1
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Hurst Z, Liu W, Shi Q, Herman PK. A distinct P-body-like granule is induced in response to the disruption of microtubule integrity in Saccharomyces cerevisiae. Genetics 2022; 222:6649695. [PMID: 35876801 PMCID: PMC9434292 DOI: 10.1093/genetics/iyac105] [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: 06/09/2022] [Accepted: 07/08/2022] [Indexed: 11/12/2022] Open
Abstract
The Processing-body (P-body) is a conserved membraneless organelle that has been implicated in the storage and/or decay of mRNAs. Although P-bodies have been shown to be induced by a variety of conditions, the mechanisms controlling their assembly and their precise physiological roles in eukaryotic cells are still being worked out. In this study, we find that a distinct subtype of P-body is induced in response to conditions that disrupt microtubule integrity in the budding yeast, Saccharomyces cerevisiae. For example, treatment with the microtubule-destabilizing agent, benomyl, led to the induction of these novel ribonucleoprotein (RNP) granules. A link to microtubules had been noted previously and the observations here extend our understanding by demonstrating that the induced foci differ from traditional P-bodies in a number of significant ways. These include differences in overall granule morphology, protein composition and the manner in which their induction is regulated. Of particular note, several key P-body constituents are absent from these Benomyl-Induced Granules (BIGs), including the Pat1 protein that is normally required for efficient P-body assembly. However, these novel RNP structures still contain many known P-body proteins and exhibit similar hallmarks of a liquid-like compartment. In all, the data suggest that the disruption of microtubule integrity leads to the formation of a novel type of P-body granule that may have distinct biological activities in the cell. Future work will aim to identify the biological activities of these BIGs and to determine, in turn, whether these P-body-like granules have any role in the regulation of microtubule dynamics.
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Affiliation(s)
- Zachary Hurst
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210 USA
| | - Wenfang Liu
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210 USA
| | - Qian Shi
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210 USA
| | - Paul K Herman
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210 USA
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2
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Lsm7 phase-separated condensates trigger stress granule formation. Nat Commun 2022; 13:3701. [PMID: 35764627 PMCID: PMC9240020 DOI: 10.1038/s41467-022-31282-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/02/2022] [Indexed: 11/09/2022] Open
Abstract
Stress granules (SGs) are non-membranous organelles facilitating stress responses and linking the pathology of age-related diseases. In a genome-wide imaging-based phenomic screen, we identify Pab1 co-localizing proteins under 2-deoxy-D-glucose (2-DG) induced stress in Saccharomyces cerevisiae. We find that deletion of one of the Pab1 co-localizing proteins, Lsm7, leads to a significant decrease in SG formation. Under 2-DG stress, Lsm7 rapidly forms foci that assist in SG formation. The Lsm7 foci form via liquid-liquid phase separation, and the intrinsically disordered region and the hydrophobic clusters within the Lsm7 sequence are the internal driving forces in promoting Lsm7 phase separation. The dynamic Lsm7 phase-separated condensates appear to work as seeding scaffolds, promoting Pab1 demixing and subsequent SG initiation, seemingly mediated by RNA interactions. The SG initiation mechanism, via Lsm7 phase separation, identified in this work provides valuable clues for understanding the mechanisms underlying SG formation and SG-associated human diseases.
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3
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Kim YK, Kim YS, Kim S, Kim YJ, Ahn Y, Kook H. Comprehensive evaluation of differentially expressed non-coding RNAs identified during macrophage activation. Mol Immunol 2020; 128:98-105. [DOI: 10.1016/j.molimm.2020.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/28/2020] [Accepted: 10/14/2020] [Indexed: 01/03/2023]
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4
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Mossanen-Parsi A, Parisi D, Browne-Marke N, Bharudin I, Connell SR, Mayans O, Fucini P, Morozov IY, Caddick MX. Histone mRNA is subject to 3' uridylation and re-adenylation in Aspergillus nidulans. Mol Microbiol 2020; 115:238-254. [PMID: 33047379 DOI: 10.1111/mmi.14613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 11/29/2022]
Abstract
The role of post-transcriptional RNA modification is of growing interest. One example is the addition of non-templated uridine residues to the 3' end of transcripts. In mammalian systems, uridylation is integral to cell cycle control of histone mRNA levels. This regulatory mechanism is dependent on the nonsense-mediated decay (NMD) component, Upf1, which promotes histone mRNA uridylation and degradation in response to the arrest of DNA synthesis. We have identified a similar system in Aspergillus nidulans, where Upf1 is required for the regulation of histone mRNA levels. However, other NMD components are also implicated, distinguishing it from the mammalian system. As in human cells, 3' uridylation of histone mRNA is induced upon replication arrest. Disruption of this 3' tagging has a significant but limited effect on histone transcript regulation, consistent with multiple mechanisms acting to regulate mRNA levels. Interestingly, 3' end degraded transcripts are also subject to re-adenylation. Both mRNA pyrimidine tagging and re-adenylation are dependent on the same terminal-nucleotidyltransferases, CutA, and CutB, and we show this is consistent with the in vitro activities of both enzymes. Based on these data we argue that mRNA 3' tagging has diverse and distinct roles associated with transcript degradation, functionality and regulation.
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Affiliation(s)
- Amir Mossanen-Parsi
- Institute of Systems, Molecular and Integrative Biology, The University of Liverpool, Liverpool, UK
| | - Daniele Parisi
- Institute of Systems, Molecular and Integrative Biology, The University of Liverpool, Liverpool, UK.,Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | | | - Izwan Bharudin
- Institute of Systems, Molecular and Integrative Biology, The University of Liverpool, Liverpool, UK
| | - Sean R Connell
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Olga Mayans
- Institute of Systems, Molecular and Integrative Biology, The University of Liverpool, Liverpool, UK
| | - Paola Fucini
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Igor Y Morozov
- Institute of Systems, Molecular and Integrative Biology, The University of Liverpool, Liverpool, UK.,Centre for Sport, Exercise and Life Sciences, Coventry University, Coventry, UK
| | - Mark X Caddick
- Institute of Systems, Molecular and Integrative Biology, The University of Liverpool, Liverpool, UK
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5
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Roithová A, Feketová Z, Vaňáčová Š, Staněk D. DIS3L2 and LSm proteins are involved in the surveillance of Sm ring-deficient snRNAs. Nucleic Acids Res 2020; 48:6184-6197. [PMID: 32374871 PMCID: PMC7293007 DOI: 10.1093/nar/gkaa301] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/06/2020] [Accepted: 04/23/2020] [Indexed: 01/31/2023] Open
Abstract
Spliceosomal small nuclear ribonucleoprotein particles (snRNPs) undergo a complex maturation pathway containing multiple steps in the nucleus and in the cytoplasm. snRNP biogenesis is strictly proofread and several quality control checkpoints are placed along the pathway. Here, we analyzed the fate of small nuclear RNAs (snRNAs) that are unable to acquire a ring of Sm proteins. We showed that snRNAs lacking the Sm ring are unstable and accumulate in P-bodies in an LSm1-dependent manner. We further provide evidence that defective snRNAs without the Sm binding site are uridylated at the 3′ end and associate with DIS3L2 3′→5′ exoribonuclease and LSm proteins. Finally, inhibition of 5′→3′ exoribonuclease XRN1 increases association of ΔSm snRNAs with DIS3L2, which indicates competition and compensation between these two degradation enzymes. Together, we provide evidence that defective snRNAs without the Sm ring are uridylated and degraded by alternative pathways involving either DIS3L2 or LSm proteins and XRN1.
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Affiliation(s)
- Adriana Roithová
- Laboratory of RNA Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic.,Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | - Zuzana Feketová
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5/A35, 625 00 Brno, Czech Republic
| | - Štěpánka Vaňáčová
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5/A35, 625 00 Brno, Czech Republic
| | - David Staněk
- Laboratory of RNA Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
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6
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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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7
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Abstract
Spliceosomal snRNPs are complex particles that proceed through a fascinating maturation pathway. Several steps of this pathway are closely linked to nuclear non-membrane structures called Cajal bodies. In this review, I summarize the last 20 y of research in this field. I primarily focus on snRNP biogenesis, specifically on the steps that involve Cajal bodies. I also evaluate the contribution of the Cajal body in snRNP quality control and discuss the role of snRNPs in Cajal body formation.
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Affiliation(s)
- David Staněk
- a Institute of Molecular Genetics, Czech Academy of Sciences , Prague , Czech Republic
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8
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Patel PH, Barbee SA, Blankenship JT. GW-Bodies and P-Bodies Constitute Two Separate Pools of Sequestered Non-Translating RNAs. PLoS One 2016; 11:e0150291. [PMID: 26930655 PMCID: PMC4773245 DOI: 10.1371/journal.pone.0150291] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/11/2016] [Indexed: 01/05/2023] Open
Abstract
Non-translating RNAs that have undergone active translational repression are culled from the cytoplasm into P-bodies for decapping-dependent decay or for sequestration. Organisms that use microRNA-mediated RNA silencing have an additional pathway to remove RNAs from active translation. Consequently, proteins that govern microRNA-mediated silencing, such as GW182/Gw and AGO1, are often associated with the P-bodies of higher eukaryotic organisms. Due to the presence of Gw, these structures have been referred to as GW-bodies. However, several reports have indicated that GW-bodies have different dynamics to P-bodies. Here, we use live imaging to examine GW-body and P-body dynamics in the early Drosophila melanogaster embryo. While P-bodies are present throughout early embryonic development, cytoplasmic GW-bodies only form in significant numbers at the midblastula transition. Unlike P-bodies, which are predominantly cytoplasmic, GW-bodies are present in both nuclei and the cytoplasm. RNA decapping factors such as DCP1, Me31B, and Hpat are not associated with GW-bodies, indicating that P-bodies and GW-bodies are distinct structures. Furthermore, known Gw interactors such as AGO1 and the CCR4-NOT deadenylation complex, which have been shown to be important for Gw function, are also not present in GW-bodies. Use of translational inhibitors puromycin and cycloheximide, which respectively increase or decrease cellular pools of non-translating RNAs, alter GW-body size, underscoring that GW-bodies are composed of non-translating RNAs. Taken together, these data indicate that active translational silencing most likely does not occur in GW-bodies. Instead GW-bodies most likely function as repositories for translationally silenced RNAs. Finally, inhibition of zygotic gene transcription is unable to block the formation of either P-bodies or GW-bodies in the early embryo, suggesting that these structures are composed of maternal RNAs.
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Affiliation(s)
- Prajal H. Patel
- Department of Biological Sciences and Eleanor Roosevelt Institute, University of Denver, Denver, Colorado, United States of America
| | - Scott A. Barbee
- Department of Biological Sciences and Eleanor Roosevelt Institute, University of Denver, Denver, Colorado, United States of America
- Molecular and Cellular Biophysics Program, University of Denver, Denver, Colorado, United States of America
- * E-mail: (JTB); (SAB)
| | - J. Todd Blankenship
- Department of Biological Sciences and Eleanor Roosevelt Institute, University of Denver, Denver, Colorado, United States of America
- Molecular and Cellular Biophysics Program, University of Denver, Denver, Colorado, United States of America
- * E-mail: (JTB); (SAB)
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9
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Cary GA, Vinh DBN, May P, Kuestner R, Dudley AM. Proteomic Analysis of Dhh1 Complexes Reveals a Role for Hsp40 Chaperone Ydj1 in Yeast P-Body Assembly. G3 (BETHESDA, MD.) 2015; 5:2497-511. [PMID: 26392412 PMCID: PMC4632068 DOI: 10.1534/g3.115.021444] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 09/16/2015] [Indexed: 12/18/2022]
Abstract
P-bodies (PB) are ribonucleoprotein (RNP) complexes that aggregate into cytoplasmic foci when cells are exposed to stress. Although the conserved mRNA decay and translational repression machineries are known components of PB, how and why cells assemble RNP complexes into large foci remain unclear. Using mass spectrometry to analyze proteins immunoisolated with the core PB protein Dhh1, we show that a considerable number of proteins contain low-complexity sequences, similar to proteins highly represented in mammalian RNP granules. We also show that the Hsp40 chaperone Ydj1, which contains an low-complexity domain and controls prion protein aggregation, is required for the formation of Dhh1-GFP foci on glucose depletion. New classes of proteins that reproducibly coenrich with Dhh1-GFP during PB induction include proteins involved in nucleotide or amino acid metabolism, glycolysis, transfer RNA aminoacylation, and protein folding. Many of these proteins have been shown to form foci in response to other stresses. Finally, analysis of RNA associated with Dhh1-GFP shows enrichment of mRNA encoding the PB protein Pat1 and catalytic RNAs along with their associated mitochondrial RNA-binding proteins. Thus, global characterization of PB composition has uncovered proteins important for PB assembly and evidence suggesting an active role for RNA in PB function.
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Affiliation(s)
- Gregory A Cary
- Institute for Systems Biology, Seattle, Washington 98109 Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195
| | - Dani B N Vinh
- Institute for Systems Biology, Seattle, Washington 98109
| | - Patrick May
- Institute for Systems Biology, Seattle, Washington 98109 Luxembourg Centre for Systems Biomedicine, Université du Luxembourg, Esch-sur-Alzette, Luxembourg L-4362
| | - Rolf Kuestner
- Institute for Systems Biology, Seattle, Washington 98109
| | - Aimée M Dudley
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195 Pacific Northwest Diabetes Research Institute, Seattle, Washington 98122
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10
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Cornes E, Porta-De-La-Riva M, Aristizábal-Corrales D, Brokate-Llanos AM, García-Rodríguez FJ, Ertl I, Díaz M, Fontrodona L, Reis K, Johnsen R, Baillie D, Muñoz MJ, Sarov M, Dupuy D, Cerón J. Cytoplasmic LSM-1 protein regulates stress responses through the insulin/IGF-1 signaling pathway in Caenorhabditis elegans. RNA (NEW YORK, N.Y.) 2015; 21:1544-53. [PMID: 26150554 PMCID: PMC4536316 DOI: 10.1261/rna.052324.115] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 06/06/2015] [Indexed: 05/04/2023]
Abstract
Genes coding for members of the Sm-like (LSm) protein family are conserved through evolution from prokaryotes to humans. These proteins have been described as forming homo- or heterocomplexes implicated in a broad range of RNA-related functions. To date, the nuclear LSm2-8 and the cytoplasmic LSm1-7 heteroheptamers are the best characterized complexes in eukaryotes. Through a comprehensive functional study of the LSm family members, we found that lsm-1 and lsm-3 are not essential for C. elegans viability, but their perturbation, by RNAi or mutations, produces defects in development, reproduction, and motility. We further investigated the function of lsm-1, which encodes the distinctive protein of the cytoplasmic complex. RNA-seq analysis of lsm-1 mutants suggests that they have impaired Insulin/IGF-1 signaling (IIS), which is conserved in metazoans and involved in the response to various types of stress through the action of the FOXO transcription factor DAF-16. Further analysis using a DAF-16::GFP reporter indicated that heat stress-induced translocation of DAF-16 to the nuclei is dependent on lsm-1. Consistent with this, we observed that lsm-1 mutants display heightened sensitivity to thermal stress and starvation, while overexpression of lsm-1 has the opposite effect. We also observed that under stress, cytoplasmic LSm proteins aggregate into granules in an LSM-1-dependent manner. Moreover, we found that lsm-1 and lsm-3 are required for other processes regulated by the IIS pathway, such as aging and pathogen resistance.
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Affiliation(s)
- Eric Cornes
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain Université Bordeaux, IECB, Laboratoire ARNA, F-33600 Pessac, France INSERM, U869, Laboratoire ARNA, F-33000 Bordeaux, France
| | - Montserrat Porta-De-La-Riva
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain C. elegans Core Facility, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - David Aristizábal-Corrales
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Ana María Brokate-Llanos
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC - UPO - Junta de Andalucía, Sevilla 41013, Spain
| | - Francisco Javier García-Rodríguez
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Iris Ertl
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Mònica Díaz
- Drug Delivery and Targeting, CIBBIM-Nanomedicine, Vall d'Hebron Research Institute, Universidad Autónoma de Barcelona, Barcelona 08035, Spain
| | - Laura Fontrodona
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Kadri Reis
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Robert Johnsen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - David Baillie
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Manuel J Muñoz
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC - UPO - Junta de Andalucía, Sevilla 41013, Spain
| | - Mihail Sarov
- TransgeneOmics Unit, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Denis Dupuy
- Université Bordeaux, IECB, Laboratoire ARNA, F-33600 Pessac, France INSERM, U869, Laboratoire ARNA, F-33000 Bordeaux, France
| | - Julián Cerón
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain
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11
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SART3-Dependent Accumulation of Incomplete Spliceosomal snRNPs in Cajal Bodies. Cell Rep 2015; 10:429-440. [PMID: 25600876 DOI: 10.1016/j.celrep.2014.12.030] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 09/18/2014] [Accepted: 12/13/2014] [Indexed: 12/16/2022] Open
Abstract
Cajal bodies (CBs) are evolutionarily conserved nuclear structures involved in the metabolism of spliceosomal small nuclear ribonucleoprotein particles (snRNPs). CBs are not present in all cell types, and the trigger for their formation is not yet known. Here, we depleted cells of factors required for the final steps of snRNP assembly and assayed for the presence of stalled intermediates in CBs. We show that depletion induces formation of CBs in cells that normally lack these nuclear compartments, suggesting that CB nucleation is triggered by an imbalance in snRNP assembly. Accumulation of stalled intermediates in CBs depends on the di-snRNP assembly factor SART3. SART3 is required for both the induction of CB formation as well as the tethering of incomplete snRNPs to coilin, the CB scaffolding protein. We propose a model wherein SART3 monitors tri-snRNP assembly and sequesters incomplete particles in CBs, thereby allowing cells to maintain a homeostatic balance of mature snRNPs in the nucleoplasm.
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12
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Yang G, Smibert CA, Kaplan DR, Miller FD. An eIF4E1/4E-T complex determines the genesis of neurons from precursors by translationally repressing a proneurogenic transcription program. Neuron 2014; 84:723-39. [PMID: 25456498 DOI: 10.1016/j.neuron.2014.10.022] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2014] [Indexed: 02/06/2023]
Abstract
Here, we have addressed the mechanisms that determine genesis of the correct numbers of neurons during development, focusing on the embryonic cortex. We identify in neural precursors a repressive complex involving eIF4E1 and its binding partner 4E-T that coordinately represses translation of proteins that determine neurogenesis. This eIF4E1/4E-T complex is present in granules with the processing body proteins Lsm1 and Rck, and disruption of this complex causes premature and enhanced neurogenesis and neural precursor depletion. Analysis of the 4E-T complex shows that it is highly enriched in mRNAs encoding transcription factors and differentiation-related proteins. These include the proneurogenic bHLH mRNAs, which colocalize with 4E-T in granules and whose protein products are aberrantly upregulated following knockdown of eIF4E, 4E-T, or processing body proteins. Thus, neural precursors are transcriptionally primed to generate neurons, but an eIF4E/4E-T complex sequesters and represses translation of proneurogenic proteins to determine appropriate neurogenesis.
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Affiliation(s)
- Guang Yang
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Craig A Smibert
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - David R Kaplan
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Freda D Miller
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada.
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13
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Stejskalová E, Staněk D. The splicing factor U1-70K interacts with the SMN complex and is required for nuclear gem integrity. J Cell Sci 2014; 127:3909-15. [PMID: 25052091 DOI: 10.1242/jcs.155838] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The nuclear SMN complex localizes to specific structures called nuclear gems. The loss of gems is a cellular marker for several neurodegenerative diseases. Here, we identify that the U1-snRNP-specific protein U1-70K localizes to nuclear gems, and we show that U1-70K is necessary for gem integrity. Furthermore, we show that the interaction between U1-70K and the SMN complex is RNA independent, and we map the SMN complex binding site to the unstructured N-terminal tail of U1-70K. Consistent with these results, the expression of the U1-70K N-terminal tail rescues gem formation. These findings show that U1-70K is an SMN-complex-associating protein, and they suggest a new function for U1-70K in the formation of nuclear gems.
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Affiliation(s)
- Eva Stejskalová
- Department of RNA Biology, Institute of Molecular Genetics AS CR, 142 20 Prague, Czech Republic Faculty of Science, Charles University in Prague, 128 43 Prague, Czech Republic
| | - David Staněk
- Department of RNA Biology, Institute of Molecular Genetics AS CR, 142 20 Prague, Czech Republic
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