1
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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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Barr J, Diegmiller R, Colonnetta MM, Ke W, Imran Alsous J, Stern T, Shvartsman SY, Schedl P. To be or not to be: orb, the fusome and oocyte specification in Drosophila. Genetics 2024; 226:iyae020. [PMID: 38345426 PMCID: PMC10990432 DOI: 10.1093/genetics/iyae020] [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: 12/17/2023] [Accepted: 01/21/2024] [Indexed: 04/05/2024] Open
Abstract
In the fruit fly Drosophila melanogaster, two cells in a cyst of 16 interconnected cells have the potential to become the oocyte, but only one of these will assume an oocyte fate as the cysts transition through regions 2a and 2b of the germarium. The mechanism of specification depends on a polarized microtubule network, a dynein dependent Egl:BicD mRNA cargo complex, a special membranous structure called the fusome and its associated proteins, and the translational regulator orb. In this work, we have investigated the role of orb and the fusome in oocyte specification. We show here that specification is a stepwise process. Initially, orb mRNAs accumulate in the two pro-oocytes in close association with the fusome. This association is accompanied by the activation of the orb autoregulatory loop, generating high levels of Orb. Subsequently, orb mRNAs become enriched in only one of the pro-oocytes, the presumptive oocyte, and this is followed, with a delay, by Orb localization to the oocyte. We find that fusome association of orb mRNAs is essential for oocyte specification in the germarium, is mediated by the orb 3' UTR, and requires Orb protein. We also show that the microtubule minus end binding protein Patronin functions downstream of orb in oocyte specification. Finally, in contrast to a previously proposed model for oocyte selection, we find that the choice of which pro-oocyte becomes the oocyte does not seem to be predetermined by the amount of fusome material in these two cells, but instead depends upon a competition for orb gene products.
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Affiliation(s)
- Justinn Barr
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Rocky Diegmiller
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Megan M Colonnetta
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Wenfan Ke
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jasmin Imran Alsous
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Tomer Stern
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Stanislav Y Shvartsman
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Paul Schedl
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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3
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Heber S, McClintock MA, Simon B, Mehtab E, Lapouge K, Hennig J, Bullock SL, Ephrussi A. Tropomyosin 1-I/C coordinates kinesin-1 and dynein motors during oskar mRNA transport. Nat Struct Mol Biol 2024; 31:476-488. [PMID: 38297086 PMCID: PMC10948360 DOI: 10.1038/s41594-024-01212-x] [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: 03/16/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024]
Abstract
Dynein and kinesin motors mediate long-range intracellular transport, translocating towards microtubule minus and plus ends, respectively. Cargoes often undergo bidirectional transport by binding to both motors simultaneously. However, it is not known how motor activities are coordinated in such circumstances. In the Drosophila female germline, sequential activities of the dynein-dynactin-BicD-Egalitarian (DDBE) complex and of kinesin-1 deliver oskar messenger RNA from nurse cells to the oocyte, and within the oocyte to the posterior pole. We show through in vitro reconstitution that Tm1-I/C, a tropomyosin-1 isoform, links kinesin-1 in a strongly inhibited state to DDBE-associated oskar mRNA. Nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and structural modeling indicate that Tm1-I/C suppresses kinesin-1 activity by stabilizing its autoinhibited conformation, thus preventing competition with dynein until kinesin-1 is activated in the oocyte. Our work reveals a new strategy for ensuring sequential activity of microtubule motors.
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Affiliation(s)
- Simone Heber
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mark A McClintock
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
| | - Eve Mehtab
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Karine Lapouge
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Bayreuth, Germany
| | - Simon L Bullock
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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4
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Badieyan S, Lichon D, Andreas MP, Gillies JP, Peng W, Shi J, DeSantis ME, Aiken CR, Böcking T, Giessen TW, Campbell EM, Cianfrocco MA. HIV-1 binds dynein directly to hijack microtubule transport machinery. bioRxiv 2023:2023.08.29.555335. [PMID: 37693451 PMCID: PMC10491134 DOI: 10.1101/2023.08.29.555335] [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: 09/12/2023]
Abstract
Viruses exploit host cytoskeletal elements and motor proteins for trafficking through the dense cytoplasm. Yet the molecular mechanism that describes how viruses connect to the motor machinery is unknown. Here, we demonstrate the first example of viral microtubule trafficking from purified components: HIV-1 hijacking microtubule transport machinery. We discover that HIV-1 directly binds to the retrograde microtubule-associated motor, dynein, and not via a cargo adaptor, as previously suggested. Moreover, we show that HIV-1 motility is supported by multiple, diverse dynein cargo adaptors as HIV-1 binds to dynein light and intermediate chains on dynein's tail. Further, we demonstrate that multiple dynein motors tethered to rigid cargoes, like HIV-1 capsids, display reduced motility, distinct from the behavior of multiple motors on membranous cargoes. Our results introduce a new model of viral trafficking wherein a pathogen opportunistically 'hijacks' the microtubule transport machinery for motility, enabling multiple transport pathways through the host cytoplasm.
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Affiliation(s)
| | - Drew Lichon
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, IL, USA
| | - Michael P Andreas
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - John P Gillies
- Department of Molecular, Cellular, and Developmental Biology, College of Literature, Sciences, and the Arts, University of Michigan, Ann Arbor, MI USA
| | - Wang Peng
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Jiong Shi
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Morgan E DeSantis
- Department of Molecular, Cellular, and Developmental Biology, College of Literature, Sciences, and the Arts, University of Michigan, Ann Arbor, MI USA
| | - Christopher R Aiken
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Till Böcking
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Tobias W Giessen
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Edward M Campbell
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, IL, USA
| | - Michael A Cianfrocco
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
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5
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Madan V, Albacete‐Albacete L, Jin L, Scaturro P, Watson JL, Muschalik N, Begum F, Boulanger J, Bauer K, Kiebler MA, Derivery E, Bullock SL. HEATR5B associates with dynein-dynactin and promotes motility of AP1-bound endosomal membranes. EMBO J 2023; 42:e114473. [PMID: 37872872 PMCID: PMC10690479 DOI: 10.15252/embj.2023114473] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/09/2023] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 10/25/2023] Open
Abstract
The microtubule motor dynein mediates polarised trafficking of a wide variety of organelles, vesicles and macromolecules. These functions are dependent on the dynactin complex, which helps recruit cargoes to dynein's tail and activates motor movement. How the dynein-dynactin complex orchestrates trafficking of diverse cargoes is unclear. Here, we identify HEATR5B, an interactor of the adaptor protein-1 (AP1) clathrin adaptor complex, as a novel player in dynein-dynactin function. HEATR5B was recovered in a biochemical screen for proteins whose association with the dynein tail is augmented by dynactin. We show that HEATR5B binds directly to the dynein tail and dynactin and stimulates motility of AP1-associated endosomal membranes in human cells. We also demonstrate that the Drosophila HEATR5B homologue is an essential gene that selectively promotes dynein-based transport of AP1-bound membranes to the Golgi apparatus. As HEATR5B lacks the coiled-coil architecture typical of dynein adaptors, our data point to a non-canonical process orchestrating motor function on a specific cargo. We additionally show that HEATR5B promotes association of AP1 with endosomal membranes independently of dynein. Thus, HEATR5B co-ordinates multiple events in AP1-based trafficking.
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Affiliation(s)
- Vanesa Madan
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
- Present address:
AbcamCambridgeUK
| | - Lucas Albacete‐Albacete
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Li Jin
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | | | - Joseph L Watson
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
- Present address:
Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | - Nadine Muschalik
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Farida Begum
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Jérôme Boulanger
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Karl Bauer
- Biomedical Center, Department for Cell Biology, Medical FacultyLudwig‐Maximilians‐University of MunichMunichGermany
| | - Michael A Kiebler
- Biomedical Center, Department for Cell Biology, Medical FacultyLudwig‐Maximilians‐University of MunichMunichGermany
| | - Emmanuel Derivery
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Simon L Bullock
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
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6
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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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7
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Lu W, Lakonishok M, Gelfand VI. The dynamic duo of microtubule polymerase Mini spindles/XMAP215 and cytoplasmic dynein is essential for maintaining Drosophila oocyte fate. Proc Natl Acad Sci U S A 2023; 120:e2303376120. [PMID: 37722034 PMCID: PMC10523470 DOI: 10.1073/pnas.2303376120] [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: 02/27/2023] [Accepted: 07/11/2023] [Indexed: 09/20/2023] Open
Abstract
In many species, only one oocyte is specified among a group of interconnected germline sister cells. In Drosophila melanogaster, 16 interconnected cells form a germline cyst, where one cell differentiates into an oocyte, while the rest become nurse cells that supply the oocyte with mRNAs, proteins, and organelles through intercellular cytoplasmic bridges named ring canals via microtubule-based transport. In this study, we find that a microtubule polymerase Mini spindles (Msps), the Drosophila homolog of XMAP215, is essential for maintenance of the oocyte specification. mRNA encoding Msps is transported and concentrated in the oocyte by dynein-dependent transport along microtubules. Translated Msps stimulates microtubule polymerization in the oocyte, causing more microtubule plus ends to grow from the oocyte through the ring canals into nurse cells, further enhancing nurse cell-to-oocyte transport by dynein. Knockdown of msps blocks the oocyte growth and causes gradual loss of oocyte determinants. Thus, the Msps-dynein duo creates a positive feedback loop, ensuring oocyte fate maintenance by promoting high microtubule polymerization activity in the oocyte, and enhancing dynein-dependent nurse cell-to-oocyte transport.
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Affiliation(s)
- Wen Lu
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Margot Lakonishok
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Vladimir I. Gelfand
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
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8
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Coscarella IL, Landim-Vieira M, Rastegarpouyani H, Chase PB, Irianto J, Pinto JR. Nucleus Mechanosensing in Cardiomyocytes. Int J Mol Sci 2023; 24:13341. [PMID: 37686151 PMCID: PMC10487505 DOI: 10.3390/ijms241713341] [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: 07/14/2023] [Revised: 08/20/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Cardiac muscle contraction is distinct from the contraction of other muscle types. The heart continuously undergoes contraction-relaxation cycles throughout an animal's lifespan. It must respond to constantly varying physical and energetic burdens over the short term on a beat-to-beat basis and relies on different mechanisms over the long term. Muscle contractility is based on actin and myosin interactions that are regulated by cytoplasmic calcium ions. Genetic variants of sarcomeric proteins can lead to the pathophysiological development of cardiac dysfunction. The sarcomere is physically connected to other cytoskeletal components. Actin filaments, microtubules and desmin proteins are responsible for these interactions. Therefore, mechanical as well as biochemical signals from sarcomeric contractions are transmitted to and sensed by other parts of the cardiomyocyte, particularly the nucleus which can respond to these stimuli. Proteins anchored to the nuclear envelope display a broad response which remodels the structure of the nucleus. In this review, we examine the central aspects of mechanotransduction in the cardiomyocyte where the transmission of mechanical signals to the nucleus can result in changes in gene expression and nucleus morphology. The correlation of nucleus sensing and dysfunction of sarcomeric proteins may assist the understanding of a wide range of functional responses in the progress of cardiomyopathic diseases.
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Affiliation(s)
| | - Maicon Landim-Vieira
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Hosna Rastegarpouyani
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
- Institute for Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Prescott Bryant Chase
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jerome Irianto
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Jose Renato Pinto
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306, USA
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9
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Salvador-Garcia D, Jin L, Hensley A, Gölcük M, Gallaud E, Chaaban S, Port F, Vagnoni A, Planelles-Herrero VJ, McClintock MA, Derivery E, Carter AP, Giet R, Gür M, Yildiz A, Bullock SL. A force-sensitive mutation reveals a spindle assembly checkpoint-independent role for dynein in anaphase progression. bioRxiv 2023:2023.08.03.551815. [PMID: 37577480 PMCID: PMC10418259 DOI: 10.1101/2023.08.03.551815] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The cytoplasmic dynein-1 (dynein) motor organizes cells by shaping microtubule networks and moving a large variety of cargoes along them. However, dynein's diverse roles complicate in vivo studies of its functions significantly. To address this issue, we have used gene editing to generate a series of missense mutations in Drosophila Dynein heavy chain (Dhc). We find that mutations associated with human neurological disease cause a range of defects in larval and adult flies, including impaired cargo trafficking in neurons. We also describe a novel mutation in the microtubule-binding domain (MTBD) of Dhc that, remarkably, causes metaphase arrest of mitotic spindles in the embryo but does not impair other dynein-dependent processes. We demonstrate that the mitotic arrest is independent of dynein's well-established roles in silencing the spindle assembly checkpoint. In vitro reconstitution and optical trapping assays reveal that the mutation only impairs the performance of dynein under load. In silico all-atom molecular dynamics simulations show that this effect correlates with increased flexibility of the MTBD, as well as an altered orientation of the stalk domain, with respect to the microtubule. Collectively, our data point to a novel role of dynein in anaphase progression that depends on the motor operating in a specific load regime. More broadly, our work illustrates how cytoskeletal transport processes can be dissected in vivo by manipulating mechanical properties of motors.
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Affiliation(s)
| | - Li Jin
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Andrew Hensley
- Department of Physics, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Mert Gölcük
- Department of Mechanical Engineering, Istanbul Technical University, Istanbul, 34437, Turkey
| | - Emmanuel Gallaud
- Institut de Génétique et Développement de Rennes - UMR 6290, Université de Rennes, F-35000 Rennes, France
| | - Sami Chaaban
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Fillip Port
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
- Current address: Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Alessio Vagnoni
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
- Current address: Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, SE5 9RX, UK
| | | | - Mark A. McClintock
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Emmanuel Derivery
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Andrew P. Carter
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Régis Giet
- Institut de Génétique et Développement de Rennes - UMR 6290, Université de Rennes, F-35000 Rennes, France
| | - Mert Gür
- Department of Mechanical Engineering, Istanbul Technical University, Istanbul, 34437, Turkey
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ahmet Yildiz
- Department of Physics, University of California at Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cellular Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Simon L. Bullock
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
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10
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Hildebrandt RP, Moss KR, Janusz-Kaminska A, Knudson LA, Denes LT, Saxena T, Boggupalli DP, Li Z, Lin K, Bassell GJ, Wang ET. Muscleblind-like proteins use modular domains to localize RNAs by riding kinesins and docking to membranes. Nat Commun 2023; 14:3427. [PMID: 37296096 PMCID: PMC10256740 DOI: 10.1038/s41467-023-38923-6] [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: 08/23/2022] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
RNA binding proteins (RBPs) act as critical facilitators of spatially regulated gene expression. Muscleblind-like (MBNL) proteins, implicated in myotonic dystrophy and cancer, localize RNAs to myoblast membranes and neurites through unknown mechanisms. We find that MBNL forms motile and anchored granules in neurons and myoblasts, and selectively associates with kinesins Kif1bα and Kif1c through its zinc finger (ZnF) domains. Other RBPs with similar ZnFs associate with these kinesins, implicating a motor-RBP specificity code. MBNL and kinesin perturbation leads to widespread mRNA mis-localization, including depletion of Nucleolin transcripts from neurites. Live cell imaging and fractionation reveal that the unstructured carboxy-terminal tail of MBNL1 allows for anchoring at membranes. An approach, termed RBP Module Recruitment and Imaging (RBP-MRI), reconstitutes kinesin- and membrane-recruitment functions using MBNL-MS2 coat protein fusions. Our findings decouple kinesin association, RNA binding, and membrane anchoring functions of MBNL while establishing general strategies for studying multi-functional, modular domains of RBPs.
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Affiliation(s)
- Ryan P Hildebrandt
- Department of Molecular Genetics & Microbiology, Center for Neurogenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Kathryn R Moss
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Luke A Knudson
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Lance T Denes
- Department of Molecular Genetics & Microbiology, Center for Neurogenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Tanvi Saxena
- Department of Molecular Genetics & Microbiology, Center for Neurogenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Devi Prasad Boggupalli
- Department of Molecular Genetics & Microbiology, Center for Neurogenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Zhuangyue Li
- Department of Molecular Genetics & Microbiology, Center for Neurogenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Kun Lin
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA.
| | - Eric T Wang
- Department of Molecular Genetics & Microbiology, Center for Neurogenetics, Genetics Institute, University of Florida, Gainesville, FL, USA.
- Myology Institute, University of Florida, Gainesville, FL, USA.
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11
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Neiswender H, Baker FC, Veeranan-Karmegam R, Allen P, Gonsalvez GB. dTtc1, a conserved tetratricopeptide repeat protein, is required for maturation of Drosophila egg chambers via its role in stabilizing electron transport chain components. Front Cell Dev Biol 2023; 11:1148773. [PMID: 37333987 PMCID: PMC10272552 DOI: 10.3389/fcell.2023.1148773] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/18/2023] [Indexed: 06/20/2023] Open
Abstract
We recently identified the Drosophila ortholog of TTC1 (dTtc1) as an interacting partner of Egalitarian, an RNA adaptor of the Dynein motor. In order to better understand the function of this relatively uncharacterized protein, we depleted dTtc1 in the Drosophila female germline. Depletion of dTtc1 resulted in defective oogenesis and no mature eggs were produced. A closer examination revealed that mRNA cargoes normally transported by Dynein were relatively unaffected. However, mitochondria in dTtc1 depleted egg chambers displayed an extremely swollen phenotype. Ultrastructural analysis revealed a lack of cristae. These phenotypes were not observed upon disruption of Dynein. Thus, this function of dTtc1 is likely to be Dynein independent. Consistent with a role for dTtc1 in mitochondrial biology, a published proteomics screen revealed that dTtc1 interacts with numerous components of electron transport chain (ETC) complexes. Our results indicate that the expression level of several of these ETC components was significantly reduced upon depletion of dTtc1. Importantly, this phenotype was completely rescued upon expression of wild-type GFP-dTtc1 in the depleted background. Lastly, we demonstrate that the mitochondrial phenotype caused by a lack of dTtc1 is not restricted to the germline but is also observed in somatic tissues. Our model suggests that dTtc1, likely in combination with cytoplasmic chaperones, is required for stabilizing ETC components.
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12
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Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24:430-447. [PMID: 36596869 PMCID: PMC10213152 DOI: 10.1038/s41580-022-00566-8] [Citation(s) in RCA: 306] [Impact Index Per Article: 306.0] [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] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia.
| | - Paulo P Amaral
- INSPER Institute of Education and Research, São Paulo, Brazil
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling-Ling Chen
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra, Pamplona, Spain
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua T Mendell
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Kathryn J Moore
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - David L Spector
- Cold Spring Harbour Laboratory, Cold Spring Harbour, NY, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yue Wan
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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13
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Lu W, Lakonishok M, Gelfand VI. Drosophila oocyte specification is maintained by the dynamic duo of microtubule polymerase Mini spindles/XMAP215 and dynein. bioRxiv 2023:2023.03.09.531953. [PMID: 36945460 PMCID: PMC10028982 DOI: 10.1101/2023.03.09.531953] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
In many species, only one oocyte is specified among a group of interconnected germline sister cells. In Drosophila melanogaster , 16-cell interconnected cells form a germline cyst, where one cell differentiates into an oocyte, while the rest become nurse cells that supply the oocyte with mRNAs, proteins, and organelles through intercellular cytoplasmic bridges named ring canals via microtubule-based transport. In this study, we find that a microtubule polymerase Mini spindles (Msps), the Drosophila homolog of XMAP215, is essential for the oocyte fate determination. mRNA encoding Msps is concentrated in the oocyte by dynein-dependent transport along microtubules. Translated Msps stimulates microtubule polymerization in the oocyte, causing more microtubule plus ends to grow from the oocyte through the ring canals into nurse cells, further enhancing nurse cell-to-oocyte transport by dynein. Knockdown of msps blocks the oocyte growth and causes gradual loss of oocyte determinants. Thus, the Msps-dynein duo creates a positive feedback loop, enhancing dynein-dependent nurse cell-to-oocyte transport and transforming a small stochastic difference in microtubule polarity among sister cells into a clear oocyte fate determination. Significance statement Oocyte determination in Drosophila melanogaster provides a valuable model for studying cell fate specification. We describe the crucial role of the duo of microtubule polymerase Mini spindles (Msps) and cytoplasmic dynein in this process. We show that Msps is essential for oocyte fate determination. Msps concentration in the oocyte is achieved through dynein-dependent transport of msps mRNA along microtubules. Translated Msps stimulates microtubule polymerization in the oocyte, further enhancing nurse cell-to-oocyte transport by dynein. This creates a positive feedback loop that transforms a small stochastic difference in microtubule polarity among sister cells into a clear oocyte fate determination. Our findings provide important insights into the mechanisms of oocyte specification and have implications for understanding the development of multicellular organisms.
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Affiliation(s)
- Wen Lu
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Margot Lakonishok
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Vladimir I Gelfand
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
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14
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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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15
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Sloan DB, Warren JM, Williams AM, Kuster SA, Forsythe ES. Incompatibility and Interchangeability in Molecular Evolution. Genome Biol Evol 2023; 15:evac184. [PMID: 36583227 PMCID: PMC9839398 DOI: 10.1093/gbe/evac184] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
There is remarkable variation in the rate at which genetic incompatibilities in molecular interactions accumulate. In some cases, minor changes-even single-nucleotide substitutions-create major incompatibilities when hybridization forces new variants to function in a novel genetic background from an isolated population. In other cases, genes or even entire functional pathways can be horizontally transferred between anciently divergent evolutionary lineages that span the tree of life with little evidence of incompatibilities. In this review, we explore whether there are general principles that can explain why certain genes are prone to incompatibilities while others maintain interchangeability. We summarize evidence pointing to four genetic features that may contribute to greater resistance to functional replacement: (1) function in multisubunit enzyme complexes and protein-protein interactions, (2) sensitivity to changes in gene dosage, (3) rapid rate of sequence evolution, and (4) overall importance to cell viability, which creates sensitivity to small perturbations in molecular function. We discuss the relative levels of support for these different hypotheses and lay out future directions that may help explain the striking contrasts in patterns of incompatibility and interchangeability throughout the history of molecular evolution.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, Colorado
| | - Jessica M Warren
- Center for Mechanisms of Evolution, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Alissa M Williams
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee
| | - Shady A Kuster
- Department of Biology, Colorado State University, Fort Collins, Colorado
| | - Evan S Forsythe
- Department of Biology, Colorado State University, Fort Collins, Colorado
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16
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Hees JT, Harbauer AB. Metabolic Regulation of Mitochondrial Protein Biogenesis from a Neuronal Perspective. Biomolecules 2022; 12:1595. [PMID: 36358945 PMCID: PMC9687362 DOI: 10.3390/biom12111595] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 09/07/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 09/29/2023] Open
Abstract
Neurons critically depend on mitochondria for ATP production and Ca2+ buffering. They are highly compartmentalized cells and therefore a finely tuned mitochondrial network constantly adapting to the local requirements is necessary. For neuronal maintenance, old or damaged mitochondria need to be degraded, while the functional mitochondrial pool needs to be replenished with freshly synthesized components. Mitochondrial biogenesis is known to be primarily regulated via the PGC-1α-NRF1/2-TFAM pathway at the transcriptional level. However, while transcriptional regulation of mitochondrial genes can change the global mitochondrial content in neurons, it does not explain how a morphologically complex cell such as a neuron adapts to local differences in mitochondrial demand. In this review, we discuss regulatory mechanisms controlling mitochondrial biogenesis thereby making a case for differential regulation at the transcriptional and translational level. In neurons, additional regulation can occur due to the axonal localization of mRNAs encoding mitochondrial proteins. Hitchhiking of mRNAs on organelles including mitochondria as well as contact site formation between mitochondria and endolysosomes are required for local mitochondrial biogenesis in axons linking defects in any of these organelles to the mitochondrial dysfunction seen in various neurological disorders.
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Affiliation(s)
- Jara Tabitha Hees
- TUM Medical Graduate Center, Technical University of Munich, 81675 Munich, Germany
- Max Planck Institute for Biological Intelligence, in Foundation, 82152 Planegg-Martinsried, Germany
| | - Angelika Bettina Harbauer
- Max Planck Institute for Biological Intelligence, in Foundation, 82152 Planegg-Martinsried, Germany
- Institute of Neuronal Cell Biology, Technical University of Munich, 80802 Munich, Germany
- Munich Cluster for Systems Neurology, 81377 Munich, Germany
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17
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Abstract
Cytoplasmic dynein is a microtubule motor that is activated by its cofactor dynactin and a coiled-coil cargo adaptor1-3. Up to two dynein dimers can be recruited per dynactin, and interactions between them affect their combined motile behaviour4-6. Different coiled-coil adaptors are linked to different cargos7,8, and some share motifs known to contact sites on dynein and dynactin4,9-13. There is limited structural information on how the resulting complex interacts with microtubules and how adaptors are recruited. Here we develop a cryo-electron microscopy processing pipeline to solve the high-resolution structure of dynein-dynactin and the adaptor BICDR1 bound to microtubules. This reveals the asymmetric interactions between neighbouring dynein motor domains and how they relate to motile behaviour. We found that two adaptors occupy the complex. Both adaptors make similar interactions with the dyneins but diverge in their contacts with each other and dynactin. Our structure has implications for the stability and stoichiometry of motor recruitment by cargos.
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Affiliation(s)
- Sami Chaaban
- Division of Structural Studies, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Andrew P Carter
- Division of Structural Studies, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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18
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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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19
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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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20
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Vargas JNS, Sleigh JN, Schiavo G. Coupling axonal mRNA transport and local translation to organelle maintenance and function. Curr Opin Cell Biol 2022; 74:97-103. [PMID: 35220080 PMCID: PMC10477965 DOI: 10.1016/j.ceb.2022.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 12/01/2021] [Revised: 01/14/2022] [Accepted: 01/22/2022] [Indexed: 12/14/2022]
Abstract
Neuronal homeostasis requires the transport of various organelles to distal compartments and defects in this process lead to neurological disorders. Although several mechanisms for the delivery of organelles to axons and dendrites have been elucidated, exactly how this process is orchestrated is not well-understood. In this review, we discuss the recent literature supporting a novel paradigm - the co-shuttling of mRNAs with different membrane-bound organelles. This model postulates that the tethering of ribonucleoprotein complexes to endolysosomes and mitochondria allows for the spatiotemporal coupling of organelle transport and the delivery of transcripts to axons. Subcellular translation of these "hitchhiking" transcripts may thus provide a proximal source of proteins required for the maintenance and function of organelles in axons.
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Affiliation(s)
- Jose Norberto S Vargas
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, UK; UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, University College London, London, UK; UK Dementia Research Institute, University College London, London, UK
| | - James N Sleigh
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, UK; UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, University College London, London, UK; UK Dementia Research Institute, University College London, London, UK
| | - Giampietro Schiavo
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, UK; UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, University College London, London, UK; UK Dementia Research Institute, University College London, London, UK.
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21
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Fu X, Rao L, Li P, Liu X, Wang Q, Son AI, Gennerich A, Liu JSH. Doublecortin and JIP3 are neural-specific counteracting regulators of dynein-mediated retrograde trafficking. eLife 2022; 11:82218. [PMID: 36476638 PMCID: PMC9799976 DOI: 10.7554/elife.82218] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022] Open
Abstract
Mutations in the microtubule (MT)-binding protein doublecortin (DCX) or in the MT-based molecular motor dynein result in lissencephaly. However, a functional link between DCX and dynein has not been defined. Here, we demonstrate that DCX negatively regulates dynein-mediated retrograde transport in neurons from Dcx-/y or Dcx-/y;Dclk1-/- mice by reducing dynein's association with MTs and disrupting the composition of the dynein motor complex. Previous work showed an increased binding of the adaptor protein C-Jun-amino-terminal kinase-interacting protein 3 (JIP3) to dynein in the absence of DCX. Using purified components, we demonstrate that JIP3 forms an active motor complex with dynein and its cofactor dynactin with two dyneins per complex. DCX competes with the binding of the second dynein, resulting in a velocity reduction of the complex. We conclude that DCX negatively regulates dynein-mediated retrograde transport through two critical interactions by regulating dynein binding to MTs and regulating the composition of the dynein motor complex.
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Affiliation(s)
- Xiaoqin Fu
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical UniversityWenzhouChina,Key Laboratory of Structural Malformations in Children of Zhejiang ProvinceWenzhouChina,Key Laboratory of Perinatal Medicine of WenzhouWenzhouChina
| | - Lu Rao
- Department of Biochemistry and Gruss-Lipper Biophotonics Center, Albert Einstein College of MedicineBronxUnited States
| | - Peijun Li
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical UniversityWenzhouChina,Key Laboratory of Structural Malformations in Children of Zhejiang ProvinceWenzhouChina,Key Laboratory of Perinatal Medicine of WenzhouWenzhouChina
| | - Xinglei Liu
- Department of Biochemistry and Gruss-Lipper Biophotonics Center, Albert Einstein College of MedicineBronxUnited States
| | - Qi Wang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical UniversityWenzhouChina
| | - Alexander I Son
- Center for Neuroscience Research, Children's National Research Institute, Children's National HospitalWashingtonUnited States
| | - Arne Gennerich
- Department of Biochemistry and Gruss-Lipper Biophotonics Center, Albert Einstein College of MedicineBronxUnited States
| | - Judy Shih-Hwa Liu
- Department of Neurology, Department of Molecular Biology, Cell Biology, and Biochemistry, Brown UniversityProvidenceUnited States
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22
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O'Connell LC, Mowry KL. Regulation of spatially restricted gene expression: linking RNA localization and phase separation. Biochem Soc Trans 2021; 49:2591-600. [PMID: 34821361 DOI: 10.1042/BST20210320] [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: 08/16/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/17/2022]
Abstract
Subcellular restriction of gene expression is crucial to the functioning of a wide variety of cell types. The cellular machinery driving spatially restricted gene expression has been studied for many years, but recent advances have highlighted novel mechanisms by which cells can generate subcellular microenvironments with specialized gene expression profiles. Particularly intriguing are recent findings that phase separation plays a role in certain RNA localization pathways. The burgeoning field of phase separation has revolutionized how we view cellular compartmentalization, revealing that, in addition to membrane-bound organelles, phase-separated cytoplasmic microenvironments - termed biomolecular condensates - are compositionally and functionally distinct from the surrounding cytoplasm, without the need for a lipid membrane. The coupling of phase separation and RNA localization allows for precise subcellular targeting, robust translational repression and dynamic recruitment of accessory proteins. Despite the growing interest in the intersection between RNA localization and phase separation, it remains to be seen how exactly components of the localization machinery, particularly motor proteins, are able to associate with these biomolecular condensates. Further studies of the formation, function, and transport of biomolecular condensates promise to provide a new mechanistic understanding of how cells restrict gene expression at a subcellular level.
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23
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Baker FC, Neiswender H, Veeranan-Karmegam R, Gonsalvez GB. In vivo proximity biotin ligation identifies the interactome of Egalitarian, a Dynein cargo adaptor. Development 2021; 148:273472. [DOI: 10.1242/dev.199935] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/18/2021] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Numerous motors of the Kinesin family contribute to plus-end-directed microtubule transport. However, almost all transport towards the minus-end of microtubules involves Dynein. Understanding the mechanism by which Dynein transports this vast diversity of cargo is the focus of intense research. In selected cases, adaptors that link a particular cargo with Dynein have been identified. However, the sheer diversity of cargo suggests that additional adaptors must exist. We used the Drosophila egg chamber as a model to address this issue. Within egg chambers, Egalitarian is required for linking mRNA with Dynein. However, in the absence of Egalitarian, Dynein transport into the oocyte is severely compromised. This suggests that additional cargoes might be linked to Dynein in an Egalitarian-dependent manner. We therefore used proximity biotin ligation to define the interactome of Egalitarian. This approach yielded several novel interacting partners, including P body components and proteins that associate with Dynein in mammalian cells. We also devised and validated a nanobody-based proximity biotinylation strategy that can be used to define the interactome of any GFP-tagged protein.
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Affiliation(s)
- Frederick C. Baker
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA
| | - Hannah Neiswender
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA
| | - Rajalakshmi Veeranan-Karmegam
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA
| | - Graydon B. Gonsalvez
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA
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24
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Müntjes K, Devan SK, Reichert AS, Feldbrügge M. Linking transport and translation of mRNAs with endosomes and mitochondria. EMBO Rep 2021; 22:e52445. [PMID: 34402186 PMCID: PMC8490996 DOI: 10.15252/embr.202152445] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 01/12/2021] [Revised: 07/06/2021] [Accepted: 07/27/2021] [Indexed: 01/01/2023] Open
Abstract
In eukaryotic cells, proteins are targeted to their final subcellular locations with precise timing. A key underlying mechanism is the active transport of cognate mRNAs, which in many systems can be linked intimately to membrane trafficking. A prominent example is the long-distance endosomal transport of mRNAs and their local translation. Here, we describe current highlights of fundamental mechanisms of the underlying transport process as well as of biological functions ranging from endosperm development in plants to fungal pathogenicity and neuronal processes. Translation of endosome-associated mRNAs often occurs at the cytoplasmic surface of endosomes, a process that is needed for membrane-assisted formation of heteromeric protein complexes and for accurate subcellular targeting of proteins. Importantly, endosome-coupled translation of mRNAs encoding mitochondrial proteins, for example, seems to be particularly important for efficient organelle import and for regulating subcellular mitochondrial activity. In essence, these findings reveal a new mechanism of loading newly synthesised proteins onto endocytic membranes enabling intimate crosstalk between organelles. The novel link between endosomes and mitochondria adds an inspiring new level of complexity to trafficking and organelle biology.
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Affiliation(s)
- Kira Müntjes
- Institute of MicrobiologyCluster of Excellence on Plant SciencesHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Senthil Kumar Devan
- Institute of MicrobiologyCluster of Excellence on Plant SciencesHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Andreas S Reichert
- Institute of Biochemistry and Molecular Biology IMedical Faculty and University Hospital DüsseldorfHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Michael Feldbrügge
- Institute of MicrobiologyCluster of Excellence on Plant SciencesHeinrich Heine University DüsseldorfDüsseldorfGermany
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25
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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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26
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Lang B, Yang JS, Garriga-Canut M, Speroni S, Aschern M, Gili M, Hoffmann T, Tartaglia GG, Maurer SP. Matrix-screening reveals a vast potential for direct protein-protein interactions among RNA binding proteins. Nucleic Acids Res 2021; 49:6702-6721. [PMID: 34133714 PMCID: PMC8266617 DOI: 10.1093/nar/gkab490] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 04/23/2021] [Accepted: 05/20/2021] [Indexed: 01/02/2023] Open
Abstract
RNA-binding proteins (RBPs) are crucial factors of post-transcriptional gene regulation and their modes of action are intensely investigated. At the center of attention are RNA motifs that guide where RBPs bind. However, sequence motifs are often poor predictors of RBP-RNA interactions in vivo. It is hence believed that many RBPs recognize RNAs as complexes, to increase specificity and regulatory possibilities. To probe the potential for complex formation among RBPs, we assembled a library of 978 mammalian RBPs and used rec-Y2H matrix screening to detect direct interactions between RBPs, sampling > 600 K interactions. We discovered 1994 new interactions and demonstrate that interacting RBPs bind RNAs adjacently in vivo. We further find that the mRNA binding region and motif preferences of RBPs deviate, depending on their adjacently binding interaction partners. Finally, we reveal novel RBP interaction networks among major RNA processing steps and show that splicing impairing RBP mutations observed in cancer rewire spliceosomal interaction networks. The dataset we provide will be a valuable resource for understanding the combinatorial interactions of RBPs with RNAs and the resulting regulatory outcomes.
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Affiliation(s)
- Benjamin Lang
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, Barcelona 08003, Spain.,Department of Structural Biology and Center of Excellence for Data-Driven Discovery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jae-Seong Yang
- Centre de Recerca en Agrigenòmica, Consortium CSIC-IRTA-UAB-UB (CRAG), Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Mireia Garriga-Canut
- Division of Engineering, New York University Abu Dhabi (NYUAD), Abu Dhabi 129188, UAE
| | - Silvia Speroni
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, Barcelona 08003, Spain
| | - Moritz Aschern
- Centre de Recerca en Agrigenòmica, Consortium CSIC-IRTA-UAB-UB (CRAG), Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Maria Gili
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, Barcelona 08003, Spain
| | - Tobias Hoffmann
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, Barcelona 08003, Spain
| | - Gian Gaetano Tartaglia
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152, Genoa, Italy.,Biology and Biotechnology Department "Charles Darwin", Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Sebastian P Maurer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Department of Experimental and Health Sciences, Barcelona, Spain
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27
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Neiswender H, Goldman CH, Veeranan-Karmegam R, Gonsalvez GB. Dynein light chain-dependent dimerization of Egalitarian is essential for maintaining oocyte fate in Drosophila. Dev Biol 2021; 478:76-88. [PMID: 34181915 DOI: 10.1016/j.ydbio.2021.06.009] [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] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/02/2021] [Accepted: 06/17/2021] [Indexed: 11/28/2022]
Abstract
Egalitarian (Egl) is an RNA adaptor for the Dynein motor and is thought to link numerous, perhaps hundreds, of mRNAs with Dynein. Dynein, in turn, is responsible for the transport and localization of these mRNAs. Studies have shown that efficient mRNA binding by Egl requires the protein to dimerize. We recently demonstrated that Dynein light chain (Dlc) is responsible for facilitating the dimerization of Egl. Mutations in Egl that fail to interact with Dlc do not dimerize, and as such, are defective for mRNA binding. Consequently, this mutant does not efficiently associate with BicaudalD (BicD), the factor responsible for linking the Egl/mRNA complex with Dynein. In this report, we tested whether artificially dimerizing this Dlc-binding mutant using a leucine zipper would restore mRNA binding and rescue mutant phenotypes in vivo. Interestingly, we found that although artificial dimerization of Egl restored BicD binding, it only partially restored mRNA binding. As a result, Egl-dependent phenotypes, such as oocyte specification and mRNA localization, were only partially rescued. We hypothesize that Dlc-mediated dimerization of Egl results in a three-dimensional conformation of the Egl dimer that is best suited for mRNA binding. Although the leucine zipper restores Egl dimerization, it likely does not enable Egl to assemble into the conformation required for maximal mRNA binding activity.
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Affiliation(s)
- Hannah Neiswender
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA, 30912, USA
| | - Chandler H Goldman
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA, 30912, USA
| | - Rajalakshmi Veeranan-Karmegam
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA, 30912, USA
| | - Graydon B Gonsalvez
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA, 30912, USA.
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28
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Rodrigues EC, Grawenhoff J, Baumann SJ, Lorenzon N, Maurer SP. Mammalian Neuronal mRNA Transport Complexes: The Few Knowns and the Many Unknowns. Front Integr Neurosci 2021; 15:692948. [PMID: 34211375 PMCID: PMC8239176 DOI: 10.3389/fnint.2021.692948] [Citation(s) in RCA: 11] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Hundreds of messenger RNAs (mRNAs) are transported into neurites to provide templates for the assembly of local protein networks. These networks enable a neuron to configure different cellular domains for specialized functions. According to current evidence, mRNAs are mostly transported in rather small packages of one to three copies, rarely containing different transcripts. This opens up fascinating logistic problems: how are hundreds of different mRNA cargoes sorted into distinct packages and how are they coupled to and released from motor proteins to produce the observed mRNA distributions? Are all mRNAs transported by the same transport machinery, or are there different adaptors or motors for different transcripts or classes of mRNAs? A variety of often indirect evidence exists for the involvement of proteins in mRNA localization, but relatively little is known about the essential activities required for the actual transport process. Here, we summarize the different types of available evidence for interactions that connect mammalian mRNAs to motor proteins to highlight at which point further research is needed to uncover critical missing links. We further argue that a combination of discovery approaches reporting direct interactions, in vitro reconstitution, and fast perturbations in cells is an ideal future strategy to unravel essential interactions and specific functions of proteins in mRNA transport processes.
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Affiliation(s)
- Elsa C. Rodrigues
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Julia Grawenhoff
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Sebastian J. Baumann
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Nicola Lorenzon
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Sebastian P. Maurer
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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29
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Abstract
In animal cells, a single cytoplasmic dynein motor mediates microtubule minus-end-directed transport, counterbalancing dozens of plus-end-directed kinesins. The remarkable ability of dynein to interact with a diverse cargo spectrum stems from its tightly regulated recruitment of cargo-specific adaptor proteins, which engage the dynactin complex to make a tripartite processive motor. Adaptor binding is governed by the homologous dynein light intermediate chain subunits LIC1 (DYNC1LI1) and LIC2 (DYNC1LI2), which exist in mutually exclusive dynein complexes that can perform both unique and overlapping functions. The intrinsically disordered and variable C-terminal domains of the LICs are indispensable for engaging a variety of structurally divergent adaptors. Here, we hypothesize that numerous spatiotemporally regulated permutations of posttranslational modifications of the LICs, as well as of the adaptors and cargoes, exponentially expand the spectrum of dynein-adaptor-cargo complexes. We thematically illustrate the possibilities that could generate a vast set of biochemical variations required to support the wide range of dynein functions.
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Affiliation(s)
- Amrita Kumari
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India.,Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Chandan Kumar
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India
| | - Neeraj Wasnik
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India
| | - Sivaram V S Mylavarapu
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India.,Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
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30
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Goldman CH, Neiswender H, Baker F, Veeranan-Karmegam R, Misra S, Gonsalvez GB. Optimal RNA binding by Egalitarian, a Dynein cargo adaptor, is critical for maintaining oocyte fate in Drosophila. RNA Biol 2021; 18:2376-2389. [PMID: 33904382 DOI: 10.1080/15476286.2021.1914422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The Dynein motor is responsible for the localization of numerous mRNAs within Drosophila oocytes and embryos. The RNA binding protein, Egalitarian (Egl), is thought to link these various RNA cargoes with Dynein. Although numerous studies have shown that Egl is able to specifically associate with these RNAs, the nature of these interactions has remained elusive. Egl contains a central RNA binding domain that shares limited homology with an exonuclease, yet Egl binds to RNA without degrading it. Mutations have been identified within Egl that disrupt its association with its protein interaction partners, BicaudalD (BicD) and Dynein light chain (Dlc), but no mutants have been described that are specifically defective for RNA binding. In this report, we identified a series of positively charged residues within Egl that are required for RNA binding. Using corresponding RNA binding mutants, we demonstrate that specific RNA cargoes are more reliant on maximal Egl RNA biding activity for their correct localization in comparison to others. We also demonstrate that specification and maintenance of oocyte fate requires maximal Egl RNA binding activity. Even a subtle reduction in Egl's RNA binding activity completely disrupts this process. Our results show that efficient RNA localization at the earliest stages of oogenesis is required for specification of the oocyte and restriction of meiosis to a single cell.
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Affiliation(s)
- Chandler H Goldman
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA.,Department of Genetics, Davidson Life Sciences Complex, University of Georgia, Athens, GA, USA
| | - Hannah Neiswender
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Frederick Baker
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | | | - Saurav Misra
- Dept. Of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS,USA
| | - Graydon B Gonsalvez
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA
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31
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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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32
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Abouward R, Schiavo G. Walking the line: mechanisms underlying directional mRNA transport and localisation in neurons and beyond. Cell Mol Life Sci 2021; 78:2665-2681. [PMID: 33341920 PMCID: PMC8004493 DOI: 10.1007/s00018-020-03724-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 09/04/2020] [Revised: 11/02/2020] [Accepted: 11/25/2020] [Indexed: 12/21/2022]
Abstract
Messenger RNA (mRNA) localisation enables a high degree of spatiotemporal control on protein synthesis, which contributes to establishing the asymmetric protein distribution required to set up and maintain cellular polarity. As such, a tight control of mRNA localisation is essential for many biological processes during development and in adulthood, such as body axes determination in Drosophila melanogaster and synaptic plasticity in neurons. The mechanisms controlling how mRNAs are localised, including diffusion and entrapment, local degradation and directed active transport, are largely conserved across evolution and have been under investigation for decades in different biological models. In this review, we will discuss the standing of the field regarding directional mRNA transport in light of the recent discovery that RNA can hitchhike on cytoplasmic organelles, such as endolysosomes, and the impact of these transport modalities on our understanding of neuronal function during development, adulthood and in neurodegeneration.
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Affiliation(s)
- Reem Abouward
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
- UK Dementia Research Institute, University College London, London, WC1E 6BT, UK
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Giampietro Schiavo
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.
- UK Dementia Research Institute, University College London, London, WC1E 6BT, UK.
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33
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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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34
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Koppers M, Özkan N, Farías GG. Complex Interactions Between Membrane-Bound Organelles, Biomolecular Condensates and the Cytoskeleton. Front Cell Dev Biol 2020; 8:618733. [PMID: 33409284 PMCID: PMC7779554 DOI: 10.3389/fcell.2020.618733] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 12/03/2020] [Indexed: 12/13/2022] Open
Abstract
Membrane-bound and membraneless organelles/biomolecular condensates ensure compartmentalization into functionally distinct units enabling proper organization of cellular processes. Membrane-bound organelles form dynamic contacts with each other to enable the exchange of molecules and to regulate organelle division and positioning in coordination with the cytoskeleton. Crosstalk between the cytoskeleton and dynamic membrane-bound organelles has more recently also been found to regulate cytoskeletal organization. Interestingly, recent work has revealed that, in addition, the cytoskeleton and membrane-bound organelles interact with cytoplasmic biomolecular condensates. The extent and relevance of these complex interactions are just beginning to emerge but may be important for cytoskeletal organization and organelle transport and remodeling. In this review, we highlight these emerging functions and emphasize the complex interplay of the cytoskeleton with these organelles. The crosstalk between membrane-bound organelles, biomolecular condensates and the cytoskeleton in highly polarized cells such as neurons could play essential roles in neuronal development, function and maintenance.
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Affiliation(s)
| | | | - Ginny G. Farías
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
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35
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Lasko P. Patterning the Drosophila embryo: A paradigm for RNA-based developmental genetic regulation. Wiley Interdiscip Rev RNA 2020; 11:e1610. [PMID: 32543002 PMCID: PMC7583483 DOI: 10.1002/wrna.1610] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/13/2020] [Accepted: 05/17/2020] [Indexed: 12/16/2022]
Abstract
Embryonic anterior–posterior patterning is established in Drosophila melanogaster by maternally expressed genes. The mRNAs of several of these genes accumulate at either the anterior or posterior pole of the oocyte via a number of mechanisms. Many of these mRNAs are also under elaborate translational regulation. Asymmetric RNA localization coupled with spatially restricted translation ensures that their proteins are restricted to the position necessary for the developmental process that they drive. Bicoid (Bcd), the anterior determinant, and Oskar (Osk), the determinant for primordial germ cells and posterior patterning, have been studied particularly closely. In early embryos an anterior–posterior gradient of Bcd is established, activating transcription of different sets of zygotic genes depending on local Bcd concentration. At the posterior pole, Osk seeds formation of polar granules, ribonucleoprotein complexes that accumulate further mRNAs and proteins involved in posterior patterning and germ cell specification. After fertilization, polar granules associate with posterior nuclei and mature into nuclear germ granules. Osk accumulates in these granules, and either by itself or as part of the granules, stimulates germ cell division. This article is categorized under:RNA Export and Localization > RNA Localization Translation > Translation Regulation RNA in Disease and Development > RNA in Development
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Affiliation(s)
- Paul Lasko
- Department of Biology, McGill University, Montréal, Québec, Canada.,Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
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36
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Abstract
Cytoplasmic dynein is an AAA+ motor that drives the transport of many intracellular cargoes towards the minus end of microtubules (MTs). Previous in vitro studies characterized isolated dynein as an exceptionally weak motor that moves slowly and diffuses on an MT. Recent studies altered this view by demonstrating that dynein remains in an autoinhibited conformation on its own, and processive motility is activated when it forms a ternary complex with dynactin and a cargo adaptor. This complex assembles more efficiently in the presence of Lis1, providing an explanation for why Lis1 is a required cofactor for most cytoplasmic dynein-driven processes in cells. This review describes how dynein motility is activated and regulated by cargo adaptors and accessory proteins.
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Affiliation(s)
- John T Canty
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Ahmet Yildiz
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cellular Biology, University of California at Berkeley, Berkeley, CA 94720, USA; Physics Department, University of California at Berkeley, Berkeley, CA 94720, USA.
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37
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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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38
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Tempes A, Weslawski J, Brzozowska A, Jaworski J. Role of dynein-dynactin complex, kinesins, motor adaptors, and their phosphorylation in dendritogenesis. J Neurochem 2020; 155:10-28. [PMID: 32196676 DOI: 10.1111/jnc.15010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 01/28/2020] [Revised: 02/24/2020] [Accepted: 03/13/2020] [Indexed: 12/21/2022]
Abstract
One of the characteristic features of different classes of neurons that is vital for their proper functioning within neuronal networks is the shape of their dendritic arbors. To properly develop dendritic trees, neurons need to accurately control the intracellular transport of various cellular cargo (e.g., mRNA, proteins, and organelles). Microtubules and motor proteins (e.g., dynein and kinesins) that move along microtubule tracks play an essential role in cargo sorting and transport to the most distal ends of neurons. Equally important are motor adaptors, which may affect motor activity and specify cargo that is transported by the motor. Such transport undergoes very dynamic fine-tuning in response to changes in the extracellular environment and synaptic transmission. Such regulation is achieved by the phosphorylation of motors, motor adaptors, and cargo, among other mechanisms. This review focuses on the contribution of the dynein-dynactin complex, kinesins, their adaptors, and the phosphorylation of these proteins in the formation of dendritic trees by maturing neurons. We primarily review the effects of the motor activity of these proteins in dendrites on dendritogenesis. We also discuss less anticipated mechanisms that contribute to dendrite growth, such as dynein-driven axonal transport and non-motor functions of kinesins.
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Affiliation(s)
- Aleksandra Tempes
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Jan Weslawski
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Agnieszka Brzozowska
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Jacek Jaworski
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, Warsaw, Poland
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39
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Bullock SL, Visa N, Pederson T. Meeting report - Nuclear and cytoplasmic molecular machines at work. J Cell Sci 2020; 133:133/7/jcs245134. [PMID: 32253357 DOI: 10.1242/jcs.245134] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This report summarizes an international conference on molecular machines convened at New York University, Abu Dhabi by Piergiorgio Percipalle, George Shubeita and Serdal Kirmizialtin. The meeting was conceived around the epistemological question of what do we understand, or not understand (if we have open minds), about the degree to which cells operate by the individual actions of single enzymes or non-catalytic protein effectors, versus combinations of these in which their heterotypic association creates an entity that is more finely tuned and efficient - a machine. This theme was explored through a vivid series of talks, summarizing the latest findings on macromolecular complexes that operate in the nucleus or cytoplasm.
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Affiliation(s)
| | - Neus Visa
- Department of Molecular Biosciences, Wenner Gren Institute, Stockholm University, Stockholm 10 691, Sweden
| | - Thoru Pederson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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40
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Abstract
RNA localization is a key biological strategy for organizing the cytoplasm and generating both cellular and developmental polarity. During RNA localization, RNAs are targeted asymmetrically to specific subcellular destinations, resulting in spatially and temporally restricted gene expression through local protein synthesis. First discovered in oocytes and embryos, RNA localization is now recognized as a significant regulatory strategy for diverse RNAs, both coding and non-coding, in a wide range of cell types. Yet, the highly polarized cytoplasm of the oocyte remains a leading model to understand not only the principles and mechanisms underlying RNA localization, but also links to the formation of biomolecular condensates through phase separation. Here, we discuss both RNA localization and biomolecular condensates in oocytes with a particular focus on the oocyte of the frog, Xenopus laevis.
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Affiliation(s)
- Sarah E Cabral
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, United States
| | - Kimberly L Mowry
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, United States.
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41
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Baumann S, Komissarov A, Gili M, Ruprecht V, Wieser S, Maurer SP. A reconstituted mammalian APC-kinesin complex selectively transports defined packages of axonal mRNAs. Sci Adv 2020; 6:eaaz1588. [PMID: 32201729 PMCID: PMC7069705 DOI: 10.1126/sciadv.aaz1588] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/17/2019] [Indexed: 05/31/2023]
Abstract
Through the asymmetric distribution of messenger RNAs (mRNAs), cells spatially regulate gene expression to create cytoplasmic domains with specialized functions. In neurons, mRNA localization is required for essential processes such as cell polarization, migration, and synaptic plasticity underlying long-term memory formation. The essential components driving cytoplasmic mRNA transport in neurons and mammalian cells are not known. We report the first reconstitution of a mammalian mRNA transport system revealing that the tumor suppressor adenomatous polyposis coli (APC) forms stable complexes with the axonally localized β-actin and β2B-tubulin mRNAs, which are linked to a kinesin-2 via the cargo adaptor KAP3. APC activates kinesin-2, and both proteins are sufficient to drive specific transport of defined mRNA packages. Guanine-rich sequences located in 3'UTRs of axonal mRNAs increase transport efficiency and balance the access of different mRNAs to the transport system. Our findings reveal a minimal set of proteins sufficient to transport mammalian mRNAs.
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Affiliation(s)
- Sebastian Baumann
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, Barcelona 08003, Spain
| | - Artem Komissarov
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, Barcelona 08003, Spain
| | - Maria Gili
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, Barcelona 08003, Spain
| | - Verena Ruprecht
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, Barcelona 08003, Spain
| | | | - Sebastian P. Maurer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Doctor Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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42
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Torisawa T, Kimura A. The Generation of Dynein Networks by Multi-Layered Regulation and Their Implication in Cell Division. Front Cell Dev Biol 2020; 8:22. [PMID: 32083077 PMCID: PMC7004958 DOI: 10.3389/fcell.2020.00022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [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: 10/15/2019] [Accepted: 01/13/2020] [Indexed: 12/13/2022] Open
Abstract
Cytoplasmic dynein-1 (hereafter referred to as dynein) is a major microtubule-based motor critical for cell division. Dynein is essential for the formation and positioning of the mitotic spindle as well as the transport of various cargos in the cell. A striking feature of dynein is that, despite having a wide variety of functions, the catalytic subunit is coded in a single gene. To perform various cellular activities, there seem to be different types of dynein that share a common catalytic subunit. In this review, we will refer to the different kinds of dynein as “dyneins.” This review attempts to classify the mechanisms underlying the emergence of multiple dyneins into four layers. Inside a cell, multiple dyneins generated through the multi-layered regulations interact with each other to form a network of dyneins. These dynein networks may be responsible for the accurate regulation of cellular activities, including cell division. How these networks function inside a cell, with a focus on the early embryogenesis of Caenorhabditis elegans embryos, is discussed, as well as future directions for the integration of our understanding of molecular layering to understand the totality of dynein’s function in living cells.
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Affiliation(s)
- Takayuki Torisawa
- Cell Architecture Laboratory, National Institute of Genetics, Mishima, Japan.,Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Japan
| | - Akatsuki Kimura
- Cell Architecture Laboratory, National Institute of Genetics, Mishima, Japan.,Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Japan
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43
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Abstract
The pathophysiology and concept of degeneration in central nervous system is very complex and overwhelming at times. There is a complex mechanism which exists among different molecules in the cytoplasm of cell bodies of neurons, antegrade and retrograde axonal transport of cargoes and accumulation of certain substances and proteins which can influence the excitatory neurotransmitter like glutamate initiating the process of neurodegeneration. Neurons have extensive processes and communication between those processes and the cell body is crucial to neuronal function, viability and survival over time with progression of age. Researchers believe neurons are uniquely dependent on microtubule-based cargo transport. There is enough evidence to support that deficits in retrograde axonal transport contribute to pathogenesis in multiple neurodegenerative diseases. Cytoplasmic dynein and its regulation by Dynactin (DCTN1) is the major molecular motor cargo involved in autophagy, mitosis and neuronal cell survival. Mutation in dynactin gene located in 2p13.1,is indeed studied very extensively and is considered to be involved directly or indirectly to various conditions like Perry syndrome, familial and sporadic Amyotrophic lateral sclerosis, Hereditary spastic paraplegia, Spinocerebellar Ataxia (SCA-5), Huntingtons disease, Alzheimers disease, Charcot marie tooth disease, Hereditary motor neuropathy 7B, prion disease, parkinsons disease, malformation of cortical development, polymicrogyria to name a few with exception of Multiple Sclerosis (MS).
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44
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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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45
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Goldman CH, Neiswender H, Veeranan-Karmegam R, Gonsalvez GB. The Egalitarian binding partners Dynein light chain and Bicaudal-D act sequentially to link mRNA to the Dynein motor. Development 2019; 146:dev.176529. [PMID: 31391195 DOI: 10.1242/dev.176529] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 02/04/2019] [Accepted: 07/15/2019] [Indexed: 01/24/2023]
Abstract
A conserved mechanism of polarity establishment is the localization of mRNA to specific cellular regions. Although it is clear that many mRNAs are transported along microtubules, much less is known about the mechanism by which these mRNAs are linked to microtubule motors. The RNA binding protein Egalitarian (Egl) is necessary for localization of several mRNAs in Drosophila oocytes and embryos. Egl also interacts with Dynein light chain (Dlc) and Bicaudal-D (BicD). The role of Dlc and BicD in mRNA localization has remained elusive. Both proteins are required for oocyte specification, as is Egl. Null alleles in these genes result in an oogenesis block. In this report, we used an shRNA-depletion strategy to overcome the oogenesis block. Our findings reveal that the primary function of Dlc is to promote Egl dimerization. Loss of dimerization compromises the ability of Egl to bind RNA. Consequently, Egl is not bound to cargo, and is not able to efficiently associate with BicD and the Dynein motor. Our results therefore identify the key molecular steps required for assembling a localization-competent mRNP.
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Affiliation(s)
- Chandler H Goldman
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1459 Laney Walker Blvd, Augusta, GA 30912, USA
| | - Hannah Neiswender
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1459 Laney Walker Blvd, Augusta, GA 30912, USA
| | - Rajalakshmi Veeranan-Karmegam
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1459 Laney Walker Blvd, Augusta, GA 30912, USA
| | - Graydon B Gonsalvez
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1459 Laney Walker Blvd, Augusta, GA 30912, USA
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46
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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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47
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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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48
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Abstract
Neurons are highly polarized cells that can extend processes far from the cell body. As such, transport of messenger RNAs serves as a set of blueprints for the synthesis of specific proteins at distal sites. RNA localization to dendrites and axons confers the ability to regulate translation with extraordinary precision in space and time. Although the rationale for RNA localization is quite compelling, it is unclear how a neuron orchestrates such a complex task of distributing over a thousand different mRNAs to their respective subcellular compartments. Recent single-molecule imaging studies have led to insights into the kinetics of individual mRNAs. We can now peer into the transport dynamics of mRNAs in both dendrites and axons.
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Affiliation(s)
- Sulagna Das
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Janelia Research Campus, Ashburn, VA, USA.
| | - Young J Yoon
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Janelia Research Campus, Ashburn, VA, USA.
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49
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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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50
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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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