers. Then, we show that the conformational cap and the GTP cap can function independently and harmoniously, signifying the pivotal role of mechanical factors. Furthermore, based on our theoretical results, we describe a Tetris-like growth style of microtubules: the stochastic tubulin assembly is regulated by energy and harmonized with the seam zipping such that the sheet keeps a practically constant length during growth.
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Affiliation(s)
- Xiang-Ying Ji
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, Tsinghua University, Beijing, China
| | - Xi-Qiao Feng
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, Tsinghua University, Beijing, China
- * E-mail:
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Zhang Y. Growth and shortening of microtubules: a two-state model approach. J Biol Chem 2011; 286:39439-49. [PMID: 21903577 PMCID: PMC3234767 DOI: 10.1074/jbc.m111.260208] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 09/06/2011] [Indexed: 11/06/2022] Open
Abstract
In this study, a two-state mechanochemical model is presented to describe the dynamic instability of microtubules (MTs) in cells. The MT switches between two states, the assembly and disassembly states. In assembly state, the growth of MTs includes two processes: free GTP-tubulin binding to the tip of protofilament (PF) and conformation change of PF, during which the first tubulin unit that curls outwards is rearranged onto the MT surface, using the energy released from the hydrolysis of GTP in the penultimate tubulin unit. In the disassembly state, the shortening of MTs also includes two processes, the release of GDP-tubulin from the tip of PF and the curling of one new tubulin unit out of the MT surface. Switches between these two states, which are usually called rescue and catastrophe, happen stochastically with external force-dependent rates. Using this two-state model with parameters obtained by fitting the recent experimental data, detailed properties of MT growth are obtained. I find that MT is mainly in the assembly state, its mean growth velocity increases with both the external force and the GTP-tubulin concentration, and an MT will shorten on average without an external force. To know more about the external force and GTP-tubulin concentration-dependent properties of MT growth, and for future experimental verification of this two-state model, 11 critical forces are defined and discussed numerically.
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Affiliation(s)
- Yunxin Zhang
- Shanghai Key Laboratory for Contemporary Applied Mathematics, Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai 200433, China.
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Ji XY, Feng XQ. Coarse-grained mechanochemical model for simulating the dynamic behavior of microtubules. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:031933. [PMID: 22060429 DOI: 10.1103/physreve.84.031933] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2011] [Revised: 08/08/2011] [Indexed: 05/31/2023]
Abstract
Modeling the structure and mechanics of microtubules, which play significant roles in various physiological functions of cells, has long been a fascinating issue. In this paper, a coarse-grained mechanochemical model is presented to study the mechanical-chemical coupling and dynamic attributes of microtubules. The interactions among tubulins are taken into account from the molecular basis. This model is used to characterize the conformations of sheet-ended microtubules, to analyze the distributions of interaction energy, and further to simulate the radial indentation process of a microtubule. This method also works for investigating the dynamic properties of microtubules, e.g., their assembly, growth, deformation, and structural evolution for different conditions. This study is helpful for understanding the structure-mechanics-function relationship of microtubules and lays a foundation for further investigation of their dynamic behavior.
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Affiliation(s)
- Xiang-Ying Ji
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China
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Abstract
The Ndc80 complex lies at the heart of the kinetochore, a large protein machine that accurately segregates chromosomes during cell division. The Ndc80 complex has structural roles in assembling the kinetochore, but also functions to congress chromosomes and to signal the spindle checkpoint. It directly binds to microtubules and is currently the best candidate for the long-sought protein that couples microtubule depolymerization to chromosome movement. A combination of structural and genetic data has recently converged to generate the first models for this fascinating motor activity. Additionally, recent data point to an increasingly dynamic role for Ndc80 in the kinetochore-one which involves not only simple binding to microtubules but also shifts in complex shape and its location within the overall kinetochore structure. In this review, we discuss recent advances in our understanding of the Ndc80 complex and address future areas of research.
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Abstract
Microtubule-depolymerizing motor proteins regulate microtubule dynamics during chromosome segregation, but whether they can independently grip the ends of shrinking kinetochore microtubules has remained unresolved. MCAK, a member of the kinesin-13 motor protein family, is now shown to grip microtubules on its own and harness the forces of microtubule disassembly.
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