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Zhao X, Quintremil S, Rodriguez Castro ED, Cui H, Moraga D, Wang T, Vallee RB, Solmaz SR. Molecular mechanism for recognition of the cargo adapter Rab6 GTP by the dynein adapter BicD2. Life Sci Alliance 2024; 7:e202302430. [PMID: 38719748 PMCID: PMC11077774 DOI: 10.26508/lsa.202302430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
Rab6 is a key modulator of protein secretion. The dynein adapter Bicaudal D2 (BicD2) recruits the motors cytoplasmic dynein and kinesin-1 to Rab6GTP-positive vesicles for transport; however, it is unknown how BicD2 recognizes Rab6. Here, we establish a structural model for recognition of Rab6GTP by BicD2, using structure prediction and mutagenesis. The binding site of BicD2 spans two regions of Rab6 that undergo structural changes upon the transition from the GDP- to GTP-bound state, and several hydrophobic interface residues are rearranged, explaining the increased affinity of the active GTP-bound state. Mutations of Rab6GTP that abolish binding to BicD2 also result in reduced co-migration of Rab6GTP/BicD2 in cells, validating our model. These mutations also severely diminished the motility of Rab6-positive vesicles in cells, highlighting the importance of the Rab6GTP/BicD2 interaction for overall motility of the multi-motor complex that contains both kinesin-1 and dynein. Our results provide insights into trafficking of secretory and Golgi-derived vesicles and will help devise therapies for diseases caused by BicD2 mutations, which selectively affect the affinity to Rab6 and other cargoes.
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Affiliation(s)
- Xiaoxin Zhao
- https://ror.org/008rmbt77 Department of Chemistry, Binghamton University, Binghamton, NY, USA
| | - Sebastian Quintremil
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | | | - Heying Cui
- https://ror.org/008rmbt77 Department of Chemistry, Binghamton University, Binghamton, NY, USA
| | - David Moraga
- https://ror.org/008rmbt77 Department of Chemistry, Binghamton University, Binghamton, NY, USA
| | - Tingyao Wang
- https://ror.org/008rmbt77 Department of Chemistry, Binghamton University, Binghamton, NY, USA
| | - Richard B Vallee
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Sozanne R Solmaz
- https://ror.org/008rmbt77 Department of Chemistry, Binghamton University, Binghamton, NY, USA
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2
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Gibson JM, Zhao X, Ali MY, Solmaz SR, Wang C. A Structural Model for the Core Nup358-BicD2 Interface. Biomolecules 2023; 13:1445. [PMID: 37892127 PMCID: PMC10604712 DOI: 10.3390/biom13101445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/08/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Dynein motors facilitate the majority of minus-end-directed transport events on microtubules. The dynein adaptor Bicaudal D2 (BicD2) recruits the dynein machinery to several cellular cargo for transport, including Nup358, which facilitates a nuclear positioning pathway that is essential for the differentiation of distinct brain progenitor cells. Previously, we showed that Nup358 forms a "cargo recognition α-helix" upon binding to BicD2; however, the specifics of the BicD2-Nup358 interface are still not well understood. Here, we used AlphaFold2, complemented by two additional docking programs (HADDOCK and ClusPro) as well as mutagenesis, to show that the Nup358 cargo-recognition α-helix binds to BicD2 between residues 747 and 774 in an anti-parallel manner, forming a helical bundle. We identified two intermolecular salt bridges that are important to stabilize the interface. In addition, we uncovered a secondary interface mediated by an intrinsically disordered region of Nup358 that is directly N-terminal to the cargo-recognition α-helix and binds to BicD2 between residues 774 and 800. This is the same BicD2 domain that binds to the competing cargo adapter Rab6, which is important for the transport of Golgi-derived and secretory vesicles. Our results establish a structural basis for cargo recognition and selection by the dynein adapter BicD2, which facilitates transport pathways that are important for brain development.
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Affiliation(s)
- James M. Gibson
- Department of Biological Sciences, Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Xiaoxin Zhao
- Department of Chemistry, Binghamton University, P.O. Box 6000, Binghamton, NY 13902, USA;
| | - M. Yusuf Ali
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT 05405, USA;
| | - Sozanne R. Solmaz
- Department of Chemistry, Binghamton University, P.O. Box 6000, Binghamton, NY 13902, USA;
| | - Chunyu Wang
- Department of Biological Sciences, Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
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Jin G, Lin L, Li K, Li J, Yu C, Wei Z. Structural basis of ELKS/Rab6B interaction and its role in vesicle capturing enhanced by liquid-liquid phase separation. J Biol Chem 2023:104808. [PMID: 37172719 DOI: 10.1016/j.jbc.2023.104808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/29/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
ELKS proteins play a key role in organizing intracellular vesicle trafficking and targeting in both neurons and non-neuronal cells. While it is known that ELKS interacts with the vesicular traffic regulator, the Rab6 GTPase, the molecular basis governing ELKS-mediated trafficking of Rab6-coated vesicles has remained unclear. In this study, we solved the Rab6B structure in complex with the Rab6-binding domain of ELKS1, revealing that a C-terminal segment of ELKS1 forms a helical hairpin to recognize Rab6B through a unique binding mode. We further showed that liquid-liquid phase separation (LLPS) of ELKS1 allows it to compete with other Rab6 effectors for binding to Rab6B and accumulate Rab6B-coated liposomes to the protein condensate formed by ELKS1. We also found that the ELKS1 condensate recruits Rab6B-coated vesicles to vesicle releasing sites and promotes vesicle exocytosis. Together, our structural, biochemical, and cellular analyses suggest that ELKS1, via the LLPS-enhanced interaction with Rab6, captures Rab6-coated vesicles from the cargo transport machine for efficient vesicle releasing at exocytotic sites. These findings shed new light on the understanding of spatiotemporal regulation of vesicle trafficking through the interplay between membranous structures and membraneless condensates.
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Affiliation(s)
- Gaowei Jin
- Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Leishu Lin
- Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Kaiyue Li
- Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Jiashan Li
- Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Cong Yu
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, and Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen, Guangdong, China 518055.
| | - Zhiyi Wei
- Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
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Yi J, Zhao X, Noell CR, Helmer P, Solmaz SR, Vallee RB. Role of Nesprin-2 and RanBP2 in BICD2-associated brain developmental disorders. PLoS Genet 2023; 19:e1010642. [PMID: 36930595 PMCID: PMC10022797 DOI: 10.1371/journal.pgen.1010642] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 01/28/2023] [Indexed: 03/18/2023] Open
Abstract
Bicaudal D2 (BICD2) is responsible for recruiting cytoplasmic dynein to diverse forms of subcellular cargo for their intracellular transport. Mutations in the human BICD2 gene have been found to cause an autosomal dominant form of spinal muscular atrophy (SMA-LED2), and brain developmental defects. Whether and how the latter mutations are related to roles we and others have identified for BICD2 in brain development remains little understood. BICD2 interacts with the nucleoporin RanBP2 to recruit dynein to the nuclear envelope (NE) of Radial Glial Progenitor cells (RGPs) to mediate their well-known but mysterious cell-cycle-regulated interkinetic nuclear migration (INM) behavior, and their subsequent differentiation to form cortical neurons. We more recently found that BICD2 also mediates NE dynein recruitment in migrating post-mitotic neurons, though via a different interactor, Nesprin-2. Here, we report that Nesprin-2 and RanBP2 compete for BICD2-binding in vitro. To test the physiological implications of this behavior, we examined the effects of known BICD2 mutations using in vitro biochemical and in vivo electroporation-mediated brain developmental assays. We find a clear relationship between the ability of BICD2 to bind RanBP2 vs. Nesprin-2 in controlling of nuclear migration and neuronal migration behavior. We propose that mutually exclusive RanBP2-BICD2 vs. Nesprin-2-BICD2 interactions at the NE play successive, critical roles in INM behavior in RGPs and in post-mitotic neuronal migration and errors in these processes contribute to specific human brain malformations.
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Affiliation(s)
- Julie Yi
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, United States of America
| | - Xiaoxin Zhao
- Department of Chemistry, Binghamton University, Binghamton, New York, New York, United States of America
| | - Crystal R. Noell
- Department of Chemistry, Binghamton University, Binghamton, New York, New York, United States of America
| | - Paige Helmer
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, United States of America
| | - Sozanne R. Solmaz
- Department of Chemistry, Binghamton University, Binghamton, New York, New York, United States of America
| | - Richard B. Vallee
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, United States of America
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5
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Wong CH, Wingett SW, Qian C, Taliaferro JM, Ross-Thriepland D, Bullock SL. Genome-scale requirements for dynein-based trafficking revealed by a high-content arrayed CRISPR screen. bioRxiv 2023:2023.03.01.530592. [PMID: 36909483 PMCID: PMC10002790 DOI: 10.1101/2023.03.01.530592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
The cytoplasmic dynein-1 (dynein) motor plays a key role in cellular organisation by transporting a wide variety of cellular constituents towards the minus ends of microtubules. However, relatively little is known about how the biosynthesis, assembly and functional diversity of the motor is orchestrated. To address this issue, we have conducted an arrayed CRISPR loss-of-function screen in human cells using the distribution of dynein-tethered peroxisomes and early endosomes as readouts. From a guide RNA library targeting 18,253 genes, 195 validated hits were recovered and parsed into those impacting multiple dynein cargoes and those whose effects are restricted to a subset of cargoes. Clustering of high-dimensional phenotypic fingerprints generated from multiplexed images revealed co-functional genes involved in many cellular processes, including several candidate novel regulators of core dynein functions. Mechanistic analysis of one of these proteins, the RNA-binding protein SUGP1, provides evidence that it promotes cargo trafficking by sustaining functional expression of the dynein activator LIS1. Our dataset represents a rich source of new hypotheses for investigating microtubule-based transport, as well as several other aspects of cellular organisation that were captured by our high-content imaging.
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Affiliation(s)
- Chun Hao Wong
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
- Discovery Biology, Discovery Sciences, AstraZeneca, R&D, Cambridge, CB4 0WG, UK
- Current address: Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Steven W. Wingett
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Chen Qian
- Quantitative Biology, Discovery Sciences, AstraZeneca, R&D, Cambridge, CB4 0WG, UK
| | - J. Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Simon L. Bullock
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
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Abstract
The microtubule minus-end-directed motility of cytoplasmic dynein 1 (dynein), arguably the most complex and versatile cytoskeletal motor, is harnessed for diverse functions, such as long-range organelle transport in neuronal axons and spindle assembly in dividing cells. The versatility of dynein raises a number of intriguing questions, including how is dynein recruited to its diverse cargo, how is recruitment coupled to activation of the motor, how is motility regulated to meet different requirements for force production and how does dynein coordinate its activity with that of other microtubule-associated proteins (MAPs) present on the same cargo. Here, these questions will be discussed in the context of dynein at the kinetochore, the supramolecular protein structure that connects segregating chromosomes to spindle microtubules in dividing cells. As the first kinetochore-localized MAP described, dynein has intrigued cell biologists for more than three decades. The first part of this Review summarizes current knowledge about how kinetochore dynein contributes to efficient and accurate spindle assembly, and the second part describes the underlying molecular mechanisms and highlights emerging commonalities with dynein regulation at other subcellular sites.
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Affiliation(s)
- Reto Gassmann
- Instituto de Investigação e Inovação em Saúde - i3S, Universidade do Porto, 4200-135 Porto, Portugal.,Instituto de Biologia Molecular e Celular - IBMC, Universidade do Porto, 4200-135 Porto, Portugal
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7
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d'Amico EA, Ud Din Ahmad M, Cmentowski V, Girbig M, Müller F, Wohlgemuth S, Brockmeyer A, Maffini S, Janning P, Vetter IR, Carter AP, Perrakis A, Musacchio A. Conformational transitions of the Spindly adaptor underlie its interaction with Dynein and Dynactin. J Cell Biol 2022; 221:213466. [PMID: 36107127 PMCID: PMC9481740 DOI: 10.1083/jcb.202206131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/02/2022] [Accepted: 08/17/2022] [Indexed: 11/22/2022] Open
Abstract
Cytoplasmic Dynein 1, or Dynein, is a microtubule minus end-directed motor. Dynein motility requires Dynactin and a family of activating adaptors that stabilize the Dynein-Dynactin complex and promote regulated interactions with cargo in space and time. How activating adaptors limit Dynein activation to specialized subcellular locales is unclear. Here, we reveal that Spindly, a mitotic Dynein adaptor at the kinetochore corona, exists natively in a closed conformation that occludes binding of Dynein-Dynactin to its CC1 box and Spindly motif. A structure-based analysis identified various mutations promoting an open conformation of Spindly that binds Dynein-Dynactin. A region of Spindly downstream from the Spindly motif and not required for cargo binding faces the CC1 box and stabilizes the intramolecular closed conformation. This region is also required for robust kinetochore localization of Spindly, suggesting that kinetochores promote Spindly activation to recruit Dynein. Thus, our work illustrates how specific Dynein activation at a defined cellular locale may require multiple factors.
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Affiliation(s)
- Ennio A d'Amico
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Misbha Ud Din Ahmad
- Oncode Institute and Department of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Verena Cmentowski
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | | | - Franziska Müller
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Sabine Wohlgemuth
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Andreas Brockmeyer
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Stefano Maffini
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Petra Janning
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Ingrid R Vetter
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | - Anastassis Perrakis
- Oncode Institute and Department of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
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8
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Fagiewicz R, Crucifix C, Klos T, Deville C, Kieffer B, Nominé Y, Busselez J, Rossolillo P, Schmidt H. In vitro characterization of the full-length human dynein-1 cargo adaptor BicD2. Structure 2022:S0969-2126(22)00353-7. [PMID: 36150379 DOI: 10.1016/j.str.2022.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 07/07/2022] [Accepted: 08/29/2022] [Indexed: 11/22/2022]
Abstract
Cargo adaptors are crucial in coupling motor proteins with their respective cargos and regulatory proteins. BicD2 is a prominent example within the cargo adaptor family. BicD2 is able to recruit the microtubule motor dynein to RNA, viral particles, and nuclei. The BicD2-mediated interaction between the nucleus and dynein is implicated in mitosis, interkinetic nuclear migration (INM) in radial glial progenitor cells, and neuron precursor migration during embryonic neocortex development. In vitro studies involving full-length cargo adaptors are difficult to perform due to the hydrophobic character, low-expression levels, and intrinsic flexibility of cargo adaptors. Here, we report the recombinant production of full-length human BicD2 and confirm its biochemical activity by interaction studies with RanBP2. We also describe pH-dependent conformational changes of BicD2 using cryoelectron microscopy (cryo-EM), template-free structure predictions, and biophysical tools. Our results will help define the biochemical parameters for the in vitro reconstitution of higher-order BicD2 protein complexes.
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9
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Chiba K, Ori-McKenney KM, Niwa S, McKenney RJ. Synergistic autoinhibition and activation mechanisms control kinesin-1 motor activity. Cell Rep 2022; 39:110900. [PMID: 35649356 PMCID: PMC9365671 DOI: 10.1016/j.celrep.2022.110900] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/22/2022] [Accepted: 05/10/2022] [Indexed: 11/03/2022] Open
Abstract
Kinesin-1 activity is regulated by autoinhibition. Intramolecular interactions within the kinesin heavy chain (KHC) are proposed to be one facet of motor regulation. The KHC also binds to the kinesin light chain (KLC), which has been implicated in both autoinhibition and activation of the motor. We show that the KLC inhibits the kinesin-microtubule interaction independently from the proposed intramolecular interaction within KHC. Cargo-adaptor proteins that bind the KLC stimulated processive movement, but the landing rate of activated kinesin complexes remained low. Mitogen-activated protein 7 (MAP7) enhanced motility by increasing the landing rate and run length of the activated kinesin motors. Our results support a model whereby the motor activity of the kinesin is regulated by synergistic inhibition mechanisms and that cargo-adaptor binding to the KLC releases both mechanisms. However, a non-motor MAP is required for robust microtubule association of the activated motor. Thus, human kinesin is regulated by synergistic autoinhibition and activation mechanisms.
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Affiliation(s)
- Kyoko Chiba
- Department of Molecular and Cellular Biology, University of California, Davis, 145 Briggs Hall, Davis, CA 95616, USA; Frontier Research Institute for Interdisciplinary Sciences (FRIS), Tohoku University, Miyagi, 6-3 Aramaki Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Kassandra M Ori-McKenney
- Department of Molecular and Cellular Biology, University of California, Davis, 145 Briggs Hall, Davis, CA 95616, USA
| | - Shinsuke Niwa
- Frontier Research Institute for Interdisciplinary Sciences (FRIS), Tohoku University, Miyagi, 6-3 Aramaki Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Richard J McKenney
- Department of Molecular and Cellular Biology, University of California, Davis, 145 Briggs Hall, Davis, CA 95616, USA.
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10
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Gibson JM, Cui H, Ali MY, Zhao X, Debler EW, Zhao J, Trybus KM, Solmaz SR, Wang C. Coil-to-α-helix transition at the Nup358-BicD2 interface activates BicD2 for dynein recruitment. eLife 2022; 11:74714. [PMID: 35229716 PMCID: PMC8956292 DOI: 10.7554/elife.74714] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Nup358, a protein of the nuclear pore complex, facilitates a nuclear positioning pathway that is essential for many biological processes, including neuromuscular and brain development. Nup358 interacts with the dynein adaptor Bicaudal D2 (BicD2), which in turn recruits the dynein machinery to position the nucleus. However, the molecular mechanisms of the Nup358/BicD2 interaction and the activation of transport remain poorly understood. Here for the first time, we show that a minimal Nup358 domain activates dynein/dynactin/BicD2 for processive motility on microtubules. Using nuclear magnetic resonance titration and chemical exchange saturation transfer, mutagenesis, and circular dichroism spectroscopy, a Nup358 α-helix encompassing residues 2162–2184 was identified, which transitioned from a random coil to an α-helical conformation upon BicD2 binding and formed the core of the Nup358-BicD2 interface. Mutations in this region of Nup358 decreased the Nup358/BicD2 interaction, resulting in decreased dynein recruitment and impaired motility. BicD2 thus recognizes Nup358 through a ‘cargo recognition α-helix,’ a structural feature that may stabilize BicD2 in its activated state and promote processive dynein motility.
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Affiliation(s)
- James M Gibson
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, United States
| | - Heying Cui
- Department of Chemistry, Binghamton University, Binghamton, United States
| | - M Yusuf Ali
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, United States
| | - Xioaxin Zhao
- Department of Biological Sciences, Binghamton University, Binghamton, United States
| | - Erik W Debler
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Jing Zhao
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, United States
| | - Kathleen M Trybus
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, United States
| | - Sozanne R Solmaz
- Department of Chemistry, Binghamton University, Binghamton, United States
| | - Chunyu Wang
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, United States
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11
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Rossor AM, Reilly MM. Neurogenic arthrogryposis and the power of phenotyping. Neuromuscul Disord 2021; 31:1062-9. [PMID: 34736627 DOI: 10.1016/j.nmd.2021.07.399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 11/23/2022]
Abstract
In this article we review the commonest cause of neurogenic arthrogryposis, termed Spinal Muscular Atrophy Lower Extremity Dominant (SMALED), due to variants in DYNC1H1 and BICD2. We discuss the characteristic clinical and radiological phenotype of this disorder and how this has facilitated the identification of the genetic cause of SMALED2. We also review the similarities and differences between the human SMALED phenotype and mouse models and how this has informed our understanding of the potential mechanisms governing motor neuron loss in these disorders.
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12
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Basyuk E, Rage F, Bertrand E. RNA transport from transcription to localized translation: a single molecule perspective. RNA Biol 2021; 18:1221-1237. [PMID: 33111627 PMCID: PMC8354613 DOI: 10.1080/15476286.2020.1842631] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/21/2022] Open
Abstract
Transport of mRNAs is an important step of gene expression, which brings the genetic message from the DNA in the nucleus to a precise cytoplasmic location in a regulated fashion. Perturbation of this process can lead to pathologies such as developmental and neurological disorders. In this review, we discuss recent advances in the field of mRNA transport made using single molecule fluorescent imaging approaches. We present an overview of these approaches in fixed and live cells and their input in understanding the key steps of mRNA journey: transport across the nucleoplasm, export through the nuclear pores and delivery to its final cytoplasmic location. This review puts a particular emphasis on the coupling of mRNA transport with translation, such as localization-dependent translational regulation and translation-dependent mRNA localization. We also highlight the recently discovered translation factories, and how cellular and viral RNAs can hijack membrane transport systems to travel in the cytoplasm.
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Affiliation(s)
- Eugenia Basyuk
- Institut de Génétique Humaine, CNRS-UMR9002, Univ Montpellier, Montpellier, France
- Present address: Laboratoire de Microbiologie Fondamentale et Pathogénicité, CNRS-UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Florence Rage
- Institut de Génétique Moléculaire de Montpellier, CNRS-UMR5535, Univ Montpellier, Montpellier, France
| | - Edouard Bertrand
- Institut de Génétique Humaine, CNRS-UMR9002, Univ Montpellier, Montpellier, France
- Institut de Génétique Moléculaire de Montpellier, CNRS-UMR5535, Univ Montpellier, Montpellier, France
- Equipe Labélisée Ligue Nationale Contre Le Cancer, Montpellier, France
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13
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Tumurkhuu M, Batbuyan U, Yuzawa S, Munkhsaikhan Y, Batmunkh G, Nishimura W. A novel BICD2 mutation of a patient with Spinal Muscular Atrophy Lower Extremity Predominant 2. Intractable Rare Dis Res 2021; 10:102-108. [PMID: 33996355 PMCID: PMC8122317 DOI: 10.5582/irdr.2021.01004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The bicaudal D homolog 2 (BICD2) gene encodes a protein required for the stable complex of dynein and dynactin, which functions as a motor protein working along the microtubule cytoskeleton. Both inherited and de novo variants of BICD2 are reported with autosomal dominant spinal muscular atrophy with lower extremity predominance (SMALED2). Here, we report a male patient with a novel mutation in the BICD2 gene caused by a heterozygous substitution of arginine with cysteine at residue 162 (Arg162Cys); inherited from his asymptomatic mother. The patient showed typical clinical symptoms of SMALED2, which was genetically confirmed by sequencing. The Arg162Cys mutant clusters with four previously reported variants (c.361C>G, p.Leu121Val; c.581A>G, p.Gln194Arg; c.320C>T, p.Ser107Leu; c.565A>T, p.Ile189Phe) in a region that binds to the dynein-dynactin complex (DDC). The BICD2 domain structures were predicted and the Arg162Cys mutation was localized in the N-terminus coiled-coil segment 1 (CC1) domain. Protein modeling of BICD2's CC1 domain predicted that the Arg162Cys missense variant disrupted interactions with dynein cytoplasmic 1 heavy chain 1 within the DDC. The mutant did this by either changing the electrostatic surface potential or making a broader hydrophobic unit with the neighboring residues. This hereditary case supports the complex and broad genotype-phenotype correlation of BICD2 mutations, which could be explained by incomplete penetrance or variable expressivity in the next generation.
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Affiliation(s)
- Munkhtuya Tumurkhuu
- Department of Molecular Biology, International University of Health and Welfare, School of Medicine, Narita, Chiba, Japan
- Department of Genetics and Molecular Biology, School of Bio-Medicine, Mongolian National University of Medical Sciences, Mongolia
- Address correspondence to:Munkhtuya Tumurkhuu, Department of Molecular Biology, School of Medicine, International University of Health and Welfare, 4-3 Kozunomori, Narita, Chiba 286-8686, Japan. E-mail: , munkhtuya.tumurkhuu@ gmail.com
| | - Uranchimeg Batbuyan
- Department of Genetics and Molecular Biology, School of Bio-Medicine, Mongolian National University of Medical Sciences, Mongolia
| | - Satoru Yuzawa
- Department of Biochemistry, International University of Health and Welfare, School of Medicine, Narita, Chiba, Japan
| | - Yanjinlkham Munkhsaikhan
- Department of Genetics and Molecular Biology, School of Bio-Medicine, Mongolian National University of Medical Sciences, Mongolia
| | - Ganbayar Batmunkh
- Laboratory of Medical Genetics, National Center of Maternal and Child Health, Mongolia
| | - Wataru Nishimura
- Department of Molecular Biology, International University of Health and Welfare, School of Medicine, Narita, Chiba, Japan
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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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Mohr S, Kenny A, Lam STY, Morgan MB, Smibert CA, Lipshitz HD, Macdonald PM. Opposing roles for Egalitarian and Staufen in transport, anchoring and localization of oskar mRNA in the Drosophila oocyte. PLoS Genet 2021; 17:e1009500. [PMID: 33798193 DOI: 10.1371/journal.pgen.1009500] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/14/2021] [Accepted: 03/19/2021] [Indexed: 11/19/2022] Open
Abstract
Localization of oskar mRNA includes two distinct phases: transport from nurse cells to the oocyte, a process typically accompanied by cortical anchoring in the oocyte, followed by posterior localization within the oocyte. Signals within the oskar 3' UTR directing transport are individually weak, a feature previously hypothesized to facilitate exchange between the different localization machineries. We show that alteration of the SL2a stem-loop structure containing the oskar transport and anchoring signal (TAS) removes an inhibitory effect such that in vitro binding by the RNA transport factor, Egalitarian, is elevated as is in vivo transport from the nurse cells into the oocyte. Cortical anchoring within the oocyte is also enhanced, interfering with posterior localization. We also show that mutation of Staufen recognized structures (SRSs), predicted binding sites for Staufen, disrupts posterior localization of oskar mRNA just as in staufen mutants. Two SRSs in SL2a, one overlapping the Egalitarian binding site, are inferred to mediate Staufen-dependent inhibition of TAS anchoring activity, thereby promoting posterior localization. The other three SRSs in the oskar 3' UTR are also required for posterior localization, including two located distant from any known transport signal. Staufen, thus, plays multiple roles in localization of oskar mRNA.
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16
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Bhagavatula S, Knust E. A putative stem-loop structure in Drosophila crumbs is required for mRNA localisation in epithelia and germline cells. J Cell Sci 2021; 134:224086. [PMID: 33310910 DOI: 10.1242/jcs.236497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/30/2020] [Indexed: 01/02/2023] Open
Abstract
Crumbs (Crb) is an evolutionarily conserved transmembrane protein localised to the apical membrane of epithelial cells. Loss or mislocalisation of Crb is often associated with disruption of apicobasal cell polarity. crb mRNA is also apically enriched in epithelial cells, and, as shown here, accumulates in the oocyte of developing egg chambers. We narrowed down the localisation element (LE) of crb mRNA to 47 nucleotides, which form a putative stem-loop structure that may be recognised by Egalitarian (Egl). Mutations in conserved nucleotides abrogate apical transport. crb mRNA enrichment in the oocyte is affected in egl mutant egg chambers. A CRISPR-based genomic deletion of the crb locus that includes the LE disrupts asymmetric crb mRNA localisation in epithelia and prevents its accumulation in the oocyte during early stages of oogenesis, but does not affect Crb protein localisation in embryonic and follicular epithelia. However, flies lacking the LE show ectopic Crb protein expression in the nurse cells. These data suggest an additional role for the Drosophila 3'-UTR in regulating translation in a tissue-specific manner.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Srija Bhagavatula
- Max-Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Elisabeth Knust
- Max-Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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17
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Henen MA, Myers W, Schmitt LR, Wade KJ, Born A, Nichols PJ, Vögeli B. The Disordered Spindly C-terminus Interacts with RZZ Subunits ROD-1 and ZWL-1 in the Kinetochore through the Same Sites in C. Elegans. J Mol Biol 2021; 433:166812. [PMID: 33450249 DOI: 10.1016/j.jmb.2021.166812] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 11/24/2022]
Abstract
Spindly is a dynein adaptor involved in chromosomal segregation during cell division. While Spindly's N-terminal domain binds to the microtubule motor dynein and its activator dynactin, the C-terminal domain (Spindly-C) binds its cargo, the ROD/ZW10/ZWILCH (RZZ) complex in the outermost layer of the kinetochore. In humans, Spindly-C binds to ROD, while in C. elegans Spindly-C binds to both Zwilch (ZWL-1) and ROD-1. Here, we employed various biophysical techniques to characterize the structure, dynamics and interaction sites of C. elegans Spindly-C. We found that despite the overall disorder, there are two regions with variable α-helical propensity. One of these regions is located in the C-terminal half and is compact; the second is sparsely populated in the N-terminal half. The interactions with both ROD-1 and ZWL-1 are mostly mediated by the same two sequentially remote disordered segments of Spindly-C, which are C-terminally adjacent to the helical regions. The findings suggest that the Spindly-C binding sites on ROD-1 in the ROD-1/ZWL-1 complex context are either shielded or conformationally weakened by the presence of ZWL-1 such that only ZWL-1 directly interacts with Spindly-C in C. elegans.
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18
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Lee IG, Cason SE, Alqassim SS, Holzbaur ELF, Dominguez R. A tunable LIC1-adaptor interaction modulates dynein activity in a cargo-specific manner. Nat Commun 2020; 11:5695. [PMID: 33173051 PMCID: PMC7655957 DOI: 10.1038/s41467-020-19538-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/16/2020] [Indexed: 01/07/2023] Open
Abstract
Cytoplasmic dynein-1 (dynein) is the motor responsible for most retrograde transport of cargoes along microtubules in eukaryotic cells, including organelles, mRNA and viruses. Cargo selectivity and activation of processive motility depend on a group of so-called "activating adaptors" that link dynein to its general cofactor, dynactin, and cargoes. The mechanism by which these adaptors regulate dynein transport is poorly understood. Here, based on crystal structures, quantitative binding studies, and in vitro motility assays, we show that BICD2, CRACR2a, and HOOK3, representing three subfamilies of unrelated adaptors, interact with the same amphipathic helix of the dynein light intermediate chain-1 (LIC1). While the hydrophobic character of the interaction is conserved, the three adaptor subfamilies use different folds (coiled-coil, EF-hand, HOOK domain) and different surface contacts to bind the LIC1 helix with affinities ranging from 1.5 to 15.0 μM. We propose that a tunable LIC1-adaptor interaction modulates dynein's motility in a cargo-specific manner.
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Affiliation(s)
- In-Gyun Lee
- grid.25879.310000 0004 1936 8972Department of Physiology and Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA ,grid.35541.360000000121053345Present Address: Korea Institute of Science and Technology (KIST), 5 Hwarangro 14-Gil, Seongbuk-Gu, Seoul, 02792 Republic of Korea
| | - Sydney E. Cason
- grid.25879.310000 0004 1936 8972Department of Physiology and Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA ,grid.25879.310000 0004 1936 8972Neuroscience Graduate Group, Biomedical Graduate Studies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Saif S. Alqassim
- grid.25879.310000 0004 1936 8972Department of Physiology and Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA ,Present Address: College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Erika L. F. Holzbaur
- grid.25879.310000 0004 1936 8972Department of Physiology and Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA ,grid.25879.310000 0004 1936 8972Neuroscience Graduate Group, Biomedical Graduate Studies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Roberto Dominguez
- grid.25879.310000 0004 1936 8972Department of Physiology and Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
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19
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Mattera R, Williamson CD, Ren X, Bonifacino JS. The FTS-Hook-FHIP (FHF) complex interacts with AP-4 to mediate perinuclear distribution of AP-4 and its cargo ATG9A. Mol Biol Cell 2020; 31:963-979. [PMID: 32073997 PMCID: PMC7185972 DOI: 10.1091/mbc.e19-11-0658] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/05/2020] [Accepted: 02/12/2020] [Indexed: 01/08/2023] Open
Abstract
The heterotetrameric adaptor protein complex 4 (AP-4) is a component of a protein coat associated with the trans-Golgi network (TGN). Mutations in AP-4 subunits cause a complicated form of autosomal-recessive hereditary spastic paraplegia termed AP-4-deficiency syndrome. Recent studies showed that AP-4 mediates export of the transmembrane autophagy protein ATG9A from the TGN to preautophagosomal structures. To identify additional proteins that cooperate with AP-4 in ATG9A trafficking, we performed affinity purification-mass spectrometry followed by validation of the hits by biochemical and functional analyses. This approach resulted in the identification of the fused toes homolog-Hook-FHIP (FHF) complex as a novel AP-4 accessory factor. We found that the AP-4-FHF interaction is mediated by direct binding of the AP-4 μ4 subunit to coiled-coil domains in the Hook1 and Hook2 subunits of FHF. Knockdown of FHF subunits resulted in dispersal of AP-4 and ATG9A from the perinuclear region of the cell, consistent with the previously demonstrated role of the FHF complex in coupling organelles to the microtubule (MT) retrograde motor dynein-dynactin. These findings thus uncover an additional mechanism for the distribution of ATG9A within cells and provide further evidence for a role of protein coats in coupling transport vesicles to MT motors.
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Affiliation(s)
- Rafael Mattera
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Chad D. Williamson
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Xuefeng Ren
- Department of Molecular and Cell Biology and California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720
| | - Juan S. Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
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20
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Abstract
Adaptation to hypoxia is essential for regulating the survival and functions of hypoxic cells; it is mainly mediated by the hypoxia-inducible factor 1 (HIF1). The alpha subunit of HIF1 (HIF1α) is a well-known regulatory component of HIF1, which is tightly controlled by various types of HIF1α-regulating processes. Previous research has shown that microtubule-regulated HIF1α nuclear translocation is a key factor for HIF1 activation under hypoxia. In this review, we summarize experimental reports on the role of microtubule-associated factors, such as microtubule, dynein, and dynein adaptor protein, in nuclear translocation of HIF1α. Based upon scientific evidence, we propose a bicaudal D homolog (BICD) as a novel HIF1α translocation regulating factor. A deeper understanding of the mechanism of the action of regulatory factors in controlling HIF1α nuclear translocation will provide novel insights into cell biology under hypoxia.
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Affiliation(s)
- Hyun Jik Lee
- Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, South Korea
| | - Ho Jae Han
- Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, South Korea
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21
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Barbosa J, Martins T, Bange T, Tao L, Conde C, Sunkel C. Polo regulates Spindly to prevent premature stabilization of kinetochore-microtubule attachments. EMBO J 2019; 39:e100789. [PMID: 31849090 DOI: 10.15252/embj.2018100789] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/26/2019] [Accepted: 12/02/2019] [Indexed: 12/13/2022] Open
Abstract
Accurate chromosome segregation in mitosis requires sister kinetochores to bind to microtubules from opposite spindle poles. The stability of kinetochore-microtubule attachments is fine-tuned to prevent or correct erroneous attachments while preserving amphitelic interactions. Polo kinase has been implicated in both stabilizing and destabilizing kinetochore-microtubule attachments. However, the mechanism underlying Polo-destabilizing activity remains elusive. Here, resorting to an RNAi screen in Drosophila for suppressors of a constitutively active Polo mutant, we identified a strong genetic interaction between Polo and the Rod-ZW10-Zwilch (RZZ) complex, whose kinetochore accumulation has been shown to antagonize microtubule stability. We find that Polo phosphorylates Spindly and impairs its ability to bind to Zwilch. This precludes dynein-mediated removal of the RZZ from kinetochores and consequently delays the formation of stable end-on attachments. We propose that high Polo-kinase activity following mitotic entry directs the RZZ complex to minimize premature stabilization of erroneous attachments, whereas a decrease in active Polo in later mitotic stages allows the formation of stable amphitelic spindle attachments. Our findings demonstrate that Polo tightly regulates the RZZ-Spindly-dynein module during mitosis to ensure the fidelity of chromosome segregation.
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Affiliation(s)
- João Barbosa
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,i3S, Instituto de Investigação e Inovação em Saúde da Universidade do Porto, Porto, Portugal
| | - Torcato Martins
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Tanja Bange
- MPI für molekulare Physiologie, Dortmund, Germany
| | - Li Tao
- Department of Biology, University of Hawaii, Hilo, HI, USA
| | - Carlos Conde
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,i3S, Instituto de Investigação e Inovação em Saúde da Universidade do Porto, Porto, Portugal
| | - Claudio Sunkel
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,i3S, Instituto de Investigação e Inovação em Saúde da Universidade do Porto, Porto, Portugal.,ICBAS-Instituto de Ciência Biomédica de Abel Salazar, Universidade do Porto, Porto, Portugal
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22
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Cui H, Noell CR, Behler RP, Zahn JB, Terry LR, Russ BB, Solmaz SR. Adapter Proteins for Opposing Motors Interact Simultaneously with Nuclear Pore Protein Nup358. Biochemistry 2019; 58:5085-5097. [PMID: 31756096 DOI: 10.1021/acs.biochem.9b00907] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Nup358 is a protein subunit of the nuclear pore complex that recruits the opposing microtubule motors kinesin-1 and dynein [via the dynein adaptor Bicaudal D2 (BicD2)] to the nuclear envelope. This pathway is important for positioning of the nucleus during the early steps of mitotic spindle assembly and also essential for an important process in brain development. It is unknown whether dynein and kinesin-1 interact with Nup358 simultaneously or whether they compete. Here, we have reconstituted and characterized a minimal complex of kinesin-1 light chain 2 (KLC2) and Nup358. The proteins interact through a W-acidic motif in Nup358, which is highly conserved among vertebrates but absent in insects. While Nup358 and KLC2 form predominantly monomers, their interaction results in the formation of 2:2 complexes, and the W-acidic motif is required for the oligomerization. In active motor complexes, BicD2 and KLC2 each form dimers. Notably, we show that the dynein adaptor BicD2 and KLC2 interact simultaneously with Nup358, resulting in the formation of 2:2:2 complexes. Mutation of the W-acidic motif results in the formation of 1:1:1 complexes. On the basis of our data, we propose that Nup358 recruits simultaneously one kinesin-1 motor and one dynein motor via BicD2 to the nucleus. We hypothesize that the binding sites are close enough to promote direct interactions between these motor recognition domains, which may be important for the regulation of the motility of these opposing motors. Our data provide important insights into a nuclear positioning pathway that is crucial for brain development and faithful chromosome segregation.
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Affiliation(s)
- Heying Cui
- Department of Chemistry , Binghamton University , P.O. Box 6000, Binghamton , New York 13902 , United States
| | - Crystal R Noell
- Department of Chemistry , Binghamton University , P.O. Box 6000, Binghamton , New York 13902 , United States
| | - Rachael P Behler
- Department of Chemistry , Binghamton University , P.O. Box 6000, Binghamton , New York 13902 , United States
| | - Jacqueline B Zahn
- Department of Chemistry , Binghamton University , P.O. Box 6000, Binghamton , New York 13902 , United States
| | - Lynn R Terry
- Department of Chemistry , Binghamton University , P.O. Box 6000, Binghamton , New York 13902 , United States
| | - Blaine B Russ
- Department of Chemistry , Binghamton University , P.O. Box 6000, Binghamton , New York 13902 , United States
| | - Sozanne R Solmaz
- Department of Chemistry , Binghamton University , P.O. Box 6000, Binghamton , New York 13902 , United States
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23
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Lee HJ, Jung YH, Choi GE, Kim JS, Chae CW, Lim JR, Kim SY, Lee JE, Park MC, Yoon JH, Choi MJ, Kim KS, Han HJ. O-cyclic phytosphingosine-1-phosphate stimulates HIF1α-dependent glycolytic reprogramming to enhance the therapeutic potential of mesenchymal stem cells. Cell Death Dis 2019; 10:590. [PMID: 31383843 PMCID: PMC6683124 DOI: 10.1038/s41419-019-1823-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/18/2019] [Accepted: 07/22/2019] [Indexed: 12/12/2022]
Abstract
O-cyclic phytosphingosine-1-phosphate (cP1P) is a novel chemically synthesized sphingosine metabolite derived from phytosphingosine-1-phosphate. Although structurally similar to sphingosine-1-phosphate (S1P), its biological properties in stem cells remain to be reported. We investigated the effect of cP1P on the therapeutic potential of mesenchymal stem cells (MSCs) and their regulatory mechanism. We found that, under hypoxia, cP1P suppressed MSC mitochondrial dysfunction and apoptosis. Metabolic data revealed that cP1P stimulated glycolysis via the upregulation of glycolysis-related genes. cP1P-induced hypoxia-inducible factor 1 alpha (HIF1α) plays a key role for MSC glycolytic reprogramming and transplantation efficacy. The intracellular calcium-dependent PKCα/mammalian target of the rapamycin (mTOR) signaling pathway triggered by cP1P regulated HIF1α translation via S6K1, which is critical for HIF1 activation. Furthermore, the cP1P-activated mTOR pathway induced bicaudal D homolog 1 expression, leading to HIF1α nuclear translocation. In conclusion, cP1P enhances the therapeutic potential of MSC through mTOR-dependent HIF1α translation and nuclear translocation.
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Affiliation(s)
- Hyun Jik Lee
- Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, 08826, Republic of Korea
| | - Young Hyun Jung
- Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, 08826, Republic of Korea
| | - Gee Euhn Choi
- Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jun Sung Kim
- Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chang Woo Chae
- Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae Ryong Lim
- Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seo Yihl Kim
- Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, 08826, Republic of Korea
| | - Joo Eun Lee
- Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, 08826, Republic of Korea
| | - Min Chul Park
- Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jee Hyeon Yoon
- Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, 08826, Republic of Korea
| | - Myeong Jun Choi
- Axcesobiopharma, 268 Hakuiro, Dongan-gu, Anyang, 14056, Republic of Korea
| | - Kye-Seong Kim
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Ho Jae Han
- Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, 08826, Republic of Korea.
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24
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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25
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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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26
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Bergendahl LT, Gerasimavicius L, Miles J, Macdonald L, Wells JN, Welburn JPI, Marsh JA. The role of protein complexes in human genetic disease. Protein Sci 2019; 28:1400-1411. [PMID: 31219644 DOI: 10.1002/pro.3667] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 06/10/2019] [Indexed: 12/20/2022]
Abstract
Many human genetic disorders are caused by mutations in protein-coding regions of DNA. Taking protein structure into account has therefore provided key insight into the molecular mechanisms underlying human genetic disease. Although most studies have focused on the intramolecular effects of mutations, the critical role of the assembly of proteins into complexes is being increasingly recognized. Here, we review multiple ways in which consideration of protein complexes can help us to understand and explain the effects of pathogenic mutations. First, we discuss disorders caused by mutations that perturb intersubunit interactions in homomeric and heteromeric complexes. Second, we address how protein complex assembly can facilitate a dominant-negative mechanism, whereby mutated subunits can disrupt the activity of wild-type protein. Third, we show how mutations that change protein expression levels can lead to damaging stoichiometric imbalances. Finally, we review how mutations affecting different subunits of the same heteromeric complex often cause similar diseases, whereas mutations in different interfaces of the same subunit can cause distinct phenotypes.
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Affiliation(s)
- L Therese Bergendahl
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Lukas Gerasimavicius
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Jamilla Miles
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Lewis Macdonald
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Jonathan N Wells
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, 14850
| | - Julie P I Welburn
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
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27
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Abstract
Cytoplasmic dynein-1 (hereafter dynein) is an essential cellular motor that drives the movement of diverse cargos along the microtubule cytoskeleton, including organelles, vesicles and RNAs. A long-standing question is how a single form of dynein can be adapted to a wide range of cellular functions in both interphase and mitosis. Recent progress has provided new insights - dynein interacts with a group of activating adaptors that provide cargo-specific and/or function-specific regulation of the motor complex. Activating adaptors such as BICD2 and Hook1 enhance the stability of the complex that dynein forms with its required activator dynactin, leading to highly processive motility toward the microtubule minus end. Furthermore, activating adaptors mediate specific interactions of the motor complex with cargos such as Rab6-positive vesicles or ribonucleoprotein particles for BICD2, and signaling endosomes for Hook1. In this Cell Science at a Glance article and accompanying poster, we highlight the conserved structural features found in dynein activators, the effects of these activators on biophysical parameters, such as motor velocity and stall force, and the specific intracellular functions they mediate.
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Affiliation(s)
- Mara A Olenick
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Erika L F Holzbaur
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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28
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Wang Y, Huynh W, Skokan TD, Lu W, Weiss A, Vale RD. CRACR2a is a calcium-activated dynein adaptor protein that regulates endocytic traffic. J Cell Biol 2019; 218:1619-1633. [PMID: 30814157 PMCID: PMC6504896 DOI: 10.1083/jcb.201806097] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 12/14/2018] [Accepted: 02/07/2019] [Indexed: 01/12/2023] Open
Abstract
Transport of intracellular cargo generally requires coiled-coil adaptor proteins that connect cargo-bound receptors, usually GTPases, to dynein motor complexes. Wang et al. report that two Rab GTPases, CRACR2a and Rab45, contain coiled-coil domains and can directly act as dynein adaptors with CRACR2a–dynein participating in calcium-regulated endocytic trafficking. Cytoplasmic dynein is a minus end–directed microtubule motor that transports intracellular cargoes. Transport is initiated by coiled-coil adaptors that (a) join dynein and its cofactor dynactin into a motile complex and (b) interact with a cargo-bound receptor, which is frequently a Rab GTPase on an organelle. Here, we report two novel dynein adaptors, CRACR2a and Rab45, that have a coiled-coil adaptor domain, a pair of EF-hands, and a Rab GTPase fused into a single polypeptide. CRACR2a-mediated, but not Rab45-mediated, dynein motility is activated by calcium in vitro. In Jurkat T cells, elevation of intracellular calcium activates CRACR2a-mediated dynein transport. We further found that T cell receptor activation induces the formation of CRACR2a puncta at the plasma membrane, which initially associate with the actin cortex and subsequently detach and travel along microtubules, suggestive of an endocytic process. These results provide the first examples of Rab GTPases that directly act as dynein adaptors and implicate CRACR2a–dynein in calcium-regulated endocytic trafficking.
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Affiliation(s)
- Yuxiao Wang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA
| | - Walter Huynh
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA
| | - Taylor D Skokan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA
| | - Wen Lu
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Arthur Weiss
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA.,Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Ronald D Vale
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA .,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA
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29
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Lee HJ, Jung YH, Oh JY, Choi GE, Chae CW, Kim JS, Lim JR, Kim SY, Lee SJ, Seong JK, Han HJ. BICD1 mediates HIF1α nuclear translocation in mesenchymal stem cells during hypoxia adaptation. Cell Death Differ 2019; 26:1716-34. [PMID: 30464225 DOI: 10.1038/s41418-018-0241-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/11/2018] [Accepted: 11/06/2018] [Indexed: 12/17/2022] Open
Abstract
Hypoxia inducible factor 1α (HIF1α) is a master regulator leading to metabolic adaptation, an essential physiological process to maintain the survival of stem cells under hypoxia. However, it is poorly understood how HIF1α translocates into the nucleus in stem cells under hypoxia. Here, we investigated the role of a motor adaptor protein Bicaudal D homolog 1 (BICD1) in dynein-mediated HIF1α nuclear translocation and the effect of BICD1 regulation on hypoxia adaptation and its therapeutic potential on human umbilical cord blood-derived mesenchymal stem cells (UCB-MSCs). In our results, silencing of BICD1 but not BICD2 abolished HIF1α nuclear translocation and its activity. BICD1 overexpression further enhanced hypoxia-induced HIF1α nuclear translocation. Hypoxia stimulated direct bindings of HIF1α to BICD1 and the intermediate chain of dynein (Dynein IC), which was abolished by BICD1 silencing. Akt inhibition reduced the binding of BICD1 to HIF1α and nuclear translocation of HIF1α. Conversely, Akt activation or GSK3β silencing further enhanced the hypoxia-induced HIF1α nuclear translocation. Furthermore, BICD1 silencing abolished hypoxia-induced glycolytic reprogramming and increased mitochondrial ROS accumulation and apoptosis in UCB-MSCs under hypoxia. In the mouse skin wound healing model, the transplanted cell survival and skin wound healing capacities of hypoxia-pretreated UCB-MSCs were reduced by BICD1 silencing and further increased by GSK3β silencing. In conclusion, we demonstrated that BICD1-induced HIF1α nuclear translocation is critical for hypoxia adaptation, which determines the regenerative potential of UCB-MSCs.
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30
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Abstract
Dynein adaptor proteins such as Bicaudal D2 (BicD2) are integral components of the dynein transport machinery, as they recognize cargoes for cell cycle-specific transport and link them to the motor complex. Human BicD2 switches from selecting secretory and Golgi-derived vesicles for transport in G1 and S phase (by recognizing Rab6GTP), to selecting the nucleus for transport in G2 phase (by recognizing nuclear pore protein Nup358), but the molecular mechanisms governing this switch are elusive. Here, we have developed a quantitative model for BicD2/cargo interactions that integrates affinities, oligomeric states, and cellular concentrations of the reactants. BicD2 and cargo form predominantly 2:2 complexes. Furthermore, the affinity of BicD2 toward its cargo Nup358 is higher than that toward Rab6GTP. Based on our calculations, an estimated 1000 BicD2 molecules per cell would be recruited to the nucleus through Nup358 in the absence of regulation. Notably, RanGTP is a negative regulator of the Nup358/BicD2 interaction that weakens the affinity by a factor of 10 and may play a role in averting dynein recruitment to the nucleus outside of the G2 phase. However, our quantitative model predicts that an additional negative regulator remains to be identified. In the absence of negative regulation, the affinity of Nup358 would likely be sufficient to recruit BicD2 to the nucleus in G2 phase. Our quantitative model makes testable predictions of how cellular transport events are orchestrated. These transport processes are important for brain development, cell cycle control, signaling, and neurotransmission at synapses.
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Affiliation(s)
- Crystal R Noell
- Department of Chemistry , State University of New York at Binghamton , Binghamton , New York 13902 , United States
| | - Kyle M Loftus
- Department of Chemistry , State University of New York at Binghamton , Binghamton , New York 13902 , United States
| | - Heying Cui
- Department of Chemistry , State University of New York at Binghamton , Binghamton , New York 13902 , United States
| | - Christof Grewer
- Department of Chemistry , State University of New York at Binghamton , Binghamton , New York 13902 , United States
| | - Megan Kizer
- Department of Chemistry , State University of New York at Binghamton , Binghamton , New York 13902 , United States
| | - Erik W Debler
- Department of Biochemistry & Molecular Biology , Thomas Jefferson University , Philadelphia , Pennsylvania 19107 , United States
| | - Sozanne R Solmaz
- Department of Chemistry , State University of New York at Binghamton , Binghamton , New York 13902 , United States
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31
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Carnes SK, Zhou J, Aiken C. HIV-1 Engages a Dynein-Dynactin-BICD2 Complex for Infection and Transport to the Nucleus. J Virol 2018; 92:e00358-18. [PMID: 30068656 DOI: 10.1128/JVI.00358-18] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/25/2018] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection depends on efficient intracytoplasmic transport of the incoming viral core to the target cell nucleus. Evidence suggests that this movement is facilitated by the microtubule motor dynein, a large multiprotein complex that interacts with dynactin and cargo-specific adaptor proteins for retrograde movement via microtubules. Dynein adaptor proteins are necessary for activating dynein movement and for linking specific cargoes to dynein. We hypothesized that HIV-1 engages the dynein motor complex via an adaptor for intracellular transport. Here, we show that small interfering RNA depletion of the dynein heavy chain, components of the dynactin complex, and the dynein adaptor BICD2 reduced cell permissiveness to HIV-1 infection. Cell depletion of dynein heavy chain and BICD2 resulted in impaired HIV-1 DNA accumulation in the nucleus and decreased retrograde movement of the virus. Biochemical studies revealed that dynein components and BICD2 associate with capsid-like assemblies of the HIV-1 CA protein in cell extracts and that purified recombinant BICD2 binds to CA assemblies in vitro Association of dynein with CA assemblies was reduced upon immunodepletion of BICD2 from cell extracts. We conclude that BICD2 is a capsid-associated dynein adaptor utilized by HIV-1 for transport to the nucleus.IMPORTANCE During HIV-1 infection, the virus must travel across the cytoplasm to enter the nucleus. The host cell motor protein complex dynein has been implicated in HIV-1 intracellular transport. We show that expression of the dynein heavy chain, components of the dynein-associated dynactin complex, and the dynein adaptor BICD2 in target cells are important for HIV-1 infection and nuclear entry. BICD2 interacts with the HIV-1 capsid in vitro, suggesting that it functions as a capsid-specific adaptor for HIV-1 intracellular transport. Our work identifies specific host proteins involved in microtubule-dependent HIV-1 intracellular transport and highlights the BICD2-capsid interaction as a potential target for antiviral therapy.
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32
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Abstract
RNA localization serves numerous purposes from controlling development and differentiation to supporting the physiological activities of cells and organisms. After a brief introduction into the history of the study of mRNA localization I will focus on animal systems, describing in which cellular compartments and in which cell types mRNA localization was observed and studied. In recent years numerous novel localization patterns have been described, and countless mRNAs have been documented to accumulate in specific subcellular compartments. These fascinating revelations prompted speculations about the purpose of localizing all these mRNAs. In recent years experimental evidence for an unexpected variety of different functions has started to emerge. Aside from focusing on the functional aspects, I will discuss various ways of localizing mRNAs with a focus on the mechanism of active and directed transport on cytoskeletal tracks. Structural studies combined with imaging of transport and biochemical studies have contributed to the enormous recent progress, particularly in understanding how dynein/dynactin/BicD (DDB) dependent transport on microtubules works. This transport process actively localizes diverse cargo in similar ways to the minus end of microtubules and, at least in flies, also individual mRNA molecules. A sophisticated mechanism ensures that cargo loading licenses processive transport.
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Affiliation(s)
- Beat Suter
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland.
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33
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McClintock MA, Dix CI, Johnson CM, McLaughlin SH, Maizels RJ, Hoang HT, Bullock SL. RNA-directed activation of cytoplasmic dynein-1 in reconstituted transport RNPs. eLife 2018; 7:36312. [PMID: 29944118 PMCID: PMC6056234 DOI: 10.7554/elife.36312] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/19/2018] [Indexed: 12/19/2022] Open
Abstract
Polarised mRNA transport is a prevalent mechanism for spatial control of protein synthesis. However, the composition of transported ribonucleoprotein particles (RNPs) and the regulation of their movement are poorly understood. We have reconstituted microtubule minus end-directed transport of mRNAs using purified components. A Bicaudal-D (BicD) adaptor protein and the RNA-binding protein Egalitarian (Egl) are sufficient for long-distance mRNA transport by the dynein motor and its accessory complex dynactin, thus defining a minimal transport-competent RNP. Unexpectedly, the RNA is required for robust activation of dynein motility. We show that a cis-acting RNA localisation signal promotes the interaction of Egl with BicD, which licenses the latter protein to recruit dynein and dynactin. Our data support a model for BicD activation based on RNA-induced occupancy of two Egl-binding sites on the BicD dimer. Scaffolding of adaptor protein assemblies by cargoes is an attractive mechanism for regulating intracellular transport. In our cells, tiny molecular motors transport the components necessary for life’s biological processes from one location to another. They do so by loading their cargo, and burning up chemical fuel to carry it along pathways made of filaments. For example, one such motor, called dynein, can move molecules of messenger RNA (mRNA) to specific locations within the cell. There, the mRNA will be used as a template to create proteins, which will operate at exactly the right place. Transporting mRNA in this way is critical in processes such as embryonic development and the formation of memories; yet, this mechanism is still poorly understood. Previous work suggested that the mRNA is simply a passenger of the dynein motor, but McClintock et al. asked if this is really the case. Instead, could mRNA regulate its own sorting by controlling the activity of dynein? Studying mRNA trafficking within the complex molecular environment of a cell is challenging, so mRNA transporting machinery was recreated in the laboratory. Only the proteins necessary to build a working system were included in the experiments. In addition to the filaments, the components included dynein and a complex of proteins known as dynactin, which allows the motor to move together with a protein called BICD2. A protein named Egalitarian was used to link the mRNA to BICD2. By filming fluorescently labelled proteins and mRNAs, McClintock et al. discovered that mRNA strongly promotes the movement of the dynein motor. A structured section in the mRNA acts as a docking area for two copies of Egalitarian. This activates BICD2, which then binds to dynein and dynactin, thereby completing the transport machinery. According to these results, the mRNA directs the assembly of the system that will carry it within the cell. Viruses such as HIV and herpesvirus hijack dynein motors to have their genetic information moved around a cell in order to propagate infection. Understanding precisely how mRNA is transported may help to develop new strategies to fight these viruses.
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Affiliation(s)
- Mark A McClintock
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Carly I Dix
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Christopher M Johnson
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Stephen H McLaughlin
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Rory J Maizels
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Ha Thi Hoang
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Simon L Bullock
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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34
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Sladewski TE, Billington N, Ali MY, Bookwalter CS, Lu H, Krementsova EB, Schroer TA, Trybus KM. Recruitment of two dyneins to an mRNA-dependent Bicaudal D transport complex. eLife 2018; 7:e36306. [PMID: 29944116 PMCID: PMC6056235 DOI: 10.7554/elife.36306] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/23/2018] [Indexed: 12/21/2022] Open
Abstract
We investigated the role of full-length Drosophila Bicaudal D (BicD) binding partners in dynein-dynactin activation for mRNA transport on microtubules. Full-length BicD robustly activated dynein-dynactin motility only when both the mRNA binding protein Egalitarian (Egl) and K10 mRNA cargo were present, and electron microscopy showed that both Egl and mRNA were needed to disrupt a looped, auto-inhibited BicD conformation. BicD can recruit two dimeric dyneins, resulting in faster speeds and longer runs than with one dynein. Moving complexes predominantly contained two Egl molecules and one K10 mRNA. This mRNA-bound configuration makes Egl bivalent, likely enhancing its avidity for BicD and thus its ability to disrupt BicD auto-inhibition. Consistent with this idea, artificially dimerized Egl activates dynein-dynactin-BicD in the absence of mRNA. The ability of mRNA cargo to orchestrate the activation of the mRNP (messenger ribonucleotide protein) complex is an elegant way to ensure that only cargo-bound motors are motile.
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Affiliation(s)
- Thomas E Sladewski
- Department of Molecular Physiology and BiophysicsUniversity of VermontBurlingtonUnited States
| | - Neil Billington
- Laboratory of PhysiologyNational Heart, Lung, and Blood Institute, National Institutes of HealthBethesdaUnited States
| | - M Yusuf Ali
- Department of Molecular Physiology and BiophysicsUniversity of VermontBurlingtonUnited States
| | - Carol S Bookwalter
- Department of Molecular Physiology and BiophysicsUniversity of VermontBurlingtonUnited States
| | - Hailong Lu
- Department of Molecular Physiology and BiophysicsUniversity of VermontBurlingtonUnited States
| | - Elena B Krementsova
- Department of Molecular Physiology and BiophysicsUniversity of VermontBurlingtonUnited States
| | - Trina A Schroer
- Department of BiologyJohns Hopkins UniversityBaltimoreUnited States
| | - Kathleen M Trybus
- Department of Molecular Physiology and BiophysicsUniversity of VermontBurlingtonUnited States
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35
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Snoberger A, Brettrager EJ, Smith DM. Conformational switching in the coiled-coil domains of a proteasomal ATPase regulates substrate processing. Nat Commun 2018; 9:2374. [PMID: 29915197 PMCID: PMC6006169 DOI: 10.1038/s41467-018-04731-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 05/18/2018] [Indexed: 12/15/2022] Open
Abstract
Protein degradation in all domains of life requires ATPases that unfold and inject proteins into compartmentalized proteolytic chambers. Proteasomal ATPases in eukaryotes and archaea contain poorly understood N-terminally conserved coiled-coil domains. In this study, we engineer disulfide crosslinks in the coiled-coils of the archaeal proteasomal ATPase (PAN) and report that its three identical coiled-coil domains can adopt three different conformations: (1) in-register and zipped, (2) in-register and partially unzipped, and (3) out-of-register. This conformational heterogeneity conflicts with PAN's symmetrical OB-coiled-coil crystal structure but resembles the conformational heterogeneity of the 26S proteasomal ATPases' coiled-coils. Furthermore, we find that one coiled-coil can be conformationally constrained even while unfolding substrates, and conformational changes in two of the coiled-coils regulate PAN switching between resting and active states. This switching functionally mimics similar states proposed for the 26S proteasome from cryo-EM. These findings thus build a mechanistic framework to understand regulation of proteasome activity.
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Affiliation(s)
- Aaron Snoberger
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, WV, 26506, USA
| | - Evan J Brettrager
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, WV, 26506, USA
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, 26501, USA
| | - David M Smith
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, WV, 26506, USA.
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36
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Huynh W, Vale RD. Disease-associated mutations in human BICD2 hyperactivate motility of dynein-dynactin. J Cell Biol 2017; 216:3051-3060. [PMID: 28883039 PMCID: PMC5626548 DOI: 10.1083/jcb.201703201] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/14/2017] [Accepted: 07/28/2017] [Indexed: 11/22/2022] Open
Abstract
Bicaudal D2 (BICD2) is an adaptor protein that recruits and activates dynein–dynactin onto Rab6 membrane vesicles. Huynh and Vale reconstitute Rab6 regulation of BICD2-mediated dynein transport in vitro and show that disease-associated mutations in BICD2 cause an increase in retrograde transport. Bicaudal D2 (BICD2) joins dynein with dynactin into a ternary complex (termed DDB) capable of processive movement. Point mutations in the BICD2 gene have been identified in patients with a dominant form of spinal muscular atrophy, but how these mutations cause disease is unknown. To investigate this question, we have developed in vitro motility assays with purified DDB and BICD2’s membrane vesicle partner, the GTPase Rab6a. Rab6a–GTP, either in solution or bound to artificial liposomes, released BICD2 from an autoinhibited state and promoted robust dynein–dynactin transport. In these assays, BICD2 mutants showed an enhanced ability to form motile DDB complexes. Increased retrograde transport by BICD2 mutants also was observed in cells using an inducible organelle transport assay. When overexpressed in rat hippocampal neurons, the hyperactive BICD2 mutants decreased neurite growth. Our results reveal that dominant mutations in BICD2 hyperactivate DDB motility and suggest that an imbalance of minus versus plus end–directed microtubule motility in neurons may underlie spinal muscular atrophy.
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Affiliation(s)
- Walter Huynh
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA
| | - Ronald D Vale
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA .,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA
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37
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Terawaki SI, Fujita S, Katsutani T, Shiomi K, Keino-Masu K, Masu M, Wakamatsu K, Shibata N, Higuchi Y. Structural basis for Ccd1 auto-inhibition in the Wnt pathway through homomerization of the DIX domain. Sci Rep 2017; 7:7739. [PMID: 28798413 DOI: 10.1038/s41598-017-08019-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/05/2017] [Indexed: 11/08/2022] Open
Abstract
Wnt signaling plays an important role in governing cell fate decisions. Coiled-coil-DIX1 (Ccd1), Dishevelled (Dvl), and Axin are signaling proteins that regulate the canonical pathway by controlling the stability of a key signal transducer β-catenin. These proteins contain the DIX domain with a ubiquitin-like fold, which mediates their interaction in the β-catenin destruction complex through dynamic head-to-tail polymerization. Despite high sequence similarities, mammalian Ccd1 shows weaker stimulation of β-catenin transcriptional activity compared with zebrafish (z) Ccd1 in cultured cells. Here, we show that the mouse (m) Ccd1 DIX domain displays weaker ability for homopolymerization than that of zCcd1. Furthermore, X-ray crystallographic analysis of mCcd1 and zCcd1 DIX domains revealed that mCcd1 was assembled into a double-helical filament by the insertion of the β1-β2 loop into the head-to-tail interface, whereas zCcd1 formed a typical single-helical polymer similar to Dvl1 and Axin. The mutation in the contact interface of mCcd1 double-helical polymer changed the hydrodynamic properties of mCcd1 so that it acquired the ability to induce Wnt-specific transcriptional activity similar to zCcd1. These findings suggest a novel regulatory mechanism by which mCcd1 modulates Wnt signaling through auto-inhibition of dynamic head-to-tail homopolymerization.
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38
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Abstract
Asymmetric localization of mRNAs is a widespread gene regulatory mechanism that is crucial for many cellular processes. The localization of a transcript involves multiple steps and requires several protein factors to mediate transport, anchoring and translational repression of the mRNA. Specific recognition of the localizing transcript is a key step that depends on linear or structured localization signals, which are bound by RNA-binding proteins. Genetic studies have identified many components involved in mRNA localization. However, mechanistic aspects of the pathway are still poorly understood. Here we provide an overview of structural studies that contributed to our understanding of the mechanisms underlying mRNA localization, highlighting open questions and future challenges.
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Affiliation(s)
| | - Fulvia Bono
- a Max Planck Institute for Developmental Biology , Tübingen , Germany
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39
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Redwine WB, DeSantis ME, Hollyer I, Htet ZM, Tran PT, Swanson SK, Florens L, Washburn MP, Reck-Peterson SL. The human cytoplasmic dynein interactome reveals novel activators of motility. eLife 2017; 6. [PMID: 28718761 PMCID: PMC5533585 DOI: 10.7554/elife.28257] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/14/2017] [Indexed: 12/25/2022] Open
Abstract
In human cells, cytoplasmic dynein-1 is essential for long-distance transport of many cargos, including organelles, RNAs, proteins, and viruses, towards microtubule minus ends. To understand how a single motor achieves cargo specificity, we identified the human dynein interactome by attaching a promiscuous biotin ligase (‘BioID’) to seven components of the dynein machinery, including a subunit of the essential cofactor dynactin. This method reported spatial information about the large cytosolic dynein/dynactin complex in living cells. To achieve maximal motile activity and to bind its cargos, human dynein/dynactin requires ‘activators’, of which only five have been described. We developed methods to identify new activators in our BioID data, and discovered that ninein and ninein-like are a new family of dynein activators. Analysis of the protein interactomes for six activators, including ninein and ninein-like, suggests that each dynein activator has multiple cargos. DOI:http://dx.doi.org/10.7554/eLife.28257.001
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Affiliation(s)
- William B Redwine
- Department of Cellular and Molecular Medicine, University of California, San Diego, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Morgan E DeSantis
- Department of Cellular and Molecular Medicine, University of California, San Diego, United States
| | - Ian Hollyer
- Department of Cellular and Molecular Medicine, University of California, San Diego, United States
| | - Zaw Min Htet
- Department of Cellular and Molecular Medicine, University of California, San Diego, United States.,Biophysics Graduate Program, Harvard Medical School, Boston, United States
| | - Phuoc Tien Tran
- Department of Cellular and Molecular Medicine, University of California, San Diego, United States
| | | | | | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas, United States.,Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas, United States
| | - Samara L Reck-Peterson
- Department of Cellular and Molecular Medicine, University of California, San Diego, United States.,Division of Biological Sciences, Cell and Developmental Biology Section, University of California, San Diego, United States
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40
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Gourinchas G, Etzl S, Göbl C, Vide U, Madl T, Winkler A. Long-range allosteric signaling in red light-regulated diguanylyl cyclases. Sci Adv 2017; 3:e1602498. [PMID: 28275738 PMCID: PMC5336353 DOI: 10.1126/sciadv.1602498] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/10/2017] [Indexed: 05/06/2023]
Abstract
Nature has evolved an astonishingly modular architecture of covalently linked protein domains with diverse functionalities to enable complex cellular networks that are critical for cell survival. The coupling of sensory modules with enzymatic effectors allows direct allosteric regulation of cellular signaling molecules in response to diverse stimuli. We present molecular details of red light-sensing bacteriophytochromes linked to cyclic dimeric guanosine monophosphate-producing diguanylyl cyclases. Elucidation of the first crystal structure of a full-length phytochrome with its enzymatic effector, in combination with the characterization of light-induced changes in conformational dynamics, reveals how allosteric light regulation is fine-tuned by the architecture and composition of the coiled-coil sensor-effector linker and also the central helical spine. We anticipate that consideration of molecular principles of sensor-effector coupling, going beyond the length of the characteristic linker, and the appreciation of dynamically driven allostery will open up new directions for the design of novel red light-regulated optogenetic tools.
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Affiliation(s)
- Geoffrey Gourinchas
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Stefan Etzl
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Christoph Göbl
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748 Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Uršula Vide
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Tobias Madl
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748 Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Harrachgasse 21/III, 8010 Graz, Austria
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
- Corresponding author.
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41
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Zheng W. Probing the Energetics of Dynactin Filament Assembly and the Binding of Cargo Adaptor Proteins Using Molecular Dynamics Simulation and Electrostatics-Based Structural Modeling. Biochemistry 2016; 56:313-323. [PMID: 27976861 DOI: 10.1021/acs.biochem.6b01002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dynactin, a large multiprotein complex, binds with the cytoplasmic dynein-1 motor and various adaptor proteins to allow recruitment and transportation of cellular cargoes toward the minus end of microtubules. The structure of the dynactin complex is built around an actin-like minifilament with a defined length, which has been visualized in a high-resolution structure of the dynactin filament determined by cryo-electron microscopy (cryo-EM). To understand the energetic basis of dynactin filament assembly, we used molecular dynamics simulation to probe the intersubunit interactions among the actin-like proteins, various capping proteins, and four extended regions of the dynactin shoulder. Our simulations revealed stronger intersubunit interactions at the barbed and pointed ends of the filament and involving the extended regions (compared with the interactions within the filament), which may energetically drive filament termination by the capping proteins and recruitment of the actin-like proteins by the extended regions, two key features of the dynactin filament assembly process. Next, we modeled the unknown binding configuration among dynactin, dynein tails, and a number of coiled-coil adaptor proteins (including several Bicaudal-D and related proteins and three HOOK proteins), and predicted a key set of charged residues involved in their electrostatic interactions. Our modeling is consistent with previous findings of conserved regions, functional sites, and disease mutations in the adaptor proteins and will provide a structural framework for future functional and mutational studies of these adaptor proteins. In sum, this study yielded rich structural and energetic information about dynactin and associated adaptor proteins that cannot be directly obtained from the cryo-EM structures with limited resolutions.
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Affiliation(s)
- Wenjun Zheng
- Department of Physics, University at Buffalo , Buffalo, New York 14260, United States
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42
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Abstract
Coiled‐coils are found in proteins throughout all three kingdoms of life. Coiled‐coil domains of some proteins are almost invariant in sequence and length, betraying a structural and functional role for amino acids along the entire length of the coiled‐coil. Other coiled‐coils are divergent in sequence, but conserved in length, thereby functioning as molecular spacers. In this capacity, coiled‐coil proteins influence the architecture of organelles such as centrioles and the Golgi, as well as permit the tethering of transport vesicles. Specialized coiled‐coils, such as those found in motor proteins, are capable of propagating conformational changes along their length that regulate cargo binding and motor processivity. Coiled‐coil domains have also been identified in enzymes, where they function as molecular rulers, positioning catalytic activities at fixed distances. Finally, while coiled‐coils have been extensively discussed for their potential to nucleate and scaffold large macromolecular complexes, structural evidence to substantiate this claim is relatively scarce.
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Affiliation(s)
- Linda Truebestein
- Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), Vienna, Austria
| | - Thomas A Leonard
- Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), Vienna, Austria.,Department of Medical Biochemistry, Medical University of Vienna, Vienna, Austria
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43
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Khanal I, Elbediwy A, Diaz de la Loza MDC, Fletcher GC, Thompson BJ. Shot and Patronin polarise microtubules to direct membrane traffic and biogenesis of microvilli in epithelia. J Cell Sci 2016; 129:2651-9. [PMID: 27231092 PMCID: PMC4958304 DOI: 10.1242/jcs.189076] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/19/2016] [Indexed: 01/08/2023] Open
Abstract
In epithelial tissues, polarisation of microtubules and actin microvilli occurs along the apical-basal axis of each cell, yet how these cytoskeletal polarisation events are coordinated remains unclear. Here, we examine the hierarchy of events during cytoskeletal polarisation in Drosophila melanogaster epithelia. Core apical-basal polarity determinants polarise the spectrin cytoskeleton to recruit the microtubule-binding proteins Patronin (CAMSAP1, CAMSAP2 and CAMSAP3 in humans) and Shortstop [Shot; MACF1 and BPAG1 (also known as DST) in humans] to the apical membrane domain. Patronin and Shot then act to polarise microtubules along the apical-basal axis to enable apical transport of Rab11 endosomes by the Nuf-Dynein microtubule motor complex. Finally, Rab11 endosomes are transferred to the MyoV (also known as Didum in Drosophila) actin motor to deliver the key microvillar determinant Cadherin 99C to the apical membrane to organise the biogenesis of actin microvilli.
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Affiliation(s)
- Ichha Khanal
- The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Ahmed Elbediwy
- The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | | | | | - Barry J Thompson
- The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
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44
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Wessels HH, Imami K, Baltz AG, Kolinski M, Beldovskaya A, Selbach M, Small S, Ohler U, Landthaler M. The mRNA-bound proteome of the early fly embryo. Genome Res 2016; 26:1000-9. [PMID: 27197210 PMCID: PMC4937569 DOI: 10.1101/gr.200386.115] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 04/26/2016] [Indexed: 12/22/2022]
Abstract
Early embryogenesis is characterized by the maternal to zygotic transition (MZT), in which maternally deposited messenger RNAs are degraded while zygotic transcription begins. Before the MZT, post-transcriptional gene regulation by RNA-binding proteins (RBPs) is the dominant force in embryo patterning. We used two mRNA interactome capture methods to identify RBPs bound to polyadenylated transcripts within the first 2 h of Drosophila melanogaster embryogenesis. We identified a high-confidence set of 476 putative RBPs and confirmed RNA-binding activities for most of 24 tested candidates. Most proteins in the interactome are known RBPs or harbor canonical RBP features, but 99 exhibited previously uncharacterized RNA-binding activity. mRNA-bound RBPs and TFs exhibit distinct expression dynamics, in which the newly identified RBPs dominate the first 2 h of embryonic development. Integrating our resource with in situ hybridization data from existing databases showed that mRNAs encoding RBPs are enriched in posterior regions of the early embryo, suggesting their general importance in posterior patterning and germ cell maturation.
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Affiliation(s)
- Hans-Hermann Wessels
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Koshi Imami
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Alexander G Baltz
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Marcin Kolinski
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | | | - Matthias Selbach
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Stephen Small
- Department of Biology, New York University, New York, New York 10003, USA
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany; Department of Biology, Humboldt University, 10115 Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
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45
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Hoogenraad CC, Akhmanova A. Bicaudal D Family of Motor Adaptors: Linking Dynein Motility to Cargo Binding. Trends Cell Biol 2016; 26:327-340. [PMID: 26822037 DOI: 10.1016/j.tcb.2016.01.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 01/03/2016] [Accepted: 01/04/2016] [Indexed: 01/24/2023]
Abstract
Transport of different intracellular cargoes along cytoskeleton filaments is essential for the morphogenesis and function of a broad variety of eukaryotic cells. Intracellular transport is mediated by cytoskeletal motors including myosin, kinesin, and dynein, which are typically linked to various cargoes by adaptor proteins. Recent studies suggest that adaptor proteins can also act as essential transport cofactors, which control motor activity and coordination. Characterization of the evolutionary conserved Bicaudal D (BICD) family of dynein adaptor proteins has provided important insights into the fundamental mechanisms governing cargo trafficking. This review highlights the advances in the current understanding of how BICD adaptors regulate microtubule-based transport and how they contribute to developmental processes and human disease.
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Affiliation(s)
- Casper C Hoogenraad
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, CH 3584 The Netherlands.
| | - Anna Akhmanova
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, CH 3584 The Netherlands.
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46
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Vagnoni A, Hoffmann PC, Bullock SL. Reducing Lissencephaly-1 levels augments mitochondrial transport and has a protective effect in adult Drosophila neurons. J Cell Sci 2015; 129:178-90. [PMID: 26598558 PMCID: PMC4732301 DOI: 10.1242/jcs.179184] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/17/2015] [Indexed: 12/22/2022] Open
Abstract
Defective transport of mitochondria in axons is implicated in the pathogenesis of several age-associated neurodegenerative diseases. However, the regulation and function of axonal mitochondrial motility during normal ageing is poorly understood. Here, we use novel imaging procedures to characterise axonal transport of these organelles in the adult Drosophila wing nerve. During early adult life there is a boost and progressive decline in the proportion of mitochondria that are motile, which is not due to general changes in cargo transport. Experimental inhibition of the mitochondrial transport machinery specifically in adulthood accelerates the appearance of focal protein accumulations in ageing axons, which is suggestive of defects in protein homeostasis. Unexpectedly, lowering levels of Lissencephaly-1 (Lis1), a dynein motor co-factor, augments axonal mitochondrial transport in ageing wing neurons. Lis1 mutations suppress focal protein accumulations in ageing neurons, including those caused by interfering with the mitochondrial transport machinery. Our data provide new insights into the dynamics of mitochondrial motility in adult neurons in vivo, identify Lis1 as a negative regulator of transport of these organelles, and provide evidence of a link between mitochondrial movement and neuronal protein homeostasis. Summary: Novel imaging procedures in the adult Drosophila wing reveal that Lissencephaly-1 restrains mitochondrial motion and that reducing levels of this protein protects against an age-related decline in protein homeostasis.
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Affiliation(s)
- Alessio Vagnoni
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Patrick C Hoffmann
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Simon L Bullock
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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47
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Jaarsma D, Hoogenraad CC. Cytoplasmic dynein and its regulatory proteins in Golgi pathology in nervous system disorders. Front Neurosci 2015; 9:397. [PMID: 26578860 PMCID: PMC4620150 DOI: 10.3389/fnins.2015.00397] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 10/09/2015] [Indexed: 12/15/2022] Open
Abstract
The Golgi apparatus is a dynamic organelle involved in processing and sorting of lipids and proteins. In neurons, the Golgi apparatus is important for the development of axons and dendrites and maintenance of their highly complex polarized morphology. The motor protein complex cytoplasmic dynein has an important role in Golgi apparatus positioning and function. Together, with dynactin and other regulatory factors it drives microtubule minus-end directed motility of Golgi membranes. Inhibition of dynein results in fragmentation and dispersion of the Golgi ribbon in the neuronal cell body, resembling the Golgi abnormalities observed in some neurodegenerative disorders, in particular motor neuron diseases. Mutations in dynein and its regulatory factors, including the dynactin subunit p150Glued, BICD2 and Lis-1, are associated with several human nervous system disorders, including cortical malformation and motor neuropathy. Here we review the role of dynein and its regulatory factors in Golgi function and positioning, and the potential role of dynein malfunction in causing Golgi apparatus abnormalities in nervous system disorders.
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Affiliation(s)
- Dick Jaarsma
- Department of Neuroscience, Erasmus MC Rotterdam, Netherlands
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48
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Abstract
Until recently, dynein was the least understood of the cytoskeletal motors. However, a wealth of new structural, mechanistic, and cell biological data is shedding light on how this complicated minus-end-directed, microtubule-based motor works. Cytoplasmic dynein-1 performs a wide array of functions in most eukaryotes, both in interphase, in which it transports organelles, proteins, mRNAs, and viruses, and in mitosis and meiosis. Mutations in dynein or its regulators are linked to neurodevelopmental and neurodegenerative diseases. Here, we begin by providing a synthesis of recent data to describe the current model of dynein's mechanochemical cycle. Next, we discuss regulators of dynein, with particular focus on those that directly interact with the motor to modulate its recruitment to microtubules, initiate cargo transport, or activate minus-end-directed motility.
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Affiliation(s)
- Michael A Cianfrocco
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093;
| | - Morgan E DeSantis
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093;
| | - Andres E Leschziner
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093;
| | - Samara L Reck-Peterson
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093;
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49
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Abstract
With the continuing trend to study larger and more complex systems, the application of protein cross-linking coupled with mass spectrometry (XL-MS) provides a varied toolkit perfectly suited to achieve these goals. By freezing the transient interactions through the formation of covalent bonds, XL-MS provides a vital insight into both the structure and organization of proteins in a wide variety of conditions. This review covers some of the established methods that underpin the field alongside the more recent developments that hold promise to further realize its potential in new directions.
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Affiliation(s)
- Andrew N Holding
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
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50
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Baffet AD, Hu DJ, Vallee RB. Cdk1 Activates Pre-mitotic Nuclear Envelope Dynein Recruitment and Apical Nuclear Migration in Neural Stem Cells. Dev Cell 2015; 33:703-16. [PMID: 26051540 DOI: 10.1016/j.devcel.2015.04.022] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 02/20/2015] [Accepted: 04/24/2015] [Indexed: 10/23/2022]
Abstract
Dynein recruitment to the nuclear envelope is required for pre-mitotic nucleus-centrosome interactions in nonneuronal cells and for apical nuclear migration in neural stem cells. In each case, dynein is recruited to the nuclear envelope (NE) specifically during G2 via two nuclear pore-mediated mechanisms involving RanBP2-BicD2 and Nup133-CENP-F. The mechanisms responsible for cell-cycle control of this behavior are unknown. We now find that Cdk1 serves as a direct master controller for NE dynein recruitment in neural stem cells and HeLa cells. Cdk1 phosphorylates conserved sites within RanBP2 and activates BicD2 binding and early dynein recruitment. Late recruitment is triggered by a Cdk1-induced export of CENP-F from the nucleus. Forced NE targeting of BicD2 overrides Cdk1 inhibition, fully rescuing dynein recruitment and nuclear migration in neural stem cells. These results reveal how NE dynein recruitment is cell-cycle regulated and identify the trigger mechanism for apical nuclear migration in the brain.
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Affiliation(s)
- Alexandre D Baffet
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA.
| | - Daniel J Hu
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Richard B Vallee
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA.
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