1
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Hu H, Kurasawa Y, Zhou Q, Li Z. A kinesin-13 family kinesin in Trypanosoma brucei regulates cytokinesis and cytoskeleton morphogenesis by promoting microtubule bundling. PLoS Pathog 2024; 20:e1012000. [PMID: 38300973 PMCID: PMC10863849 DOI: 10.1371/journal.ppat.1012000] [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: 09/28/2023] [Revised: 02/13/2024] [Accepted: 01/26/2024] [Indexed: 02/03/2024] Open
Abstract
The early branching eukaryote Trypanosoma brucei divides uni-directionally along the longitudinal cell axis from the cell anterior toward the cell posterior, and the cleavage furrow ingresses along the cell division plane between the new and the old flagella of a dividing bi-flagellated cell. Regulation of cytokinesis in T. brucei involves actomyosin-independent machineries and trypanosome-specific signaling pathways, but the molecular mechanisms underlying cell division plane positioning remain poorly understood. Here we report a kinesin-13 family protein, KIN13-5, that functions downstream of FPRC in the cytokinesis regulatory pathway and determines cell division plane placement. KIN13-5 localizes to multiple cytoskeletal structures, interacts with FPRC, and depends on FPRC for localization to the site of cytokinesis initiation. Knockdown of KIN13-5 causes loss of microtubule bundling at both ends of the cell division plane, leading to mis-placement of the cleavage furrow and unequal cytokinesis, and at the posterior cell tip, causing the formation of a blunt posterior. In vitro biochemical assays demonstrate that KIN13-5 bundles microtubules, providing mechanistic insights into the role of KIN13-5 in cytokinesis and posterior morphogenesis. Altogether, KIN13-5 promotes microtubule bundle formation to ensure cleavage furrow placement and to maintain posterior cytoskeleton morphology in T. brucei.
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Affiliation(s)
- Huiqing Hu
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Yasuhiro Kurasawa
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Qing Zhou
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Ziyin Li
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
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2
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Henkin G, Brito C, Thomas C, Surrey T. The minus-end depolymerase KIF2A drives flux-like treadmilling of γTuRC-uncapped microtubules. J Cell Biol 2023; 222:e202304020. [PMID: 37615667 PMCID: PMC10450741 DOI: 10.1083/jcb.202304020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/27/2023] [Accepted: 08/04/2023] [Indexed: 08/25/2023] Open
Abstract
During mitosis, microtubules in the spindle turn over continuously. At spindle poles, where microtubule minus ends are concentrated, microtubule nucleation and depolymerization, the latter required for poleward microtubule flux, happen side by side. How these seemingly antagonistic processes of nucleation and depolymerization are coordinated is not understood. Here, we reconstitute this coordination in vitro combining different pole-localized activities. We find that the spindle pole-localized kinesin-13 KIF2A is a microtubule minus-end depolymerase, in contrast to its paralog MCAK. Due to its asymmetric activity, KIF2A still allows microtubule nucleation from the γ-tubulin ring complex (γTuRC), which serves as a protective cap shielding the minus end against KIF2A binding. Efficient γTuRC uncapping requires the combined action of KIF2A and a microtubule severing enzyme, leading to treadmilling of the uncapped microtubule driven by KIF2A. Together, these results provide insight into the molecular mechanisms by which a minimal protein module coordinates microtubule nucleation and depolymerization at spindle poles consistent with their role in poleward microtubule flux.
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Affiliation(s)
- Gil Henkin
- Centre for Genomic Regulation(CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Cláudia Brito
- Centre for Genomic Regulation(CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | - Thomas Surrey
- Centre for Genomic Regulation(CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
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3
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Zhou J, Wang A, Song Y, Liu N, Wang J, Li Y, Liang X, Li G, Chu H, Wang HW. Structural insights into the mechanism of GTP initiation of microtubule assembly. Nat Commun 2023; 14:5980. [PMID: 37749104 PMCID: PMC10519996 DOI: 10.1038/s41467-023-41615-w] [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: 11/06/2022] [Accepted: 09/08/2023] [Indexed: 09/27/2023] Open
Abstract
In eukaryotes, the dynamic assembly of microtubules (MT) plays an important role in numerous cellular processes. The underlying mechanism of GTP triggering MT assembly is still unknown. Here, we present cryo-EM structures of tubulin heterodimer at their GTP- and GDP-bound states, intermediate assembly states of GTP-tubulin, and final assembly stages of MT. Both GTP- and GDP-tubulin heterodimers adopt similar curved conformations with subtle flexibility differences. In head-to-tail oligomers of tubulin heterodimers, the inter-dimer interface of GDP-tubulin exhibits greater flexibility, particularly in tangential bending. Cryo-EM of the intermediate assembly states reveals two types of tubulin lateral contacts, "Tube-bond" and "MT-bond". Further, molecular dynamics (MD) simulations show that GTP triggers lateral contact formation in MT assembly in multiple sequential steps, gradually straightening the curved tubulin heterodimers. Therefore, we propose a flexible model of GTP-initiated MT assembly, including the formation of longitudinal and lateral contacts, to explain the nucleation and assembly of MT.
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Affiliation(s)
- Ju Zhou
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
- University of California Berkeley, Berkeley, CA, USA
| | - Anhui Wang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Yinlong Song
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Nan Liu
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
| | - Jia Wang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
| | - Yan Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Xin Liang
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China.
| | - Hong-Wei Wang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China.
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4
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Pandey H, Singh SK, Sadan M, Popov M, Singh M, Davidov G, Inagaki S, Al-Bassam J, Zarivach R, Rosenfeld SS, Gheber L. Flexible microtubule anchoring modulates the bi-directional motility of the kinesin-5 Cin8. Cell Mol Life Sci 2021; 78:6051-6068. [PMID: 34274977 PMCID: PMC11072411 DOI: 10.1007/s00018-021-03891-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/08/2021] [Accepted: 06/18/2021] [Indexed: 10/20/2022]
Abstract
Two modes of motility have been reported for bi-directional kinesin-5 motors: (a) context-dependent directionality reversal, a mode in which motors undergo persistent minus-end directed motility at the single-molecule level and switch to plus-end directed motility in different assays or under different conditions, such as during MT gliding or antiparallel sliding or as a function of motor clustering; and (b) bi-directional motility, defined as movement in two directions in the same assay, without persistent unidirectional motility. Here, we examine how modulation of motor-microtubule (MT) interactions affects these two modes of motility for the bi-directional kinesin-5, Cin8. We report that the large insert in loop 8 (L8) within the motor domain of Cin8 increases the MT affinity of Cin8 in vivo and in vitro and is required for Cin8 intracellular functions. We consistently found that recombinant purified L8 directly binds MTs and L8 induces single Cin8 motors to behave according to context-dependent directionality reversal and bi-directional motility modes at intermediate ionic strength and according to a bi-directional motility mode in an MT surface-gliding assay under low motor density conditions. We propose that the largely unstructured L8 facilitates flexible anchoring of Cin8 to the MTs. This flexible anchoring enables the direct observation of bi-directional motility in motility assays. Remarkably, although L8-deleted Cin8 variants exhibit a strong minus-end directed bias at the single-molecule level, they also exhibit plus-end directed motility in an MT-gliding assay. Thus, L8-induced flexible MT anchoring is required for bi-directional motility of single Cin8 molecules but is not necessary for context-dependent directionality reversal of Cin8 in an MT-gliding assay.
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Affiliation(s)
- Himanshu Pandey
- Department of Chemistry, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Sudhir Kumar Singh
- Department of Chemistry, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Mayan Sadan
- Department of Chemistry, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Mary Popov
- Department of Chemistry, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Meenakshi Singh
- Department of Chemistry, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Geula Davidov
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Sayaka Inagaki
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Jawdat Al-Bassam
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, 95616, USA
| | - Raz Zarivach
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | | | - Larisa Gheber
- Department of Chemistry, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel.
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel.
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5
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Parts list for a microtubule depolymerising kinesin. Biochem Soc Trans 2018; 46:1665-1672. [PMID: 30467119 PMCID: PMC6299235 DOI: 10.1042/bst20180350] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/11/2018] [Accepted: 10/15/2018] [Indexed: 12/12/2022]
Abstract
The Kinesin superfamily is a large group of molecular motors that use the turnover of ATP to regulate their interaction with the microtubule cytoskeleton. The coupled relationship between nucleotide turnover and microtubule binding is harnessed in various ways by these motors allowing them to carry out a variety of cellular functions. The Kinesin-13 family is a group of specialist microtubule depolymerising motors. Members of this family use their microtubule destabilising activity to regulate processes such as chromosome segregation, maintenance of cilia and neuronal development. Here, we describe the current understanding of the structure of this family of kinesins and the role different parts of these proteins play in their microtubule depolymerisation activity and in the wider function of this family of kinesins.
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6
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Benoit MPMH, Asenjo AB, Sosa H. Cryo-EM reveals the structural basis of microtubule depolymerization by kinesin-13s. Nat Commun 2018; 9:1662. [PMID: 29695795 PMCID: PMC5916938 DOI: 10.1038/s41467-018-04044-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 03/27/2018] [Indexed: 11/25/2022] Open
Abstract
Kinesin-13s constitute a distinct group within the kinesin superfamily of motor proteins that promote microtubule depolymerization and lack motile activity. The molecular mechanism by which kinesin-13s depolymerize microtubules and are adapted to perform a seemingly very different activity from other kinesins is still unclear. To address this issue, here we report the near atomic resolution cryo-electron microscopy (cryo-EM) structures of Drosophila melanogaster kinesin-13 KLP10A protein constructs bound to curved or straight tubulin in different nucleotide states. These structures show how nucleotide induced conformational changes near the catalytic site are coupled with movement of the kinesin-13-specific loop-2 to induce tubulin curvature leading to microtubule depolymerization. The data highlight a modular structure that allows similar kinesin core motor-domains to be used for different functions, such as motility or microtubule depolymerization. Kinesin-13s are microtubule depolymerases that lack motile activity. Here the authors present the cryo-EM structures of kinesin-13 microtubule complexes in different nucleotide bound states, which reveal how ATP hydrolysis is linked to conformational changes and propose a model for kinesin induced depolymerisation.
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Affiliation(s)
- Matthieu P M H Benoit
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ana B Asenjo
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Hernando Sosa
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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7
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Monda JK, Whitney IP, Tarasovetc EV, Wilson-Kubalek E, Milligan RA, Grishchuk EL, Cheeseman IM. Microtubule Tip Tracking by the Spindle and Kinetochore Protein Ska1 Requires Diverse Tubulin-Interacting Surfaces. Curr Biol 2017; 27:3666-3675.e6. [PMID: 29153323 DOI: 10.1016/j.cub.2017.10.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 08/02/2017] [Accepted: 10/05/2017] [Indexed: 12/14/2022]
Abstract
The macromolecular kinetochore functions to generate interactions between chromosomal DNA and spindle microtubules [1]. To facilitate chromosome movement and segregation, kinetochores must maintain associations with both growing and shrinking microtubule ends. It is critical to define the proteins and their properties that allow kinetochores to associate with dynamic microtubules. The kinetochore-localized human Ska1 complex binds to microtubules and tracks with depolymerizing microtubule ends [2]. We now demonstrate that the Ska1 complex also autonomously tracks with growing microtubule ends in vitro, a key property that would allow this complex to act at kinetochores to mediate persistent associations with dynamic microtubules. To define the basis for Ska1 complex interactions with dynamic microtubules, we investigated the tubulin-binding properties of the Ska1 microtubule binding domain. In addition to binding to the microtubule lattice and dolastatin-induced protofilament-like structures, we demonstrate that the Ska1 microtubule binding domain can associate with soluble tubulin heterodimers and promote assembly of oligomeric ring-like tubulin structures. We generated mutations on distinct surfaces of the Ska1 microtubule binding domain that disrupt binding to soluble tubulin but do not prevent microtubule binding. These mutants display compromised microtubule tracking activity in vitro and result in defective chromosome alignment and mitotic progression in cells using a CRISPR/Cas9-based replacement assay. Our work supports a model in which multiple surfaces of Ska1 interact with diverse tubulin substrates to associate with dynamic microtubule polymers and facilitate optimal chromosome segregation.
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Affiliation(s)
- Julie K Monda
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Ian P Whitney
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Ekaterina V Tarasovetc
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | | | - Ronald A Milligan
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ekaterina L Grishchuk
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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8
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Asbury CL. Anaphase A: Disassembling Microtubules Move Chromosomes toward Spindle Poles. BIOLOGY 2017; 6:E15. [PMID: 28218660 PMCID: PMC5372008 DOI: 10.3390/biology6010015] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/04/2017] [Accepted: 02/10/2017] [Indexed: 11/16/2022]
Abstract
The separation of sister chromatids during anaphase is the culmination of mitosis and one of the most strikingly beautiful examples of cellular movement. It consists of two distinct processes: Anaphase A, the movement of chromosomes toward spindle poles via shortening of the connecting fibers, and anaphase B, separation of the two poles from one another via spindle elongation. I focus here on anaphase A chromosome-to-pole movement. The chapter begins by summarizing classical observations of chromosome movements, which support the current understanding of anaphase mechanisms. Live cell fluorescence microscopy studies showed that poleward chromosome movement is associated with disassembly of the kinetochore-attached microtubule fibers that link chromosomes to poles. Microtubule-marking techniques established that kinetochore-fiber disassembly often occurs through loss of tubulin subunits from the kinetochore-attached plus ends. In addition, kinetochore-fiber disassembly in many cells occurs partly through 'flux', where the microtubules flow continuously toward the poles and tubulin subunits are lost from minus ends. Molecular mechanistic models for how load-bearing attachments are maintained to disassembling microtubule ends, and how the forces are generated to drive these disassembly-coupled movements, are discussed.
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Affiliation(s)
- Charles L Asbury
- Department of Physiology & Biophysics, University of Washington, Seattle, WA 98195, USA.
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9
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Chatterjee C, Benoit MPMH, DePaoli V, Diaz-Valencia JD, Asenjo AB, Gerfen GJ, Sharp DJ, Sosa H. Distinct Interaction Modes of the Kinesin-13 Motor Domain with the Microtubule. Biophys J 2016; 110:1593-1604. [PMID: 27074684 DOI: 10.1016/j.bpj.2016.02.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 01/28/2016] [Accepted: 02/16/2016] [Indexed: 01/12/2023] Open
Abstract
Kinesins-13s are members of the kinesin superfamily of motor proteins that depolymerize microtubules (MTs) and have no motile activity. Instead of generating unidirectional movement over the MT lattice, like most other kinesins, kinesins-13s undergo one-dimensional diffusion (ODD) and induce depolymerization at the MT ends. To understand the mechanism of ODD and the origin of the distinct kinesin-13 functionality, we used ensemble and single-molecule fluorescence polarization microscopy to analyze the behavior and conformation of Drosophila melanogaster kinesin-13 KLP10A protein constructs bound to the MT lattice. We found that KLP10A interacts with the MT in two coexisting modes: one in which the motor domain binds with a specific orientation to the MT lattice and another where the motor domain is very mobile and able to undergo ODD. By comparing the orientation and dynamic behavior of mutated and deletion constructs we conclude that 1) the Kinesin-13 class specific neck domain and loop-2 help orienting the motor domain relative to the MT. 2) During ODD the KLP10A motor-domain changes orientation rapidly (rocks or tumbles). 3) The motor domain alone is capable of undergoing ODD. 4) A second tubulin binding site in the KLP10A motor domain is not critical for ODD. 5) The neck domain is not the element preventing KLP10A from binding to the MT lattice like motile kinesins.
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Affiliation(s)
- Chandrima Chatterjee
- Departments of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York
| | - Matthieu P M H Benoit
- Departments of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York
| | - Vania DePaoli
- Departments of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York
| | - Juan D Diaz-Valencia
- Departments of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York
| | - Ana B Asenjo
- Departments of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York
| | - Gary J Gerfen
- Departments of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York
| | - David J Sharp
- Departments of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York
| | - Hernando Sosa
- Departments of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York.
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10
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Ghiretti AE, Thies E, Tokito MK, Lin T, Ostap EM, Kneussel M, Holzbaur ELF. Activity-Dependent Regulation of Distinct Transport and Cytoskeletal Remodeling Functions of the Dendritic Kinesin KIF21B. Neuron 2016; 92:857-872. [PMID: 27817978 DOI: 10.1016/j.neuron.2016.10.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 08/05/2016] [Accepted: 09/20/2016] [Indexed: 01/19/2023]
Abstract
The dendritic arbor is subject to continual activity-dependent remodeling, requiring a balance between directed cargo trafficking and dynamic restructuring of the underlying microtubule tracks. How cytoskeletal components are able to dynamically regulate these processes to maintain this balance remains largely unknown. By combining single-molecule assays and live imaging in rat hippocampal neurons, we have identified the kinesin-4 KIF21B as a molecular regulator of activity-dependent trafficking and microtubule dynamicity in dendrites. We find that KIF21B contributes to the retrograde trafficking of brain-derived neurotrophic factor (BDNF)-TrkB complexes and also regulates microtubule dynamics through a separable, non-motor microtubule-binding domain. Neuronal activity enhances the motility of KIF21B at the expense of its role in cytoskeletal remodeling, the first example of a kinesin whose function is directly tuned to neuronal activity state. These studies suggest a model in which KIF21B navigates the complex cytoskeletal environment of dendrites by compartmentalizing functions in an activity-dependent manner.
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Affiliation(s)
- Amy E Ghiretti
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, 415 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Edda Thies
- Department of Molecular Neurogenetics, ZMNH, University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany
| | - Mariko K Tokito
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, 415 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Tianming Lin
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, 415 Curie Boulevard, Philadelphia, PA 19104, USA
| | - E Michael Ostap
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, 415 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Matthias Kneussel
- Department of Molecular Neurogenetics, ZMNH, University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany
| | - Erika L F Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, 415 Curie Boulevard, Philadelphia, PA 19104, USA.
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11
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Shojania Feizabadi M, Janakaloti Narayanareddy BR, Vadpey O, Jun Y, Chapman D, Rosenfeld S, Gross SP. Microtubule C-Terminal Tails Can Change Characteristics of Motor Force Production. Traffic 2015; 16:1075-87. [PMID: 26094820 DOI: 10.1111/tra.12307] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 06/15/2015] [Accepted: 06/16/2015] [Indexed: 12/21/2022]
Abstract
Control of intracellular transport is poorly understood, and functional ramifications of tubulin isoform differences between cell types are mostly unexplored. Motors' force production and detachment kinetics are critical for their group function, but how microtubule (MT) details affect these properties--if at all--is unknown. We investigated these questions using both a vesicular transport human kinesin, kinesin-1, and also a mitotic kinesin likely optimized for group function, kinesin-5, moving along either bovine brain or MCF7(breast cancer) MTs. We found that kinesin-1 functioned similarly on the two sets of MTs--in particular, its mean force production was approximately the same, though due to its previously reported decreased processivity, the mean duration of kinesin-1 force production was slightly decreased on MCF7 MTs. In contrast, kinesin-5's function changed dramatically on MCF7 MTs: its average detachment force was reduced and its force-velocity curve was different. In spite of the reduced detachment force, the force-velocity alteration surprisingly improved high-load group function for kinesin-5 on the cancer-cell MTs, potentially contributing to functions such as spindle-mediated chromosome separation. Significant differences were previously reported for C-terminal tubulin tails in MCF7 versus bovine brain tubulin. Consistent with this difference being functionally important, elimination of the tails made transport along the two sets of MTs similar.
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Affiliation(s)
- Mitra Shojania Feizabadi
- Department of Physics, Seton Hall University, South Orange, NJ 07079, USA.,Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | | | - Omid Vadpey
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Yonggun Jun
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Dail Chapman
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Steven Rosenfeld
- Department of Cancer Biology, Cleveland Clinic, Cleveland, OH, USA
| | - Steven P Gross
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
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12
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Burns KM, Sarpe V, Wagenbach M, Wordeman L, Schriemer DC. HX-MS2 for high performance conformational analysis of complex protein states. Protein Sci 2015; 24:1313-24. [PMID: 26009873 DOI: 10.1002/pro.2707] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 05/05/2015] [Accepted: 05/14/2015] [Indexed: 01/15/2023]
Abstract
Water-mediated hydrogen exchange (HX) processes involving the protein main chain are sensitive to structural dynamics and molecular interactions. Measuring deuterium uptake in amide bonds provides information on conformational states, structural transitions and binding events. Increasingly, deuterium levels are measured by mass spectrometry (MS) from proteolytically generated peptide fragments of large molecular systems. However, this bottom-up method has limited spectral capacity and requires a burdensome manual validation exercise, both of which restrict analysis of protein systems to generally less than 150 kDa. In this study, we present a bottom-up HX-MS(2) method that improves peptide identification rates, localizes high-quality HX data and simplifies validation. The method combines a new peptide scoring algorithm (WUF, weighted unique fragment) with data-independent acquisition of peptide fragmentation data. Scoring incorporates the validation process and emphasizes identification accuracy. The HX-MS(2) method is illustrated using data from a conformational analysis of microtubules treated with dimeric kinesin MCAK. When compared to a conventional Mascot-driven HX-MS method, HX-MS(2) produces two-fold higher α/β-tubulin sequence depth at a peptide utilization rate of 74%. A Mascot approach delivers a utilization rate of 44%. The WUF score can be constrained by false utilization rate (FUR) calculations to return utilization values exceeding 90% without serious data loss, indicating that automated validation should be possible. The HX-MS(2) data confirm that N-terminal MCAK domains anchor kinesin force generation in kinesin-mediated depolymerization, while the C-terminal tails regulate MCAK-tubulin interactions.
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Affiliation(s)
- Kyle M Burns
- Department of Biochemistry and Molecular Biology and the Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada, T2N 4N1
| | - Vladimir Sarpe
- Department of Biochemistry and Molecular Biology and the Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada, T2N 4N1
| | - Mike Wagenbach
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, Washington, 98195-7290
| | - Linda Wordeman
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, Washington, 98195-7290
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology and the Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada, T2N 4N1
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13
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Talapatra SK, Harker B, Welburn JPI. The C-terminal region of the motor protein MCAK controls its structure and activity through a conformational switch. eLife 2015; 4. [PMID: 25915621 PMCID: PMC4443670 DOI: 10.7554/elife.06421] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/24/2015] [Indexed: 11/29/2022] Open
Abstract
The precise regulation of microtubule dynamics is essential during cell division. The
kinesin-13 motor protein MCAK is a potent microtubule depolymerase. The divergent
non-motor regions flanking the ATPase domain are critical in regulating its targeting
and activity. However, the molecular basis for the function of the non-motor regions
within the context of full-length MCAK is unknown. Here, we determine the structure
of MCAK motor domain bound to its regulatory C-terminus. Our analysis reveals that
the MCAK C-terminus binds to two motor domains in solution and is displaced
allosterically upon microtubule binding, which allows its robust accumulation at
microtubule ends. These results demonstrate that MCAK undergoes long-range
conformational changes involving its C-terminus during the soluble to
microtubule-bound transition and that the C-terminus-motor interaction represents a
structural intermediate in the MCAK catalytic cycle. Together, our work reveals
intrinsic molecular mechanisms underlying the regulation of kinesin-13 activity. DOI:http://dx.doi.org/10.7554/eLife.06421.001 Within a cell, there is a scaffold-like structure called the cytoskeleton that
provides shape and structural support, and acts as a transport network for the
movement of molecules around the cell. This scaffold contains highly dynamic polymers
called microtubules that are made from a protein called tubulin. The constant growth
and shrinking of the ends of the microtubules is essential to rebuild and adapt the
cytoskeleton according to the needs of the cell. A protein called MCAK belongs to a family of motor proteins that can move along
microtubules. It generally binds to the ends of the microtubules to shorten them.
Previous studies have found that a single MCAK protein binds to another MCAK protein
to form a larger molecule known as a dimer. Part of the MCAK protein forms a
so-called motor domain, which enables this protein to bind to the microtubules. One
end of the protein, known as the C-terminus, controls the activity of this motor
domain. However, it is not clear how this works. Talapatra et al. have now revealed the three-dimensional structure of MCAK's
motor domain with the C-terminus using a technique called X-ray crystallography. The
experiments show that the C-terminus binds to the motor domain, which promotes the
formation of the dimers. A short stretch of amino acids—the building blocks of
proteins—in the C-terminus interacts with two motor molecules. This
‘motif’ is also found in other similar proteins from a variety of
animals. However, once MCAK binds to a microtubule, the microtubule triggers the
release of the C-terminus from the motor domain. This allows MCAK to bind more
strongly to the microtubule. The experiments also show that the binding of the C-terminus to the motor domain
alters the ability of MCAK to associate with microtubules, which encourages the
protein to reach the ends of the polymers. Future work is required to see whether
other motor proteins work in a similar way. DOI:http://dx.doi.org/10.7554/eLife.06421.002
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Affiliation(s)
- Sandeep K Talapatra
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Bethany Harker
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Julie P I Welburn
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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14
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Rey M, Sarpe V, Burns KM, Buse J, Baker CAH, van Dijk M, Wordeman L, Bonvin AMJJ, Schriemer DC. Mass spec studio for integrative structural biology. Structure 2014; 22:1538-48. [PMID: 25242457 DOI: 10.1016/j.str.2014.08.013] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/30/2014] [Accepted: 08/06/2014] [Indexed: 02/01/2023]
Abstract
The integration of biophysical data from multiple sources is critical for developing accurate structural models of large multiprotein systems and their regulators. Mass spectrometry (MS) can be used to measure the insertion location for a wide range of topographically sensitive chemical probes, and such insertion data provide a rich, but disparate set of modeling restraints. We have developed a software platform that integrates the analysis of label-based MS and tandem MS (MS(2)) data with protein modeling activities (Mass Spec Studio). Analysis packages can mine any labeling data from any mass spectrometer in a proteomics-grade manner, and link labeling methods with data-directed protein interaction modeling using HADDOCK. Support is provided for hydrogen/deuterium exchange (HX) and covalent labeling chemistries, including novel acquisition strategies such as targeted HX-MS(2) and data-independent HX-MS(2). The latter permits the modeling of highly complex systems, which we demonstrate by the analysis of microtubule interactions.
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Affiliation(s)
- Martial Rey
- Department of Biochemistry and Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Vladimir Sarpe
- Department of Biochemistry and Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Kyle M Burns
- Department of Biochemistry and Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Joshua Buse
- Department of Biochemistry and Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | | | - Marc van Dijk
- Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Padualaan 8, Utrecht CH 3584, the Netherlands
| | - Linda Wordeman
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, WA 98195-7290, USA
| | - Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Padualaan 8, Utrecht CH 3584, the Netherlands
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada.
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15
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Nucleotide exchange in dimeric MCAK induces longitudinal and lateral stress at microtubule ends to support depolymerization. Structure 2014; 22:1173-1183. [PMID: 25066134 DOI: 10.1016/j.str.2014.06.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/13/2014] [Accepted: 06/14/2014] [Indexed: 10/25/2022]
Abstract
Members of the kinesin-13 subfamily use motor domains in an unconventional fashion to initiate microtubule (MT) depolymerization at MT ends, suggesting unique conformational transitions for lattice engagement, end adaptation, or both. Using hydrogen-deuterium exchange and electron microscopy, we explored conformational changes in free dimeric mitotic centromere-associated kinesin (MCAK) and when bound to a depolymerization intermediate. ATP hydrolysis relaxes the conformation of the dimer, notably in the neck and N-terminal domain. Exchanging ADP in dimeric MCAK with ATP at the MT plus end induces outward curvature in α/β-tubulin, accompanied by a restructuring of the MCAK neck and N terminus, as it returns to a closed state. Reestablishing a closed dimer induces lateral separation of paired tubulin dimers, which may assist in depolymerization. Thus, full-length ADP-MCAK transitions from an open diffusion-competent configuration to a closed state upon plus end-mediated nucleotide exchange, which is mediated by conformational changes in the N-terminal domains of the dimer.
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Abstract
We review the properties and uses of cell lines in Drosophila research, emphasizing the variety of lines, the large body of genomic and transcriptional data available for many of the lines, and the variety of ways the lines have been used to provide tools for and insights into the developmental, molecular, and cell biology of Drosophila and mammals.
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Affiliation(s)
- Lucy Cherbas
- Drosophila Genomics Resource Center, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA; Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA.
| | - Lei Gong
- Drosophila Genomics Resource Center, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA.
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