101
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Lumb JH, Li Q, Popov LM, Ding S, Keith MT, Merrill BD, Greenberg HB, Li JB, Carette JE. DDX6 Represses Aberrant Activation of Interferon-Stimulated Genes. Cell Rep 2018; 20:819-831. [PMID: 28746868 DOI: 10.1016/j.celrep.2017.06.085] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/30/2017] [Accepted: 06/28/2017] [Indexed: 12/31/2022] Open
Abstract
The innate immune system tightly regulates activation of interferon-stimulated genes (ISGs) to avoid inappropriate expression. Pathological ISG activation resulting from aberrant nucleic acid metabolism has been implicated in autoimmune disease; however, the mechanisms governing ISG suppression are unknown. Through a genome-wide genetic screen, we identified DEAD-box helicase 6 (DDX6) as a suppressor of ISGs. Genetic ablation of DDX6 induced global upregulation of ISGs and other immune genes. ISG upregulation proved cell intrinsic, imposing an antiviral state and making cells refractory to divergent families of RNA viruses. Epistatic analysis revealed that ISG activation could not be overcome by deletion of canonical RNA sensors. However, DDX6 deficiency was suppressed by disrupting LSM1, a core component of mRNA degradation machinery, suggesting that dysregulation of RNA processing underlies ISG activation in the DDX6 mutant. DDX6 is distinct among DExD/H helicases that regulate the antiviral response in its singular ability to negatively regulate immunity.
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Affiliation(s)
- Jennifer H Lumb
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Qin Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Lauren M Popov
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Siyuan Ding
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA; Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Palo Alto Veterans Institute of Research, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Marie T Keith
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Bryan D Merrill
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Harry B Greenberg
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA; Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Palo Alto Veterans Institute of Research, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
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102
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Courel M, Bénard M, Ernoult-Lange M, Chouaib R, Hubstenberger A, Kress M, Weil D. [P-bodies: microscopic droplets to store mRNAs encoding regulatory proteins]. Med Sci (Paris) 2018; 34:306-308. [PMID: 29658471 DOI: 10.1051/medsci/20183404009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Maïté Courel
- Sorbonne université, CNRS, institut de biologie Paris-Seine (IBPS), Laboratoire de biologie du développement, 7, quai Saint Bernard, F-75005 Paris, France
| | - Marianne Bénard
- Sorbonne université, CNRS, institut de biologie Paris-Seine (IBPS), Laboratoire de biologie du développement, 7, quai Saint Bernard, F-75005 Paris, France
| | - Michèle Ernoult-Lange
- Sorbonne université, CNRS, institut de biologie Paris-Seine (IBPS), Laboratoire de biologie du développement, 7, quai Saint Bernard, F-75005 Paris, France
| | - Racha Chouaib
- Sorbonne université, CNRS, institut de biologie Paris-Seine (IBPS), Laboratoire de biologie du développement, 7, quai Saint Bernard, F-75005 Paris, France - Département de biologie, faculté de sciences, université du Liban, Beyrouth, Liban
| | - Arnaud Hubstenberger
- Sorbonne université, CNRS, institut de biologie Paris-Seine (IBPS), Laboratoire de biologie du développement, 7, quai Saint Bernard, F-75005 Paris, France - Université Côte d'Azur, CNRS, Inserm, institut de biologie Valrose, Nice, France
| | - Michel Kress
- Sorbonne université, CNRS, institut de biologie Paris-Seine (IBPS), Laboratoire de biologie du développement, 7, quai Saint Bernard, F-75005 Paris, France
| | - Dominique Weil
- Sorbonne université, CNRS, institut de biologie Paris-Seine (IBPS), Laboratoire de biologie du développement, 7, quai Saint Bernard, F-75005 Paris, France
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103
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Vindry C, Marnef A, Broomhead H, Twyffels L, Ozgur S, Stoecklin G, Llorian M, Smith CW, Mata J, Weil D, Standart N. Dual RNA Processing Roles of Pat1b via Cytoplasmic Lsm1-7 and Nuclear Lsm2-8 Complexes. Cell Rep 2018; 20:1187-1200. [PMID: 28768202 PMCID: PMC5554784 DOI: 10.1016/j.celrep.2017.06.091] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/12/2017] [Accepted: 06/28/2017] [Indexed: 12/16/2022] Open
Abstract
Pat1 RNA-binding proteins, enriched in processing bodies (P bodies), are key players in cytoplasmic 5' to 3' mRNA decay, activating decapping of mRNA in complex with the Lsm1-7 heptamer. Using co-immunoprecipitation and immunofluorescence approaches coupled with RNAi, we provide evidence for a nuclear complex of Pat1b with the Lsm2-8 heptamer, which binds to the spliceosomal U6 small nuclear RNA (snRNA). Furthermore, we establish the set of interactions connecting Pat1b/Lsm2-8/U6 snRNA/SART3 and additional U4/U6.U5 tri-small nuclear ribonucleoprotein particle (tri-snRNP) components in Cajal bodies, the site of snRNP biogenesis. RNA sequencing following Pat1b depletion revealed the preferential upregulation of mRNAs normally found in P bodies and enriched in 3' UTR AU-rich elements. Changes in >180 alternative splicing events were also observed, characterized by skipping of regulated exons with weak donor sites. Our data demonstrate the dual role of a decapping enhancer in pre-mRNA processing as well as in mRNA decay via distinct nuclear and cytoplasmic Lsm complexes.
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Affiliation(s)
- Caroline Vindry
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Aline Marnef
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse UT3, 31062 Toulouse, France
| | - Helen Broomhead
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Laure Twyffels
- Center for Microscopy and Molecular Imaging (CMMI), Université libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Sevim Ozgur
- Max Planck Institute of Biochemistry, Am Klopferspitz, 82152 Martinsried, Germany
| | - Georg Stoecklin
- Division of Biochemistry, Center for Biomedicine and Medical Technology Mannheim, Medical Faculty Mannheim, Heidelberg University, 69047 Heidelberg, Germany; Center for Molecular Biology of Heidelberg University (ZMBH), 69047 Heidelberg, Germany; German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 68167 Mannheim, Germany
| | - Miriam Llorian
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Christopher W Smith
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Juan Mata
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Dominique Weil
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie du développement Paris Seine - Institut de Biologie Paris Seine (LBD - IBPS), 75005 Paris, France
| | - Nancy Standart
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK.
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104
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Qi MY, Song JW, Zhang Z, Huang S, Jing Q. P38 activation induces the dissociation of tristetraprolin from Argonaute 2 to increase ARE-mRNA stabilization. Mol Biol Cell 2018; 29:988-1002. [PMID: 29444957 PMCID: PMC5896936 DOI: 10.1091/mbc.e17-02-0105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
ARE-mRNAs are actively degraded with tristetraprolin (TTP) in resting cells while they turn into stable messengers in activated cells. P38 plays a crucial role in stabilizing ARE-mRNA. Here we reveal that P38 activation represses the interaction between TTP and Ago2, thus restraining TTP from being targeted into processing bodies and stabilizing ARE-mRNA.
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Affiliation(s)
- Mei-Yan Qi
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jing-Wen Song
- Department of Cardiology, Changhai Hospital, Shanghai 200433, China
| | - Zhuo Zhang
- Department of Cardiology, Changhai Hospital, Shanghai 200433, China.,Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Shuang Huang
- Department of Cardiology, Changhai Hospital, Shanghai 200433, China
| | - Qing Jing
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Department of Cardiology, Changhai Hospital, Shanghai 200433, China
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105
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Abstract
Processing bodies (P-bodies) are cytoplasmic ribonucleoprotein (RNP) granules primarily composed of translationally repressed mRNAs and proteins related to mRNA decay, suggesting roles in post-transcriptional regulation. P-bodies are conserved in eukaryotic cells and exhibit properties of liquid droplets. However, the function of P-bodies in translational repression and/or mRNA decay remains contentious. Here we review recent advances in our understanding of the molecular composition of P-bodies, the interactions and processes that regulate P-body liquid-liquid phase separation (LLPS), and the cellular localization of mRNA decay machinery, in the context of how these discoveries refine models of P-body function.
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Affiliation(s)
- Yang Luo
- Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States.,Chemical Biology Institute , Yale University , West Haven , Connecticut 06516 , United States
| | - Zhenkun Na
- Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States.,Chemical Biology Institute , Yale University , West Haven , Connecticut 06516 , United States
| | - Sarah A Slavoff
- Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States.,Chemical Biology Institute , Yale University , West Haven , Connecticut 06516 , United States.,Department of Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06529 , United States
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106
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Kershaw CJ, Ashe MP. Untangling P-Bodies: Dissecting the Complex Web of Interactions that Enable Tiered Control of Gene Expression. Mol Cell 2017; 68:3-4. [PMID: 28985509 DOI: 10.1016/j.molcel.2017.09.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In this issue of Molecular Cell, Hubstenberger et al. (2017) define the molecular composition of P-bodies isolated from human epithelial cells to propose that these foci act as mRNA storage depots rather than mRNA decay facilities.
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Affiliation(s)
- Christopher J Kershaw
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Mark P Ashe
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.
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107
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Regulation of epithelial-mesenchymal transition and metastasis by TGF-β, P-bodies, and autophagy. Oncotarget 2017; 8:103302-103314. [PMID: 29262563 PMCID: PMC5732729 DOI: 10.18632/oncotarget.21871] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 09/29/2017] [Indexed: 12/19/2022] Open
Abstract
Processing bodies (P-bodies) are ribonucleoprotein complexes involved in post-transcriptional mRNA metabolism that accumulate in cells exposed to various stress stimuli. The treatment of mammary epithelial cells with transforming growth factor-beta (TGF-β), triggers epithelial-mesenchymal transition (EMT), and induces the formation of P-bodies. Ectopic expression of the transcription factor TWIST, which stimulates EMT downstream of the TGF-β receptor, also promotes P-body formation. Removal of TGF-β from treated cells results in the clearance of P-bodies by a process that is blocked by inhibitors of autophagy. Activators of autophagy enhance P-body clearance and block EMT. Blockage of P-body formation by disruption of the gene for DDX6, a protein essential for P-body assembly, blocks EMT and prevents tumor cell metastasis in vivo. These studies suggest critical roles for P-body formation and autophagy in transitions of cancer cells between epithelial and mesenchymal phenotypes and help explain how autophagy functions to promote or suppress tumor cell growth during different stages of tumorigenesis.
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108
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Götze M, Dufourt J, Ihling C, Rammelt C, Pierson S, Sambrani N, Temme C, Sinz A, Simonelig M, Wahle E. Translational repression of the Drosophila nanos mRNA involves the RNA helicase Belle and RNA coating by Me31B and Trailer hitch. RNA (NEW YORK, N.Y.) 2017; 23:1552-1568. [PMID: 28701521 PMCID: PMC5602113 DOI: 10.1261/rna.062208.117] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/10/2017] [Indexed: 05/10/2023]
Abstract
Translational repression of maternal mRNAs is an essential regulatory mechanism during early embryonic development. Repression of the Drosophila nanos mRNA, required for the formation of the anterior-posterior body axis, depends on the protein Smaug binding to two Smaug recognition elements (SREs) in the nanos 3' UTR. In a comprehensive mass spectrometric analysis of the SRE-dependent repressor complex, we identified Smaug, Cup, Me31B, Trailer hitch, eIF4E, and PABPC, in agreement with earlier data. As a novel component, the RNA-dependent ATPase Belle (DDX3) was found, and its involvement in deadenylation and repression of nanos was confirmed in vivo. Smaug, Cup, and Belle bound stoichiometrically to the SREs, independently of RNA length. Binding of Me31B and Tral was also SRE-dependent, but their amounts were proportional to the length of the RNA and equimolar to each other. We suggest that "coating" of the RNA by a Me31B•Tral complex may be at the core of repression.
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Affiliation(s)
- Michael Götze
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Jérémy Dufourt
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34396 Montpellier Cedex 5, France
| | - Christian Ihling
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Christiane Rammelt
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Stephanie Pierson
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34396 Montpellier Cedex 5, France
| | - Nagraj Sambrani
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34396 Montpellier Cedex 5, France
| | - Claudia Temme
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Martine Simonelig
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34396 Montpellier Cedex 5, France
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
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109
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Hubstenberger A, Courel M, Bénard M, Souquere S, Ernoult-Lange M, Chouaib R, Yi Z, Morlot JB, Munier A, Fradet M, Daunesse M, Bertrand E, Pierron G, Mozziconacci J, Kress M, Weil D. P-Body Purification Reveals the Condensation of Repressed mRNA Regulons. Mol Cell 2017; 68:144-157.e5. [PMID: 28965817 DOI: 10.1016/j.molcel.2017.09.003] [Citation(s) in RCA: 455] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 06/05/2017] [Accepted: 08/31/2017] [Indexed: 01/27/2023]
Abstract
Within cells, soluble RNPs can switch states to coassemble and condense into liquid or solid bodies. Although these phase transitions have been reconstituted in vitro, for endogenous bodies the diversity of the components, the specificity of the interaction networks, and the function of the coassemblies remain to be characterized. Here, by developing a fluorescence-activated particle sorting (FAPS) method to purify cytosolic processing bodies (P-bodies) from human epithelial cells, we identified hundreds of proteins and thousands of mRNAs that structure a dense network of interactions, separating P-body from non-P-body RNPs. mRNAs segregating into P-bodies are translationally repressed, but not decayed, and this repression explains part of the poor genome-wide correlation between RNA and protein abundance. P-bodies condense thousands of mRNAs that strikingly encode regulatory processes. Thus, we uncovered how P-bodies, by condensing and segregating repressed mRNAs, provide a physical substrate for the coordinated regulation of posttranscriptional mRNA regulons.
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Affiliation(s)
- Arnaud Hubstenberger
- UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 7622, F-75005 Paris, France; Université Côte d'Azur, CNRS, Inserm, iBV, Nice, France.
| | - Maïté Courel
- UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 7622, F-75005 Paris, France
| | - Marianne Bénard
- UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 7622, F-75005 Paris, France
| | - Sylvie Souquere
- CNRS UMR-9196, Institut Gustave Roussy, F-94800 Villejuif, France
| | - Michèle Ernoult-Lange
- UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 7622, F-75005 Paris, France
| | - Racha Chouaib
- UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 7622, F-75005 Paris, France; IGMM, CNRS, University Montpellier, F-34090 Montpellier, France
| | - Zhou Yi
- UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 7622, F-75005 Paris, France
| | | | - Annie Munier
- UPMC Univ Paris 06, LUMIC, UMS30, F-75005 Paris, France
| | | | - Maëlle Daunesse
- École Normale Supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l'École Normale Supérieure (IBENS), Genomic Paris Centre, IBENS, F-75005 Paris, France
| | | | - Gérard Pierron
- CNRS UMR-9196, Institut Gustave Roussy, F-94800 Villejuif, France
| | | | - Michel Kress
- UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 7622, F-75005 Paris, France
| | - Dominique Weil
- UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 7622, F-75005 Paris, France.
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110
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Lee J, Yoo E, Lee H, Park K, Hur JH, Lim C. LSM12 and ME31B/DDX6 Define Distinct Modes of Posttranscriptional Regulation by ATAXIN-2 Protein Complex in Drosophila Circadian Pacemaker Neurons. Mol Cell 2017; 66:129-140.e7. [PMID: 28388438 DOI: 10.1016/j.molcel.2017.03.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 01/04/2017] [Accepted: 03/03/2017] [Indexed: 01/12/2023]
Abstract
ATAXIN-2 (ATX2) has been implicated in human neurodegenerative diseases, yet it remains elusive how ATX2 assembles specific protein complexes to execute its physiological roles. Here we employ the posttranscriptional co-activator function of Drosophila ATX2 to demonstrate that LSM12 and ME31B/DDX6 are two ATX2-associating factors crucial for sustaining circadian rhythms. LSM12 acts as a molecular adaptor for the recruitment of TWENTY-FOUR (TYF) to ATX2. The ATX2-LSM12-TYF complex thereby stimulates TYF-dependent translation of the rate-limiting clock gene period (per) to maintain 24 hr periodicity in circadian behaviors. In contrast, ATX2 contributes to NOT1-mediated gene silencing and associates with NOT1 in a ME31B/DDX6-dependent manner. The ME31B/DDX6-NOT1 complex does not affect PER translation but supports high-amplitude behavioral rhythms along with ATX2, indicating a PER-independent clock function of ATX2. Taken together, these data suggest that the ATX2 complex may switch distinct modes of posttranscriptional regulation through its associating factors to control circadian clocks and ATX2-related physiology.
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Affiliation(s)
- Jongbo Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Eunseok Yoo
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Hoyeon Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Keunhee Park
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jin-Hoe Hur
- UNIST-Olympus Biomed Imaging Center, UNIST, Ulsan 44919, Republic of Korea
| | - Chunghun Lim
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
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111
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DEAD-box helicase 6 (DDX6) is a new negative regulator for milk synthesis and proliferation of bovine mammary epithelial cells. In Vitro Cell Dev Biol Anim 2017; 54:52-60. [DOI: 10.1007/s11626-017-0195-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 08/09/2017] [Indexed: 12/11/2022]
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112
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Auburger G, Sen NE, Meierhofer D, Başak AN, Gitler AD. Efficient Prevention of Neurodegenerative Diseases by Depletion of Starvation Response Factor Ataxin-2. Trends Neurosci 2017; 40:507-516. [DOI: 10.1016/j.tins.2017.06.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 06/09/2017] [Indexed: 12/13/2022]
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113
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Wang X, Chang L, Wang H, Su A, Wu Z. Dcp1a and GW182 Induce Distinct Cellular Aggregates and Have Different Effects on microRNA Pathway. DNA Cell Biol 2017; 36:565-570. [DOI: 10.1089/dna.2017.3633] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Xiaohui Wang
- Department of Hematology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, People's Republic of China
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Liang Chang
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Huanru Wang
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Airong Su
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Zhiwei Wu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, People's Republic of China
- State Key Lab of Analytical Chemistry for Life Science, Nanjing University, Nanjing, People's Republic of China
- Jiangsu Laboratory for Molecular Medicines, Nanjing University, Nanjing, People's Republic of China
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114
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Huang JH, Ku WC, Chen YC, Chang YL, Chu CY. Dual mechanisms regulate the nucleocytoplasmic localization of human DDX6. Sci Rep 2017; 7:42853. [PMID: 28216671 PMCID: PMC5316971 DOI: 10.1038/srep42853] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/18/2017] [Indexed: 12/14/2022] Open
Abstract
DDX6 is a conserved DEAD-box protein (DBP) that plays central roles in cytoplasmic RNA regulation, including processing body (P-body) assembly, mRNA decapping, and translational repression. Beyond its cytoplasmic functions, DDX6 may also have nuclear functions because its orthologues are known to localize to nuclei in several biological contexts. However, it is unclear whether DDX6 is generally present in human cell nuclei, and the molecular mechanism underlying DDX6 subcellular distribution remains elusive. In this study, we showed that DDX6 is commonly present in the nuclei of human-derived cells. Our structural and molecular analyses deviate from the current model that the shuttling of DDX6 is directly mediated by the canonical nuclear localization signal (NLS) and nuclear export signal (NES), which are recognized and transported by Importin-α/β and CRM1, respectively. Instead, we show that DDX6 can be transported by 4E-T in a piggyback manner. Furthermore, we provide evidence for a novel nuclear targeting mechanism in which DDX6 enters the newly formed nuclei by "hitch-hiking" on mitotic chromosomes with its C-terminal domain during M phase progression. Together, our results indicate that the nucleocytoplasmic localization of DDX6 is regulated by these dual mechanisms.
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Affiliation(s)
- Jo-Hsi Huang
- Department of Life Science, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Wei-Chi Ku
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei 24205, Taiwan
| | - Yen-Chun Chen
- Department of Life Science, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Ling Chang
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei 24205, Taiwan
| | - Chia-Ying Chu
- Department of Life Science, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
- Center for Systems Biology, National Taiwan University, Taipei 10617, Taiwan
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115
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Attacked from All Sides: RNA Decay in Antiviral Defense. Viruses 2017; 9:v9010002. [PMID: 28054965 PMCID: PMC5294971 DOI: 10.3390/v9010002] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/22/2016] [Accepted: 12/26/2016] [Indexed: 12/22/2022] Open
Abstract
The innate immune system has evolved a number of sensors that recognize viral RNA (vRNA) to restrict infection, yet the full spectrum of host-encoded RNA binding proteins that target these foreign RNAs is still unknown. The RNA decay machinery, which uses exonucleases to degrade aberrant RNAs largely from the 5′ or 3′ end, is increasingly recognized as playing an important role in antiviral defense. The 5′ degradation pathway can directly target viral messenger RNA (mRNA) for degradation, as well as indirectly attenuate replication by limiting specific pools of endogenous RNAs. The 3′ degradation machinery (RNA exosome) is emerging as a downstream effector of a diverse array of vRNA sensors. This review discusses our current understanding of the roles of the RNA decay machinery in controlling viral infection.
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Jungfleisch J, Blasco-Moreno B, Díez J. Use of Cellular Decapping Activators by Positive-Strand RNA Viruses. Viruses 2016; 8:v8120340. [PMID: 28009841 PMCID: PMC5192400 DOI: 10.3390/v8120340] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/06/2016] [Accepted: 12/19/2016] [Indexed: 12/14/2022] Open
Abstract
Positive-strand RNA viruses have evolved multiple strategies to not only circumvent the hostile decay machinery but to trick it into being a priceless collaborator supporting viral RNA translation and replication. In this review, we describe the versatile interaction of positive-strand RNA viruses and the 5′-3′ mRNA decay machinery with a focus on the viral subversion of decapping activators. This highly conserved viral trickery is exemplified with the plant Brome mosaic virus, the animal Flock house virus and the human hepatitis C virus.
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Affiliation(s)
- Jennifer Jungfleisch
- Molecular Virology Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain.
| | - Bernat Blasco-Moreno
- Molecular Virology Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain.
| | - Juana Díez
- Molecular Virology Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain.
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Frydryskova K, Masek T, Borcin K, Mrvova S, Venturi V, Pospisek M. Distinct recruitment of human eIF4E isoforms to processing bodies and stress granules. BMC Mol Biol 2016; 17:21. [PMID: 27578149 PMCID: PMC5006505 DOI: 10.1186/s12867-016-0072-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/16/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Eukaryotic translation initiation factor 4E (eIF4E) plays a pivotal role in the control of cap-dependent translation initiation, modulates the fate of specific mRNAs, occurs in processing bodies (PBs) and is required for formation of stress granules (SGs). In this study, we focused on the subcellular localization of a representative compendium of eIF4E protein isoforms, particularly on the less studied members of the human eIF4E protein family, eIF4E2 and eIF4E3. RESULTS We showed that unlike eIF4E1, its less studied isoform eIF4E3_A, encoded by human chromosome 3, localized to stress granules but not PBs upon both heat shock and arsenite stress. Furthermore, we found that eIF4E3_A interacts with human translation initiation factors eIF4G1, eIF4G3 and PABP1 in vivo and sediments into the same fractions as canonical eIF4E1 during polysome analysis in sucrose gradients. Contrary to this finding, the truncated human eIF4E3 isoform, eIF4E3_B, showed no localization to SGs and no binding to eIF4G. We also highlighted that eIF4E2 may exhibit distinct functions under different stresses as it readily localizes to P-bodies during arsenite and heat stresses, whereas it is redirected to stress granules only upon heat shock. We extended our study to a number of protein variants, arising from alternative mRNA splicing, of each of the three eIF4E isoforms. Our results surprisingly uncovered differences in the ability of eIF4E1_1 and eIF4E1_3 to form stress granules in response to cellular stresses. CONCLUSION Our comparison of all three human eIF4E isoforms and their protein variants enriches the intriguing spectrum of roles attributed to the eukaryotic initiation translation factors of the 4E family, which exhibit a distinctive localization within different RNA granules under different stresses. The localization of eIF4E3_A to stress granules, but not to processing bodies, along with its binding to eIF4G and PABP1 suggests a role of human eIF4E3_A in translation initiation rather than its involvement in a translational repression and mRNA decay and turnover. The localization of eIF4E2 to stress granules under heat shock but not arsenite stress indicates its distinct function in cellular response to these stresses and points to the variable protein content of SGs as a consequence of different stress insults.
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Affiliation(s)
- Klara Frydryskova
- Laboratory of RNA Biochemistry, Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 00, Prague 2, Czech Republic
| | - Tomas Masek
- Laboratory of RNA Biochemistry, Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 00, Prague 2, Czech Republic.
| | - Katerina Borcin
- Laboratory of RNA Biochemistry, Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 00, Prague 2, Czech Republic
| | - Silvia Mrvova
- Laboratory of RNA Biochemistry, Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 00, Prague 2, Czech Republic
| | - Veronica Venturi
- Laboratory of RNA Biochemistry, Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 00, Prague 2, Czech Republic.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Martin Pospisek
- Laboratory of RNA Biochemistry, Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 00, Prague 2, Czech Republic.
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Kamenska A, Simpson C, Vindry C, Broomhead H, Bénard M, Ernoult-Lange M, Lee BP, Harries LW, Weil D, Standart N. The DDX6-4E-T interaction mediates translational repression and P-body assembly. Nucleic Acids Res 2016; 44:6318-34. [PMID: 27342281 PMCID: PMC5291280 DOI: 10.1093/nar/gkw565] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/10/2016] [Accepted: 06/14/2016] [Indexed: 12/13/2022] Open
Abstract
4E-Transporter binds eIF4E via its consensus sequence YXXXXLΦ, shared with eIF4G, and is a nucleocytoplasmic shuttling protein found enriched in P-(rocessing) bodies. 4E-T inhibits general protein synthesis by reducing available eIF4E levels. Recently, we showed that 4E-T bound to mRNA however represses its translation in an eIF4E-independent manner, and contributes to silencing of mRNAs targeted by miRNAs. Here, we address further the mechanism of translational repression by 4E-T by first identifying and delineating the interacting sites of its major partners by mass spectrometry and western blotting, including DDX6, UNR, unrip, PAT1B, LSM14A and CNOT4. Furthermore, we document novel binding between 4E-T partners including UNR-CNOT4 and unrip-LSM14A, altogether suggesting 4E-T nucleates a complex network of RNA-binding protein interactions. In functional assays, we demonstrate that joint deletion of two short conserved motifs that bind UNR and DDX6 relieves repression of 4E-T-bound mRNA, in part reliant on the 4E-T-DDX6-CNOT1 axis. We also show that the DDX6-4E-T interaction mediates miRNA-dependent translational repression and de novo P-body assembly, implying that translational repression and formation of new P-bodies are coupled processes. Altogether these findings considerably extend our understanding of the role of 4E-T in gene regulation, important in development and neurogenesis.
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Affiliation(s)
- Anastasiia Kamenska
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK
| | - Clare Simpson
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK
| | - Caroline Vindry
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK
| | - Helen Broomhead
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK
| | - Marianne Bénard
- Sorbonne Universités, UPMC, CNRS, IBPS, Developmental Biology Laboratory, 75005 Paris, France
| | - Michèle Ernoult-Lange
- Sorbonne Universités, UPMC, CNRS, IBPS, Developmental Biology Laboratory, 75005 Paris, France
| | - Benjamin P Lee
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter EX2 5DW
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter EX2 5DW
| | - Dominique Weil
- Sorbonne Universités, UPMC, CNRS, IBPS, Developmental Biology Laboratory, 75005 Paris, France
| | - Nancy Standart
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK
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Ozgur S, Basquin J, Kamenska A, Filipowicz W, Standart N, Conti E. Structure of a Human 4E-T/DDX6/CNOT1 Complex Reveals the Different Interplay of DDX6-Binding Proteins with the CCR4-NOT Complex. Cell Rep 2015; 13:703-711. [DOI: 10.1016/j.celrep.2015.09.033] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 08/05/2015] [Accepted: 09/10/2015] [Indexed: 01/09/2023] Open
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Bish R, Cuevas-Polo N, Cheng Z, Hambardzumyan D, Munschauer M, Landthaler M, Vogel C. Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins. Biomolecules 2015; 5:1441-66. [PMID: 26184334 PMCID: PMC4598758 DOI: 10.3390/biom5031441] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 06/15/2015] [Indexed: 12/24/2022] Open
Abstract
DDX6 (p54/RCK) is a human RNA helicase with central roles in mRNA decay and translation repression. To help our understanding of how DDX6 performs these multiple functions, we conducted the first unbiased, large-scale study to map the DDX6-centric protein-protein interactome using immunoprecipitation and mass spectrometry. Using DDX6 as bait, we identify a high-confidence and high-quality set of protein interaction partners which are enriched for functions in RNA metabolism and ribosomal proteins. The screen is highly specific, maximizing the number of true positives, as demonstrated by the validation of 81% (47/58) of the RNA-independent interactors through known functions and interactions. Importantly, we minimize the number of indirect interaction partners through use of a nuclease-based digestion to eliminate RNA. We describe eleven new interactors, including proteins involved in splicing which is an as-yet unknown role for DDX6. We validated and characterized in more detail the interaction of DDX6 with Nuclear fragile X mental retardation-interacting protein 2 (NUFIP2) and with two previously uncharacterized proteins, FAM195A and FAM195B (here referred to as granulin-1 and granulin-2, or GRAN1 and GRAN2). We show that NUFIP2, GRAN1, and GRAN2 are not P-body components, but re-localize to stress granules upon exposure to stress, suggesting a function in translation repression in the cellular stress response. Using a complementary analysis that resolved DDX6's multiple complex memberships, we further validated these interaction partners and the presence of splicing factors. As DDX6 also interacts with the E3 SUMO ligase TIF1β, we tested for and observed a significant enrichment of sumoylation amongst DDX6's interaction partners. Our results represent the most comprehensive screen for direct interaction partners of a key regulator of RNA life cycle and localization, highlighting new stress granule components and possible DDX6 functions-many of which are likely conserved across eukaryotes.
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Affiliation(s)
- Rebecca Bish
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA.
| | - Nerea Cuevas-Polo
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA.
| | - Zhe Cheng
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA.
| | - Dolores Hambardzumyan
- The Cleveland Clinic, Department of Neurosciences, Lerner Research Institute, 9500 Euclid Avenue, Cleveland, OH 44195, USA.
| | - Mathias Munschauer
- RNA Biology and Post-Transcriptional Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin-Buch, Robert-Rössle-Str. 10, Berlin 13092, Germany.
| | - Markus Landthaler
- RNA Biology and Post-Transcriptional Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin-Buch, Robert-Rössle-Str. 10, Berlin 13092, Germany.
| | - Christine Vogel
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA.
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