1
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Neahring L, Cho NH, He Y, Liu G, Fernandes J, Rux CJ, Nakos K, Subramanian R, Upadhyayula S, Yildiz A, Dumont S. Torques within and outside the human spindle balance twist at anaphase. J Cell Biol 2024; 223:e202312046. [PMID: 38869473 PMCID: PMC11176257 DOI: 10.1083/jcb.202312046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/14/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024] Open
Abstract
At each cell division, nanometer-scale motors and microtubules give rise to the micron-scale spindle. Many mitotic motors step helically around microtubules in vitro, and most are predicted to twist the spindle in a left-handed direction. However, the human spindle exhibits only slight global twist, raising the question of how these molecular torques are balanced. Here, we find that anaphase spindles in the epithelial cell line MCF10A have a high baseline twist, and we identify factors that both increase and decrease this twist. The midzone motors KIF4A and MKLP1 are together required for left-handed twist at anaphase, and we show that KIF4A generates left-handed torque in vitro. The actin cytoskeleton also contributes to left-handed twist, but dynein and its cortical recruitment factor LGN counteract it. Together, our work demonstrates that force generators regulate twist in opposite directions from both within and outside the spindle, preventing strong spindle twist during chromosome segregation.
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Affiliation(s)
- Lila Neahring
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Nathan H. Cho
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Tetrad Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Yifei He
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Gaoxiang Liu
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jonathan Fernandes
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Caleb J. Rux
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- UC Berkeley/UC San Francisco Graduate Group in Bioengineering, Berkeley, CA, USA
| | - Konstantinos Nakos
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Radhika Subramanian
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Srigokul Upadhyayula
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Ahmet Yildiz
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Physics Department, University of California Berkeley, Berkeley, CA, USA
| | - Sophie Dumont
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Tetrad Graduate Program, University of California San Francisco, San Francisco, CA, USA
- UC Berkeley/UC San Francisco Graduate Group in Bioengineering, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
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2
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Zimmermann N, Ishikawa T. Comparative structural study on axonemal and cytoplasmic dyneins. Cytoskeleton (Hoboken) 2024. [PMID: 39073294 DOI: 10.1002/cm.21897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/30/2024]
Abstract
Axonemal dyneins are the driving force of motile cilia, while cytoplasmic dyneins play an essential role in minus-end oriented intracellular transport. Their molecular structure is indispensable for an understanding of the molecular mechanism of ciliary beating and cargo transport. After some initial structural analysis of cytoplasmic dyneins, which are easier to manipulate with genetic engineering, using X-ray crystallography and single-particle cryo-electron microscopy, a number of atomic and pseudo-atomic structural analyses of axonemal dyneins have been published. Currently, several structures of dyneins in the post-power stroke conformation as well as a few structures in the pre-power stroke conformation are available. It will be worth systematically comparing conformations of dynein motor proteins from different sources and at different states, to understand their role in biological function. In this review, we will overview published high- and intermediate-resolution structures of cytoplasmic and axonemal dyneins, compare the high-resolution structures of their core motor domains and overall tail conformations at various nucleotide states, and discuss their force generation mechanism.
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Affiliation(s)
- Noemi Zimmermann
- Laboratory of Nanoscale Biology, Paul Scherrer Institute, Villigen, Switzerland
- Department of Biology, ETH Zurich, Zürich, Switzerland
| | - Takashi Ishikawa
- Laboratory of Nanoscale Biology, Paul Scherrer Institute, Villigen, Switzerland
- Department of Biology, ETH Zurich, Zürich, Switzerland
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3
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Slivka J, Gleave E, Wijewardena DP, Canty JT, Selvin PR, Carter AP, Yildiz A. Stepping dynamics of dynein characterized by MINFLUX. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603667. [PMID: 39071311 PMCID: PMC11275781 DOI: 10.1101/2024.07.16.603667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Cytoplasmic dynein is a dimeric motor that drives minus-end directed transport on microtubules (MTs). To couple ATP hydrolysis to a mechanical step, a dynein monomer must be released from the MT before undergoing a conformational change that generates a bias towards the minus end. However, the dynamics of dynein stepping have been poorly characterized by tracking flexible regions of the motor with limited resolution. Here, we developed a cysteine-light mutant of yeast dynein and site-specifically labeled its MT-binding domain in vitro. MINFLUX tracking at sub-millisecond resolution revealed that dynein hydrolyzes one ATP per step and takes multitudes of 8 nm steps at physiological ATP. Steps are preceded by the transient movement towards the plus end. We propose that these backward "dips" correspond to MT release and subsequent diffusion of the stepping monomer around its MT-bound partner before taking a minus-end-directed conformational change of its linker. Our results reveal the order of sub-millisecond events that result in a productive step of dynein.
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Affiliation(s)
- Joseph Slivka
- Department of Physics, University of California at Berkeley, Berkeley CA 94720 USA
| | - Emma Gleave
- Medical Research Council Laboratory of Molecular Biology, Division of Structural Studies, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Devinda P Wijewardena
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana IL 61801 USA
| | - John T Canty
- Biophysics Graduate Group, University of California at Berkeley, Berkeley CA 94720 USA
| | - Paul R Selvin
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana IL 61801 USA
| | - Andrew P Carter
- Medical Research Council Laboratory of Molecular Biology, Division of Structural Studies, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Ahmet Yildiz
- Department of Physics, University of California at Berkeley, Berkeley CA 94720 USA
- Biophysics Graduate Group, University of California at Berkeley, Berkeley CA 94720 USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley CA 94720 USA
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4
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Rao L, Gennerich A. Structure and Function of Dynein's Non-Catalytic Subunits. Cells 2024; 13:330. [PMID: 38391943 PMCID: PMC10886578 DOI: 10.3390/cells13040330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024] Open
Abstract
Dynein, an ancient microtubule-based motor protein, performs diverse cellular functions in nearly all eukaryotic cells, with the exception of land plants. It has evolved into three subfamilies-cytoplasmic dynein-1, cytoplasmic dynein-2, and axonemal dyneins-each differentiated by their cellular functions. These megadalton complexes consist of multiple subunits, with the heavy chain being the largest subunit that generates motion and force along microtubules by converting the chemical energy of ATP hydrolysis into mechanical work. Beyond this catalytic core, the functionality of dynein is significantly enhanced by numerous non-catalytic subunits. These subunits are integral to the complex, contributing to its stability, regulating its enzymatic activities, targeting it to specific cellular locations, and mediating its interactions with other cofactors. The diversity of non-catalytic subunits expands dynein's cellular roles, enabling it to perform critical tasks despite the conservation of its heavy chains. In this review, we discuss recent findings and insights regarding these non-catalytic subunits.
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Affiliation(s)
- Lu Rao
- Department of Biochemistry and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Arne Gennerich
- Department of Biochemistry and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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5
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Neahring L, He Y, Cho NH, Liu G, Fernandes J, Rux CJ, Nakos K, Subramanian R, Upadhyayula S, Yildiz A, Dumont S. Torques within and outside the human spindle balance twist at anaphase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.10.570990. [PMID: 38405786 PMCID: PMC10888964 DOI: 10.1101/2023.12.10.570990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
At each cell division, nanometer-scale motors and microtubules give rise to the micron-scale spindle. Many mitotic motors step helically around microtubules in vitro, and most are predicted to twist the spindle in a left-handed direction. However, the human spindle exhibits only slight global twist, raising the question of how these molecular torques are balanced. Here, using lattice light sheet microscopy, we find that anaphase spindles in the epithelial cell line MCF10A have a high baseline twist, and we identify factors that both increase and decrease this twist. The midzone motors KIF4A and MKLP1 are redundantly required for left-handed twist at anaphase, and we show that KIF4A generates left-handed torque in vitro. The actin cytoskeleton also contributes to left-handed twist, but dynein and its cortical recruitment factor LGN counteract it. Together, our work demonstrates that force generators regulate twist in opposite directions from both within and outside the spindle, preventing strong spindle twist during chromosome segregation.
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Affiliation(s)
- Lila Neahring
- Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Developmental & Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Yifei He
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Nathan H. Cho
- Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Tetrad Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Gaoxiang Liu
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jonathan Fernandes
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Caleb J. Rux
- Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- UC Berkeley/UC San Francisco Graduate Group in Bioengineering, Berkeley, CA, USA
| | - Konstantinos Nakos
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Radhika Subramanian
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Srigokul Upadhyayula
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Ahmet Yildiz
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Physics Department, University of California Berkeley, Berkeley, CA, USA
| | - Sophie Dumont
- Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Developmental & Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Tetrad Graduate Program, University of California San Francisco, San Francisco, CA, USA
- UC Berkeley/UC San Francisco Graduate Group in Bioengineering, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, CA, USA
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6
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Kikkawa M. A quest to unravel the role of the stalk and microtubule-binding domain of axonemal dyneins. FEBS Lett 2023; 597:2147-2148. [PMID: 37599096 DOI: 10.1002/1873-3468.14707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023]
Affiliation(s)
- Masahide Kikkawa
- Department of Cell Biology & Anatomy, Graduate School of Medicine, The University of Tokyo, Japan
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7
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Ton WD, Wang Y, Chai P, Beauchamp-Perez C, Flint NT, Lammers LG, Xiong H, Zhang K, Markus SM. Microtubule-binding-induced allostery triggers LIS1 dissociation from dynein prior to cargo transport. Nat Struct Mol Biol 2023; 30:1365-1379. [PMID: 37322240 PMCID: PMC10590275 DOI: 10.1038/s41594-023-01010-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/28/2023] [Indexed: 06/17/2023]
Abstract
The lissencephaly-related protein LIS1 is a critical regulator of cytoplasmic dynein that governs motor function and intracellular localization (for example, to microtubule plus-ends). Although LIS1 binding is required for dynein activity, its unbinding prior to initiation of cargo transport is equally important, since preventing dissociation leads to dynein dysfunction. To understand whether and how dynein-LIS1 binding is modulated, we engineered dynein mutants locked in a microtubule-bound (MT-B) or microtubule-unbound (MT-U) state. Whereas the MT-B mutant exhibits low LIS1 affinity, the MT-U mutant binds LIS1 with high affinity, and as a consequence remains almost irreversibly associated with microtubule plus-ends. We find that a monomeric motor domain is sufficient to exhibit these opposing LIS1 affinities, and that this is evolutionarily conserved between yeast and humans. Three cryo-EM structures of human dynein with and without LIS1 reveal microtubule-binding induced conformational changes responsible for this regulation. Our work reveals key biochemical and structural insight into LIS1-mediated dynein activation.
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Affiliation(s)
- William D Ton
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Yue Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Pengxin Chai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Nicholas T Flint
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Lindsay G Lammers
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Hao Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Kai Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
| | - Steven M Markus
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.
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8
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Ko S, Toda A, Tanaka H, Yu J, Kurisu G. Crystal structure of the stalk region of axonemal inner-arm dynein-d reveals unique features in the coiled-coil and microtubule-binding domain. FEBS Lett 2023; 597:2149-2160. [PMID: 37400274 DOI: 10.1002/1873-3468.14690] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 07/05/2023]
Abstract
Axonemal dynein is an ATP-dependent microtubular motor protein responsible for cilia and flagella beating, and its dysfunction can cause diseases such as primary ciliary dyskinesia and sperm dysmotility. Despite its biological importance, structure-based mechanisms underlying axonemal dynein motors remain unclear. Here, we determined the X-ray crystal structure of the human inner-arm dynein-d (DNAH1) stalk region, which contains a long antiparallel coiled-coil and a microtubule-binding domain (MTBD), at 2.7 Å resolution. Notably, differences in the relative orientation of the coiled-coil and MTBD in comparison with other dyneins, as well as the diverse orientations of the MTBD flap region among various isoforms, lead us to propose a 'spike shoe model' with an altered stepping angle for the interaction between IAD-d and microtubules. Based on these findings, we discuss isoform-specific functions of the axonemal dynein stalk MTBDs.
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Affiliation(s)
- Seolmin Ko
- Protein Crystallography Laboratory, Institute for Protein Research, Osaka University, Suita, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Akiyuki Toda
- Protein Crystallography Laboratory, Institute for Protein Research, Osaka University, Suita, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Hideaki Tanaka
- Protein Crystallography Laboratory, Institute for Protein Research, Osaka University, Suita, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Jian Yu
- Protein Crystallography Laboratory, Institute for Protein Research, Osaka University, Suita, Japan
| | - Genji Kurisu
- Protein Crystallography Laboratory, Institute for Protein Research, Osaka University, Suita, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Japan
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9
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Minckley TF, Salvagio LA, Fudge DH, Verhey K, Markus SM, Qin Y. Zn2+ decoration of microtubules arrests axonal transport and displaces tau, doublecortin, and MAP2C. J Cell Biol 2023; 222:e202208121. [PMID: 37326602 PMCID: PMC10276529 DOI: 10.1083/jcb.202208121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 03/31/2023] [Accepted: 05/11/2023] [Indexed: 06/17/2023] Open
Abstract
Intracellular Zn2+ concentrations increase via depolarization-mediated influx or intracellular release, but the immediate effects of Zn2+ signals on neuron function are not fully understood. By simultaneous recording of cytosolic Zn2+ and organelle motility, we find that elevated Zn2+ (IC50 ≈ 5-10 nM) reduces both lysosomal and mitochondrial motility in primary rat hippocampal neurons and HeLa cells. Using live-cell confocal microscopy and in vitro single-molecule TIRF imaging, we reveal that Zn2+ inhibits activity of motor proteins (kinesin and dynein) without disrupting their microtubule binding. Instead, Zn2+ directly binds to microtubules and selectively promotes detachment of tau, DCX, and MAP2C, but not MAP1B, MAP4, MAP7, MAP9, or p150glued. Bioinformatic predictions and structural modeling show that the Zn2+ binding sites on microtubules partially overlap with the microtubule binding sites of tau, DCX, dynein, and kinesin. Our results reveal that intraneuronal Zn2+ regulates axonal transport and microtubule-based processes by interacting with microtubules.
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Affiliation(s)
- Taylor F. Minckley
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | | | - Dylan H. Fudge
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Kristen Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Steven M. Markus
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Yan Qin
- Department of Biological Sciences, University of Denver, Denver, CO, USA
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10
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Yonemura Y, Sakai Y, Nakata R, Hagita-Tatsumoto A, Miyasaka T, Misonou H. Active Transport by Cytoplasmic Dynein Maintains the Localization of MAP2 in Developing Neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538370. [PMID: 37163107 PMCID: PMC10168327 DOI: 10.1101/2023.04.26.538370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
MAP2 has been widely used as a marker of neuronal dendrites because of its extensive restriction in the somatodendritic region of neurons. Despite that, how the precise localization of such a soluble protein is established and maintained against thermal forces and diffusion has been elusive and long remained a mystery in neuroscience. In this study, we aimed to uncover the mechanism behind how MAP2 is retained in the somatodendritic region. Using GFP-tagged MAP2 expressed in cultured hippocampal neurons, we discovered a crucial protein region responsible for the localization of MAP2, the serine/proline-rich (S/P) region. Our pulse-chase live-cell imaging revealed the slow but steady migration of MAP2 toward distal dendrites, which was not observed in a MAP2 mutant lacking the S/P region, indicating that S/P-dependent transport is vital for the proper localization of MAP2. Furthermore, our experiments using an inhibitor of cytoplasmic Dynein, ciliobrevin D, as well as Dynein knockdown, showed that cytoplasmic Dynein is involved in the transport of MAP2 in dendrites. We also found that Dynein complex binds to MAP2 through the S/P region in heterologous cells. Using mathematical modeling based on experimental data, we confirmed that an intermittent active transport mechanism is essential. Thus, we propose that the cytoplasmic Dynein recruits and transports free MAP2 toward distal dendrites, thereby maintaining the precise dendritic localization of MAP2 in neurons. Our findings shed light on the previously unknown mechanism behind MAP2 localization and provide a new direction for soluble protein trafficking research in the field of cell biology of neurons.
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11
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Reimer JM, DeSantis ME, Reck-Peterson SL, Leschziner AE. Structures of human dynein in complex with the lissencephaly 1 protein, LIS1. eLife 2023; 12:84302. [PMID: 36692009 PMCID: PMC9889085 DOI: 10.7554/elife.84302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/08/2023] [Indexed: 01/25/2023] Open
Abstract
The lissencephaly 1 protein, LIS1, is mutated in type-1 lissencephaly and is a key regulator of cytoplasmic dynein-1. At a molecular level, current models propose that LIS1 activates dynein by relieving its autoinhibited form. Previously we reported a 3.1 Å structure of yeast dynein bound to Pac1, the yeast homologue of LIS1, which revealed the details of their interactions (Gillies et al., 2022). Based on this structure, we made mutations that disrupted these interactions and showed that they were required for dynein's function in vivo in yeast. We also used our yeast dynein-Pac1 structure to design mutations in human dynein to probe the role of LIS1 in promoting the assembly of active dynein complexes. These mutations had relatively mild effects on dynein activation, suggesting that there may be differences in how dynein and Pac1/LIS1 interact between yeast and humans. Here, we report cryo-EM structures of human dynein-LIS1 complexes. Our new structures reveal the differences between the yeast and human systems, provide a blueprint to disrupt the human dynein-LIS1 interactions more accurately, and map type-1 lissencephaly disease mutations, as well as mutations in dynein linked to malformations of cortical development/intellectual disability, in the context of the dynein-LIS1 complex.
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Affiliation(s)
- Janice M Reimer
- Department of Cellular and Molecular Medicine, University of California, San DiegoSan DiegoUnited States
| | - Morgan E DeSantis
- Department of Molecular, Cellular and Developmental Biology, University of MichiganAnn ArborUnited States
| | - Samara L Reck-Peterson
- Department of Cellular and Molecular Medicine, University of California, San DiegoSan DiegoUnited States
- Department of Cell and Developmental Biology, University of California, San DiegoLa JollaUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Andres E Leschziner
- Department of Cellular and Molecular Medicine, University of California, San DiegoSan DiegoUnited States
- Department of Molecular Biology, University of California, San DiegoLa JollaUnited States
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12
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Studying Dynein Mechanochemistry with an Optical Trap. Methods Mol Biol 2023; 2623:201-219. [PMID: 36602688 DOI: 10.1007/978-1-0716-2958-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Molecular motors generate force and mechanical work to perform some of the most energy-demanding cellular processes, such as whole cell motility and cell division. These motors experience resistance from the viscoelastic environment of the surrounding cytoplasm, and opposing forces that can originate from other motors bound to cytoskeleton. Optical trapping is the most widely used method to measure the force-generating and force-response characteristics of motor proteins. Here we present the methodologies of three different optical trapping assays we use to measure how forces originating from external factors affect the microtubule-detachment rate and velocity of dynein. We also briefly discuss the remaining challenges and future directions of optical trapping studies of dyneins and other microtubule-based motors.
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13
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Pabbathi A, Coleman L, Godar S, Paul A, Garlapati A, Spencer M, Eller J, Alper JD. Long-range electrostatic interactions significantly modulate the affinity of dynein for microtubules. Biophys J 2022; 121:1715-1726. [PMID: 35346642 PMCID: PMC9117880 DOI: 10.1016/j.bpj.2022.03.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/13/2022] [Accepted: 03/24/2022] [Indexed: 11/02/2022] Open
Abstract
The dynein family of microtubule minus-end-directed motor proteins drives diverse functions in eukaryotic cells, including cell division, intracellular transport, and flagellar beating. Motor protein processivity, which characterizes how far a motor walks before detaching from its filament, depends on the interaction between its microtubule-binding domain (MTBD) and the microtubule. Dynein's MTBD switches between high- and low-binding affinity states as it steps. Significant structural and functional data show that specific salt bridges within the MTBD and between the MTBD and the microtubule govern these affinity state shifts. However, recent computational work suggests that nonspecific, long-range electrostatic interactions between the MTBD and the microtubule may also play an important role in the processivity of dynein. To investigate this hypothesis, we mutated negatively charged amino acids remote from the dynein MTBD-microtubule-binding interface to neutral residues and measured the binding affinity using microscale thermophoresis and optical tweezers. We found a significant increase in the binding affinity of the mutated MTBDs for microtubules. Furthermore, we found that charge screening by free ions in solution differentially affected the binding and unbinding rates of MTBDs to microtubules. Together, these results demonstrate a significant role for long-range electrostatic interactions in regulating dynein-microtubule affinity. Moreover, these results provide insight into the principles that potentially underlie the biophysical differences between molecular motors with various processivities and protein-protein interactions more generally.
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Affiliation(s)
- Ashok Pabbathi
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina
| | - Lawrence Coleman
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina
| | - Subash Godar
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina
| | - Apurba Paul
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina; Eukaryotic Pathogen Innovations Center, Clemson, University, Clemson, South Carolina
| | - Aman Garlapati
- School of Mathematical and Statistical Sciences, Clemson University, Clemson, South Carolina
| | - Matheu Spencer
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina
| | - Jared Eller
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina; Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina
| | - Joshua Daniel Alper
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina; Eukaryotic Pathogen Innovations Center, Clemson, University, Clemson, South Carolina; Department of Biological Sciences, Clemson University, Clemson, South Carolina.
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14
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Three-color single-molecule imaging reveals conformational dynamics of dynein undergoing motility. Proc Natl Acad Sci U S A 2021; 118:2101391118. [PMID: 34326255 PMCID: PMC8346880 DOI: 10.1073/pnas.2101391118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Dynein, a dimeric motor protein, moves along microtubules through adenosine 5′-triphosphate- and thermal-driven motions of two large ring domains (AAA rings) and small microtubule-binding domains (MTBDs) separated by a long coiled-coil. Previous single-molecule studies have tracked the positions of the AAA rings during motility, but not the MTBDs. Here, we tracked the relative positions of both MTBDs and one AAA ring by three-color, nanometer-resolution imaging. The observation of both MTBDs provided a direct measurement of how dynein steps on the tubulin subunits, and the simultaneous observation of three fiducial markers revealed extraordinary flexibility and previously unknown conformational states of the motor during motility. The techniques presented here can be used to explore conformational dynamics of many other macromolecular complexes. The motor protein dynein undergoes coordinated conformational changes of its domains during motility along microtubules. Previous single-molecule studies analyzed the motion of the AAA rings of the dynein homodimer, but not the distal microtubule-binding domains (MTBDs) that step along the track. Here, we simultaneously tracked with nanometer precision two MTBDs and one AAA ring of a single dynein as it underwent hundreds of steps using three-color imaging. We show that the AAA ring and the MTBDs do not always step simultaneously and can take differently sized steps. This variability in the movement between the AAA ring and MTBDs results in an unexpectedly large number of conformational states of dynein during motility. Extracting data on conformational transition biases, we could accurately model dynein stepping in silico. Our results reveal that the flexibility between major dynein domains is critical for dynein motility.
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15
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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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16
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Cui H, Ali MY, Goyal P, Zhang K, Loh JY, Trybus KM, Solmaz SR. Coiled-coil registry shifts in the F684I mutant of Bicaudal D result in cargo-independent activation of dynein motility. Traffic 2021; 21:463-478. [PMID: 32378283 DOI: 10.1111/tra.12734] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 04/29/2020] [Accepted: 05/01/2020] [Indexed: 11/28/2022]
Abstract
The dynein adaptor Drosophila Bicaudal D (BicD) is auto-inhibited and activates dynein motility only after cargo is bound, but the underlying mechanism is elusive. In contrast, we show that the full-length BicD/F684I mutant activates dynein processivity even in the absence of cargo. Our X-ray structure of the C-terminal domain of the BicD/F684I mutant reveals a coiled-coil registry shift; in the N-terminal region, the two helices of the homodimer are aligned, whereas they are vertically shifted in the wild-type. One chain is partially disordered and this structural flexibility is confirmed by computations, which reveal that the mutant transitions back and forth between the two registries. We propose that a coiled-coil registry shift upon cargo-binding activates BicD for dynein recruitment. Moreover, the human homolog BicD2/F743I exhibits diminished binding of cargo adaptor Nup358, implying that a coiled-coil registry shift may be a mechanism to modulate cargo selection for BicD2-dependent transport pathways.
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Affiliation(s)
- Heying Cui
- Department of Chemistry, State University of New York at Binghamton, Binghamton, New York, USA
| | - M Yusuf Ali
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, Vermont, USA
| | - Puja Goyal
- Department of Chemistry, State University of New York at Binghamton, Binghamton, New York, USA
| | - Kaiqi Zhang
- Department of Chemistry, State University of New York at Binghamton, Binghamton, New York, USA
| | - Jia Ying Loh
- Department of Chemistry, State University of New York at Binghamton, Binghamton, New York, USA
| | - Kathleen M Trybus
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, Vermont, USA
| | - Sozanne R Solmaz
- Department of Chemistry, State University of New York at Binghamton, Binghamton, New York, USA
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17
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Liu X, Rao L, Gennerich A. The regulatory function of the AAA4 ATPase domain of cytoplasmic dynein. Nat Commun 2020; 11:5952. [PMID: 33230227 PMCID: PMC7683685 DOI: 10.1038/s41467-020-19477-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/19/2020] [Indexed: 11/08/2022] Open
Abstract
Cytoplasmic dynein is the primary motor for microtubule minus-end-directed transport and is indispensable to eukaryotic cells. Although each motor domain of dynein contains three active AAA+ ATPases (AAA1, 3, and 4), only the functions of AAA1 and 3 are known. Here, we use single-molecule fluorescence and optical tweezers studies to elucidate the role of AAA4 in dynein's mechanochemical cycle. We demonstrate that AAA4 controls the priming stroke of the motion-generating linker, which connects the dimerizing tail of the motor to the AAA+ ring. Before ATP binds to AAA4, dynein remains incapable of generating motion. However, when AAA4 is bound to ATP, the gating of AAA1 by AAA3 prevails and dynein motion can occur. Thus, AAA1, 3, and 4 work together to regulate dynein function. Our work elucidates an essential role for AAA4 in dynein's stepping cycle and underscores the complexity and crosstalk among the motor's multiple AAA+ domains.
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Affiliation(s)
- Xinglei Liu
- Department of Anatomy and Structural Biology and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Lu Rao
- Department of Anatomy and Structural Biology and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Arne Gennerich
- Department of Anatomy and Structural Biology and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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18
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Xiang X, Qiu R. Cargo-Mediated Activation of Cytoplasmic Dynein in vivo. Front Cell Dev Biol 2020; 8:598952. [PMID: 33195284 PMCID: PMC7649786 DOI: 10.3389/fcell.2020.598952] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
Cytoplasmic dynein-1 is a minus-end-directed microtubule motor that transports a variety of cargoes including early endosomes, late endosomes and other organelles. In many cell types, dynein accumulates at the microtubule plus end, where it interacts with its cargo to be moved toward the minus end. Dynein binds to its various cargoes via the dynactin complex and specific cargo adapters. Dynactin and some of the coiled-coil-domain-containing cargo adapters not only link dynein to cargo but also activate dynein motility, which implies that dynein is activated by its cellular cargo. Structural studies indicate that a dynein dimer switches between the autoinhibited phi state and an open state; and the binding of dynactin and a cargo adapter to the dynein tails causes the dynein motor domains to have a parallel configuration, allowing dynein to walk processively along a microtubule. Recently, the dynein regulator LIS1 has been shown to be required for dynein activation in vivo, and its mechanism of action involves preventing dynein from switching back to the autoinhibited state. In this review, we will discuss our current understanding of dynein activation and point out the gaps of knowledge on the spatial regulation of dynein in live cells. In addition, we will emphasize the importance of studying a complete set of dynein regulators for a better understanding of dynein regulation in vivo.
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Affiliation(s)
- Xin Xiang
- Department of Biochemistry and Molecular Biology, The Uniformed Services University of the Health Sciences - F. Edward Hébert School of Medicine, Bethesda, MD, United States
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19
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Heale KA, Alisaraie L. C-terminal Tail of β-Tubulin and its Role in the Alterations of Dynein Binding Mode. Cell Biochem Biophys 2020; 78:331-345. [PMID: 32462384 PMCID: PMC10020315 DOI: 10.1007/s12013-020-00920-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/18/2020] [Indexed: 12/25/2022]
Abstract
Dynein is a cytoskeletal molecular motor protein that moves along the microtubule (MT) and transports various cellular cargos during its movement. Using standard Molecular Dynamics (MD) simulation, Principle Component Analysis (PCA), and Normal Mode Analysis (NMA) methods, this investigation studied large-scale movements and local interactions of dynein's Microtubule Binding Domain (MTBD) when bound to tubulin heterodimer subunits. Examination of the interactions between the MTBD segments, and their adjustments in terms of intra- and intermolecular distances at the interfacial area with tubulin heterodimer, particularly at α-H16, β-H18, and β-tubulin C-terminal tail (CTT), was the main focus of this study. The specific intramolecular interactions, electrostatic forces, and the salt bridge residue pairs were shown to be the dominating factors in orchestrating movements of the MTBD and MT interfacial segments in the dynein's low-high-affinity binding modes. Important interactions included β-Glu447 and β-Glu449 (CTT) with Arg3469 (MTBD-H6), Lys3472 (MTBD-H6-H7 loop) and Lys3479 (MTBD-H7); β-Glu449 with Lys3384 (MTBD-H8), Lys3386 and His3387 (MTBD-H1). The structural and precise position, orientation, and functional effects of the CTTs on the MT-MTBD, within reasonable cut-off distance for non-bonding interactions and under physiological conditions, are unavailable from previous studies. The absence of the residues in the highly flexible MT-CTTs in the experimentally solved structures is perhaps in some cases due to insufficient data from density maps, but these segments are crucial in protein binding. The presented work contributes to the information useful for the MT-MTBD structure refinement.
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Affiliation(s)
- Kali A Heale
- School of Pharmacy, Memorial University of Newfoundland, 300 Prince Philip Dr., St. John's, NL, A1B 3V6, Canada
| | - Laleh Alisaraie
- School of Pharmacy, Memorial University of Newfoundland, 300 Prince Philip Dr., St. John's, NL, A1B 3V6, Canada.
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20
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Canty JT, Yildiz A. Activation and Regulation of Cytoplasmic Dynein. Trends Biochem Sci 2020; 45:440-453. [PMID: 32311337 PMCID: PMC7179903 DOI: 10.1016/j.tibs.2020.02.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/30/2020] [Accepted: 02/04/2020] [Indexed: 12/30/2022]
Abstract
Cytoplasmic dynein is an AAA+ motor that drives the transport of many intracellular cargoes towards the minus end of microtubules (MTs). Previous in vitro studies characterized isolated dynein as an exceptionally weak motor that moves slowly and diffuses on an MT. Recent studies altered this view by demonstrating that dynein remains in an autoinhibited conformation on its own, and processive motility is activated when it forms a ternary complex with dynactin and a cargo adaptor. This complex assembles more efficiently in the presence of Lis1, providing an explanation for why Lis1 is a required cofactor for most cytoplasmic dynein-driven processes in cells. This review describes how dynein motility is activated and regulated by cargo adaptors and accessory proteins.
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Affiliation(s)
- John T Canty
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Ahmet Yildiz
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cellular Biology, University of California at Berkeley, Berkeley, CA 94720, USA; Physics Department, University of California at Berkeley, Berkeley, CA 94720, USA.
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21
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Marzo MG, Griswold JM, Markus SM. Pac1/LIS1 stabilizes an uninhibited conformation of dynein to coordinate its localization and activity. Nat Cell Biol 2020; 22:559-569. [PMID: 32341548 DOI: 10.1038/s41556-020-0492-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 02/23/2020] [Indexed: 12/20/2022]
Abstract
Dynein is a microtubule motor that transports many different cargos in various cell types and contexts. How dynein is regulated to perform these activities with spatial and temporal precision remains unclear. Human dynein is regulated by autoinhibition, whereby intermolecular contacts limit motor activity. Whether this mechanism is conserved throughout evolution, whether it can be affected by extrinsic factors, and its role in regulating dynein function remain unclear. Here, we use a combination of negative stain electron microscopy, single-molecule assays, genetic, and cell biological techniques to show that autoinhibition is conserved in budding yeast, and plays a key role in coordinating in vivo dynein function. Moreover, we find that the Lissencephaly-related protein, LIS1 (Pac1 in yeast), plays an important role in regulating dynein autoinhibition. Our studies demonstrate that, rather than inhibiting dynein motility, Pac1/LIS1 promotes dynein activity by stabilizing the uninhibited conformation, which ensures appropriate dynein localization and activity in cells.
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Affiliation(s)
- Matthew G Marzo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Jacqueline M Griswold
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Steven M Markus
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.
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22
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Force-Generating Mechanism of Axonemal Dynein in Solo and Ensemble. Int J Mol Sci 2020; 21:ijms21082843. [PMID: 32325779 PMCID: PMC7215579 DOI: 10.3390/ijms21082843] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/12/2020] [Accepted: 04/15/2020] [Indexed: 11/17/2022] Open
Abstract
In eukaryotic cilia and flagella, various types of axonemal dyneins orchestrate their distinct functions to generate oscillatory bending of axonemes. The force-generating mechanism of dyneins has recently been well elucidated, mainly in cytoplasmic dyneins, thanks to progress in single-molecule measurements, X-ray crystallography, and advanced electron microscopy. These techniques have shed light on several important questions concerning what conformational changes accompany ATP hydrolysis and whether multiple motor domains are coordinated in the movements of dynein. However, due to the lack of a proper expression system for axonemal dyneins, no atomic coordinates of the entire motor domain of axonemal dynein have been reported. Therefore, a substantial amount of knowledge on the molecular architecture of axonemal dynein has been derived from electron microscopic observations on dynein arms in axonemes or on isolated axonemal dynein molecules. This review describes our current knowledge and perspectives of the force-generating mechanism of axonemal dyneins in solo and in ensemble.
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23
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Self-organized networks: Darwinian evolution of dynein rings, stalks, and stalk heads. Proc Natl Acad Sci U S A 2020; 117:7799-7802. [PMID: 32205434 DOI: 10.1073/pnas.1920840117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cytoskeletons are self-organized networks based on polymerized proteins: actin, tubulin, and driven by motor proteins, such as myosin, kinesin, and dynein. Their positive Darwinian evolution enables them to approach optimized functionality (self-organized criticality). Dynein has three distinct titled subunits, but how these units connect to function as a molecular motor is mysterious. Dynein binds to tubulin through two coiled coil stalks and a stalk head. The energy used to alter the head binding and propel cargo along tubulin is supplied by ATP at a ring 1,500 amino acids away. Here, we show how many details of this extremely distant interaction are explained by water waves quantified by thermodynamic scaling. Water waves have shaped all proteins throughout positive Darwinian evolution, and many aspects of long-range water-protein interactions are universal (described by self-organized criticality). Dynein water waves resembling tsunami produce nearly optimal energy transport over 1,500 amino acids along dynein's one-dimensional peptide backbone. More specifically, this paper identifies many similarities in the function and evolution of dynein compared to other cytoskeleton proteins such as actin, myosin, and tubulin.
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24
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Toda A, Nishikawa Y, Tanaka H, Yagi T, Kurisu G. The complex of outer-arm dynein light chain-1 and the microtubule-binding domain of the γ heavy chain shows how axonemal dynein tunes ciliary beating. J Biol Chem 2020; 295:3982-3989. [PMID: 32014992 PMCID: PMC7086020 DOI: 10.1074/jbc.ra119.011541] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/29/2020] [Indexed: 01/07/2023] Open
Abstract
Axonemal dynein is a microtubule-based molecular motor that drives ciliary/flagellar beating in eukaryotes. In axonemal dynein, the outer-arm dynein (OAD) complex, which comprises three heavy chains (α, β, and γ), produces the main driving force for ciliary/flagellar motility. It has recently been shown that axonemal dynein light chain-1 (LC1) binds to the microtubule-binding domain (MTBD) of OADγ, leading to a decrease in its microtubule-binding affinity. However, it remains unclear how LC1 interacts with the MTBD and controls the microtubule-binding affinity of OADγ. Here, we have used X-ray crystallography and pulldown assays to examine the interaction between LC1 and the MTBD, identifying two important sites of interaction in the MTBD. Solving the LC1-MTBD complex from Chlamydomonas reinhardtii at 1.7 Å resolution, we observed that one site is located in the H5 helix and that the other is located in the flap region that is unique to some axonemal dynein MTBDs. Mutational analysis of key residues in these sites indicated that the H5 helix is the main LC1-binding site. We modeled the ternary structure of the LC1-MTBD complex bound to microtubules based on the known dynein-microtubule complex. This enabled us to propose a structural basis for both formations of the ternary LC1-MTBD-microtubule complex and LC1-mediated tuning of MTBD binding to the microtubule, suggesting a molecular model for how axonemal dynein senses the curvature of the axoneme and tunes ciliary/flagellar beating.
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Affiliation(s)
- Akiyuki Toda
- Department of Biological Sciences, Osaka University, Toyonaka, Osaka 560-0043, Japan,Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yosuke Nishikawa
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hideaki Tanaka
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Toshiki Yagi
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Hiroshima 727-0023, Japan
| | - Genji Kurisu
- Department of Biological Sciences, Osaka University, Toyonaka, Osaka 560-0043, Japan,Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan, To whom correspondence should be addressed. E-mail:
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25
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Beeby M, Ferreira JL, Tripp P, Albers SV, Mitchell DR. Propulsive nanomachines: the convergent evolution of archaella, flagella and cilia. FEMS Microbiol Rev 2020; 44:253-304. [DOI: 10.1093/femsre/fuaa006] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
ABSTRACT
Echoing the repeated convergent evolution of flight and vision in large eukaryotes, propulsive swimming motility has evolved independently in microbes in each of the three domains of life. Filamentous appendages – archaella in Archaea, flagella in Bacteria and cilia in Eukaryotes – wave, whip or rotate to propel microbes, overcoming diffusion and enabling colonization of new environments. The implementations of the three propulsive nanomachines are distinct, however: archaella and flagella rotate, while cilia beat or wave; flagella and cilia assemble at their tips, while archaella assemble at their base; archaella and cilia use ATP for motility, while flagella use ion-motive force. These underlying differences reflect the tinkering required to evolve a molecular machine, in which pre-existing machines in the appropriate contexts were iteratively co-opted for new functions and whose origins are reflected in their resultant mechanisms. Contemporary homologies suggest that archaella evolved from a non-rotary pilus, flagella from a non-rotary appendage or secretion system, and cilia from a passive sensory structure. Here, we review the structure, assembly, mechanism and homologies of the three distinct solutions as a foundation to better understand how propulsive nanomachines evolved three times independently and to highlight principles of molecular evolution.
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Affiliation(s)
- Morgan Beeby
- Department of Life Sciences, Frankland Road, Imperial College of London, London, SW7 2AZ, UK
| | - Josie L Ferreira
- Department of Life Sciences, Frankland Road, Imperial College of London, London, SW7 2AZ, UK
| | - Patrick Tripp
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Schaenzlestrasse 1, 79211 Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Schaenzlestrasse 1, 79211 Freiburg, Germany
| | - David R Mitchell
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, 750 E. Adams St., Syracuse, NY 13210, USA
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26
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Nishida N, Komori Y, Takarada O, Watanabe A, Tamura S, Kubo S, Shimada I, Kikkawa M. Structural basis for two-way communication between dynein and microtubules. Nat Commun 2020; 11:1038. [PMID: 32098965 PMCID: PMC7042235 DOI: 10.1038/s41467-020-14842-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/05/2020] [Indexed: 12/14/2022] Open
Abstract
The movements of cytoplasmic dynein on microtubule (MT) tracks is achieved by two-way communication between the microtubule-binding domain (MTBD) and the ATPase domain via a coiled-coil stalk, but the structural basis of this communication remains elusive. Here, we regulate MTBD either in high-affinity or low-affinity states by introducing a disulfide bond to the stalk and analyze the resulting structures by NMR and cryo-EM. In the MT-unbound state, the affinity changes of MTBD are achieved by sliding of the stalk α-helix by a half-turn, which suggests that structural changes propagate from the ATPase-domain to MTBD. In addition, MT binding induces further sliding of the stalk α-helix even without the disulfide bond, suggesting how the MT-induced conformational changes propagate toward the ATPase domain. Based on differences in the MT-binding surface between the high- and low-affinity states, we propose a potential mechanism for the directional bias of dynein movement on MT tracks.
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Affiliation(s)
- Noritaka Nishida
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - Yuta Komori
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Osamu Takarada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Atsushi Watanabe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Satoko Tamura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Satoshi Kubo
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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27
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Elshenawy MM, Canty JT, Oster L, Ferro LS, Zhou Z, Blanchard SC, Yildiz A. Cargo adaptors regulate stepping and force generation of mammalian dynein-dynactin. Nat Chem Biol 2019; 15:1093-1101. [PMID: 31501589 PMCID: PMC6810841 DOI: 10.1038/s41589-019-0352-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/18/2019] [Indexed: 12/24/2022]
Abstract
Cytoplasmic dynein is an ATP-driven motor that transports intracellular cargos along microtubules. Dynein adopts an inactive conformation when not attached to a cargo, and motility is activated when dynein assembles with dynactin and a cargo adaptor. It was unclear how active dynein-dynactin complexes step along microtubules and transport cargos under tension. Using single-molecule imaging, we showed that dynein-dynactin advances by taking 8 to 32-nm steps toward the microtubule minus end with frequent sideways and backward steps. Multiple dyneins collectively bear a large amount of tension because the backward stepping rate of dynein is insensitive to load. Recruitment of two dyneins to dynactin increases the force generation and the likelihood of winning against kinesin in a tug-of-war but does not directly affect velocity. Instead, velocity is determined by cargo adaptors and tail-tail interactions between two closely packed dyneins. Our results show that cargo adaptors modulate dynein motility and force generation for a wide range of cellular functions.
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Affiliation(s)
- Mohamed M Elshenawy
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - John T Canty
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA
| | - Liya Oster
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA
| | - Luke S Ferro
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Zhou Zhou
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ahmet Yildiz
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA.
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA.
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28
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Tirumala NA, Ananthanarayanan V. Role of Dynactin in the Intracellular Localization and Activation of Cytoplasmic Dynein. Biochemistry 2019; 59:156-162. [PMID: 31591892 DOI: 10.1021/acs.biochem.9b00772] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytoplasmic dynein, the major minus end-directed motor protein in several cell types, transports a variety of intracellular cargo upon forming a processive tripartite complex with its activator dynactin and cargo adaptors such as Hook3 and BicD2. Our current understanding of dynein regulation stems from a combination of in vivo studies of cargo movement upon perturbation of dynein activity, in vitro single-molecule experiments, and cryo-electron microscopy studies of dynein structure and its interaction with dynactin and cargo adaptors. In this Perspective, we first consolidate data from recent publications to understand how perturbations to the dynein-dynactin interaction and dynactin's in vivo localization alter the behavior of dynein-driven cargo transport in a cell type- and experimental condition-specific manner. In addition, we touch upon results from in vivo and in vitro studies to elucidate how dynein's interaction with dynactin and cargo adaptors activates dynein and enhances its processivity. Finally, we propose questions that need to be addressed in the future with appropriate experimental designs so as to improve our understanding of the spatiotemporal regulation of dynein's function in the context of the distribution and dynamics of dynactin in living cells.
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29
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Clinical and Genetic Analysis of Children with Kartagener Syndrome. Cells 2019; 8:cells8080900. [PMID: 31443223 PMCID: PMC6721662 DOI: 10.3390/cells8080900] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/05/2019] [Accepted: 08/13/2019] [Indexed: 12/28/2022] Open
Abstract
Primary ciliary dyskinesia (PCD) is a rare autosomal recessive disorder characterized by dysfunction of motile cilia causing ineffective mucus clearance and organ laterality defects. In this study, two unrelated Portuguese children with strong PCD suspicion underwent extensive clinical and genetic assessments by whole-exome sequencing (WES), as well as ultrastructural analysis of cilia by transmission electron microscopy (TEM) to identify their genetic etiology. These analyses confirmed the diagnostic of Kartagener syndrome (KS) (PCD with situs inversus). Patient-1 showed a predominance of the absence of the inner dynein arms with two disease-causing variants in the CCDC40 gene. Patient-2 showed the absence of both dynein arms and WES disclosed two novel high impact variants in the DNAH5 gene and two missense variants in the DNAH7 gene, all possibly deleterious. Moreover, in Patient-2, functional data revealed a reduction of gene expression and protein mislocalization in both genes' products. Our work calls the researcher's attention to the complexity of the PCD and to the possibility of gene interactions modelling the PCD phenotype. Further, it is demonstrated that even for well-known PCD genes, novel pathogenic variants could have importance for a PCD/KS diagnosis, reinforcing the difficulty of providing genetic counselling and prenatal diagnosis to families.
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30
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Noell CR, Loh JY, Debler EW, Loftus KM, Cui H, Russ BB, Zhang K, Goyal P, Solmaz SR. Role of Coiled-Coil Registry Shifts in the Activation of Human Bicaudal D2 for Dynein Recruitment upon Cargo Binding. J Phys Chem Lett 2019; 10:4362-4367. [PMID: 31306018 PMCID: PMC7243283 DOI: 10.1021/acs.jpclett.9b01865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Dynein adaptors such as Bicaudal D2 (BicD2) recognize cargo for dynein-dependent transport, and cargo-bound adaptors are required to activate dynein for processive transport, but the mechanism of action is unknown. Here we report the X-ray structure of the cargo-binding domain of human BicD2 and investigate the structural dynamics of the coiled-coil. Our molecular dynamics simulations support the fact that BicD2 can switch from a homotypic coiled-coil registry, in which both helices of the homodimer are aligned, to an asymmetric registry, where a portion of one helix is vertically shifted, as both states are similarly stable and defined by distinct conformations of F743. The F743I variant increases dynein recruitment in the Drosophila homologue, whereas the human R747C variant causes spinal muscular atrophy. We report spontaneous registry shifts for both variants, which may be the cause for BicD2 hyperactivation and disease. We propose that a registry shift upon cargo binding may activate autoinhibited BicD2 for dynein recruitment.
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Affiliation(s)
- Crystal R. Noell
- Department of Chemistry, State University of New York at Binghamton, P.O. Box 6000, Binghamton, New York 13902, United States
| | - Jia Ying Loh
- Department of Chemistry, State University of New York at Binghamton, P.O. Box 6000, Binghamton, New York 13902, United States
| | - Erik W. Debler
- Department of Biochemistry & Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, Pennsylvania 19107, United States
| | - Kyle M. Loftus
- Department of Chemistry, State University of New York at Binghamton, P.O. Box 6000, Binghamton, New York 13902, United States
| | - Heying Cui
- Department of Chemistry, State University of New York at Binghamton, P.O. Box 6000, Binghamton, New York 13902, United States
| | - Blaine B. Russ
- Department of Chemistry, State University of New York at Binghamton, P.O. Box 6000, Binghamton, New York 13902, United States
| | - Kaiqi Zhang
- Department of Chemistry, State University of New York at Binghamton, P.O. Box 6000, Binghamton, New York 13902, United States
| | - Puja Goyal
- Department of Chemistry, State University of New York at Binghamton, P.O. Box 6000, Binghamton, New York 13902, United States
- Corresponding Authors:. Tel: +1 607 777 4308 (P.G.)., . Tel: +1 607 777 2089 (S.R.S.)
| | - Sozanne R. Solmaz
- Department of Chemistry, State University of New York at Binghamton, P.O. Box 6000, Binghamton, New York 13902, United States
- Corresponding Authors:. Tel: +1 607 777 4308 (P.G.)., . Tel: +1 607 777 2089 (S.R.S.)
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31
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Rao L, Berger F, Nicholas MP, Gennerich A. Molecular mechanism of cytoplasmic dynein tension sensing. Nat Commun 2019; 10:3332. [PMID: 31350388 PMCID: PMC6659695 DOI: 10.1038/s41467-019-11231-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 07/02/2019] [Indexed: 12/21/2022] Open
Abstract
Cytoplasmic dynein is the most complex cytoskeletal motor protein and is responsible for numerous biological functions. Essential to dynein’s function is its capacity to respond anisotropically to tension, so that its microtubule-binding domains bind microtubules more strongly when under backward load than forward load. The structural mechanisms by which dynein senses directional tension, however, are unknown. Using a combination of optical tweezers, mutagenesis, and chemical cross-linking, we show that three structural elements protruding from the motor domain—the linker, buttress, and stalk—together regulate directional tension-sensing. We demonstrate that dynein’s anisotropic response to directional tension is mediated by sliding of the coiled-coils of the stalk, and that coordinated conformational changes of dynein’s linker and buttress control this process. We also demonstrate that the stalk coiled-coils assume a previously undescribed registry during dynein’s stepping cycle. We propose a revised model of dynein’s mechanochemical cycle which accounts for our findings. The cytoplasmic motor protein dynein senses directional tension; its microtubule-binding domains bind microtubules more strongly when under backward load. Here the authors use optical tweezers to show that the linker, buttress, and stalk domains together regulate directional tension-sensing.
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Affiliation(s)
- Lu Rao
- Department of Anatomy and Structural Biology and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Florian Berger
- Laboratory of Sensory Neuroscience, Rockefeller University, New York, NY, 10065, USA
| | - Matthew P Nicholas
- Department of Anatomy and Structural Biology and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.,Medical Scientist Training Program, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.,Flaum Eye Institute, University of Rochester Medical Center, 210 Crittenden Blvd, Rochester, NY, 14642, USA
| | - Arne Gennerich
- Department of Anatomy and Structural Biology and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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32
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Grotjahn DA, Lander GC. Setting the dynein motor in motion: New insights from electron tomography. J Biol Chem 2019; 294:13202-13217. [PMID: 31285262 DOI: 10.1074/jbc.rev119.003095] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Dyneins are ATP-fueled macromolecular machines that power all minus-end microtubule-based transport processes of molecular cargo within eukaryotic cells and play essential roles in a wide variety of cellular functions. These complex and fascinating motors have been the target of countless structural and biophysical studies. These investigations have elucidated the mechanism of ATP-driven force production and have helped unravel the conformational rearrangements associated with the dynein mechanochemical cycle. However, despite decades of research, it remains unknown how these molecular motions are harnessed to power massive cellular reorganization and what are the regulatory mechanisms that drive these processes. Recent advancements in electron tomography imaging have enabled researchers to visualize dynein motors in their transport environment with unprecedented detail and have led to exciting discoveries regarding dynein motor function and regulation. In this review, we will highlight how these recent structural studies have fundamentally propelled our understanding of the dynein motor and have revealed some unexpected, unifying mechanisms of regulation.
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Affiliation(s)
- Danielle A Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037.
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33
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A model for the chemomechanical coupling of the mammalian cytoplasmic dynein molecular motor. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:609-619. [PMID: 31278451 DOI: 10.1007/s00249-019-01386-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/17/2019] [Accepted: 07/01/2019] [Indexed: 01/07/2023]
Abstract
Available single-molecule data have shown that some mammalian cytoplasmic dynein dimers move on microtubules with a constant step size of about 8.2 nm. Here, a model is presented for the chemomechanical coupling of these mammalian cytoplasmic dynein dimers. In contrast to the previous models, a peculiar feature of the current model is that the rate constants of ATPase activity are independent of the external force. Based on this model, analytical studies of the motor dynamics are presented. With only four adjustable parameters, the theoretical results reproduce quantitatively diverse available single-molecule data on the force dependence of stepping ratio, velocity, mean dwell time, and dwell-time distribution between two mechanical steps. Predicted results are also provided for the force dependence of the number of ATP molecules consumed per mechanical step, indicating that under no or low force the motors exhibit a tight chemomechanical coupling, and as the force increases the number of ATPs consumed per step increases greatly.
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34
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Lacey SE, He S, Scheres SHW, Carter AP. Cryo-EM of dynein microtubule-binding domains shows how an axonemal dynein distorts the microtubule. eLife 2019; 8:e47145. [PMID: 31264960 PMCID: PMC6629372 DOI: 10.7554/elife.47145] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/01/2019] [Indexed: 01/14/2023] Open
Abstract
Dyneins are motor proteins responsible for transport in the cytoplasm and the beating of axonemes in cilia and flagella. They bind and release microtubules via a compact microtubule-binding domain (MTBD) at the end of a coiled-coil stalk. We address how cytoplasmic and axonemal dynein MTBDs bind microtubules at near atomic resolution. We decorated microtubules with MTBDs of cytoplasmic dynein-1 and axonemal dynein DNAH7 and determined their cryo-EM structures using helical Relion. The majority of the MTBD is rigid upon binding, with the transition to the high-affinity state controlled by the movement of a single helix at the MTBD interface. DNAH7 contains an 18-residue insertion, found in many axonemal dyneins, that contacts the adjacent protofilament. Unexpectedly, we observe that DNAH7, but not dynein-1, induces large distortions in the microtubule cross-sectional curvature. This raises the possibility that dynein coordination in axonemes is mediated via conformational changes in the microtubule.
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Affiliation(s)
- Samuel E Lacey
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Shaoda He
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
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35
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Niekamp S, Coudray N, Zhang N, Vale RD, Bhabha G. Coupling of ATPase activity, microtubule binding, and mechanics in the dynein motor domain. EMBO J 2019; 38:e101414. [PMID: 31268607 PMCID: PMC6600642 DOI: 10.15252/embj.2018101414] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 04/24/2019] [Accepted: 04/30/2019] [Indexed: 01/10/2023] Open
Abstract
The movement of a molecular motor protein along a cytoskeletal track requires communication between enzymatic, polymer-binding, and mechanical elements. Such communication is particularly complex and not well understood in the dynein motor, an ATPase that is comprised of a ring of six AAA domains, a large mechanical element (linker) spanning over the ring, and a microtubule-binding domain (MTBD) that is separated from the AAA ring by a ~ 135 Å coiled-coil stalk. We identified mutations in the stalk that disrupt directional motion, have microtubule-independent hyperactive ATPase activity, and nucleotide-independent low affinity for microtubules. Cryo-electron microscopy structures of a mutant that uncouples ATPase activity from directional movement reveal that nucleotide-dependent conformational changes occur normally in one-half of the AAA ring, but are disrupted in the other half. The large-scale linker conformational change observed in the wild-type protein is also inhibited, revealing that this conformational change is not required for ATP hydrolysis. These results demonstrate an essential role of the stalk in regulating motor activity and coupling conformational changes across the two halves of the AAA ring.
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Affiliation(s)
- Stefan Niekamp
- Department of Cellular and Molecular PharmacologyHoward Hughes Medical InstituteUniversity of California San FranciscoSan FranciscoCAUSA
| | - Nicolas Coudray
- Department of Cell BiologySkirball Institute of Biomolecular MedicineNew York University School of MedicineNew YorkNYUSA
- Applied Bioinformatics LaboratoriesNew York University School of MedicineNew YorkNYUSA
| | - Nan Zhang
- Department of Cellular and Molecular PharmacologyHoward Hughes Medical InstituteUniversity of California San FranciscoSan FranciscoCAUSA
| | - Ronald D Vale
- Department of Cellular and Molecular PharmacologyHoward Hughes Medical InstituteUniversity of California San FranciscoSan FranciscoCAUSA
| | - Gira Bhabha
- Department of Cell BiologySkirball Institute of Biomolecular MedicineNew York University School of MedicineNew YorkNYUSA
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36
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Tajielyato N, Alexov E. Processivity vs. Beating: Comparing Cytoplasmic and Axonemal Dynein Microtubule Binding Domain Association with Microtubule. Int J Mol Sci 2019; 20:ijms20051090. [PMID: 30832428 PMCID: PMC6429364 DOI: 10.3390/ijms20051090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 02/24/2019] [Accepted: 02/26/2019] [Indexed: 12/25/2022] Open
Abstract
This study compares the role of electrostatics in the binding process between microtubules and two dynein microtubule-binding domains (MTBDs): cytoplasmic and axonemal. These two dyneins are distinctively different in terms of their functionalities: cytoplasmic dynein is processive, while axonemal dynein is involved in beating. In both cases, the binding requires frequent association/disassociation between the microtubule and MTBD, and involves highly negatively charged microtubules, including non-structured C-terminal domains (E-hooks), and an MTBD interface that is positively charged. This indicates that electrostatics play an important role in the association process. Here, we show that the cytoplasmic MTBD binds electrostatically tighter to microtubules than to the axonemal MTBD, but the axonemal MTBD experiences interactions with microtubule E-hooks at longer distances compared with the cytoplasmic MTBD. This allows the axonemal MTBD to be weakly bound to the microtubule, while at the same time acting onto the microtubule via the flexible E-hooks, even at MTBD⁻microtubule distances of 45 Å. In part, this is due to the charge distribution of MTBDs: in the cytoplasmic MTBD, the positive charges are concentrated at the binding interface with the microtubule, while in the axonemal MTBD, they are more distributed over the entire structure, allowing E-hooks to interact at longer distances. The dissimilarities of electrostatics in the cases of axonemal and cytoplasmic MTBDs were found not to result in a difference in conformational dynamics on MTBDs, while causing differences in the conformational states of E-hooks. The E-hooks' conformations in the presence of the axonemal MTBD were less restricted than in the presence of the cytoplasmic MTBD. In parallel with the differences, the common effect was found that the structural fluctuations of MTBDs decrease as either the number of contacts with E-hooks increases or the distance to the microtubule decreases.
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Affiliation(s)
- Nayere Tajielyato
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29630, USA.
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29630, USA.
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37
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Nanometer-accuracy distance measurements between fluorophores at the single-molecule level. Proc Natl Acad Sci U S A 2019; 116:4275-4284. [PMID: 30770448 PMCID: PMC6410877 DOI: 10.1073/pnas.1815826116] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Measurements of macromolecular shapes provide insight into the mechanism of molecular machines. Distance measurements at the scale of biological macromolecules are often pursued by single-molecule fluorescence techniques. However, while single-molecule Förster resonance energy transfer can estimate distances of less than 8 nm, distances on the scale of 8 to 25 nm are difficult to determine. Here, we report two-color fluorescent distance measurement techniques capable of determining distances with ∼1-nm accuracy over a wide range of length scales. These methods can be implemented in high throughput on commonly available microscopes. As an example of their utility, we used our methods to uncover an unexpected conformational change in the antiparallel coiled-coil stalk of the dynein motor domain in different nucleotide states. Light microscopy is a powerful tool for probing the conformations of molecular machines at the single-molecule level. Single-molecule Förster resonance energy transfer can measure intramolecular distance changes of single molecules in the range of 2 to 8 nm. However, current superresolution measurements become error-prone below 25 nm. Thus, new single-molecule methods are needed for measuring distances in the 8- to 25-nm range. Here, we describe methods that utilize information about localization and imaging errors to measure distances between two different color fluorophores with ∼1-nm accuracy at distances >2 nm. These techniques can be implemented in high throughput using a standard total internal reflection fluorescence microscope and open-source software. We applied our two-color localization method to uncover an unexpected ∼4-nm nucleotide-dependent conformational change in the coiled-coil “stalk” of the motor protein dynein. We anticipate that these methods will be useful for high-accuracy distance measurements of single molecules over a wide range of length scales.
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38
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Can S, Lacey S, Gur M, Carter AP, Yildiz A. Directionality of dynein is controlled by the angle and length of its stalk. Nature 2019; 566:407-410. [PMID: 30728497 PMCID: PMC6450657 DOI: 10.1038/s41586-019-0914-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 01/09/2019] [Indexed: 02/02/2023]
Abstract
The ability of cytoskeletal motors to move unidirectionally along filamentous tracks is central to their role in cargo transport, motility and cell division. Kinesin and myosin motor families have a subclass that moves towards the opposite end of the microtubule or actin filament with respect to the rest of the motor family1,2, whereas all dynein motors that have been studied so far exclusively move towards the minus end of the microtubule3. Guided by cryo-electron microscopy and molecular dynamics simulations, we sought to understand the mechanism that underpins the directionality of dynein by engineering a Saccharomyces cerevisiae dynein that is directed towards the plus end of the microtubule. Here, using single-molecule assays, we show that elongation or shortening of the coiled-coil stalk that connects the motor to the microtubule controls the helical directionality of dynein around microtubules. By changing the length and angle of the stalk, we successfully reversed the motility towards the plus end of the microtubule. These modifications act by altering the direction in which the dynein linker swings relative to the microtubule, rather than by reversing the asymmetric unbinding of the motor from the microtubule. Because the length and angle of the dynein stalk are fully conserved among species, our findings provide an explanation for why all dyneins move towards the minus end of the microtubule.
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Affiliation(s)
- Sinan Can
- Physics Department, University of California at Berkeley, Berkeley, CA, USA
| | - Samuel Lacey
- Medical Research Council, Laboratory of Molecular Biology, Division of Structural Studies, Cambridge, UK
| | - Mert Gur
- Department of Mechanical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Andrew P Carter
- Medical Research Council, Laboratory of Molecular Biology, Division of Structural Studies, Cambridge, UK
| | - Ahmet Yildiz
- Physics Department, University of California at Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cellular Biology, University of California at Berkeley, Berkeley, CA, USA.
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39
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Behrens VA, Walter WJ, Peters C, Wang T, Brenner B, Geeves MA, Scholz T, Steffen W. Mg 2+ -free ATP regulates the processivity of native cytoplasmic dynein. FEBS Lett 2019; 593:296-307. [PMID: 30575960 DOI: 10.1002/1873-3468.13319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/15/2018] [Accepted: 12/12/2018] [Indexed: 11/07/2022]
Abstract
Cytoplasmic dynein, a microtubule-based motor protein, is responsible for many cellular functions ranging from cargo transport to cell division. The various functions are carried out by a single isoform of cytoplasmic dynein, thus requiring different forms of motor regulation. A possible pathway to regulate motor function was revealed in optical trap experiments. Switching motor function from single steps to processive runs could be achieved by changing Mg2+ and ATP concentrations. Here, we confirm by single molecule total internal reflection fluorescence microscopy that a native cytoplasmic dynein dimer is able to switch to processive runs of more than 680 consecutive steps or 5.5 μm. We also identified the ratio of Mg2+ -free ATP to Mg.ATP as the regulating factor and propose a model for dynein processive stepping.
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Affiliation(s)
| | | | - Carsten Peters
- Molecular and Cell Physiology, Hannover Medical School, Germany
| | - Tianbang Wang
- Molecular and Cell Physiology, Hannover Medical School, Germany
| | | | | | - Tim Scholz
- Molecular and Cell Physiology, Hannover Medical School, Germany
| | - Walter Steffen
- Molecular and Cell Physiology, Hannover Medical School, Germany
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40
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Wang Q, Jana B, Diehl MR, Cheung MS, Kolomeisky AB, Onuchic JN. Molecular mechanisms of the interhead coordination by interhead tension in cytoplasmic dyneins. Proc Natl Acad Sci U S A 2018; 115:10052-10057. [PMID: 30224489 PMCID: PMC6176594 DOI: 10.1073/pnas.1806688115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Cytoplasmic dyneins play a major role in retrograde cellular transport by moving vesicles and organelles along microtubule filaments. Dyneins are multidomain motor proteins with two heads that coordinate their motion via their interhead tension. Compared with the leading head, the trailing head has a higher detachment rate from microtubules, facilitating the movement. However, the molecular mechanism of such coordination is unknown. To elucidate this mechanism, we performed molecular dynamics simulations on a cytoplasmic dynein with a structure-based coarse-grained model that probes the effect of the interhead tension on the structure. The tension creates a torque that influences the head rotating about its stalk. The conformation of the stalk switches from the α registry to the β registry during the rotation, weakening the binding affinity to microtubules. The directions of the tension and the torque of the leading head are opposite to those of the trailing head, breaking the structural symmetry between the heads. The leading head transitions less often to the β registry than the trailing head. The former thus has a greater binding affinity to the microtubule than the latter. We measured the moment arm of the torque from a dynein structure in the simulations to develop a phenomenological model that captures the influence of the head rotating about its stalk on the differential detachment rates of the two heads. Our study provides a consistent molecular picture for interhead coordination via interhead tension.
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Affiliation(s)
- Qian Wang
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, 700032 Kolkata, India
| | - Michael R Diehl
- Department of Bioengineering, Rice University, Houston, TX 77030
- Department of Chemistry, Rice University, Houston, TX 77030
| | - Margaret S Cheung
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005
- Department of Physics, University of Houston, Houston, TX 77204
| | - Anatoly B Kolomeisky
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005
- Department of Bioengineering, Rice University, Houston, TX 77030
- Department of Chemistry, Rice University, Houston, TX 77030
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005;
- Department of Chemistry, Rice University, Houston, TX 77030
- Department of Physics and Astronomy, Rice University, Houston, TX 77005
- Department of Biosciences, Rice University, Houston, TX 77005
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41
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Goldtzvik Y, Mugnai ML, Thirumalai D. Dynamics of Allosteric Transitions in Dynein. Structure 2018; 26:1664-1677.e5. [PMID: 30270176 DOI: 10.1016/j.str.2018.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/19/2018] [Accepted: 08/08/2018] [Indexed: 12/20/2022]
Abstract
Cytoplasmic dynein, whose motor domain belongs to the AAA+ family, walks on microtubules toward the minus end. Using the available structures in different nucleotide states, we performed simulations of a coarse-grained model to elucidate the dynamics of allosteric transitions. Binding of ATP closes the cleft between the AAA1 and AAA2 domains, triggering conformational changes in the rest of the motor domain, thus forming the pre-power stroke state. Interactions with the microtubule, modeled implicitly, enhance ADP release rate, and the formation of the post-power stroke state. The dynamics of the linker (LN), which reversibly changes from a straight to a bent state, is heterogeneous. Persistent interactions between the LN and the insert loops in the AAA2 domain prevent the formation of pre-power stroke state when ATP is bound to AAA3, thus locking dynein in a repressed non-functional state. Application of mechanical force to the LN restores motility in the repressed state.
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Affiliation(s)
- Yonathan Goldtzvik
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | | | - D Thirumalai
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
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42
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Goktas M, Luo C, Sullan RMA, Bergues-Pupo AE, Lipowsky R, Vila Verde A, Blank KG. Molecular mechanics of coiled coils loaded in the shear geometry. Chem Sci 2018; 9:4610-4621. [PMID: 29899954 PMCID: PMC5969510 DOI: 10.1039/c8sc01037d] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 04/19/2018] [Indexed: 01/25/2023] Open
Abstract
Coiled coils are important nanomechanical building blocks in biological and biomimetic materials. A mechanistic molecular understanding of their structural response to mechanical load is essential for elucidating their role in tissues and for utilizing and tuning these building blocks in materials applications. Using a combination of single-molecule force spectroscopy (SMFS) and steered molecular dynamics (SMD) simulations, we have investigated the mechanics of synthetic heterodimeric coiled coils of different length (3-4 heptads) when loaded in shear geometry. Upon shearing, we observe an initial rise in the force, which is followed by a constant force plateau and ultimately strand separation. The force required for strand separation depends on the coiled coil length and the applied loading rate, suggesting that coiled coil shearing occurs out of equilibrium. This out-of-equilibrium behaviour is determined by a complex structural response which involves helix uncoiling, uncoiling-assisted sliding of the helices relative to each other in the direction of the applied force as well as uncoiling-assisted dissociation perpendicular to the force axis. These processes follow a hierarchy of timescales with helix uncoiling being faster than sliding and sliding being faster than dissociation. In SMFS experiments, strand separation is dominated by uncoiling-assisted dissociation and occurs at forces between 25-45 pN for the shortest 3-heptad coiled coil and between 35-50 pN for the longest 4-heptad coiled coil. These values are highly similar to the forces required for shearing apart short double-stranded DNA oligonucleotides, reinforcing the potential role of coiled coils as nanomechanical building blocks in applications where protein-based structures are desired.
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Affiliation(s)
- Melis Goktas
- Max Planck Institute of Colloids and Interfaces , Mechano(bio)chemistry , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
| | - Chuanfu Luo
- Max Planck Institute of Colloids and Interfaces , Department of Theory & Bio-Systems , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
| | - Ruby May A Sullan
- Max Planck Institute of Colloids and Interfaces , Mechano(bio)chemistry , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
| | - Ana E Bergues-Pupo
- Max Planck Institute of Colloids and Interfaces , Department of Theory & Bio-Systems , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
| | - Reinhard Lipowsky
- Max Planck Institute of Colloids and Interfaces , Department of Theory & Bio-Systems , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
| | - Ana Vila Verde
- Max Planck Institute of Colloids and Interfaces , Department of Theory & Bio-Systems , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
| | - Kerstin G Blank
- Max Planck Institute of Colloids and Interfaces , Mechano(bio)chemistry , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
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43
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Kato Y, Miyakawa T, Tanokura M. Overview of the mechanism of cytoskeletal motors based on structure. Biophys Rev 2018; 10:571-581. [PMID: 29235081 PMCID: PMC5899727 DOI: 10.1007/s12551-017-0368-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/19/2017] [Indexed: 12/31/2022] Open
Abstract
In the last two decades, a wealth of structural and functional knowledge has been obtained for the three major cytoskeletal motor proteins, myosin, kinesin and dynein, which we review here. The cytoskeletal motor proteins myosin and kinesin are structurally similar in the core architecture of their motor domains and have similar force-producing mechanisms that are coupled with the chemical cycles of ATP binding, hydrolysis, Pi release and subsequent ADP release. The force is generated through conformational changes in the motor domain during Pi release and ATP binding in myosin and kinesin, respectively, and then converted into the rotation of the lever arm or neck linker (referred to as a power stroke) through the common structural pathways. On the other hand, the dynein cytoskeletal motor is an AAA+ protein and has a different structure and power stroke mechanism from those of myosins and kinesins. The linker protruding from the AAA+ ring of dynein swings according to the ATPase states, which, presumably, generates force to carry cargos within a cell. The communication mechanism between the track-binding and ATPase domains of dynein is unique because the two helices that presumably slide with respect to each other work as coordinators for these domains. Details of the mechanism underlying the power stroke and interdomain communication were revealed through recent progress in the structural studies of myosin, kinesin and dynein.
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Affiliation(s)
- Yusuke Kato
- Institute for Enzyme Research, Tokushima University, Tokushima, Japan
| | - Takuya Miyakawa
- Laboratory of Basic Science on Healthy Longevity, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masaru Tanokura
- Laboratory of Basic Science on Healthy Longevity, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
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Hou R, Wang N, Bao W, Wang Z. Mechanical transduction via a single soft polymer. Phys Rev E 2018; 97:042504. [PMID: 29758660 DOI: 10.1103/physreve.97.042504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Indexed: 06/08/2023]
Abstract
Molecular machines from biology and nanotechnology often depend on soft structures to perform mechanical functions, but the underlying mechanisms and advantages or disadvantages over rigid structures are not fully understood. We report here a rigorous study of mechanical transduction along a single soft polymer based on exact solutions to the realistic three-dimensional wormlike-chain model and augmented with analytical relations derived from simpler polymer models. The results reveal surprisingly that a soft polymer with vanishingly small persistence length below a single chemical bond still transduces biased displacement and mechanical work up to practically significant amounts. This "soft" approach possesses unique advantages over the conventional wisdom of rigidity-based transduction, and potentially leads to a unified mechanism for effective allosterylike transduction and relay of mechanical actions, information, control, and molecules from one position to another in molecular devices and motors. This study also identifies an entropy limit unique to the soft transduction, and thereby suggests a possibility of detecting higher efficiency for kinesin motor and mutants in future experiments.
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Affiliation(s)
- Ruizheng Hou
- School of Science and Institute of Quantum Optics and Quantum Information, Xi'an Jiaotong University, Shaan Xi 710049, China
| | - Nan Wang
- Department of Mathematics, National University of Singapore, Singapore 119076
| | - Weizhu Bao
- Department of Mathematics, National University of Singapore, Singapore 119076
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119076
| | - Zhisong Wang
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119076
- Department of Physics, National University of Singapore, Singapore 117542
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45
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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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She1 affects dynein through direct interactions with the microtubule and the dynein microtubule-binding domain. Nat Commun 2017; 8:2151. [PMID: 29247176 PMCID: PMC5732302 DOI: 10.1038/s41467-017-02004-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/31/2017] [Indexed: 01/31/2023] Open
Abstract
Cytoplasmic dynein is an enormous minus end-directed microtubule motor. Rather than existing as bare tracks, microtubules are bound by numerous microtubule-associated proteins (MAPs) that have the capacity to affect various cellular functions, including motor-mediated transport. One such MAP is She1, a dynein effector that polarizes dynein-mediated spindle movements in budding yeast. Here, we characterize the molecular basis by which She1 affects dynein, providing the first such insight into which a MAP can modulate motor motility. We find that She1 affects the ATPase rate, microtubule-binding affinity, and stepping behavior of dynein, and that microtubule binding by She1 is required for its effects on dynein motility. Moreover, we find that She1 directly contacts the microtubule-binding domain of dynein, and that their interaction is sensitive to the nucleotide-bound state of the motor. Our data support a model in which simultaneous interactions between the microtubule and dynein enables She1 to directly affect dynein motility. Dynein is a microtubule motor the motility of which is affected by the microtubule-associated protein She1. Here, the authors show that She1 alters dynein stepping behavior and increases its microtubule affinity through simultaneous interactions with the microtubule and dynein microtubule binding domain.
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Furuta K, Furuta A. Re-engineering of protein motors to understand mechanisms biasing random motion and generating collective dynamics. Curr Opin Biotechnol 2017; 51:39-46. [PMID: 29179022 DOI: 10.1016/j.copbio.2017.11.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 11/12/2017] [Accepted: 11/14/2017] [Indexed: 11/25/2022]
Abstract
A considerable amount of insight into the mechanisms of protein-based biomolecular motors has been accumulated over decades of research. However, our knowledge about the design principles of these motors is still limited. Even less is known about the design of multi-motor systems that perform various functions within the cell. Here we focus on constructive (or synthetic) approaches to biomolecular motors that could make a breakthrough in our understanding. Recent achievements include studies at different hierarchical levels of complexity: re-engineering of individual motors, construction of multi-motor systems, and generation of large-scale complex behaviour. We then propose a strategy where the collective behaviour can be repeatedly tested upon modifying individual motors, which may provide important clues about how biomolecular motors and their systems are designed.
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Affiliation(s)
- Ken'ya Furuta
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo 651-2492, Japan.
| | - Akane Furuta
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo 651-2492, Japan
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48
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Peptides mediating DNA transport on microtubules and their impact on non-viral gene transfer efficiency. Biosci Rep 2017; 37:BSR20170995. [PMID: 28899926 PMCID: PMC5643739 DOI: 10.1042/bsr20170995] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/05/2017] [Accepted: 09/07/2017] [Indexed: 11/17/2022] Open
Abstract
Synthetic vectors such as cationic polymers and cationic lipids remain attractive tools for non-viral gene transfer which is a complex process whose effectiveness relies on the ability to deliver a plasmid DNA (pDNA) into the nucleus of non-dividing cells. Once in the cytosol, the transport of pDNAs towards the nuclear envelope is strongly impaired by their very low cytosolic mobility due to their large size. To promote their movement towards the cell nucleus, few strategies have been implemented to exploit dynein, the microtubule’s (MT’s) motor protein, for propagation of cytosolic pDNA along the MTs towards the cell nucleus. In the first part of this review, an overview on MTs, dynein, dynein/virus interaction feature is presented followed by a summary of the results obtained by exploitation of LC8 and TCTEL1 dynein light chain association sequence (DLC-AS) for non-viral transfection. The second part dedicated to the adenoviral protein E3-14.7K, reports the transfection efficiency of polyplexes and lipoplexes containing the E3-14.7K-derived P79-98 peptide linked to pDNA. Here, several lines of evidence are given showing that dynein can be targeted to improve cytosolic pDNA mobility and accumulate pDNA near nuclear envelope in order to facilitate its transport through the nuclear pores. The linkage of various DLC-AS to pDNA carriers led to modest transfection improvements and their direct interaction with MTs was not demonstrated. In contrast, pDNA linked to the P79-98 peptide interacting with TCTEL1 via a cytosolic protein (fourteen seven K-interacting protein-1 (FIP-1)), interaction with MTs is evidenced in cellulo and transfection efficiency is improved.
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Šarlah A, Vilfan A. Minimum requirements for motility of a processive motor protein. PLoS One 2017; 12:e0185948. [PMID: 29016643 PMCID: PMC5634618 DOI: 10.1371/journal.pone.0185948] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/21/2017] [Indexed: 11/19/2022] Open
Abstract
Motor proteins generally have a two-way coupling between the ATP hydrolysis site, the lever movement and the binding affinity for their track, which allows them to perform efficient stepping. Here we explore the minimal requirements for directed motility based on simpler schemes in which the binding/unbinding from the track is decoupled from the ATPase cycle. We show that a directed power stroke alone is not sufficient for motility, but combined with an asymmetry in force-induced unbinding rates it can generate stepping. The energetic efficiency of such stepping is limited to approximately 20%. We conclude that the allosteric coupling between the ATP hydrolysis and the track binding is not strictly necessary for motility, but it greatly improves its efficiency.
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Affiliation(s)
- Andreja Šarlah
- Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia
- * E-mail: (AŠ); (AV)
| | - Andrej Vilfan
- J. Stefan Institute, Ljubljana, Slovenia
- * E-mail: (AŠ); (AV)
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Kobayashi T, Miyashita T, Murayama T, Toyoshima YY. Dynactin has two antagonistic regulatory domains and exerts opposing effects on dynein motility. PLoS One 2017; 12:e0183672. [PMID: 28850609 PMCID: PMC5574551 DOI: 10.1371/journal.pone.0183672] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 07/31/2017] [Indexed: 01/01/2023] Open
Abstract
Dynactin is a dynein-regulating protein that increases the processivity of dynein movement on microtubules. Recent studies have shown that a tripartite complex of dynein–dynactin–Bicaudal D2 is essential for highly processive movement. To elucidate the regulation of dynein motility by dynactin, we focused on two isoforms (A and B) of dynactin 1 (DCTN1), the largest subunit of dynactin that contains both microtubule- and dynein-binding domains. The only difference between the primary structures of the two isoforms is that DCTN1B lacks the K-rich domain, a cluster of basic residues. We measured dynein motility by single molecule observation of recombinant dynein and dynactin. Whereas the tripartite complex containing DCTN1A exhibited highly processive movement, the complex containing DCTN1B dissociated from microtubules with no apparent processive movement. This inhibitory effect of DCTN1B was caused by reductions of the microtubule-binding affinities of both dynein and dynactin, which was attributed to the coiled-coil 1 domain of DCTN1. In DCTN1A, the K-rich domain antagonized these inhibitory effects. Therefore, dynactin has two antagonistic domains and promotes or suppresses dynein motility to accomplish correct localization and functions of dynein within a cell.
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Affiliation(s)
- Takuya Kobayashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Takuya Miyashita
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Takashi Murayama
- Department of Pharmacology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Yoko Y. Toyoshima
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
- * E-mail:
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