1
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Abstract
Dyneins make up a family of AAA+ motors that move toward the minus end of microtubules. Cytoplasmic dynein is responsible for transporting intracellular cargos in interphase cells and mediating spindle assembly and chromosome positioning during cell division. Other dynein isoforms transport cargos in cilia and power ciliary beating. Dyneins were the least studied of the cytoskeletal motors due to challenges in the reconstitution of active dynein complexes in vitro and the scarcity of high-resolution methods for in-depth structural and biophysical characterization of these motors. These challenges have been recently addressed, and there have been major advances in our understanding of the activation, mechanism, and regulation of dyneins. This review synthesizes the results of structural and biophysical studies for each class of dynein motors. We highlight several outstanding questions about the regulation of bidirectional transport along microtubules and the mechanisms that sustain self-coordinated oscillations within motile cilia.
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Affiliation(s)
- John T Canty
- Biophysics Graduate Group, University of California, Berkeley, California 94720, USA;
| | - Ruensern Tan
- Department of Molecular and Cellular Biology, University of California, Berkeley, California 94720, USA
| | - Emre Kusakci
- Biophysics Graduate Group, University of California, Berkeley, California 94720, USA;
| | - Jonathan Fernandes
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Ahmet Yildiz
- Biophysics Graduate Group, University of California, Berkeley, California 94720, USA; .,Department of Molecular and Cellular Biology, University of California, Berkeley, California 94720, USA.,Physics Department, University of California, Berkeley, California 94720, USA
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2
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Palenzuela H, Lacroix B, Sallé J, Minami K, Shima T, Jegou A, Romet-Lemonne G, Minc N. In Vitro Reconstitution of Dynein Force Exertion in a Bulk Viscous Medium. Curr Biol 2020; 30:4534-4540.e7. [PMID: 32946749 DOI: 10.1016/j.cub.2020.08.078] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/03/2020] [Accepted: 08/24/2020] [Indexed: 11/28/2022]
Abstract
The forces generated by microtubules (MTs) and their associated motors orchestrate essential cellular processes ranging from vesicular trafficking to centrosome positioning [1, 2]. To date, most studies have focused on MT force exertion by motors anchored to a static surface, such as the cell cortex in vivo or glass surfaces in vitro [2-4]. However, motors also transport large cargos and endomembrane networks, whose hydrodynamic interactions with the viscous cytoplasm should generate sizable forces in bulk. Such forces may contribute to MT aster centration, organization, and orientation [5-14] but have yet to be evidenced and studied in a minimal reconstituted system. By developing a bulk motility assay, based on stabilized MTs and dynein-coated beads freely floating in a viscous medium away from any surface, we demonstrate that the motion of a cargo exerts a pulling force on the MT and propels it in opposite direction. Quantification of resulting MT movements for different motors, motor velocities, over a range of cargo sizes and medium viscosities shows that the efficiency of this mechanism is primarily determined by cargo size and MT length. Forces exerted by cargos are additive, allowing us to recapitulate tug-of-war situations or bi-dimensional motions of minimal asters. These data also reveal unappreciated effects of the nature of viscous crowders and hydrodynamic interactions between cargos and MTs, likely relevant to understand this mode of force exertion in living cells. This study reinforces the notion that endomembrane transport can exert significant forces on MTs.
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Affiliation(s)
| | - Benjamin Lacroix
- Institut Jacques Monod, Université de Paris, CNRS, 75006 Paris, France
| | - Jérémy Sallé
- Institut Jacques Monod, Université de Paris, CNRS, 75006 Paris, France
| | - Katsuhiko Minami
- Graduate School of Science, The University of Tokyo, 113-0033 Tokyo, Japan
| | - Tomohiro Shima
- Graduate School of Science, The University of Tokyo, 113-0033 Tokyo, Japan
| | - Antoine Jegou
- Institut Jacques Monod, Université de Paris, CNRS, 75006 Paris, France
| | | | - Nicolas Minc
- Institut Jacques Monod, Université de Paris, CNRS, 75006 Paris, France.
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3
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Kubo S, Shima T, Takada S. How Cytoplasmic Dynein Couples ATP Hydrolysis Cycle to Diverse Stepping Motions: Kinetic Modeling. Biophys J 2020; 118:1930-1945. [PMID: 32272056 DOI: 10.1016/j.bpj.2020.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/07/2020] [Accepted: 03/17/2020] [Indexed: 01/20/2023] Open
Abstract
Cytoplasmic dynein is a two-headed molecular motor that moves to the minus end of a microtubule by ATP hydrolysis free energy. By employing its two heads (motor domains), cytoplasmic dynein exhibits various bipedal stepping motions: inchworm and hand-over-hand motions, as well as nonalternating steps of one head. However, the molecular basis to achieve such diverse stepping manners remains unclear because of the lack of an experimental method to observe stepping and the ATPase reaction of dynein simultaneously. Here, we propose a kinetic model for bipedal motions of cytoplasmic dynein and perform Gillespie Monte Carlo simulations that qualitatively reproduce most experimental data obtained to date. The model represents the status of each motor domain as five states according to conformation and nucleotide- and microtubule-binding conditions of the domain. In addition, the relative positions of the two domains were approximated by three discrete states. Accompanied by ATP hydrolysis cycles, the model dynein stochastically and processively moved forward in multiple steps via diverse pathways, including inchworm and hand-over-hand motions, similarly to experimental data. The model reproduced key experimental motility-related properties, including velocity and run length, as functions of the ATP concentration and external force, therefore providing a plausible explanation of how dynein achieves various stepping manners with explicit characterization of nucleotide states. Our model highlights the uniqueness of dynein in the coupling of ATPase with its movement during both inchworm and hand-over-hand stepping.
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Affiliation(s)
- Shintaroh Kubo
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Tomohiro Shima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.
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4
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Torisawa T, Kimura A. The Generation of Dynein Networks by Multi-Layered Regulation and Their Implication in Cell Division. Front Cell Dev Biol 2020; 8:22. [PMID: 32083077 PMCID: PMC7004958 DOI: 10.3389/fcell.2020.00022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/13/2020] [Indexed: 12/13/2022] Open
Abstract
Cytoplasmic dynein-1 (hereafter referred to as dynein) is a major microtubule-based motor critical for cell division. Dynein is essential for the formation and positioning of the mitotic spindle as well as the transport of various cargos in the cell. A striking feature of dynein is that, despite having a wide variety of functions, the catalytic subunit is coded in a single gene. To perform various cellular activities, there seem to be different types of dynein that share a common catalytic subunit. In this review, we will refer to the different kinds of dynein as “dyneins.” This review attempts to classify the mechanisms underlying the emergence of multiple dyneins into four layers. Inside a cell, multiple dyneins generated through the multi-layered regulations interact with each other to form a network of dyneins. These dynein networks may be responsible for the accurate regulation of cellular activities, including cell division. How these networks function inside a cell, with a focus on the early embryogenesis of Caenorhabditis elegans embryos, is discussed, as well as future directions for the integration of our understanding of molecular layering to understand the totality of dynein’s function in living cells.
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Affiliation(s)
- Takayuki Torisawa
- Cell Architecture Laboratory, National Institute of Genetics, Mishima, Japan.,Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Japan
| | - Akatsuki Kimura
- Cell Architecture Laboratory, National Institute of Genetics, Mishima, Japan.,Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Japan
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5
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Ando J, Shima T, Kanazawa R, Shimo-Kon R, Nakamura A, Yamamoto M, Kon T, Iino R. Small stepping motion of processive dynein revealed by load-free high-speed single-particle tracking. Sci Rep 2020; 10:1080. [PMID: 31974448 PMCID: PMC6978368 DOI: 10.1038/s41598-020-58070-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/10/2020] [Indexed: 12/13/2022] Open
Abstract
Cytoplasmic dynein is a dimeric motor protein which processively moves along microtubule. Its motor domain (head) hydrolyzes ATP and induces conformational changes of linker, stalk, and microtubule binding domain (MTBD) to trigger stepping motion. Here we applied scattering imaging of gold nanoparticle (AuNP) to visualize load-free stepping motion of processive dynein. We observed artificially-dimerized chimeric dynein, which has the head, linker, and stalk from Dictyostelium discoideum cytoplasmic dynein and the MTBD from human axonemal dynein, whose structure has been well-studied by cryo-electron microscopy. One head of a dimer was labeled with 30 nm AuNP, and stepping motions were observed with 100 μs time resolution and sub-nanometer localization precision at physiologically-relevant 1 mM ATP. We found 8 nm forward and backward steps and 5 nm side steps, consistent with on- and off-axes pitches of binding cleft between αβ-tubulin dimers on the microtubule. Probability of the forward step was 1.8 times higher than that of the backward step, and similar to those of the side steps. One-head bound states were not clearly observed, and the steps were limited by a single rate constant. Our results indicate dynein mainly moves with biased small stepping motion in which only backward steps are slightly suppressed.
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Affiliation(s)
- Jun Ando
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8787, Aichi, Japan.,The Graduate University for Advanced Studies (SOKENDAI), Hayama, 240-0193, Kanagawa, Japan
| | - Tomohiro Shima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, 113-0033, Tokyo, Japan
| | - Riko Kanazawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Rieko Shimo-Kon
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Akihiko Nakamura
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8787, Aichi, Japan.,The Graduate University for Advanced Studies (SOKENDAI), Hayama, 240-0193, Kanagawa, Japan
| | - Mayuko Yamamoto
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8787, Aichi, Japan
| | - Takahide Kon
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Ryota Iino
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8787, Aichi, Japan. .,The Graduate University for Advanced Studies (SOKENDAI), Hayama, 240-0193, Kanagawa, Japan.
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6
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Farhana TI, Nakagawa T, Ohara S, Shintaku H, Kotera H, Yokokawa R. Spatial Patterning of Kinesin-1 and Dynein Motor Proteins in an In Vitro Assay using Aqueous Two-Phase Systems (ATPS). LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:13003-13010. [PMID: 31510745 DOI: 10.1021/acs.langmuir.9b01411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Cooperativity of motor proteins is essential for intracellular transport. Although their motion is unidirectional, they often cause bidirectional movement by different types of motors as seen in organelles. However, in vitro assessments of such cellular functions are still inadequate owing to the experimental limitations in precisely patterning multiple motors. Here, we present an approach to immobilize two motor proteins, kinesin-1 and dynein, using the aqueous two-phase system (ATPS) made of poly(ethylene glycol) and dextran polymers. The negligible influence of polymer solutions on the attachment and velocity of motor proteins ensures the compatibility of using ATPS as the patterning technique. The selective fixation of kinesin and dynein was assessed using polarity-marked microtubules (PMMTs). Our experimental results show that on a patterned kinesin surface, 72% of PMMTs display minus-end leading motility, while on a dynein surface, 79% of PMMTs display plus-end leading motility. This work offers a universal and biocompatible method to pattern motor proteins of different classes at the nanoscale, providing a new route to study different cellular functions performed by molecular motors such as the formation of mitotic spindles.
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Affiliation(s)
- Tamanna Ishrat Farhana
- Department of Micro Engineering , Kyoto University , Kyoto Daigaku-Katsura , Nishikyo-ku, Kyoto 615-8540 , Japan
| | - Tomohiro Nakagawa
- Department of Micro Engineering , Kyoto University , Kyoto Daigaku-Katsura , Nishikyo-ku, Kyoto 615-8540 , Japan
| | - Shumpei Ohara
- Department of Micro Engineering , Kyoto University , Kyoto Daigaku-Katsura , Nishikyo-ku, Kyoto 615-8540 , Japan
| | - Hirofumi Shintaku
- Cluster for Pioneering Research, RIKEN , 2-1, Hirosawa , Wako , Saitama 351-0198 , Japan
| | | | - Ryuji Yokokawa
- Department of Micro Engineering , Kyoto University , Kyoto Daigaku-Katsura , Nishikyo-ku, Kyoto 615-8540 , Japan
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7
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Kinoshita Y, Kambara T, Nishikawa K, Kaya M, Higuchi H. Step Sizes and Rate Constants of Single-headed Cytoplasmic Dynein Measured with Optical Tweezers. Sci Rep 2018; 8:16333. [PMID: 30397249 PMCID: PMC6218510 DOI: 10.1038/s41598-018-34549-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 10/19/2018] [Indexed: 01/04/2023] Open
Abstract
A power stroke of dynein is thought to be responsible for the stepping of dimeric dynein. However, the actual size of the displacement driven by a power stroke has not been directly measured. Here, the displacements of single-headed cytoplasmic dynein were measured by optical tweezers. The mean displacement of dynein interacting with microtubule was ~8 nm at 100 µM ATP, and decreased sigmoidally with a decrease in the ATP concentration. The ATP dependence of the mean displacement was explained by a model that some dynein molecules bind to microtubule in pre-stroke conformation and generate 8-nm displacement, while others bind in the post-stroke one and detach without producing a power stroke. Biochemical assays showed that the binding affinity of the post-stroke dynein to a microtubule was ~5 times higher than that of pre-stroke dynein, and the dissociation rate was ~4 times lower. Taking account of these rates, we conclude that the displacement driven by a power stroke is 8.3 nm. A working model of dimeric dynein driven by the 8-nm power stroke was proposed.
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Affiliation(s)
- Yoshimi Kinoshita
- Department of Physics, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Taketoshi Kambara
- Department of Physics, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-0033, Japan.,Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Kaori Nishikawa
- Department of Physics, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Motoshi Kaya
- Department of Physics, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hideo Higuchi
- Department of Physics, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-0033, Japan.
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8
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Dwivedi D, Sharma M. Multiple Roles, Multiple Adaptors: Dynein During Cell Cycle. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1112:13-30. [PMID: 30637687 DOI: 10.1007/978-981-13-3065-0_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Dynein is an essential protein complex present in most eukaryotes that regulate biological processes ranging from ciliary beating, intracellular transport, to cell division. Elucidating the detailed mechanism of dynein function has been a challenging task owing to its large molecular weight and high complexity of the motor. With the advent of technologies in the last two decades, studies have uncovered a wealth of information about the structural, biochemical, and cell biological roles of this motor protein. Cytoplasmic dynein associates with dynactin through adaptor proteins to mediate retrograde transport of vesicles, mRNA, proteins, and organelles on the microtubule tracts. In a mitotic cell, dynein has multiple localizations, such as at the nuclear envelope, kinetochores, mitotic spindle and spindle poles, and cell cortex. In line with this, dynein regulates multiple events during the cell cycle, such as centrosome separation, nuclear envelope breakdown, spindle assembly checkpoint inactivation, chromosome segregation, and spindle positioning. Here, we provide an overview of dynein structure and function with focus on the roles played by this motor during different stages of the cell cycle. Further, we review in detail the role of dynactin and dynein adaptors that regulate both recruitment and activity of dynein during the cell cycle.
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Affiliation(s)
- Devashish Dwivedi
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Punjab, India.
| | - Mahak Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Punjab, India.
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9
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Cianfrocco MA, DeSantis ME, Leschziner AE, Reck-Peterson SL. Mechanism and regulation of cytoplasmic dynein. Annu Rev Cell Dev Biol 2015; 31:83-108. [PMID: 26436706 DOI: 10.1146/annurev-cellbio-100814-125438] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Until recently, dynein was the least understood of the cytoskeletal motors. However, a wealth of new structural, mechanistic, and cell biological data is shedding light on how this complicated minus-end-directed, microtubule-based motor works. Cytoplasmic dynein-1 performs a wide array of functions in most eukaryotes, both in interphase, in which it transports organelles, proteins, mRNAs, and viruses, and in mitosis and meiosis. Mutations in dynein or its regulators are linked to neurodevelopmental and neurodegenerative diseases. Here, we begin by providing a synthesis of recent data to describe the current model of dynein's mechanochemical cycle. Next, we discuss regulators of dynein, with particular focus on those that directly interact with the motor to modulate its recruitment to microtubules, initiate cargo transport, or activate minus-end-directed motility.
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Affiliation(s)
- Michael A Cianfrocco
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093;
| | - Morgan E DeSantis
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093;
| | - Andres E Leschziner
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093;
| | - Samara L Reck-Peterson
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093;
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10
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Imai H, Shima T, Sutoh K, Walker ML, Knight PJ, Kon T, Burgess SA. Direct observation shows superposition and large scale flexibility within cytoplasmic dynein motors moving along microtubules. Nat Commun 2015; 6:8179. [PMID: 26365535 PMCID: PMC4579568 DOI: 10.1038/ncomms9179] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 07/25/2015] [Indexed: 12/16/2022] Open
Abstract
Cytoplasmic dynein is a dimeric AAA(+) motor protein that performs critical roles in eukaryotic cells by moving along microtubules using ATP. Here using cryo-electron microscopy we directly observe the structure of Dictyostelium discoideum dynein dimers on microtubules at near-physiological ATP concentrations. They display remarkable flexibility at a hinge close to the microtubule binding domain (the stalkhead) producing a wide range of head positions. About half the molecules have the two heads separated from one another, with both leading and trailing motors attached to the microtubule. The other half have the two heads and stalks closely superposed in a front-to-back arrangement of the AAA(+) rings, suggesting specific contact between the heads. All stalks point towards the microtubule minus end. Mean stalk angles depend on the separation between their stalkheads, which allows estimation of inter-head tension. These findings provide a structural framework for understanding dynein's directionality and unusual stepping behaviour.
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Affiliation(s)
- Hiroshi Imai
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Tomohiro Shima
- Quantitative Biology Center, Riken, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Kazuo Sutoh
- Faculty of Science and Engineering, Waseda University, Takada 1-17-22, Toshima-ku, Tokyo 171-0033, Japan
| | | | - Peter J. Knight
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Takahide Kon
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, 560-0043 Osaka, Japan
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, Kawaguchi, 332-0012 Saitama, Japan
| | - Stan A. Burgess
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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11
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Bosch PJ, Corrêa IR, Sonntag MH, Ibach J, Brunsveld L, Kanger JS, Subramaniam V. Evaluation of fluorophores to label SNAP-tag fused proteins for multicolor single-molecule tracking microscopy in live cells. Biophys J 2015; 107:803-14. [PMID: 25140415 DOI: 10.1016/j.bpj.2014.06.040] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 05/22/2014] [Accepted: 06/10/2014] [Indexed: 11/19/2022] Open
Abstract
Single-molecule tracking has become a widely used technique for studying protein dynamics and their organization in the complex environment of the cell. In particular, the spatiotemporal distribution of membrane receptors is an active field of study due to its putative role in the regulation of signal transduction. The SNAP-tag is an intrinsically monovalent and highly specific genetic tag for attaching a fluorescent label to a protein of interest. Little information is currently available on the choice of optimal fluorescent dyes for single-molecule microscopy utilizing the SNAP-tag labeling system. We surveyed 6 green and 16 red excitable dyes for their suitability in single-molecule microscopy of SNAP-tag fusion proteins in live cells. We determined the nonspecific binding levels and photostability of these dye conjugates when bound to a SNAP-tag fused membrane protein in live cells. We found that only a limited subset of the dyes tested is suitable for single-molecule tracking microscopy. The results show that a careful choice of the dye to conjugate to the SNAP-substrate to label SNAP-tag fusion proteins is very important, as many dyes suffer from either rapid photobleaching or high nonspecific staining. These characteristics appear to be unpredictable, which motivated the need to perform the systematic survey presented here. We have developed a protocol for evaluating the best dyes, and for the conditions that we evaluated, we find that Dy 549 and CF 640 are the best choices tested for single-molecule tracking. Using an optimal dye pair, we also demonstrate the possibility of dual-color single-molecule imaging of SNAP-tag fusion proteins. This survey provides an overview of the photophysical and imaging properties of a range of SNAP-tag fluorescent substrates, enabling the selection of optimal dyes and conditions for single-molecule imaging of SNAP-tagged fusion proteins in eukaryotic cell lines.
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Affiliation(s)
- Peter J Bosch
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | | | - Michael H Sonntag
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Jenny Ibach
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Johannes S Kanger
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | - Vinod Subramaniam
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands.
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12
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Schmidt H. Dynein motors: How AAA+ ring opening and closing coordinates microtubule binding and linker movement. Bioessays 2015; 37:532-43. [DOI: 10.1002/bies.201400215] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Helgo Schmidt
- Medical Research Council Laboratory of Molecular Biology; Division of Structural Studies; Cambridge UK
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13
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Nicholas MP, Höök P, Brenner S, Wynne CL, Vallee RB, Gennerich A. Control of cytoplasmic dynein force production and processivity by its C-terminal domain. Nat Commun 2015; 6:6206. [PMID: 25670086 PMCID: PMC4339881 DOI: 10.1038/ncomms7206] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 01/05/2015] [Indexed: 02/07/2023] Open
Abstract
Cytoplasmic dynein is a microtubule motor involved in cargo transport, nuclear migration and cell division. Despite structural conservation of the dynein motor domain from yeast to higher eukaryotes, the extensively studied S. cerevisiae dynein behaves distinctly from mammalian dyneins, which produce far less force and travel over shorter distances. However, isolated reports of yeast-like force production by mammalian dynein have called interspecies differences into question. We report that functional differences between yeast and mammalian dynein are real and attributable to a C-terminal motor element absent in yeast, which resembles a ‘cap’ over the central pore of the mammalian dynein motor domain. Removal of this cap increases the force generation of rat dynein from 1 pN to a yeast-like 6 pN and greatly increases its travel distance. Our findings identify the CT-cap as a novel regulator of dynein function. Cytoplasmic dynein from the yeast S. cerevisiae behaves distinctly from mammalian dyneins, despite structural conservation. Here, Nicholas et al. identify a C-terminal domain in mammalian dynein that restricts force generation and travel distance, which, when removed, allows mammalian dynein to behave like its yeast counterpart.
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Affiliation(s)
- Matthew P Nicholas
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Peter Höök
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
| | - Sibylle Brenner
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Caitlin L Wynne
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
| | - Richard B Vallee
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
| | - Arne Gennerich
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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14
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Jha R, Surrey T. Regulation of processive motion and microtubule localization of cytoplasmic dynein. Biochem Soc Trans 2015; 43:48-57. [PMID: 25619245 DOI: 10.1042/bst20140252] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The cytoplasmic dynein complex is the major minus-end-directed microtubule motor. Although its directionality is evolutionary well conserved, differences exist among cytoplasmic dyneins from different species in their stepping behaviour, maximum velocity and force production. Recent experiments also suggest differences in processivity regulation. In the present article, we give an overview of dynein's motile properties, with a special emphasis on processivity and its regulation. Furthermore, we summarize recent findings of different pathways for microtubule plus-end loading of dynein. The present review highlights how distinct functions in different cell types or organisms appear to require different mechanochemical dynein properties and localization pathways.
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Affiliation(s)
- Rupam Jha
- *London Research Institute, Cancer Research UK, 44 Lincoln's Inn Fields, London WC2A 3LY, U.K
| | - Thomas Surrey
- *London Research Institute, Cancer Research UK, 44 Lincoln's Inn Fields, London WC2A 3LY, U.K
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15
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Uchimura S, Fujii T, Takazaki H, Ayukawa R, Nishikawa Y, Minoura I, Hachikubo Y, Kurisu G, Sutoh K, Kon T, Namba K, Muto E. A flipped ion pair at the dynein-microtubule interface is critical for dynein motility and ATPase activation. ACTA ACUST UNITED AC 2015; 208:211-22. [PMID: 25583999 PMCID: PMC4298687 DOI: 10.1083/jcb.201407039] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Dynein is a motor protein that moves on microtubules (MTs) using the energy of adenosine triphosphate (ATP) hydrolysis. To understand its motility mechanism, it is crucial to know how the signal of MT binding is transmitted to the ATPase domain to enhance ATP hydrolysis. However, the molecular basis of signal transmission at the dynein-MT interface remains unclear. Scanning mutagenesis of tubulin identified two residues in α-tubulin, R403 and E416, that are critical for ATPase activation and directional movement of dynein. Electron cryomicroscopy and biochemical analyses revealed that these residues form salt bridges with the residues in the dynein MT-binding domain (MTBD) that work in concert to induce registry change in the stalk coiled coil and activate the ATPase. The R403-E3390 salt bridge functions as a switch for this mechanism because of its reversed charge relative to other residues at the interface. This study unveils the structural basis for coupling between MT binding and ATPase activation and implicates the MTBD in the control of directional movement.
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Affiliation(s)
- Seiichi Uchimura
- Laboratory for Molecular Biophysics, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Takashi Fujii
- Graduate School of Frontier Biosciences and Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, Kawaguchi, Saitama 332-0012, Japan Quantitative Biology Center, Institute of Physical and Chemical Research, Suita, Osaka 565-0871, Japan
| | - Hiroko Takazaki
- Laboratory for Molecular Biophysics, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Rie Ayukawa
- Laboratory for Molecular Biophysics, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Yosuke Nishikawa
- Graduate School of Frontier Biosciences and Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Itsushi Minoura
- Laboratory for Molecular Biophysics, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - You Hachikubo
- Laboratory for Molecular Biophysics, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Genji Kurisu
- Graduate School of Frontier Biosciences and Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Kazuo Sutoh
- Research Institute for Science and Engineering, Waseda University, Toshima-ku, Tokyo 171-0033, Japan
| | - Takahide Kon
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, Kawaguchi, Saitama 332-0012, Japan Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan Department of Frontier Bioscience, Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences and Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan Quantitative Biology Center, Institute of Physical and Chemical Research, Suita, Osaka 565-0871, Japan
| | - Etsuko Muto
- Laboratory for Molecular Biophysics, RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
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16
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Tug-of-war of microtubule filaments at the boundary of a kinesin- and dynein-patterned surface. Sci Rep 2014; 4:5281. [PMID: 24923426 PMCID: PMC4055898 DOI: 10.1038/srep05281] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 05/20/2014] [Indexed: 01/09/2023] Open
Abstract
Intracellular cargo is transported by multiple motor proteins. Because of the force balance of motors with mixed polarities, cargo moves bidirectionally to achieve biological functions. Here, we propose a microtubule gliding assay for a tug-of-war study of kinesin and dynein. A boundary of the two motor groups is created by photolithographically patterning gold to selectively attach kinesin to the glass and dynein to the gold surface using a self-assembled monolayer. The relationship between the ratio of two antagonistic motor numbers and the velocity is derived from a force-velocity relationship for each motor to calculate the detachment force and motor backward velocity. Although the tug-of-war involves >100 motors, values are calculated for a single molecule and reflect the collective dynein and non-collective kinesin functions when they work as a team. This assay would be useful for detailed in vitro analysis of intracellular motility, e.g., mitosis, where a large number of motors with mixed polarities are involved.
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17
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Gleave ES, Schmidt H, Carter AP. A structural analysis of the AAA+ domains in Saccharomyces cerevisiae cytoplasmic dynein. J Struct Biol 2014; 186:367-75. [PMID: 24680784 PMCID: PMC4047620 DOI: 10.1016/j.jsb.2014.03.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/21/2014] [Accepted: 03/22/2014] [Indexed: 11/05/2022]
Abstract
Dyneins are large protein complexes that act as microtubule based molecular motors. The dynein heavy chain contains a motor domain which is a member of the AAA+ protein family (ATPases Associated with diverse cellular Activities). Proteins of the AAA+ family show a diverse range of functionalities, but share a related core AAA+ domain, which often assembles into hexameric rings. Dynein is unusual because it has all six AAA+ domains linked together, in one long polypeptide. The dynein motor domain generates movement by coupling ATP driven conformational changes in the AAA+ ring to the swing of a motile element called the linker. Dynein binds to its microtubule track via a long antiparallel coiled-coil stalk that emanates from the AAA+ ring. Recently the first high resolution structures of the dynein motor domain were published. Here we provide a detailed structural analysis of the six AAA+ domains using our Saccharomycescerevisiae crystal structure. We describe how structural similarities in the dynein AAA+ domains suggest they share a common evolutionary origin. We analyse how the different AAA+ domains have diverged from each other. We discuss how this is related to the function of dynein as a motor protein and how the AAA+ domains of dynein compare to those of other AAA+ proteins.
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Affiliation(s)
- Emma S Gleave
- MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, UK
| | - Helgo Schmidt
- MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, UK
| | - Andrew P Carter
- MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, UK.
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18
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Roberts AJ, Kon T, Knight PJ, Sutoh K, Burgess SA. Functions and mechanics of dynein motor proteins. Nat Rev Mol Cell Biol 2013; 14:713-26. [PMID: 24064538 DOI: 10.1038/nrm3667] [Citation(s) in RCA: 346] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Fuelled by ATP hydrolysis, dyneins generate force and movement on microtubules in a wealth of biological processes, including ciliary beating, cell division and intracellular transport. The large mass and complexity of dynein motors have made elucidating their mechanisms a sizable task. Yet, through a combination of approaches, including X-ray crystallography, cryo-electron microscopy, single-molecule assays and biochemical experiments, important progress has been made towards understanding how these giant motor proteins work. From these studies, a model for the mechanochemical cycle of dynein is emerging, in which nucleotide-driven flexing motions within the AAA+ ring of dynein alter the affinity of its microtubule-binding stalk and reshape its mechanical element to generate movement.
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Affiliation(s)
- Anthony J Roberts
- 1] Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. [2] Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
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19
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Rao L, Romes EM, Nicholas MP, Brenner S, Tripathy A, Gennerich A, Slep KC. The yeast dynein Dyn2-Pac11 complex is a dynein dimerization/processivity factor: structural and single-molecule characterization. Mol Biol Cell 2013; 24:2362-77. [PMID: 23761070 PMCID: PMC3727929 DOI: 10.1091/mbc.e13-03-0166] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Studying the role of accessory chains in dynein single-molecule motility shows that the dynein light chain (LC) and intermediate chain (IC) promote motor dimerization, increase velocity, and potentiate processivity. The crystal structure of the yeast LC–IC complex is determined, and the interaction is biochemically characterized. Cytoplasmic dynein is the major microtubule minus end–directed motor. Although studies have probed the mechanism of the C-terminal motor domain, if and how dynein's N-terminal tail and the accessory chains it binds regulate motor activity remain to be determined. Here, we investigate the structure and function of the Saccharomyces cerevisiae dynein light (Dyn2) and intermediate (Pac11) chains in dynein heavy chain (Dyn1) movement. We present the crystal structure of a Dyn2-Pac11 complex, showing Dyn2-mediated Pac11 dimerization. To determine the molecular effects of Dyn2 and Pac11 on Dyn1 function, we generated dyn2Δ and dyn2Δpac11Δ strains and analyzed Dyn1 single-molecule motor activity. We find that the Dyn2-Pac11 complex promotes Dyn1 homodimerization and potentiates processivity. The absence of Dyn2 and Pac11 yields motors with decreased velocity, dramatically reduced processivity, increased monomerization, aggregation, and immobility as determined by single-molecule measurements. Deleting dyn2 significantly reduces Pac11-Dyn1 complex formation, yielding Dyn1 motors with activity similar to Dyn1 from the dyn2Δpac11Δ strain. Of interest, motor phenotypes resulting from Dyn2-Pac11 complex depletion bear similarity to a point mutation in the mammalian dynein N-terminal tail (Loa), highlighting this region as a conserved, regulatory motor element.
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Affiliation(s)
- Lu Rao
- Department of Anatomy and Structural Biology and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, NY 10461, USA
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20
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Engel BD, Ishikawa H, Wemmer KA, Geimer S, Wakabayashi KI, Hirono M, Craige B, Pazour GJ, Witman GB, Kamiya R, Marshall WF. The role of retrograde intraflagellar transport in flagellar assembly, maintenance, and function. ACTA ACUST UNITED AC 2013; 199:151-67. [PMID: 23027906 PMCID: PMC3461521 DOI: 10.1083/jcb.201206068] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
An inducible dynein heavy chain 1b mutant reveals that robust retrograde intraflagellar transport is required for flagellar assembly and function but not the maintenance of flagellar length. The maintenance of flagellar length is believed to require both anterograde and retrograde intraflagellar transport (IFT). However, it is difficult to uncouple the functions of retrograde transport from anterograde, as null mutants in dynein heavy chain 1b (DHC1b) have stumpy flagella, demonstrating solely that retrograde IFT is required for flagellar assembly. We isolated a Chlamydomonas reinhardtii mutant (dhc1b-3) with a temperature-sensitive defect in DHC1b, enabling inducible inhibition of retrograde IFT in full-length flagella. Although dhc1b-3 flagella at the nonpermissive temperature (34°C) showed a dramatic reduction of retrograde IFT, they remained nearly full-length for many hours. However, dhc1b-3 cells at 34°C had strong defects in flagellar assembly after cell division or pH shock. Furthermore, dhc1b-3 cells displayed altered phototaxis and flagellar beat. Thus, robust retrograde IFT is required for flagellar assembly and function but is dispensable for the maintenance of flagellar length. Proteomic analysis of dhc1b-3 flagella revealed distinct classes of proteins that change in abundance when retrograde IFT is inhibited.
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Affiliation(s)
- Benjamin D Engel
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
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21
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Fujimoto K, Kitamura M, Yokokawa M, Kanno I, Kotera H, Yokokawa R. Colocalization of quantum dots by reactive molecules carried by motor proteins on polarized microtubule arrays. ACS NANO 2013; 7:447-455. [PMID: 23230973 DOI: 10.1021/nn3045038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The field of microfluidics has drastically contributed to downscale the size of benchtop experiments to the dimensions of a chip without compromising results. However, further miniaturization and the ability to directly manipulate individual molecules require a platform that permits organized molecular transport. The motor proteins and microtubules that carry out orderly intracellular transport are ideal for driving in vitro nanotransport. Here, we demonstrate that a reconstruction of the cellular kinesin/dynein-microtubule system in nanotracks provides a molecular total analysis system (MTAS) to control massively parallel chemical reactions. The mobility of kinesin and a microtubule dissociation method enable orientation of a microtubule in an array for directed transport of reactive molecules carried by kinesin or dynein. The binding of glutathione S-transferase (GST) to glutathione (GSH) and the binding of streptavidin to biotin are visualized as colocalizations of quantum dots (Q-dots) when motor motilities bring them into contact. The organized nanotransport demonstrated here suggests the feasibility of using our platform to perform parallel biochemical reactions focused at the molecular level.
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Affiliation(s)
- Kazuya Fujimoto
- Department of Micro Engineering, Kyoto University, Yoshida-Honmachi, Sakyo, Kyoto 606-8501, Japan
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22
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Abstract
Cytoplasmic dynein is the major motor protein responsible for microtubule minus-end-directed movements in most eukaryotic cells. It transports a variety of cargoes and has numerous functions during spindle assembly and chromosome segregation. It is a large complex of about 1.4 MDa composed of six different subunits, interacting with a multitude of different partners. Most biochemical studies have been performed either with the native mammalian cytoplasmic dynein complex purified from tissue or, more recently, with recombinant dynein fragments from budding yeast and Dictyostelium. Hardly any information exists about the properties of human dynein. Moreover, experiments with an entire human dynein complex prepared from recombinant subunits with a well-defined composition are lacking. Here, we reconstitute a complete cytoplasmic dynein complex using recombinant human subunits and characterize its biochemical and motile properties. Using analytical gel filtration, sedimentation-velocity ultracentrifugation, and negative-stain electron microscopy, we demonstrate that the smaller subunits of the complex have an important structural function for complex integrity. Fluorescence microscopy experiments reveal that while engaged in collective microtubule transport, the recombinant human cytoplasmic dynein complex is an active, microtubule minus-end-directed motor, as expected. However, in contrast to recombinant dynein of nonmetazoans, individual reconstituted human dynein complexes did not show robust processive motility, suggesting a more intricate mechanism of processivity regulation for the human dynein complex. In the future, the comparison of reconstituted dynein complexes from different species promises to provide molecular insight into the mechanisms regulating the various functions of these large molecular machines.
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Affiliation(s)
- Martina Trokter
- Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; and
| | - Norbert Mücke
- Division of Biophysics of Macromolecules, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Thomas Surrey
- Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; and
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23
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ATP-driven remodeling of the linker domain in the dynein motor. Structure 2012; 20:1670-80. [PMID: 22863569 PMCID: PMC3469822 DOI: 10.1016/j.str.2012.07.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 07/03/2012] [Accepted: 07/05/2012] [Indexed: 01/13/2023]
Abstract
Dynein ATPases are the largest known cytoskeletal motors and perform critical functions in cells: carrying cargo along microtubules in the cytoplasm and powering flagellar beating. Dyneins are members of the AAA+ superfamily of ring-shaped enzymes, but how they harness this architecture to produce movement is poorly understood. Here, we have used cryo-EM to determine 3D maps of native flagellar dynein-c and a cytoplasmic dynein motor domain in different nucleotide states. The structures show key sites of conformational change within the AAA+ ring and a large rearrangement of the “linker” domain, involving a hinge near its middle. Analysis of a mutant in which the linker “undocks” from the ring indicates that linker remodeling requires energy that is supplied by interactions with the AAA+ modules. Fitting the dynein-c structures into flagellar tomograms suggests how this mechanism could drive sliding between microtubules, and also has implications for cytoplasmic cargo transport.
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24
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Kon T, Oyama T, Shimo-Kon R, Imamula K, Shima T, Sutoh K, Kurisu G. The 2.8 Å crystal structure of the dynein motor domain. Nature 2012; 484:345-50. [PMID: 22398446 DOI: 10.1038/nature10955] [Citation(s) in RCA: 181] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 02/17/2012] [Indexed: 01/04/2023]
Abstract
Dyneins are microtubule-based AAA(+) motor complexes that power ciliary beating, cell division, cell migration and intracellular transport. Here we report the most complete structure obtained so far, to our knowledge, of the 380-kDa motor domain of Dictyostelium discoideum cytoplasmic dynein at 2.8 Å resolution; the data are reliable enough to discuss the structure and mechanism at the level of individual amino acid residues. Features that can be clearly visualized at this resolution include the coordination of ADP in each of four distinct nucleotide-binding sites in the ring-shaped AAA(+) ATPase unit, a newly identified interaction interface between the ring and mechanical linker, and junctional structures between the ring and microtubule-binding stalk, all of which should be critical for the mechanism of dynein motility. We also identify a long-range allosteric communication pathway between the primary ATPase and the microtubule-binding sites. Our work provides a framework for understanding the mechanism of dynein-based motility.
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Affiliation(s)
- Takahide Kon
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
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25
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26
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Qiu W, Derr ND, Goodman BS, Villa E, Wu D, Shih W, Reck-Peterson SL. Dynein achieves processive motion using both stochastic and coordinated stepping. Nat Struct Mol Biol 2012; 19:193-200. [PMID: 22231401 PMCID: PMC3272163 DOI: 10.1038/nsmb.2205] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 11/18/2011] [Indexed: 12/18/2022]
Abstract
Processivity, the ability of single molecules to move continuously along a track, is a fundamental requirement of cargo-transporting molecular motors. Here, we investigate how cytoplasmic dynein, a homodimeric, microtubule-based motor, achieves processive motion. To do this, we developed a versatile method for assembling Saccharomyces cerevisiae dynein heterodimers, using complementary DNA oligonucleotides covalently linked to dynein monomers labeled with different organic fluorophores. Using two-color, single-molecule microscopy and high-precision, two-dimensional tracking, we find that dynein has a highly variable stepping pattern that is distinct from all other processive cytoskeletal motors, which use 'hand-over-hand' mechanisms. Uniquely, dynein stepping is stochastic when its two motor domains are close together. However, coordination emerges as the distance between motor domains increases, implying that a tension-based mechanism governs these steps. This plasticity may allow tuning of dynein for its diverse cellular functions.
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Affiliation(s)
- Weihong Qiu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
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27
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Cho C, Vale RD. The mechanism of dynein motility: insight from crystal structures of the motor domain. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1823:182-91. [PMID: 22062687 DOI: 10.1016/j.bbamcr.2011.10.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2011] [Revised: 10/22/2011] [Accepted: 10/24/2011] [Indexed: 12/30/2022]
Abstract
Dynein is a large cytoskeletal motor protein that belongs to the AAA+ (ATPases associated with diverse cellular activities) superfamily. While dynein has had a rich history of cellular research, its molecular mechanism of motility remains poorly understood. Here we describe recent X-ray crystallographic studies that reveal the architecture of dynein's catalytic ring, mechanical linker element, and microtubule binding domain. This structural information has given rise to new hypotheses on how the dynein motor domain might change its conformation in order to produce motility along microtubules.
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Affiliation(s)
- Carol Cho
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, USA
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28
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Tsygankov D, Serohijos AWR, Dokholyan NV, Elston TC. A physical model reveals the mechanochemistry responsible for dynein's processive motion. Biophys J 2011; 101:144-50. [PMID: 21723824 DOI: 10.1016/j.bpj.2011.05.043] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 05/06/2011] [Accepted: 05/18/2011] [Indexed: 12/22/2022] Open
Abstract
The molecular motor dynein is associated with various cellular activities, such as directed transport along microtubules and the rhythmic beating of the axoneme. Because of the size and complexity of the protein, a detailed understanding of the mechanochemistry that drives dynein's processive motion is lacking. To overcome this deficiency, we developed the first (to our knowledge) computational model for two-headed dynein that couples conformational changes of the motor's subunits to the biochemical steps involved in ATP hydrolysis. Analysis of the model provides what we believe are several novel insights into how the protein functions: 1), structural constraints limit the motion of the free microtubule binding domain to one dimension, increasing the efficiency with which this domain finds a binding site; 2), in addition to the power stroke of the bound head, recovery of the free head to a pre-power-stroke conformation is required for this head to reach a forward binding site; 3), the order in which the power stroke and recovery transitions occur affects the probability of back-stepping; and 4), the existence of multiple equilibria in the motor's bending energy provides a mechanism for processive back-stepping. To the best of our knowledge, our computational model provides the first complete mechanochemical description of the motor protein dynein, and the findings presented here should motivate new experimental investigations to test its predictions.
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Affiliation(s)
- Denis Tsygankov
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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