1
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Riggs CL, Kedersha N, Amarsanaa M, Zubair SN, Ivanov P, Anderson P. UBAP2L contributes to formation of P-bodies and modulates their association with stress granules. J Cell Biol 2024; 223:e202307146. [PMID: 39007803 PMCID: PMC11248227 DOI: 10.1083/jcb.202307146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 03/06/2024] [Accepted: 06/10/2024] [Indexed: 07/16/2024] Open
Abstract
Stress triggers the formation of two distinct cytoplasmic biomolecular condensates: stress granules (SGs) and processing bodies (PBs), both of which may contribute to stress-responsive translation regulation. Though PBs can be present constitutively, stress can increase their number and size and lead to their interaction with stress-induced SGs. The mechanism of such interaction, however, is largely unknown. Formation of canonical SGs requires the RNA binding protein Ubiquitin-Associated Protein 2-Like (UBAP2L), which is a central SG node protein in the RNA-protein interaction network of SGs and PBs. UBAP2L binds to the essential SG and PB proteins G3BP and DDX6, respectively. Research on UBAP2L has mostly focused on its role in SGs, but not its connection to PBs. We find that UBAP2L is not solely an SG protein but also localizes to PBs in certain conditions, contributes to PB biogenesis and SG-PB interactions, and can nucleate hybrid granules containing SG and PB components in cells. These findings inform a new model for SG and PB formation in the context of UBAP2L's role.
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Affiliation(s)
- Claire L Riggs
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nancy Kedersha
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Misheel Amarsanaa
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Biological Sciences, Wellesley College, Wellesley, MA, USA
| | - Safiyah Noor Zubair
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Paul Anderson
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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2
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Asano-Inami E, Yokoi A, Sugiyama M, Hyodo T, Hamaguchi T, Kajiyama H. The association of UBAP2L and G3BP1 mediated by small nucleolar RNA is essential for stress granule formation. Commun Biol 2023; 6:415. [PMID: 37059803 PMCID: PMC10104854 DOI: 10.1038/s42003-023-04754-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 03/24/2023] [Indexed: 04/16/2023] Open
Abstract
Stress granules (SGs) are dynamic, non-membranous structures composed of non-translating mRNAs and various proteins and play critical roles in cell survival under stressed conditions. Extensive proteomics analyses have been performed to identify proteins in SGs; however, the molecular functions of these components in SG formation remain unclear. In this report, we show that ubiquitin-associated protein 2-like (UBAP2L) is a crucial component of SGs. UBAP2L localized to SGs in response to various stresses, and its depletion significantly suppressed SG organization. Proteomics and RNA sequencing analyses found that UBAP2L formed a protein-RNA complex with Ras-GTP-activating protein SH3 domain binding protein 1 (G3BP1) and small nucleolar RNAs (snoRNAs). In vitro binding analysis demonstrated that snoRNAs were required for UBAP2L association with G3BP1. In addition, decreased expression of snoRNAs reduced the interaction between UBAP2L and G3BP1 and suppressed SG formation. Our results reveal a critical role of SG component, the UBAP2L/snoRNA/G3BP1 protein-RNA complex, and provide new insights into the regulation of SG assembly.
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Affiliation(s)
- Eri Asano-Inami
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan.
- Bell Research Center for Reproductive Health and Cancer, Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan.
| | - Akira Yokoi
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan.
- Institute for Advanced Research, Nagoya University, Nagoya, Japan.
| | - Mai Sugiyama
- Bell Research Center for Reproductive Health and Cancer, Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan
| | - Toshinori Hyodo
- Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Aichi, 480-1195, Japan
| | - Tomonari Hamaguchi
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan
| | - Hiroaki Kajiyama
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku Nagoya, 466-8550, Japan
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3
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Guerber L, Pangou E, Sumara I. Ubiquitin Binding Protein 2-Like (UBAP2L): is it so NICE After All? Front Cell Dev Biol 2022; 10:931115. [PMID: 35794863 PMCID: PMC9250975 DOI: 10.3389/fcell.2022.931115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/01/2022] [Indexed: 12/30/2022] Open
Abstract
Ubiquitin Binding Protein 2-like (UBAP2L, also known as NICE-4) is a ubiquitin- and RNA-binding protein, highly conserved in metazoans. Despite its abundance, its functions have only recently started to be characterized. Several studies have demonstrated the crucial involvement of UBAP2L in various cellular processes such as cell cycle regulation, stem cell activity and stress-response signaling. In addition, UBAP2L has recently emerged as a master regulator of growth and proliferation in several human cancers, where it is suggested to display oncogenic properties. Given that this versatile protein is involved in the regulation of multiple and distinct cellular pathways, actively contributing to the maintenance of cell homeostasis and survival, UBAP2L might represent a good candidate for future therapeutic studies. In this review, we discuss the current knowledge and latest advances on elucidating UBAP2L cellular functions, with an aim to highlight the importance of targeting UBAP2L for future therapies.
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Affiliation(s)
- Lucile Guerber
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Centre National de la Recherche Scientifique UMR 7104, Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale U964, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Evanthia Pangou
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Centre National de la Recherche Scientifique UMR 7104, Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale U964, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Izabela Sumara
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Centre National de la Recherche Scientifique UMR 7104, Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale U964, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- *Correspondence: Izabela Sumara,
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4
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Singh A, Kandi AR, Jayaprakashappa D, Thuery G, Purohit DJ, Huelsmeier J, Singh R, Pothapragada SS, Ramaswami M, Bakthavachalu B. The Transcriptional Response to Oxidative Stress is Independent of Stress-Granule Formation. Mol Biol Cell 2022; 33:ar25. [PMID: 34985933 PMCID: PMC9250384 DOI: 10.1091/mbc.e21-08-0418] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Cells respond to stress with translational arrest, robust transcriptional changes, and transcription-independent formation of mRNP assemblies termed stress granules (SGs). Despite considerable interest in the role of SGs in oxidative, unfolded-protein and viral stress responses, whether and how SGs contribute to stress-induced transcription has not been rigorously examined. To address this, we characterized transcriptional changes in Drosophila S2 cells induced by acute oxidative-stress and assessed how these were altered under conditions that disrupted SG assembly. Oxidative stress for 3-hours predominantly resulted in induction or upregulation of stress-responsive mRNAs whose levels peaked during recovery after stress cessation. The stress-transcriptome is enriched in mRNAs coding for chaperones, including HSP70s, small heat shock proteins, glutathione transferases, and several non-coding RNAs. Oxidative stress also induced cytoplasmic SGs that disassembled 3-hours after stress cessation. As expected, RNAi-mediated knockdown of the conserved G3BP1/Rasputin protein inhibited SG assembly. However, this disruption had no significant effect on the stress-induced transcriptional response or stress-induced translational arrest. Thus, SG assembly and stress-induced gene expression alterations appear to be driven by distinctive signaling processes. We suggest that while SG assembly represents a fast, transient mechanism, the transcriptional response enables a slower, longer-lasting mechanism for adaptation to and recovery from cell stress.
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Affiliation(s)
- Amanjot Singh
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India
| | - Arvind Reddy Kandi
- Tata Institute for Genetics and Society Centre at inStem, Bellary Road, Bangalore 560065, India
| | | | - Guillaume Thuery
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin-2 Ireland
| | - Devam J Purohit
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India
| | - Joern Huelsmeier
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin-2 Ireland
| | - Rashi Singh
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India
| | | | - Mani Ramaswami
- National Centre for Biological Sciences, TIFR, Bangalore 560065, India.,Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin-2 Ireland
| | - Baskar Bakthavachalu
- Tata Institute for Genetics and Society Centre at inStem, Bellary Road, Bangalore 560065, India.,School of Basic Sciences, Indian Institute of Technology, Mandi 175005, India
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5
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Lachke SA. RNA-binding proteins and post-transcriptional regulation in lens biology and cataract: Mediating spatiotemporal expression of key factors that control the cell cycle, transcription, cytoskeleton and transparency. Exp Eye Res 2022; 214:108889. [PMID: 34906599 PMCID: PMC8792301 DOI: 10.1016/j.exer.2021.108889] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 01/03/2023]
Abstract
Development of the ocular lens - a transparent tissue capable of sustaining frequent shape changes for optimal focusing power - pushes the boundaries of what cells can achieve using the molecular toolkit encoded by their genomes. The mammalian lens contains broadly two types of cells, the anteriorly located monolayer of epithelial cells which, at the equatorial region of the lens, initiate differentiation into fiber cells that contribute to the bulk of the tissue. This differentiation program involves massive upregulation of select fiber cell-expressed RNAs and their subsequent translation into high amounts of proteins, such as crystallins. But intriguingly, fiber cells achieve this while also simultaneously undergoing significant morphological changes such as elongation - involving about 1000-fold length-wise increase - and migration, which requires modulation of cytoskeletal and cell adhesion factors. Adding further to the challenges, these molecular and cellular events have to be coordinated as fiber cells progress toward loss of their nuclei and organelles, which irreversibly compromises their potential for harnessing genetically hardwired information. A long-standing question is how processes downstream of signaling and transcription, which may also participate in feedback regulation, contribute toward orchestrating these cellular differentiation events in the lens. It is now becoming clear from findings over the past decade that post-transcriptional gene expression regulatory mechanisms are critical in controlling cellular proteomes and coordinating key processes in lens development and fiber cell differentiation. Indeed, RNA-binding proteins (RBPs) such as Caprin2, Celf1, Rbm24 and Tdrd7 have now been described in mediating post-transcriptional control over key factors (e.g. Actn2, Cdkn1a (p21Cip1), Cdkn1b (p27Kip1), various crystallins, Dnase2b, Hspb1, Pax6, Prox1, Sox2) that are variously involved in cell cycle, transcription, cytoskeleton maintenance and differentiation in the lens. Furthermore, deficiencies of these RBPs have been shown to result in various eye and lens defects and/or cataract. Because fiber cell differentiation in the lens occurs throughout life, the underlying regulatory mechanisms operational in development are expected to also be recruited for the maintenance of transparency in aged lenses. Indeed, in support of this, TDRD7 and CAPRIN2 loci have been linked to age-related cataract in humans. Here, I will review the role of key RBPs in the lens and their importance in understanding the pathology of lens defects. I will discuss advances in RBP-based gene expression control, in general, and the important challenges that need to be addressed in the lens to define the mechanisms that determine the epithelial and fiber cell proteome. Finally, I will also discuss in detail several key future directions including the application of bioinformatics approaches such as iSyTE to study RBP-based post-transcriptional gene expression control in the aging lens and in the context of age-related cataract.
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Affiliation(s)
- Salil A Lachke
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA; Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, 19716, USA.
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6
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Kruse T, Benz C, Garvanska DH, Lindqvist R, Mihalic F, Coscia F, Inturi R, Sayadi A, Simonetti L, Nilsson E, Ali M, Kliche J, Moliner Morro A, Mund A, Andersson E, McInerney G, Mann M, Jemth P, Davey NE, Överby AK, Nilsson J, Ivarsson Y. Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities. Nat Commun 2021; 12:6761. [PMID: 34799561 PMCID: PMC8605023 DOI: 10.1038/s41467-021-26498-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/06/2021] [Indexed: 12/13/2022] Open
Abstract
Viral proteins make extensive use of short peptide interaction motifs to hijack cellular host factors. However, most current large-scale methods do not identify this important class of protein-protein interactions. Uncovering peptide mediated interactions provides both a molecular understanding of viral interactions with their host and the foundation for developing novel antiviral reagents. Here we describe a viral peptide discovery approach covering 23 coronavirus strains that provides high resolution information on direct virus-host interactions. We identify 269 peptide-based interactions for 18 coronaviruses including a specific interaction between the human G3BP1/2 proteins and an ΦxFG peptide motif in the SARS-CoV-2 nucleocapsid (N) protein. This interaction supports viral replication and through its ΦxFG motif N rewires the G3BP1/2 interactome to disrupt stress granules. A peptide-based inhibitor disrupting the G3BP1/2-N interaction dampened SARS-CoV-2 infection showing that our results can be directly translated into novel specific antiviral reagents.
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Affiliation(s)
- Thomas Kruse
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Caroline Benz
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Dimitriya H Garvanska
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Richard Lindqvist
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186, Umeå, Sweden
| | - Filip Mihalic
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Fabian Coscia
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200, Copenhagen, Denmark
- Spatial Proteomics Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Raviteja Inturi
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ahmed Sayadi
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Emma Nilsson
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186, Umeå, Sweden
| | - Muhammad Ali
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Johanna Kliche
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ainhoa Moliner Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andreas Mund
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Matthias Mann
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Anna K Överby
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden.
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186, Umeå, Sweden.
| | - Jakob Nilsson
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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7
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Abbatemarco S, Bondaz A, Schwager F, Wang J, Hammell CM, Gotta M. PQN-59 and GTBP-1 contribute to stress granule formation but are not essential for their assembly in C. elegans embryos. J Cell Sci 2021; 134:273437. [PMID: 34661238 PMCID: PMC8645233 DOI: 10.1242/jcs.258834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/09/2021] [Indexed: 11/04/2022] Open
Abstract
When exposed to stressful conditions, eukaryotic cells respond by inducing the formation of cytoplasmic ribonucleoprotein complexes called stress granules. Here, we use C. elegans to study two proteins that are important for stress granule assembly in human cells – PQN-59, the human UBAP2L ortholog, and GTBP-1, the human G3BP1 and G3BP2 ortholog. Both proteins assemble into stress granules in the embryo and in the germline when C. elegans is exposed to stressful conditions. Neither of the two proteins is essential for the assembly of stress-induced granules, as shown by the single and combined depletions by RNAi, and neither pqn-59 nor gtbp-1 mutant embryos show higher sensitivity to stress than control embryos. We find that pqn-59 mutants display reduced progeny and a high percentage of embryonic lethality, phenotypes that are not dependent on stress exposure and that are not shared with gtbp-1 mutants. Our data indicate that, in contrast to human cells, PQN-59 and GTBP-1 are not required for stress granule formation but that PQN-59 is important for C. elegans development. Summary: In contrast to human cells, where the UBAP2L and G3BP1 and G3BP2 proteins are crucial nucleators of stress granules, the C. elegans orthologs are not essential for this process in worms.
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Affiliation(s)
- Simona Abbatemarco
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
| | - Alexandra Bondaz
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
| | - Francoise Schwager
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
| | - Jing Wang
- Cold Spring Harbor Laboratory, New York, NY 11724, USA
| | | | - Monica Gotta
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
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8
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Sharp KA, Khoury MJ, Wirtz-Peitz F, Bilder D. Evidence for a nuclear role for Drosophila Dlg as a regulator of the NURF complex. Mol Biol Cell 2021; 32:ar23. [PMID: 34495684 PMCID: PMC8693970 DOI: 10.1091/mbc.e21-04-0187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Scribble (Scrib), Discs-large (Dlg), and Lethal giant larvae (Lgl) are basolateral regulators of epithelial polarity and tumor suppressors whose molecular mechanisms of action remain unclear. We used proximity biotinylation to identify proteins localized near Dlg in the Drosophila wing imaginal disc epithelium. In addition to expected membrane- and cytoskeleton-associated protein classes, nuclear proteins were prevalent in the resulting mass spectrometry dataset, including all four members of the nucleosome remodeling factor (NURF) chromatin remodeling complex. Subcellular fractionation demonstrated a nuclear pool of Dlg and proximity ligation confirmed its position near the NURF complex. Genetic analysis showed that NURF activity is also required for the overgrowth of dlg tumors, and this growth suppression correlated with a reduction in Hippo pathway gene expression. Together, these data suggest a nuclear role for Dlg in regulating chromatin and transcription through a more direct mechanism than previously thought.
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Affiliation(s)
- Katherine A Sharp
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley CA 94720
| | - Mark J Khoury
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley CA 94720
| | | | - David Bilder
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley CA 94720
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9
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Carlston C, Weinmann R, Stec N, Abbatemarco S, Schwager F, Wang J, Ouyang H, Ewald CY, Gotta M, Hammell CM. PQN-59 antagonizes microRNA-mediated repression during post-embryonic temporal patterning and modulates translation and stress granule formation in C. elegans. PLoS Genet 2021; 17:e1009599. [PMID: 34807903 PMCID: PMC8648105 DOI: 10.1371/journal.pgen.1009599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 12/06/2021] [Accepted: 10/27/2021] [Indexed: 12/14/2022] Open
Abstract
microRNAs (miRNAs) are potent regulators of gene expression that function in a variety of developmental and physiological processes by dampening the expression of their target genes at a post-transcriptional level. In many gene regulatory networks (GRNs), miRNAs function in a switch-like manner whereby their expression and activity elicit a transition from one stable pattern of gene expression to a distinct, equally stable pattern required to define a nascent cell fate. While the importance of miRNAs that function in this capacity are clear, we have less of an understanding of the cellular factors and mechanisms that ensure the robustness of this form of regulatory bistability. In a screen to identify suppressors of temporal patterning phenotypes that result from ineffective miRNA-mediated target repression, we identified pqn-59, an ortholog of human UBAP2L, as a novel factor that antagonizes the activities of multiple heterochronic miRNAs. Specifically, we find that depletion of pqn-59 can restore normal development in animals with reduced lin-4 and let-7-family miRNA activity. Importantly, inactivation of pqn-59 is not sufficient to bypass the requirement of these regulatory RNAs within the heterochronic GRN. The pqn-59 gene encodes an abundant, cytoplasmically-localized, unstructured protein that harbors three essential "prion-like" domains. These domains exhibit LLPS properties in vitro and normally function to limit PQN-59 diffusion in the cytoplasm in vivo. Like human UBAP2L, PQN-59's localization becomes highly dynamic during stress conditions where it re-distributes to cytoplasmic stress granules and is important for their formation. Proteomic analysis of PQN-59 complexes from embryonic extracts indicates that PQN-59 and human UBAP2L interact with orthologous cellular components involved in RNA metabolism and promoting protein translation and that PQN-59 additionally interacts with proteins involved in transcription and intracellular transport. Finally, we demonstrate that pqn-59 depletion reduces protein translation and also results in the stabilization of several mature miRNAs (including those involved in temporal patterning). These data suggest that PQN-59 may ensure the bistability of some GRNs that require miRNA functions by promoting miRNA turnover and, like UBAP2L, enhancing protein translation.
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Affiliation(s)
- Colleen Carlston
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Robin Weinmann
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Natalia Stec
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Simona Abbatemarco
- Department of Cellular Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Francoise Schwager
- Department of Cellular Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Jing Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Huiwu Ouyang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Collin Y. Ewald
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach, Switzerland
| | - Monica Gotta
- Department of Cellular Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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10
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Hecw controls oogenesis and neuronal homeostasis by promoting the liquid state of ribonucleoprotein particles. Nat Commun 2021; 12:5488. [PMID: 34531401 PMCID: PMC8446043 DOI: 10.1038/s41467-021-25809-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 08/31/2021] [Indexed: 01/17/2023] Open
Abstract
Specialised ribonucleoprotein (RNP) granules are a hallmark of polarized cells, like neurons and germ cells. Among their main functions is the spatial and temporal modulation of the activity of specific mRNA transcripts that allow specification of primary embryonic axes. While RNPs composition and role are well established, their regulation is poorly defined. Here, we demonstrate that Hecw, a newly identified Drosophila ubiquitin ligase, is a key modulator of RNPs in oogenesis and neurons. Hecw depletion leads to the formation of enlarged granules that transition from a liquid to a gel-like state. Loss of Hecw activity results in defective oogenesis, premature aging and climbing defects associated with neuronal loss. At the molecular level, reduced ubiquitination of the Fmrp impairs its translational repressor activity, resulting in altered Orb expression in nurse cells and Profilin in neurons. Ribonucleoprotein (RNP) granules are responsible for mRNA transport and local translation required for neuronal and oocyte maturation. Here the authors show that loss of the Drosophila Ub ligase Hecw enlarges RNP granules, leads to a liquid to gel-like transition, and results in defective oogenesis and neuronal loss.
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11
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Schoville SD, Simon S, Bai M, Beethem Z, Dudko RY, Eberhard MJB, Frandsen PB, Küpper SC, Machida R, Verheij M, Willadsen PC, Zhou X, Wipfler B. Comparative transcriptomics of ice-crawlers demonstrates cold specialization constrains niche evolution in a relict lineage. Evol Appl 2021; 14:360-382. [PMID: 33664782 PMCID: PMC7896716 DOI: 10.1111/eva.13120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/25/2020] [Accepted: 08/17/2020] [Indexed: 12/26/2022] Open
Abstract
Key changes in ecological niche space are often critical to understanding how lineages diversify during adaptive radiations. However, the converse, or understanding why some lineages are depauperate and relictual, is more challenging, as many factors may constrain niche evolution. In the case of the insect order Grylloblattodea, highly conserved thermal breadth is assumed to be closely tied to their relictual status, but has not been formerly tested. Here, we investigate whether evolutionary constraints in the physiological tolerance of temperature can help explain relictualism in this lineage. Using a comparative transcriptomics approach, we investigate gene expression following acute heat and cold stress across members of Grylloblattodea and their sister group, Mantophasmatodea. We additionally examine patterns of protein evolution, to identify candidate genes of positive selection. We demonstrate that cold specialization in Grylloblattodea has been accompanied by the loss of the inducible heat shock response under both acute heat and cold stress. Additionally, there is widespread evidence of selection on protein-coding genes consistent with evolutionary constraints due to cold specialization. This includes positive selection on genes involved in trehalose transport, metabolic function, mitochondrial function, oxygen reduction, oxidative stress, and protein synthesis. These patterns of molecular adaptation suggest that Grylloblattodea have undergone evolutionary trade-offs to survive in cold habitats and should be considered highly vulnerable to climate change. Finally, our transcriptomic data provide a robust backbone phylogeny for generic relationships within Grylloblattodea and Mantophasmatodea. Major phylogenetic splits in each group relate to arid conditions driving biogeographical patterns, with support for a sister-group relationship between North American Grylloblatta and Altai-Sayan Grylloblattella, and a range disjunction in Namibia splitting major clades within Mantophasmatodea.
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Affiliation(s)
| | - Sabrina Simon
- Biosystematics GroupWageningen University & ResearchPB WageningenThe Netherlands
| | - Ming Bai
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina
| | - Zachary Beethem
- Department of EntomologyUniversity of Wisconsin‐MadisonMadisonWIUSA
- Present address:
Department of Biomedical SciencesSchool of Veterinary MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Roman Y. Dudko
- Institute of Systematics and Ecology of AnimalsSiberian Branch of the Russian Academy of SciencesNovosibirskRussia
- Tomsk State UniversityTomskRussia
| | - Monika J. B. Eberhard
- Zoological Institute and MuseumGeneral Zoology and Zoological SystematicsUniversity of GreifswaldGreifswaldGermany
| | - Paul B. Frandsen
- Department of Plant & Wildlife SciencesBrigham Young UniversityProvoUTUSA
- Data Science LabOffice of the Chief Information OfficerSmithsonian InstitutionWashingtonDCU.S.A
| | - Simon C. Küpper
- Zoological Institute and MuseumGeneral Zoology and Zoological SystematicsUniversity of GreifswaldGreifswaldGermany
| | - Ryuichiro Machida
- Sugadaira Research StationMountain Science CenterUniversity of TsukubaUeda, NaganoJapan
| | - Max Verheij
- Biosystematics GroupWageningen University & ResearchPB WageningenThe Netherlands
| | - Peter C. Willadsen
- Department of EntomologyUniversity of Wisconsin‐MadisonMadisonWIUSA
- Present address:
Department of Entomology and Plant PathologyNorth Carolina State UniversityCampus Box 7613RaleighNCUSA
| | - Xin Zhou
- Department of EntomologyCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
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12
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Zhu J, Zhou X, Huang X, Du Z. Crystal structure of a 123 amino acids dimerization domain of Drosophila Caprin. Proteins 2020; 88:1701-1711. [PMID: 32725918 DOI: 10.1002/prot.25987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/12/2020] [Accepted: 07/26/2020] [Indexed: 11/12/2022]
Abstract
Cytoplasmic activation/proliferation-associated protein (Caprin) proteins assume diverse functions in many important biological processes, including synaptic plasticity, stress response, innate immune response, and cellular proliferation. The Caprin family members are characterized by the presence of a highly conserved homologous region (HR1) at the N-terminus and arginine-glycine-rich (RGG) boxes at the C-terminus. We had previously determined the crystal structures of human Caprin-1 and Caprin-2 fragments corresponding to the C-terminal 2/3 of HR1. Both fragments adopt homodimeric structures. Based on sequence conservation, we speculated that all Caprin proteins should have similar homodimeric structures. Here we report the crystal structure of a fragment (residues 187-309) of Drosophila melanogaster Caprin (dCaprin). The dCaprin fragment adopts an all α-helical fold which self-associates to form a homodimer. The overall dCaprin homodimeric structure is similar to the Caprin-1 and Caprin-2 homodimeric structures. Most of the amino acids residues mediating homodimerization in the three structures are conserved among all Caprin family members. These structural and sequence data suggest that homodimerization through a conserved dimerization domain is a common structural feature of the Caprin protein family. The dimeric structures may also be involved in interaction with Caprin partners. Dimer formation creates a V-shape concave surface that may serve as a protein binding groove. The concave surfaces in Caprin-1, Caprin-2, and dCaprin should have different and specific binding partners due to the large difference in electrostatic potentials. We propose the existence of a multi-functional domain in Caprin proteins, which not only mediate homodimerization but also involve in interaction with specific Caprin partners.
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Affiliation(s)
- Jiang Zhu
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
| | - Xia Zhou
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
| | - Xiaolan Huang
- Department of Computer Science, Southern Illinois University, Carbondale, Illinois, USA
| | - Zhihua Du
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
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13
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Gupta A, Stocker H. FoxO suppresses endoplasmic reticulum stress to inhibit growth of Tsc1-deficient tissues under nutrient restriction. eLife 2020; 9:53159. [PMID: 32525804 PMCID: PMC7289595 DOI: 10.7554/elife.53159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 05/22/2020] [Indexed: 12/27/2022] Open
Abstract
The transcription factor FoxO has been shown to block proliferation and progression in mTORC1-driven tumorigenesis but the picture of the relevant FoxO target genes remains incomplete. Here, we employed RNA-seq profiling on single clones isolated using laser capture microdissection from Drosophila larval eye imaginal discs to identify FoxO targets that restrict the proliferation of Tsc1-deficient cells under nutrient restriction (NR). Transcriptomics analysis revealed downregulation of endoplasmic reticulum-associated protein degradation pathway components upon foxo knockdown. Induction of ER stress pharmacologically or by suppression of other ER stress response pathway components led to an enhanced overgrowth of Tsc1 knockdown tissue. Increase of ER stress in Tsc1 loss-of-function cells upon foxo knockdown was also confirmed by elevated expression levels of known ER stress markers. These results highlight the role of FoxO in limiting ER stress to regulate Tsc1 mutant overgrowth.
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Affiliation(s)
- Avantika Gupta
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Hugo Stocker
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
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14
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Sanders DW, Kedersha N, Lee DSW, Strom AR, Drake V, Riback JA, Bracha D, Eeftens JM, Iwanicki A, Wang A, Wei MT, Whitney G, Lyons SM, Anderson P, Jacobs WM, Ivanov P, Brangwynne CP. Competing Protein-RNA Interaction Networks Control Multiphase Intracellular Organization. Cell 2020; 181:306-324.e28. [PMID: 32302570 PMCID: PMC7816278 DOI: 10.1016/j.cell.2020.03.050] [Citation(s) in RCA: 447] [Impact Index Per Article: 111.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 10/24/2019] [Accepted: 03/20/2020] [Indexed: 12/22/2022]
Abstract
Liquid-liquid phase separation (LLPS) mediates formation of membraneless condensates such as those associated with RNA processing, but the rules that dictate their assembly, substructure, and coexistence with other liquid-like compartments remain elusive. Here, we address the biophysical mechanism of this multiphase organization using quantitative reconstitution of cytoplasmic stress granules (SGs) with attached P-bodies in human cells. Protein-interaction networks can be viewed as interconnected complexes (nodes) of RNA-binding domains (RBDs), whose integrated RNA-binding capacity determines whether LLPS occurs upon RNA influx. Surprisingly, both RBD-RNA specificity and disordered segments of key proteins are non-essential, but modulate multiphase condensation. Instead, stoichiometry-dependent competition between protein networks for connecting nodes determines SG and P-body composition and miscibility, while competitive binding of unconnected proteins disengages networks and prevents LLPS. Inspired by patchy colloid theory, we propose a general framework by which competing networks give rise to compositionally specific and tunable condensates, while relative linkage between nodes underlies multiphase organization.
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Affiliation(s)
- David W Sanders
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Nancy Kedersha
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Daniel S W Lee
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Amy R Strom
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Victoria Drake
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Joshua A Riback
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Dan Bracha
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Jorine M Eeftens
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Allana Iwanicki
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Alicia Wang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Ming-Tzo Wei
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Gena Whitney
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Shawn M Lyons
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Paul Anderson
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - William M Jacobs
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton, NJ 08544, USA.
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15
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Laver JD, Ly J, Winn JK, Karaiskakis A, Lin S, Nie K, Benic G, Jaberi-Lashkari N, Cao WX, Khademi A, Westwood JT, Sidhu SS, Morris Q, Angers S, Smibert CA, Lipshitz HD. The RNA-Binding Protein Rasputin/G3BP Enhances the Stability and Translation of Its Target mRNAs. Cell Rep 2020; 30:3353-3367.e7. [PMID: 32160542 DOI: 10.1016/j.celrep.2020.02.066] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 01/13/2020] [Accepted: 02/14/2020] [Indexed: 12/14/2022] Open
Abstract
G3BP RNA-binding proteins are important components of stress granules (SGs). Here, we analyze the role of the Drosophila G3BP Rasputin (RIN) in unstressed cells, where RIN is not SG associated. Immunoprecipitation followed by microarray analysis identifies over 550 mRNAs that copurify with RIN. The mRNAs found in SGs are long and translationally silent. In contrast, we find that RIN-bound mRNAs, which encode core components of the transcription, splicing, and translation machinery, are short, stable, and highly translated. We show that RIN is associated with polysomes and provide evidence for a direct role for RIN and its human homologs in stabilizing and upregulating the translation of their target mRNAs. We propose that when cells are stressed, the resulting incorporation of RIN/G3BPs into SGs sequesters them away from their short target mRNAs. This would downregulate the expression of these transcripts, even though they are not incorporated into stress granules.
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Affiliation(s)
- John D Laver
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Jimmy Ly
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Jamie K Winn
- Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Angelo Karaiskakis
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Sichun Lin
- Department of Pharmaceutical Sciences, University of Toronto, 144 College Street, Toronto, ON M5S 3M2, Canada
| | - Kun Nie
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Giulia Benic
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Nima Jaberi-Lashkari
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Wen Xi Cao
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Alireza Khademi
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - J Timothy Westwood
- Department of Biology, University of Toronto, 3359 Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Sachdev S Sidhu
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Quaid Morris
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Vector Institute, 661 University Ave, Toronto, Ontario, Canada, M160 College Street, Toronto, ON M5G 1M1, Canada
| | - Stephane Angers
- Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Department of Pharmaceutical Sciences, University of Toronto, 144 College Street, Toronto, ON M5S 3M2, Canada
| | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada.
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada.
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16
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Durdevic Z, Ephrussi A. Germ Cell Lineage Homeostasis in Drosophila Requires the Vasa RNA Helicase. Genetics 2019; 213:911-922. [PMID: 31484689 PMCID: PMC6827371 DOI: 10.1534/genetics.119.302558] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 08/29/2019] [Indexed: 11/18/2022] Open
Abstract
The conserved RNA helicase Vasa is required for germ cell development in many organisms. In Drosophila melanogaster loss of PIWI-interacting RNA pathway components, including Vasa, causes Chk2-dependent oogenesis arrest. However, whether the arrest is due to Chk2 signaling at a specific stage and whether continuous Chk2 signaling is required for the arrest is unknown. Here, we show that absence of Vasa during the germarial stages causes Chk2-dependent oogenesis arrest. Additionally, we report the age-dependent decline of the ovariole number both in flies lacking Vasa expression only in the germarium and in loss-of-function vasa mutant flies. We show that Chk2 activation exclusively in the germarium is sufficient to interrupt oogenesis and to reduce ovariole number in aging flies. Once induced in the germarium, Chk2-mediated arrest of germ cell development cannot be overcome by restoration of Vasa or by downregulation of Chk2 in the arrested egg chambers. These findings, together with the identity of Vasa-associated proteins identified in this study, demonstrate an essential role of the helicase in the germ cell lineage maintenance and indicate a function of Vasa in germline stem cell homeostasis.
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Affiliation(s)
- Zeljko Durdevic
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany
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17
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UBAP2L arginine methylation by PRMT1 modulates stress granule assembly. Cell Death Differ 2019; 27:227-241. [PMID: 31114027 PMCID: PMC7205891 DOI: 10.1038/s41418-019-0350-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 04/28/2019] [Accepted: 05/03/2019] [Indexed: 02/06/2023] Open
Abstract
Stress granules (SGs) are discrete assemblies of stalled messenger ribonucleoprotein complexes (mRNPs) that form when eukaryotic cells encounter environmental stress. RNA-binding proteins (RBPs) mediate their condensation by recruiting populations of mRNPs. However, the cellular and molecular mechanisms underlying the role of ubiquitin-associated protein 2-like (UBAP2L) in the regulation of SG dynamics remain elusive. Here, we show that UBAP2L is required for both SG assembly and disassembly. UBAP2L overexpression nucleated SGs under stress-null conditions. The UBAP2L Arg–Gly–Gly (RGG) motif was required for SG competence, and mediated the recruitment of SG components, including mRNPs, RBPs, and ribosomal subunits. The domain of unknown function (DUF) of UBAP2L-mediated interaction with ras GTPase-activating protein-binding protein (G3BP)1/2, and its deletion caused the cytoplasmic–nuclear transport of UBAP2L and G3BP1/2, thereby compromising SG formation. The protein arginine methyltransferase PRMT1 asymmetrically dimethylated UBAP2L by targeting the RGG motif. Increased arginine methylation blocked, whereas its decrease enhanced UBAP2L interactions with SG components, ablating and promoting SG assembly, respectively. These results provide new insights into the mechanisms by which UBAP2L regulates SG dynamics and RNA metabolism.
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18
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Ivanov P, Kedersha N, Anderson P. Stress Granules and Processing Bodies in Translational Control. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032813. [PMID: 30082464 DOI: 10.1101/cshperspect.a032813] [Citation(s) in RCA: 272] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Stress granules (SGs) and processing bodies (PBs) are non-membrane-enclosed RNA granules that dynamically sequester translationally inactive messenger ribonucleoprotein particles (mRNPs) into compartments that are distinct from the surrounding cytoplasm. mRNP remodeling, silencing, and/or storage involves the dynamic partitioning of closed-loop polyadenylated mRNPs into SGs, or the sequestration of deadenylated, linear mRNPs into PBs. SGs form when stress-activated pathways stall translation initiation but allow elongation and termination to occur normally, resulting in a sudden excess of mRNPs that are spatially condensed into discrete foci by protein:protein, protein:RNA, and RNA:RNA interactions. In contrast, PBs can exist in the absence of stress, when specific factors promote mRNA deadenylation, condensation, and sequestration from the translational machinery. The formation and dissolution of SGs and PBs reflect changes in messenger RNA (mRNA) metabolism and allow cells to modulate the proteome and/or mediate life or death decisions during changing environmental conditions.
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Affiliation(s)
- Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, Massachusetts 02115.,Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115.,The Broad Institute of Harvard and M.I.T., Cambridge, Massachusetts 02142
| | - Nancy Kedersha
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, Massachusetts 02115.,Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115
| | - Paul Anderson
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, Massachusetts 02115.,Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115
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19
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Trivedi S, Starz-Gaiano M. Drosophila Jak/STAT Signaling: Regulation and Relevance in Human Cancer and Metastasis. Int J Mol Sci 2018; 19:ijms19124056. [PMID: 30558204 PMCID: PMC6320922 DOI: 10.3390/ijms19124056] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/08/2018] [Accepted: 12/11/2018] [Indexed: 12/26/2022] Open
Abstract
Over the past three-decades, Janus kinase (Jak) and signal transducer and activator of transcription (STAT) signaling has emerged as a paradigm to understand the involvement of signal transduction in development and disease pathology. At the molecular level, cytokines and interleukins steer Jak/STAT signaling to transcriptional regulation of target genes, which are involved in cell differentiation, migration, and proliferation. Jak/STAT signaling is involved in various types of blood cell disorders and cancers in humans, and its activation is associated with carcinomas that are more invasive or likely to become metastatic. Despite immense information regarding Jak/STAT regulation, the signaling network has numerous missing links, which is slowing the progress towards developing drug therapies. In mammals, many components act in this cascade, with substantial cross-talk with other signaling pathways. In Drosophila, there are fewer pathway components, which has enabled significant discoveries regarding well-conserved regulatory mechanisms. Work across species illustrates the relevance of these regulators in humans. In this review, we showcase fundamental Jak/STAT regulation mechanisms in blood cells, stem cells, and cell motility. We examine the functional relevance of key conserved regulators from Drosophila to human cancer stem cells and metastasis. Finally, we spotlight less characterized regulators of Drosophila Jak/STAT signaling, which stand as promising candidates to be investigated in cancer biology. These comparisons illustrate the value of using Drosophila as a model for uncovering the roles of Jak/STAT signaling and the molecular means by which the pathway is controlled.
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Affiliation(s)
- Sunny Trivedi
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
| | - Michelle Starz-Gaiano
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
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20
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Youn JY, Dunham WH, Hong SJ, Knight JDR, Bashkurov M, Chen GI, Bagci H, Rathod B, MacLeod G, Eng SWM, Angers S, Morris Q, Fabian M, Côté JF, Gingras AC. High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies. Mol Cell 2018; 69:517-532.e11. [PMID: 29395067 DOI: 10.1016/j.molcel.2017.12.020] [Citation(s) in RCA: 456] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 12/02/2017] [Accepted: 12/21/2017] [Indexed: 12/11/2022]
Abstract
mRNA processing, transport, translation, and ultimately degradation involve a series of dedicated protein complexes that often assemble into large membraneless structures such as stress granules (SGs) and processing bodies (PBs). Here, systematic in vivo proximity-dependent biotinylation (BioID) analysis of 119 human proteins associated with different aspects of mRNA biology uncovers 7424 unique proximity interactions with 1,792 proteins. Classical bait-prey analysis reveals connections of hundreds of proteins to distinct mRNA-associated processes or complexes, including the splicing and transcriptional elongation machineries (protein phosphatase 4) and the CCR4-NOT deadenylase complex (CEP85, RNF219, and KIAA0355). Analysis of correlated patterns between endogenous preys uncovers the spatial organization of RNA regulatory structures and enables the definition of 144 core components of SGs and PBs. We report preexisting contacts between most core SG proteins under normal growth conditions and demonstrate that several core SG proteins (UBAP2L, CSDE1, and PRRC2C) are critical for the formation of microscopically visible SGs.
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Affiliation(s)
- Ji-Young Youn
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Wade H Dunham
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Seo Jung Hong
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - James D R Knight
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Mikhail Bashkurov
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Ginny I Chen
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Halil Bagci
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada; Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada
| | - Bhavisha Rathod
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Graham MacLeod
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Simon W M Eng
- Department of Immunology, University of Toronto, Toronto, ON, Canada; Division of Rheumatology, The Hospital for Sick Children (SickKids), Toronto, ON, Canada
| | - Stéphane Angers
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Quaid Morris
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada; Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON, Canada
| | - Marc Fabian
- Department of Oncology, McGill University, Montréal, QC, Canada; Segal Cancer Centre, Jewish General Hospital, Lady Davis Institute for Medical Research, Montréal, QC, Canada
| | - Jean-François Côté
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada; Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada; Département de Biochimie, Université de Montréal, Montréal, QC, Canada; Département de Médecine (Programmes de Biologie Moléculaire), Université de Montréal, Montréal, QC, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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21
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He J, Chen Y, Cai L, Li Z, Guo X. UBAP2L silencing inhibits cell proliferation and G2/M phase transition in breast cancer. Breast Cancer 2017; 25:224-232. [PMID: 29196913 PMCID: PMC5818569 DOI: 10.1007/s12282-017-0820-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/15/2017] [Indexed: 12/21/2022]
Abstract
Background Ubiquitin-associated protein 2-like (UBAP2L) contains a ubiquitin-associated domain near its N-terminus, which has been demonstrated to be overexpressed in multiple tumors, including hepatocellular carcinoma and colorectal carcinoma but its role has not been well studied in breast cancer. Thus, this study was designed to evaluate whether UBAP2L can serve as a potential molecular target for breast cancer therapy. Methods The expression of UBAP2L was determined in breast cancer tissues and cell lines by Western blotting and Oncomine database mining. Then the expression of UBAP2L was silenced using RNA interference and the effects of UBAP2L knockdown on breast cancer cell proliferation and cell cycle progression by MTT and colony formation assay, and Flow cytometry, respectively. Results We found the expression of UBAP2L was significantly up-regulated in breast cancer tissues and cell lines. Knockdown of UBAP2L suppressed cell proliferation, impaired colony formation ability and induced cell cycle arrest at G2/M phase. At molecular levels, knockdown of UBAP2L increased p21 expression, but decreased the expression of CDK1 and Cyclin B1 in breast cancer cells. Conclusion Our findings suggest that UBAP2L plays an important role in breast cancer cell proliferation and might serve as a potential target for breast cancer treatment.
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Affiliation(s)
- Jing He
- Department of Oncology, The Affiliated Ganzhou Hospital of Nanchang University, No. 17 Hongqi Avenue, Ganzhou, 341000, Jiangxi, China
| | - Yuanping Chen
- Department of Oncology, The Affiliated Ganzhou Hospital of Nanchang University, No. 17 Hongqi Avenue, Ganzhou, 341000, Jiangxi, China
| | - Lu Cai
- Department of Oncology, The Affiliated Ganzhou Hospital of Nanchang University, No. 17 Hongqi Avenue, Ganzhou, 341000, Jiangxi, China
| | - Zelei Li
- Department of Oncology, The Affiliated Ganzhou Hospital of Nanchang University, No. 17 Hongqi Avenue, Ganzhou, 341000, Jiangxi, China
| | - Xiaoqing Guo
- Department of Oncology, The Affiliated Ganzhou Hospital of Nanchang University, No. 17 Hongqi Avenue, Ganzhou, 341000, Jiangxi, China.
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22
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Wu P, Jie W, Shang Q, Annan E, Jiang X, Hou C, Chen T, Guo X. DNA methylation in silkworm genome may provide insights into epigenetic regulation of response to Bombyx mori cypovirus infection. Sci Rep 2017; 7:16013. [PMID: 29167521 PMCID: PMC5700172 DOI: 10.1038/s41598-017-16357-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/10/2017] [Indexed: 12/27/2022] Open
Abstract
DNA methylation is an important epigenetic modification that regulates a wide range of biological processes including immune response. However, information on the epigenetics-mediated immune mechanisms in insects is limited. Therefore, in this study, we examined transcriptomes and DNA methylomes in the fat body and midgut tissues of silkworm, Bombyx mori with or without B. mori cytoplasmic polyhedrosis virus (BmCPV) infection. The transcriptional profile and the genomic DNA methylation patterns in the midgut and fat body were tissue-specific and dynamically altered after BmCPV challenge. KEGG pathway analysis revealed that differentially methylated genes (DMGs) could be involved in pathways of RNA transport, RNA degradation, nucleotide excision repair, DNA replication, etc. 27 genes were shown to have both differential expression and differential methylation in the midgut and fat body of infected larvae, respectively, indicating that the BmCPV infection-induced expression changes of these genes could be mediated by variations in DNA methylation. BS-PCR validated the hypomethylation of G2/M phase-specific E3 ubiquitin-protein ligase-like gene in the BmCPV infected midgut. These results demonstrated that epigenetic regulation may play roles in host-virus interaction in silkworm and would be potential value for further studies on mechanism of BmCPV epithelial-specific infection and epigenetic regulation in the silkworm.
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Affiliation(s)
- Ping Wu
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Wencai Jie
- Beijing Genomics Institute (BGI), Shenzhen, Guangdong, China
| | - Qi Shang
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Enoch Annan
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Xiaoxu Jiang
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Chenxiang Hou
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Tao Chen
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Xijie Guo
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China.
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23
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Aucagne R, Girard S, Mayotte N, Lehnertz B, Lopes-Paciencia S, Gendron P, Boucher G, Chagraoui J, Sauvageau G. UBAP2L is amplified in a large subset of human lung adenocarcinoma and is critical for epithelial lung cell identity and tumor metastasis. FASEB J 2017; 31:5012-5018. [PMID: 28754713 DOI: 10.1096/fj.201601219rrr] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 07/17/2017] [Indexed: 02/03/2023]
Abstract
The ubiquitin-associated protein 2-like (UBAP2L) gene remains poorly studied in human and mouse development. UBAP2L interacts with the Polycomb group protein B lymphoma Mo-MLV insertion region 1 homolog (BMI1) and determines the activity of mouse hematopoietic stem cells in vivo Here we show that loss of Ubap2l leads to disorganized respiratory epithelium of mutant neonates, which die of respiratory failure. We also show that UBAP2L overexpression leads to epithelial-mesenchymal transition-like phenotype in a non-small cell lung carcinoma (NSCLC) cell line. UBAP2L is amplified in 15% of human primary lung adenocarcinoma specimens. Such patients express higher levels of UBAP2L and show a reduction in survival when compared with those who do not have this gene amplification. Supporting a possible role for UBAP2L in lung tumor progression, NSCLC cells engineered to express low levels of this gene produce much smaller tumors in vivo than wild-type control cells. Together, these results suggest that UBAP2L contributes to epithelial lung cell identity in mice and that it plays an important role in human lung adenocarcinoma.-Aucagne, R., Girard, S., Mayotte, N., Lehnertz, B., Lopes-Paciencia, S., Gendron, P., Boucher, G., Chagraoui, J., Sauvageau, G. UBAP2L is amplified in a large subset of human lung adenocarcinoma and is critical for epithelial lung cell identity and tumor metastasis.
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Affiliation(s)
- Romain Aucagne
- Laboratory of Molecular Genetics of Stem Cells, Université de Montréal, Montreal, Québec, Canada
| | - Simon Girard
- Laboratory of Molecular Genetics of Stem Cells, Université de Montréal, Montreal, Québec, Canada
| | - Nadine Mayotte
- Laboratory of Molecular Genetics of Stem Cells, Université de Montréal, Montreal, Québec, Canada
| | - Bernhard Lehnertz
- Laboratory of Molecular Genetics of Stem Cells, Université de Montréal, Montreal, Québec, Canada
| | - Stéphane Lopes-Paciencia
- Laboratory of Molecular Genetics of Stem Cells, Université de Montréal, Montreal, Québec, Canada
| | - Patrick Gendron
- Bioinformatics Platform, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Québec, Canada
| | - Geneviève Boucher
- Bioinformatics Platform, Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Québec, Canada
| | - Jalila Chagraoui
- Laboratory of Molecular Genetics of Stem Cells, Université de Montréal, Montreal, Québec, Canada
| | - Guy Sauvageau
- Laboratory of Molecular Genetics of Stem Cells, Université de Montréal, Montreal, Québec, Canada; .,Department of Medicine, Université de Montréal, Montreal, Québec, Canada; and.,Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, Québec, Canada
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Wu Y, Zhu J, Huang X, Du Z. Crystal structure of a dimerization domain of human Caprin-1: insights into the assembly of an evolutionarily conserved ribonucleoprotein complex consisting of Caprin-1, FMRP and G3BP1. Acta Crystallogr D Struct Biol 2016; 72:718-27. [PMID: 27303792 PMCID: PMC4908866 DOI: 10.1107/s2059798316004903] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 03/23/2016] [Indexed: 01/04/2023] Open
Abstract
Caprin-1 plays roles in many important biological processes, including cellular proliferation, innate immune response, stress response and synaptic plasticity. Caprin-1 has been implicated in several human diseases, including osteosarcoma, breast cancer, viral infection, hearing loss and neurodegenerative disorders. The functions of Caprin-1 depend on its molecular-interaction network. Direct interactions have been established between Caprin-1 and the fragile X mental retardation protein (FMRP), Ras GAP-activating protein-binding protein 1 (G3BP1) and the Japanese encephalitis virus (JEV) core protein. Here, crystal structures of a fragment (residues 132-251) of Caprin-1, which adopts a novel all-α-helical fold and mediates homodimerization through a substantial interface, are reported. Homodimerization creates a large and highly negatively charged concave surface suggestive of a protein-binding groove. The FMRP-interacting sequence motif forms an integral α-helix in the dimeric Caprin-1 structure in such a way that the binding of FMRP would not disrupt the homodimerization of Caprin-1. Based on insights from the structures and existing biochemical data, the existence of an evolutionarily conserved ribonucleoprotein (RNP) complex consisting of Caprin-1, FMRP and G3BP1 is proposed. The JEV core protein may bind Caprin-1 at the negatively charged putative protein-binding groove and an adjacent E-rich sequence to hijack the RNP complex.
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Affiliation(s)
- Yuhong Wu
- Department of Chemistry and Biochemistry, Southern Illinois University, 1245 Lincoln Drive, Carbondale, IL 62901, USA
| | - Jiang Zhu
- Department of Chemistry and Biochemistry, Southern Illinois University, 1245 Lincoln Drive, Carbondale, IL 62901, USA
| | - Xiaolan Huang
- Department of Computer Science, Southern Illinois University, 1000 Faner Drive, Carbondale, IL 62901, USA
| | - Zhihua Du
- Department of Chemistry and Biochemistry, Southern Illinois University, 1245 Lincoln Drive, Carbondale, IL 62901, USA
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25
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Lecona-Valera AN, Tao D, Rodríguez MH, López T, Dinglasan RR, Rodríguez MC. An antibody against an Anopheles albimanus midgut myosin reduces Plasmodium berghei oocyst development. Parasit Vectors 2016; 9:274. [PMID: 27165123 PMCID: PMC4863318 DOI: 10.1186/s13071-016-1548-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/27/2016] [Indexed: 11/13/2022] Open
Abstract
Background Malaria parasites are transmitted by Anopheles mosquitoes. Although several studies have identified mosquito midgut surface proteins that are putatively important for Plasmodium ookinete invasion, only a few have characterized these protein targets and demonstrated transmission-blocking activity. Molecular information about these proteins is essential for the development of transmission-blocking vaccines (TBV). The aim of the present study was to test three monoclonal antibodies (mAbs), A-140, A-78 and A-10, for their ability to recognize antigens and block oocyst infection of the midgut of Anopheles albimanus, a major malaria vector in Latin America. Method Western-blot of mAbs on antigens from midgut brush border membrane vesicles was used to select antibodies. Three mAbs were tested by membrane feeding assays to evaluate their potential transmission-blocking activity against Plasmodium berghei. The cognate antigens recognized by mAbs with oocyst-reducing activity were determined by immunoprecipitation followed by liquid chromatography tandem mass spectrometry. Results Only one mAb, A-140, significantly reduced oocyst infection intensity. Hence, its probable protein target in the Anopheles albimanus midgut was identified and characterized. It recognized three high-molecular mass proteins from a midgut brush border microvilli vesicle preparation. Chemical deglycosylation assays confirmed the peptide nature of the epitope recognized by mAb A-140. Immunoprecipitation followed by proteomic identification with tandem mass spectrometry revealed five proteins, presumably extracted together as a complex. Of these, AALB007909 had the highest mascot score and corresponds to a protein with a myosin head motor domain, indicating that the target of mAb A-140 is probably myosin located on the microvilli of the mosquito midgut. Conclusion These results provide support for the participation of myosin in mosquito midgut invasion by Plasmodium ookinetes. The potential inclusion of this protein in the design of new multivalent vaccine strategies for blocking Plasmodium transmission is discussed. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1548-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alba N Lecona-Valera
- Center of Research on Infectious Diseases, National Institute of Public Health, Av. Universidad 655, Col. Santa María Ahuacatitlán, Cuernavaca, Morelos, C. P. 62508, Mexico
| | - Dingyin Tao
- W. Harry Feinstone Department of Molecular Microbiology & Immunology and the Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland, 21205, USA
| | - Mario H Rodríguez
- Center of Research on Infectious Diseases, National Institute of Public Health, Av. Universidad 655, Col. Santa María Ahuacatitlán, Cuernavaca, Morelos, C. P. 62508, Mexico
| | - Tomás López
- Instituto de Biotecnología, Universidad Nacional Autónoma de Méxic006F, Av. Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, 62210, Mexico
| | - Rhoel R Dinglasan
- W. Harry Feinstone Department of Molecular Microbiology & Immunology and the Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland, 21205, USA
| | - María C Rodríguez
- Center of Research on Infectious Diseases, National Institute of Public Health, Av. Universidad 655, Col. Santa María Ahuacatitlán, Cuernavaca, Morelos, C. P. 62508, Mexico.
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26
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Dash S, Siddam AD, Barnum CE, Janga SC, Lachke SA. RNA-binding proteins in eye development and disease: implication of conserved RNA granule components. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:527-57. [PMID: 27133484 DOI: 10.1002/wrna.1355] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/21/2016] [Indexed: 01/16/2023]
Abstract
The molecular biology of metazoan eye development is an area of intense investigation. These efforts have led to the surprising recognition that although insect and vertebrate eyes have dramatically different structures, the orthologs or family members of several conserved transcription and signaling regulators such as Pax6, Six3, Prox1, and Bmp4 are commonly required for their development. In contrast, our understanding of posttranscriptional regulation in eye development and disease, particularly regarding the function of RNA-binding proteins (RBPs), is limited. We examine the present knowledge of RBPs in eye development in the insect model Drosophila as well as several vertebrate models such as fish, frog, chicken, and mouse. Interestingly, of the 42 RBPs that have been investigated for their expression or function in vertebrate eye development, 24 (~60%) are recognized in eukaryotic cells as components of RNA granules such as processing bodies, stress granules, or other specialized ribonucleoprotein (RNP) complexes. We discuss the distinct developmental and cellular events that may necessitate potential RBP/RNA granule-associated RNA regulon models to facilitate posttranscriptional control of gene expression in eye morphogenesis. In support of these hypotheses, three RBPs and RNP/RNA granule components Tdrd7, Caprin2, and Stau2 are linked to ocular developmental defects such as congenital cataract, Peters anomaly, and microphthalmia in human patients or animal models. We conclude by discussing the utility of interdisciplinary approaches such as the bioinformatics tool iSyTE (integrated Systems Tool for Eye gene discovery) to prioritize RBPs for deriving posttranscriptional regulatory networks in eye development and disease. WIREs RNA 2016, 7:527-557. doi: 10.1002/wrna.1355 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Soma Dash
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Archana D Siddam
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Carrie E Barnum
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Sarath Chandra Janga
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University & Purdue University Indianapolis, Indianapolis, IN, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
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27
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Fros JJ, Geertsema C, Zouache K, Baggen J, Domeradzka N, van Leeuwen DM, Flipse J, Vlak JM, Failloux AB, Pijlman GP. Mosquito Rasputin interacts with chikungunya virus nsP3 and determines the infection rate in Aedes albopictus. Parasit Vectors 2015; 8:464. [PMID: 26384002 PMCID: PMC4573678 DOI: 10.1186/s13071-015-1070-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/03/2015] [Indexed: 01/22/2023] Open
Abstract
Background Chikungunya virus (CHIKV) is an arthritogenic alphavirus (family Togaviridae), transmitted by Aedes species mosquitoes. CHIKV re-emerged in 2004 with multiple outbreaks worldwide and recently reached the Americas where it has infected over a million individuals in a rapidly expanding epidemic. While alphavirus replication is well understood in general, the specific function (s) of non-structural protein nsP3 remain elusive. CHIKV nsP3 modulates the mammalian stress response by preventing stress granule formation through sequestration of G3BP. In mosquitoes, nsP3 is a determinant of vector specificity, but its functional interaction with mosquito proteins is unclear. Methods In this research we studied the domains required for localization of CHIKV nsP3 in insect cells and demonstrated its molecular interaction with Rasputin (Rin), the mosquito homologue of G3BP. The biological involvement of Rin in CHIKV infection was investigated in live Ae. albopictus mosquitoes. Results In insect cells, nsP3 localized as cytoplasmic granules, which was dependent on the central domain and the C-terminal variable region but independent of the N-terminal macrodomain. Ae. albopictus Rin displayed a diffuse, cytoplasmic localization, but was effectively sequestered into nsP3-granules upon nsP3 co-expression. Site-directed mutagenesis showed that the Rin-nsP3 interaction involved the NTF2-like domain of Rin and two conserved TFGD repeats in the C-terminal variable domain of nsP3. Although in vitro silencing of Rin did not impact nsP3 localization or CHIKV replication in cell culture, Rin depletion in vivo significantly decreased the CHIKV infection rate and transmissibility in Ae.albopictus. Conclusions We identified the nsP3 hypervariable C-terminal domain as a critical factor for granular localization and sequestration of mosquito Rin. Our study offers novel insight into a conserved virus-mosquito interaction at the molecular level, and reveals a strong proviral role for G3BP homologue Rin in live mosquitoes, making the nsP3-Rin interaction a putative target to interfere with the CHIKV transmission cycle.
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Affiliation(s)
- Jelke J Fros
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Corinne Geertsema
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Karima Zouache
- Institut Pasteur, Department of Virology, Arboviruses and Insect Vectors, 25-28 rue du Docteur Roux, 75724, Paris, cedex 15, France.
| | - Jim Baggen
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Natalia Domeradzka
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Daniël M van Leeuwen
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Jacky Flipse
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Just M Vlak
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Anna-Bella Failloux
- Institut Pasteur, Department of Virology, Arboviruses and Insect Vectors, 25-28 rue du Docteur Roux, 75724, Paris, cedex 15, France.
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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28
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Maeda M, Hasegawa H, Sugiyama M, Hyodo T, Ito S, Chen D, Asano E, Masuda A, Hasegawa Y, Hamaguchi M, Senga T. Arginine methylation of ubiquitin-associated protein 2-like is required for the accurate distribution of chromosomes. FASEB J 2015; 30:312-23. [PMID: 26381755 DOI: 10.1096/fj.14-268987] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 09/08/2015] [Indexed: 01/01/2023]
Abstract
Proper bioriented attachment of microtubules and kinetochores is essential for the precise distribution of duplicated chromosomes to each daughter cell. An aberrant kinetochore-microtubule attachment results in chromosome instability, which leads to cellular transformation or apoptosis. In this article, we show that ubiquitin-associated protein 2-like (UBAP2L) is necessary for correct kinetochore-microtubule attachment. Depletion of UBAP2L inhibited chromosome alignment in metaphase and delayed progression to anaphase by activating spindle assembly checkpoint signaling. In addition, UBAP2L knockdown increased side-on attachment of kinetochores along the microtubules and suppressed stable kinetochore fiber formation. A proteomics analysis identified protein arginine methyltransferase (PRMT)1 as a direct interaction partner of UBAP2L. UBAP2L has an arginine- and glycine-rich motif called the RGG/RG or GAR motif in the N terminus. Biochemical analysis confirmed that arginine residues in the RGG/RG motif of UBAP2L were directly methylated by PRMT1. Finally, we demonstrated that the RGG/RG motif of UBAP2L is essential for the proper alignment of chromosomes in metaphase for the accurate distribution of chromosomes. Our results show a possible role for arginine methylation in UBAP2L for the progression of mitosis.
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Affiliation(s)
- Masao Maeda
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hitoki Hasegawa
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mai Sugiyama
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toshinori Hyodo
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satoko Ito
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Dan Chen
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Eri Asano
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akio Masuda
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshinori Hasegawa
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Michinari Hamaguchi
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takeshi Senga
- *Division of Cancer Biology, Division of Neurogenetics, and Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Dong L, Li J, Huang H, Yin MX, Xu J, Li P, Lu Y, Wu W, Yang H, Zhao Y, Zhang L. Growth suppressor lingerer regulates bantam microRNA to restrict organ size. J Mol Cell Biol 2015; 7:415-28. [PMID: 26117838 DOI: 10.1093/jmcb/mjv045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 04/27/2015] [Indexed: 01/05/2023] Open
Abstract
The evolutionarily conserved Hippo signaling pathway plays an important role in organ size control by regulating cell proliferation and apoptosis. Here, we identify Lingerer (Lig) as a growth suppressor using RNAi modifying screen in Drosophila melanogaster. Loss of lig increases organ size and upregulates bantam (ban) and the expression of the Hippo pathway target genes, while overexpression of lig results in diminished ban expression and organ size reduction. We demonstrate that Lig C-terminal exhibits dominant-negative function on growth and ban expression, and thus plays an important role in organ size control and ban regulation. In addition, we provide evidence that both Yki and Mad are essential for Lig-induced ban expression. We also show that Lig regulates the expression of the Hippo pathway target genes partially via Yorkie. Moreover, we find that Lig physically interacts with and requires Salvador to restrict cell growth. Taken together, we demonstrate that Lig functions as a critical growth suppressor to control organ size via ban and Hippo signaling.
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Affiliation(s)
- Liang Dong
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jinhui Li
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hongling Huang
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Meng-Xin Yin
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jinjin Xu
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Peixue Li
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yi Lu
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wenqing Wu
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hang Yang
- Department of Biochemistry and Molecular Biology, USC Health Science Campus, Los Angeles, CA 90033, USA
| | - Yun Zhao
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lei Zhang
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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Kimura S, Sakakibara Y, Sato K, Ote M, Ito H, Koganezawa M, Yamamoto D. TheDrosophilalingerer protein cooperates with Orb2 in long-term memory formation. J Neurogenet 2014; 29:8-17. [DOI: 10.3109/01677063.2014.917644] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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