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Su Y, Wu J, Chen W, Shan J, Chen D, Zhu G, Ge S, Liu Y. Spliceosomal snRNAs, the Essential Players in pre-mRNA Processing in Eukaryotic Nucleus: From Biogenesis to Functions and Spatiotemporal Characteristics. Adv Biol (Weinh) 2024; 8:e2400006. [PMID: 38797893 DOI: 10.1002/adbi.202400006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/30/2024] [Indexed: 05/29/2024]
Abstract
Spliceosomal small nuclear RNAs (snRNAs) are a fundamental class of non-coding small RNAs abundant in the nucleoplasm of eukaryotic cells, playing a crucial role in splicing precursor messenger RNAs (pre-mRNAs). They are transcribed by DNA-dependent RNA polymerase II (Pol II) or III (Pol III), and undergo subsequent processing and 3' end cleavage to become mature snRNAs. Numerous protein factors are involved in the transcription initiation, elongation, termination, splicing, cellular localization, and terminal modification processes of snRNAs. The transcription and processing of snRNAs are regulated spatiotemporally by various mechanisms, and the homeostatic balance of snRNAs within cells is of great significance for the growth and development of organisms. snRNAs assemble with specific accessory proteins to form small nuclear ribonucleoprotein particles (snRNPs) that are the basal components of spliceosomes responsible for pre-mRNA maturation. This article provides an overview of the biological functions, biosynthesis, terminal structure, and tissue-specific regulation of snRNAs.
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Affiliation(s)
- Yuan Su
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Jiaming Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Wei Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Junling Shan
- Department of basic medicine, Guangxi Medical University of Nursing College, Nanning, Guangxi, 530021, China
| | - Dan Chen
- Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, Guangxi, 530011, China
| | - Guangyu Zhu
- Guangxi Medical University Hospital of Stomatology, Nanning, Guangxi, 530021, China
| | - Shengchao Ge
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Yunfeng Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
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2
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Matera AG, Steiner RE, Mills CA, Herring LE, Garcia EL. Chaperoning the chaperones: Proteomic analysis of the SMN complex reveals conserved and etiologic connections to the proteostasis network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594402. [PMID: 38903116 PMCID: PMC11188114 DOI: 10.1101/2024.05.15.594402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Molecular chaperones and co-chaperones are highly conserved cellular components that perform variety of duties related to the proper three-dimensional folding of the proteome. The web of factors that carries out this essential task is called the proteostasis network (PN). Ribonucleoproteins (RNPs) represent an underexplored area in terms of the connections they make with the PN. The Survival Motor Neuron (SMN) complex is an RNP assembly chaperone and serves as a paradigm for studying how specific small nuclear (sn)RNAs are identified and paired with their client substrate proteins. SMN protein is the eponymous component of a large complex required for the biogenesis of uridine-rich small nuclear ribonucleoproteins (U-snRNPs) and localizes to distinct membraneless organelles in both the nucleus and cytoplasm of animal cells. SMN forms the oligomeric core of this complex, and missense mutations in its YG box self-interaction domain are known to cause Spinal Muscular Atrophy (SMA). The basic framework for understanding how snRNAs are assembled into U-snRNPs is known, the pathways and mechanisms used by cells to regulate their biogenesis are poorly understood. Given the importance of these processes to normal development as well as neurodegenerative disease, we set out to identify and characterize novel SMN binding partners. Here, we carried out affinity purification mass spectrometry (AP-MS) of SMN using stable fly lines exclusively expressing either wildtype or SMA-causing missense alleles. Bioinformatic analyses of the pulldown data, along with comparisons to proximity labeling studies carried out in human cells, revealed conserved connections to at least two other major chaperone systems including heat shock folding chaperones (HSPs) and histone/nucleosome assembly chaperones. Notably, we found that heat shock cognate protein Hsc70-4 and other HspA family members preferentially interacted with SMA-causing alleles of SMN. Hsc70-4 is particularly interesting because its mRNA is aberrantly sequestered by a mutant form of TDP-43 in mouse and Drosophila ALS (Amyotrophic Lateral Sclerosis) disease models. Most important, a missense allele of Hsc70-4 (HspA8 in mammals) was recently identified as a bypass suppressor of the SMA phenotype in mice. Collectively, these findings suggest that chaperone-related dysfunction lies at the etiological root of both ALS and SMA.
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Affiliation(s)
- A. Gregory Matera
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill NC, USA
- Departments of Biology and Genetics, University of North Carolina at Chapel Hill
- RNA Discovery and Lineberger Comprehensive Cancer Centers, University of North Carolina at Chapel Hill
| | - Rebecca E. Steiner
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill NC, USA
| | - C. Alison Mills
- Department of Pharmacology, University of North Carolina at Chapel Hill
| | - Laura E. Herring
- Department of Pharmacology, University of North Carolina at Chapel Hill
| | - Eric L. Garcia
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill NC, USA
- Department of Biology, University of Kentucky, Lexington KY, USA
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Yang XC, Desotell A, Lin MH, Paige AS, Malinowska A, Sun Y, Aik WS, Dadlez M, Tong L, Dominski Z. In vitro methylation of the U7 snRNP subunits Lsm11 and SmE by the PRMT5/MEP50/pICln methylosome. RNA (NEW YORK, N.Y.) 2023; 29:1673-1690. [PMID: 37562960 PMCID: PMC10578488 DOI: 10.1261/rna.079709.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/08/2023] [Indexed: 08/12/2023]
Abstract
U7 snRNP is a multisubunit endonuclease required for 3' end processing of metazoan replication-dependent histone pre-mRNAs. In contrast to the spliceosomal snRNPs, U7 snRNP lacks the Sm subunits D1 and D2 and instead contains two related proteins, Lsm10 and Lsm11. The remaining five subunits of the U7 heptameric Sm ring, SmE, F, G, B, and D3, are shared with the spliceosomal snRNPs. The pathway that assembles the unique ring of U7 snRNP is unknown. Here, we show that a heterodimer of Lsm10 and Lsm11 tightly interacts with the methylosome, a complex of the arginine methyltransferase PRMT5, MEP50, and pICln known to methylate arginines in the carboxy-terminal regions of the Sm proteins B, D1, and D3 during the spliceosomal Sm ring assembly. Both biochemical and cryo-EM structural studies demonstrate that the interaction is mediated by PRMT5, which binds and methylates two arginine residues in the amino-terminal region of Lsm11. Surprisingly, PRMT5 also methylates an amino-terminal arginine in SmE, a subunit that does not undergo this type of modification during the biogenesis of the spliceosomal snRNPs. An intriguing possibility is that the unique methylation pattern of Lsm11 and SmE plays a vital role in the assembly of the U7 snRNP.
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Affiliation(s)
- Xiao-Cui Yang
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Anthony Desotell
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Min-Han Lin
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Andrew S Paige
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Agata Malinowska
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Yadong Sun
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Wei Shen Aik
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Michał Dadlez
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Warsaw University, 02-106 Warsaw, Poland
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Zbigniew Dominski
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Pánek J, Roithová A, Radivojević N, Sýkora M, Prusty AB, Huston N, Wan H, Pyle AM, Fischer U, Staněk D. The SMN complex drives structural changes in human snRNAs to enable snRNP assembly. Nat Commun 2023; 14:6580. [PMID: 37852981 PMCID: PMC10584915 DOI: 10.1038/s41467-023-42324-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
Spliceosomal snRNPs are multicomponent particles that undergo a complex maturation pathway. Human Sm-class snRNAs are generated as 3'-end extended precursors, which are exported to the cytoplasm and assembled together with Sm proteins into core RNPs by the SMN complex. Here, we provide evidence that these pre-snRNA substrates contain compact, evolutionarily conserved secondary structures that overlap with the Sm binding site. These structural motifs in pre-snRNAs are predicted to interfere with Sm core assembly. We model structural rearrangements that lead to an open pre-snRNA conformation compatible with Sm protein interaction. The predicted rearrangement pathway is conserved in Metazoa and requires an external factor that initiates snRNA remodeling. We show that the essential helicase Gemin3, which is a component of the SMN complex, is crucial for snRNA structural rearrangements during snRNP maturation. The SMN complex thus facilitates ATP-driven structural changes in snRNAs that expose the Sm site and enable Sm protein binding.
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Affiliation(s)
- Josef Pánek
- Laboratory of Bioinformatics, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic.
| | - Adriana Roithová
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
- Laboratory of Regulation of Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Nenad Radivojević
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Sýkora
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | | | - Nicholas Huston
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, USA
| | - Han Wan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, USA
- Department of Chemistry, Yale University, New Haven, USA
- Howard Hughes Medical Institute, Chevy Chase, USA
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
| | - David Staněk
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic.
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5
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Šimčíková D, Gelles-Watnick S, Neugebauer KM. Tudor-dimethylarginine interactions: the condensed version. Trends Biochem Sci 2023; 48:689-698. [PMID: 37156649 PMCID: PMC10524826 DOI: 10.1016/j.tibs.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 04/09/2023] [Accepted: 04/10/2023] [Indexed: 05/10/2023]
Abstract
Biomolecular condensates (BMCs) can facilitate or inhibit diverse cellular functions. BMC formation is driven by noncovalent protein-protein, protein-RNA, and RNA-RNA interactions. Here, we focus on Tudor domain-containing proteins - such as survival motor neuron protein (SMN) - that contribute to BMC formation by binding to dimethylarginine (DMA) modifications on protein ligands. SMN is present in RNA-rich BMCs, and its absence causes spinal muscular atrophy (SMA). SMN's Tudor domain forms cytoplasmic and nuclear BMCs, but its DMA ligands are largely unknown, highlighting open questions about the function of SMN. Moreover, DMA modification can alter intramolecular interactions and affect protein localization. Despite these emerging functions, the lack of direct methods of DMA detection remains an obstacle to understanding Tudor-DMA interactions in cells.
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Affiliation(s)
- Daniela Šimčíková
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Sara Gelles-Watnick
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
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6
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Yang XC, Desotell A, Lin MH, Paige AS, Malinowska A, Sun Y, Aik WS, Dadlez M, Tong L, Dominski Z. In vitro methylation of the U7 snRNP subunits Lsm11 and SmE by the PRMT5/MEP50/pICln methylosome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.10.540203. [PMID: 37215023 PMCID: PMC10197641 DOI: 10.1101/2023.05.10.540203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
U7 snRNP is a multi-subunit endonuclease required for 3' end processing of metazoan replication-dependent histone pre-mRNAs. In contrast to the spliceosomal snRNPs, U7 snRNP lacks the Sm subunits D1 and D2 and instead contains two related proteins, Lsm10 and Lsm11. The remaining five subunits of the U7 heptameric Sm ring, SmE, F, G, B and D3, are shared with the spliceosomal snRNPs. The pathway that assembles the unique ring of U7 snRNP is unknown. Here, we show that a heterodimer of Lsm10 and Lsm11 tightly interacts with the methylosome, a complex of the arginine methyltransferase PRMT5, MEP50 and pICln known to methylate arginines in the C-terminal regions of the Sm proteins B, D1 and D3 during the spliceosomal Sm ring assembly. Both biochemical and Cryo-EM structural studies demonstrate that the interaction is mediated by PRMT5, which binds and methylates two arginine residues in the N-terminal region of Lsm11. Surprisingly, PRMT5 also methylates an N-terminal arginine in SmE, a subunit that does not undergo this type of modification during the biogenesis of the spliceosomal snRNPs. An intriguing possibility is that the unique methylation pattern of Lsm11 and SmE plays a vital role in the assembly of the U7 snRNP.
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7
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Almentina Ramos Shidi F, Cologne A, Delous M, Besson A, Putoux A, Leutenegger AL, Lacroix V, Edery P, Mazoyer S, Bordonné R. Mutations in the non-coding RNU4ATAC gene affect the homeostasis and function of the Integrator complex. Nucleic Acids Res 2022; 51:712-727. [PMID: 36537210 PMCID: PMC9881141 DOI: 10.1093/nar/gkac1182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 11/17/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Various genetic diseases associated with microcephaly and developmental defects are due to pathogenic variants in the U4atac small nuclear RNA (snRNA), a component of the minor spliceosome essential for the removal of U12-type introns from eukaryotic mRNAs. While it has been shown that a few RNU4ATAC mutations result in impaired binding of essential protein components, the molecular defects of the vast majority of variants are still unknown. Here, we used lymphoblastoid cells derived from RNU4ATAC compound heterozygous (g.108_126del;g.111G>A) twin patients with MOPD1 phenotypes to analyze the molecular consequences of the mutations on small nuclear ribonucleoproteins (snRNPs) formation and on splicing. We found that the U4atac108_126del mutant is unstable and that the U4atac111G>A mutant as well as the minor di- and tri-snRNPs are present at reduced levels. Our results also reveal the existence of 3'-extended snRNA transcripts in patients' cells. Moreover, we show that the mutant cells have alterations in splicing of INTS7 and INTS10 minor introns, contain lower levels of the INTS7 and INTS10 proteins and display changes in the assembly of Integrator subunits. Altogether, our results show that compound heterozygous g.108_126del;g.111G>A mutations induce splicing defects and affect the homeostasis and function of the Integrator complex.
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Affiliation(s)
- Fatimat Almentina Ramos Shidi
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR5535, 34293 Montpellier, France
| | - Audric Cologne
- INRIA Erable, CNRS LBBE UMR 5558, University Lyon 1, University of Lyon, 69622 Villeurbanne, France
| | - Marion Delous
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon U1028 UMR5292, GENDEV, 69500 Bron, France
| | - Alicia Besson
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon U1028 UMR5292, GENDEV, 69500 Bron, France
| | - Audrey Putoux
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon U1028 UMR5292, GENDEV, 69500 Bron, France,Clinical Genetics Unit, Department of Genetics, Centre de Référence Anomalies du Développement et Syndromes Polymalformatifs, Hospices Civils de Lyon, University Lyon 1, Bron, France
| | | | - Vincent Lacroix
- INRIA Erable, CNRS LBBE UMR 5558, University Lyon 1, University of Lyon, 69622 Villeurbanne, France
| | - Patrick Edery
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon U1028 UMR5292, GENDEV, 69500 Bron, France,Clinical Genetics Unit, Department of Genetics, Centre de Référence Anomalies du Développement et Syndromes Polymalformatifs, Hospices Civils de Lyon, University Lyon 1, Bron, France
| | - Sylvie Mazoyer
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon U1028 UMR5292, GENDEV, 69500 Bron, France
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Preussner M, Santos KF, Alles J, Heroven C, Heyd F, Wahl MC, Weber G. Structural and functional investigation of the human snRNP assembly factor AAR2 in complex with the RNase H-like domain of PRPF8. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:1373-1383. [PMID: 36322420 PMCID: PMC9629490 DOI: 10.1107/s2059798322009755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/05/2022] [Indexed: 11/07/2022]
Abstract
The crystal structure of human AAR2 bound to the central spliceosomal factor PRPF8 and in vitro functional data yield insights into the structural basis of snRNP assembly in humans. Small nuclear ribonucleoprotein complexes (snRNPs) represent the main subunits of the spliceosome. While the assembly of the snRNP core particles has been well characterized, comparably little is known of the incorporation of snRNP-specific proteins and the mechanisms of snRNP recycling. U5 snRNP assembly in yeast requires binding of the the Aar2 protein to Prp8p as a placeholder to preclude premature assembly of the SNRNP200 helicase, but the role of the human AAR2 homolog has not yet been investigated in detail. Here, a crystal structure of human AAR2 in complex with the RNase H-like domain of the U5-specific PRPF8 (PRP8F RH) is reported, revealing a significantly different interaction between the two proteins compared with that in yeast. Based on the structure of the AAR2–PRPF8 RH complex, the importance of the interacting regions and residues was probed and AAR2 variants were designed that failed to stably bind PRPF8 in vitro. Protein-interaction studies of AAR2 with U5 proteins using size-exclusion chromatography reveal similarities and marked differences in the interaction patterns compared with yeast Aar2p and imply phosphorylation-dependent regulation of AAR2 reminiscent of that in yeast. It is found that in vitro AAR2 seems to lock PRPF8 RH in a conformation that is only compatible with the first transesterification step of the splicing reaction and blocks a conformational switch to the step 2-like, Mg2+-coordinated conformation that is likely during U5 snRNP biogenesis. These findings extend the picture of AAR2 PRP8 interaction from yeast to humans and indicate a function for AAR2 in the spliceosomal assembly process beyond its role as an SNRNP200 placeholder in yeast.
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Bergfort A, Hilal T, Kuropka B, Ilik İA, Weber G, Aktaş T, Freund C, Wahl MC. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2938-2958. [PMID: 35188580 PMCID: PMC8934646 DOI: 10.1093/nar/gkac087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/21/2022] [Accepted: 01/26/2022] [Indexed: 11/16/2022] Open
Abstract
Biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and their recycling after splicing require numerous assembly/recycling factors whose modes of action are often poorly understood. The intrinsically disordered TSSC4 protein has been identified as a nuclear-localized U5 snRNP and U4/U6-U5 tri-snRNP assembly/recycling factor, but how TSSC4’s intrinsic disorder supports TSSC4 functions remains unknown. Using diverse interaction assays and cryogenic electron microscopy-based structural analysis, we show that TSSC4 employs four conserved, non-contiguous regions to bind the PRPF8 Jab1/MPN domain and the SNRNP200 helicase at functionally important sites. It thereby inhibits SNRNP200 helicase activity, spatially aligns the proteins, coordinates formation of a U5 sub-module and transiently blocks premature interaction of SNRNP200 with at least three other spliceosomal factors. Guided by the structure, we designed a TSSC4 variant that lacks stable binding to the PRPF8 Jab1/MPN domain or SNRNP200 in vitro. Comparative immunoprecipitation/mass spectrometry from HEK293 nuclear extract revealed distinct interaction profiles of wild type TSSC4 and the variant deficient in PRPF8/SNRNP200 binding with snRNP proteins, other spliceosomal proteins as well as snRNP assembly/recycling factors and chaperones. Our findings elucidate molecular strategies employed by an intrinsically disordered protein to promote snRNP assembly, and suggest multiple TSSC4-dependent stages during snRNP assembly/recycling.
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Affiliation(s)
- Alexandra Bergfort
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany
| | - Tarek Hilal
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Research Center of Electron Microscopy, Fabeckstr. 36a, 14195 Berlin, Germany
| | - Benno Kuropka
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Protein Biochemistry, Thielallee 63, D-14195, Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Core Facility BioSupraMol, Thielallee 63, D-14195, Berlin, Germany
| | - İbrahim Avşar Ilik
- Max Planck Institute for Molecular Genetics, Ihnestr. 63, D-14195 Berlin, Germany
| | - Gert Weber
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Tuğçe Aktaş
- Max Planck Institute for Molecular Genetics, Ihnestr. 63, D-14195 Berlin, Germany
| | - Christian Freund
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Protein Biochemistry, Thielallee 63, D-14195, Berlin, Germany
| | - Markus C Wahl
- To whom correspondence should be addressed. Tel: +49 30 838 53456; Fax: +49 30 8384 53456;
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10
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Mabin JW, Lewis PW, Brow DA, Dvinge H. Human spliceosomal snRNA sequence variants generate variant spliceosomes. RNA (NEW YORK, N.Y.) 2021; 27:1186-1203. [PMID: 34234030 PMCID: PMC8457000 DOI: 10.1261/rna.078768.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/29/2021] [Indexed: 06/02/2023]
Abstract
Human pre-mRNA splicing is primarily catalyzed by the major spliceosome, comprising five small nuclear ribonucleoprotein complexes, U1, U2, U4, U5, and U6 snRNPs, each of which contains the corresponding U-rich snRNA. These snRNAs are encoded by large gene families exhibiting significant sequence variation, but it remains unknown if most human snRNA genes are untranscribed pseudogenes or produce variant snRNAs with the potential to differentially influence splicing. Since gene duplication and variation are powerful mechanisms of evolutionary adaptation, we sought to address this knowledge gap by systematically profiling human U1, U2, U4, and U5 snRNA variant gene transcripts. We identified 55 transcripts that are detectably expressed in human cells, 38 of which incorporate into snRNPs and spliceosomes in 293T cells. All U1 snRNA variants are more than 1000-fold less abundant in spliceosomes than the canonical U1, whereas at least 1% of spliceosomes contain a variant of U2 or U4. In contrast, eight U5 snRNA sequence variants occupy spliceosomes at levels of 1% to 46%. Furthermore, snRNA variants display distinct expression patterns across five human cell lines and adult and fetal tissues. Different RNA degradation rates contribute to the diverse steady state levels of snRNA variants. Our findings suggest that variant spliceosomes containing noncanonical snRNAs may contribute to different tissue- and cell-type-specific alternative splicing patterns.
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Affiliation(s)
- Justin W Mabin
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
| | - Peter W Lewis
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
| | - David A Brow
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
| | - Heidi Dvinge
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
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11
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Veepaschit J, Viswanathan A, Bordonné R, Grimm C, Fischer U. Identification and structural analysis of the Schizosaccharomyces pombe SMN complex. Nucleic Acids Res 2021; 49:7207-7223. [PMID: 33754639 PMCID: PMC8287938 DOI: 10.1093/nar/gkab158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/11/2021] [Accepted: 02/26/2021] [Indexed: 01/20/2023] Open
Abstract
The macromolecular SMN complex facilitates the formation of Sm-class ribonucleoproteins involved in mRNA processing (UsnRNPs). While biochemical studies have revealed key activities of the SMN complex, its structural investigation is lagging behind. Here we report on the identification and structural determination of the SMN complex from the lower eukaryote Schizosaccharomyces pombe, consisting of SMN, Gemin2, 6, 7, 8 and Sm proteins. The core of the SMN complex is formed by several copies of SMN tethered through its C-terminal alpha-helices arranged with alternating polarity. This creates a central platform onto which Gemin8 binds and recruits Gemins 6 and 7. The N-terminal parts of the SMN molecules extrude via flexible linkers from the core and enable binding of Gemin2 and Sm proteins. Our data identify the SMN complex as a multivalent hub where Sm proteins are collected in its periphery to allow their joining with UsnRNA.
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Affiliation(s)
- Jyotishman Veepaschit
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Aravindan Viswanathan
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Rémy Bordonné
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier 34293, France
| | - Clemens Grimm
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Utz Fischer
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg 97074, Germany
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12
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Gupta K, Wen Y, Ninan NS, Raimer AC, Sharp R, Spring A, Sarachan KL, Johnson MC, Van Duyne GD, Matera AG. Assembly of higher-order SMN oligomers is essential for metazoan viability and requires an exposed structural motif present in the YG zipper dimer. Nucleic Acids Res 2021; 49:7644-7664. [PMID: 34181727 PMCID: PMC8287954 DOI: 10.1093/nar/gkab508] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 06/03/2021] [Indexed: 12/16/2022] Open
Abstract
Protein oligomerization is one mechanism by which homogenous solutions can separate into distinct liquid phases, enabling assembly of membraneless organelles. Survival Motor Neuron (SMN) is the eponymous component of a large macromolecular complex that chaperones biogenesis of eukaryotic ribonucleoproteins and localizes to distinct membraneless organelles in both the nucleus and cytoplasm. SMN forms the oligomeric core of this complex, and missense mutations within its YG box domain are known to cause Spinal Muscular Atrophy (SMA). The SMN YG box utilizes a unique variant of the glycine zipper motif to form dimers, but the mechanism of higher-order oligomerization remains unknown. Here, we use a combination of molecular genetic, phylogenetic, biophysical, biochemical and computational approaches to show that formation of higher-order SMN oligomers depends on a set of YG box residues that are not involved in dimerization. Mutation of key residues within this new structural motif restricts assembly of SMN to dimers and causes locomotor dysfunction and viability defects in animal models.
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Affiliation(s)
- Kushol Gupta
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19105-6059, USA
| | - Ying Wen
- Integrative Program for Biological & Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Nisha S Ninan
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19105-6059, USA
| | - Amanda C Raimer
- Integrative Program for Biological & Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Robert Sharp
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19105-6059, USA
| | - Ashlyn M Spring
- Integrative Program for Biological & Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kathryn L Sarachan
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19105-6059, USA
| | - Meghan C Johnson
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Gregory D Van Duyne
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19105-6059, USA
| | - A Gregory Matera
- Integrative Program for Biological & Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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13
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Schilling M, Prusty AB, Boysen B, Oppermann FS, Riedel YL, Husedzinovic A, Rasouli H, König A, Ramanathan P, Reymann J, Erfle H, Daub H, Fischer U, Gruss OJ. TOR signaling regulates liquid phase separation of the SMN complex governing snRNP biogenesis. Cell Rep 2021; 35:109277. [PMID: 34161763 DOI: 10.1016/j.celrep.2021.109277] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 04/23/2021] [Accepted: 05/27/2021] [Indexed: 01/10/2023] Open
Abstract
The activity of the SMN complex in promoting the assembly of pre-mRNA processing UsnRNPs correlates with condensation of the complex in nuclear Cajal bodies. While mechanistic details of its activity have been elucidated, the molecular basis for condensation remains unclear. High SMN complex phosphorylation suggests extensive regulation. Here, we report on systematic siRNA-based screening for modulators of the capacity of SMN to condense in Cajal bodies and identify mTOR and ribosomal protein S6 kinase β-1 as key regulators. Proteomic analysis reveals TOR-dependent phosphorylations in SMN complex subunits. Using stably expressed or optogenetically controlled phospho mutants, we demonstrate that serine 49 and 63 phosphorylation of human SMN controls the capacity of the complex to condense in Cajal bodies via liquid-liquid phase separation. Our findings link SMN complex condensation and UsnRNP biogenesis to cellular energy levels and suggest modulation of TOR signaling as a rational concept for therapy of the SMN-linked neuromuscular disorder spinal muscular atrophy.
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Affiliation(s)
- Maximilian Schilling
- Institut für Genetik, Rheinische Friedrich-Wilhelms Universität Bonn, 53115 Bonn, Germany
| | - Archana B Prusty
- Theodor Boveri Institute, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Björn Boysen
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | | | - Yannick L Riedel
- Institut für Genetik, Rheinische Friedrich-Wilhelms Universität Bonn, 53115 Bonn, Germany
| | - Alma Husedzinovic
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Homa Rasouli
- Evotec SE, Am Klopferspitz 19a, 82152 Martinsried, Germany
| | - Angelika König
- Institut für Genetik, Rheinische Friedrich-Wilhelms Universität Bonn, 53115 Bonn, Germany
| | - Pradhipa Ramanathan
- Theodor Boveri Institute, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Jürgen Reymann
- Advanced Biological Screening Facility, BioQuant Centre, Universität Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Holger Erfle
- Advanced Biological Screening Facility, BioQuant Centre, Universität Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Henrik Daub
- Evotec SE, Am Klopferspitz 19a, 82152 Martinsried, Germany
| | - Utz Fischer
- Theodor Boveri Institute, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Oliver J Gruss
- Institut für Genetik, Rheinische Friedrich-Wilhelms Universität Bonn, 53115 Bonn, Germany; Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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14
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Solomon DA, Smikle R, Reid MJ, Mizielinska S. Altered Phase Separation and Cellular Impact in C9orf72-Linked ALS/FTD. Front Cell Neurosci 2021; 15:664151. [PMID: 33967699 PMCID: PMC8096919 DOI: 10.3389/fncel.2021.664151] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/19/2021] [Indexed: 12/21/2022] Open
Abstract
Since the discovery of the C9orf72 repeat expansion mutation as causative for chromosome 9-linked amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) in 2011, a multitude of cellular pathways have been implicated. However, evidence has also been accumulating for a key mechanism of cellular compartmentalization—phase separation. Liquid-liquid phase separation (LLPS) is fundamental for the formation of membraneless organelles including stress granules, the nucleolus, Cajal bodies, nuclear speckles and the central channel of the nuclear pore. Evidence has now accumulated showing that the formation and function of these membraneless organelles is impaired by both the toxic arginine rich dipeptide repeat proteins (DPRs), translated from the C9orf72 repeat RNA transcript, and the repeat RNA itself. Both the arginine rich DPRs and repeat RNA themselves undergo phase separation and disrupt the physiological phase separation of proteins involved in the formation of these liquid-like organelles. Hence abnormal phase separation may explain a number of pathological cellular phenomena associated with C9orf72-ALS/FTD. In this review article, we will discuss the principles of phase separation, phase separation of the DPRs and repeat RNA themselves and how they perturb LLPS associated with membraneless organelles and the functional consequences of this. We will then discuss how phase separation may impact the major pathological feature of C9orf72-ALS/FTD, TDP-43 proteinopathy, and how LLPS may be targeted therapeutically in disease.
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Affiliation(s)
- Daniel A Solomon
- UK Dementia Research Institute at King's College London, London, United Kingdom.,Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
| | - Rebekah Smikle
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
| | - Matthew J Reid
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
| | - Sarah Mizielinska
- UK Dementia Research Institute at King's College London, London, United Kingdom.,Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
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15
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Small noncoding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology. Proc Natl Acad Sci U S A 2021; 118:2011574118. [PMID: 33879606 PMCID: PMC8092379 DOI: 10.1073/pnas.2011574118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Dysregulation of microRNAs (miRNAs), a type of small noncoding RNAs (sncRNAs), has frequently been associated with multiple sclerosis (MS). However, most studies have focused on peripheral blood, and few investigated other classes of sncRNAs. To address this, we analyzed all classes of sncRNAs in matching peripheral blood mononuclear cells, plasma, cerebrospinal fluid (CSF) cells, and cell-free CSF from MS patients and controls. We demonstrate widespread alterations of small nuclear (snRNA)–derived RNAs, small nucleolar-derived RNAs (sdRNAs), transfer RNA–derived fragments, and miRNAs, particularly in CSF cells. The striking contrast between the periphery and central nervous system and between relapse and remission phases of disease highlights the importance of sncRNA-mediated mechanisms in MS, in particular alternative splicing and mRNA translation. Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease affecting the central nervous system (CNS). Small non-coding RNAs (sncRNAs) and, in particular, microRNAs (miRNAs) have frequently been associated with MS. Here, we performed a comprehensive analysis of all classes of sncRNAs in matching samples of peripheral blood mononuclear cells (PBMCs), plasma, cerebrospinal fluid (CSF) cells, and cell-free CSF from relapsing-remitting (RRMS, n = 12 in relapse and n = 11 in remission) patients, secondary progressive (SPMS, n = 6) MS patients, and noninflammatory and inflammatory neurological disease controls (NINDC, n = 11; INDC, n = 5). We show widespread changes in miRNAs and sncRNA-derived fragments of small nuclear, nucleolar, and transfer RNAs. In CSF cells, 133 out of 133 and 115 out of 117 differentially expressed sncRNAs were increased in RRMS relapse compared to remission and RRMS compared to NINDC, respectively. In contrast, 65 out of 67 differentially expressed PBMC sncRNAs were decreased in RRMS compared to NINDC. The striking contrast between the periphery and CNS suggests that sncRNA-mediated mechanisms, including alternative splicing, RNA degradation, and mRNA translation, regulate the transcriptome of pathogenic cells primarily in the CNS target organ.
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16
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Metz PJ, Ching KA, Xie T, Delgado Cuenca P, Niessen S, Tatlock JH, Jensen-Pergakes K, Murray BW. Symmetric Arginine Dimethylation Is Selectively Required for mRNA Splicing and the Initiation of Type I and Type III Interferon Signaling. Cell Rep 2021; 30:1935-1950.e8. [PMID: 32049022 DOI: 10.1016/j.celrep.2020.01.054] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/07/2019] [Accepted: 01/16/2020] [Indexed: 12/13/2022] Open
Abstract
Alternative splicing is well understood to enhance proteome diversity as cells respond to stimuli. However, mechanistic understanding for how the spliceosome processes precursor messenger RNA (mRNA) transcripts to achieve template diversification is incomplete. We use recently developed enzymatic inhibitors of protein arginine methyltransferase 5 (PRMT5) and human naive T lymphocyte activation as a model system to uncover a precise set of mRNA transcripts that require symmetric arginine dimethylation. This methylation-dependent splicing selectivity is associated with a limited set of signaling pathways that are affected when PRMT5 is inhibited. Specifically, we identify a conserved role for symmetric arginine dimethylation in the induction of antiviral type I and type III interferon signaling following T cell receptor and pattern recognition receptor stimulation in human T lymphocytes and undifferentiated human THP-1 monocytes. Altogether, these findings reveal a mechanism by which cells may be enabled to precisely modulate transcript heterogeneity to orchestrate specific functional outcomes.
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Affiliation(s)
- Patrick J Metz
- Tumor Cell Biology, Pfizer Oncology Research & Development, La Jolla, Pfizer Inc., 10777 Science Center Drive, San Diego, CA 92121, USA.
| | - Keith A Ching
- Computational Biology, Pfizer Oncology Research & Development, La Jolla, Pfizer Inc., 10777 Science Center Drive, San Diego, CA 92121, USA
| | - Tao Xie
- Computational Biology, Pfizer Oncology Research & Development, La Jolla, Pfizer Inc., 10777 Science Center Drive, San Diego, CA 92121, USA
| | - Paulina Delgado Cuenca
- Tumor Cell Biology, Pfizer Oncology Research & Development, La Jolla, Pfizer Inc., 10777 Science Center Drive, San Diego, CA 92121, USA
| | - Sherry Niessen
- Tumor Cell Biology, Pfizer Oncology Research & Development, La Jolla, Pfizer Inc., 10777 Science Center Drive, San Diego, CA 92121, USA
| | - John H Tatlock
- Worldwide Medicinal Chemistry, Pfizer Oncology Research & Development, La Jolla, Pfizer Inc., 10777 Science Center Drive, San Diego, CA 92121, USA
| | - Kristen Jensen-Pergakes
- Tumor Cell Biology, Pfizer Oncology Research & Development, La Jolla, Pfizer Inc., 10777 Science Center Drive, San Diego, CA 92121, USA
| | - Brion W Murray
- Tumor Cell Biology, Pfizer Oncology Research & Development, La Jolla, Pfizer Inc., 10777 Science Center Drive, San Diego, CA 92121, USA
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17
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Chen TH. Circulating microRNAs as potential biomarkers and therapeutic targets in spinal muscular atrophy. Ther Adv Neurol Disord 2021; 13:1756286420979954. [PMID: 33488772 PMCID: PMC7768327 DOI: 10.1177/1756286420979954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
Spinal muscular atrophy (SMA), a leading genetic cause of infant death, is a neurodegenerative disease characterized by the selective loss of particular groups of motor neurons (MNs) in the anterior horn of the spinal cord with progressive muscle wasting. SMA is caused by a deficiency of the survival motor neuron (SMN) protein due to a homozygous deletion or mutation of the SMN1 gene. However, the molecular mechanisms whereby the SMN complex regulates MN functions are not fully elucidated. Emerging studies on SMA pathogenesis have turned the attention of researchers to RNA metabolism, given that increasingly identified SMN-associated modifiers are involved in both coding and non-coding RNA (ncRNA) processing. Among various ncRNAs, microRNAs (miRNAs) are the most studied in terms of regulation of posttranscriptional gene expression. Recently, the discovery that miRNAs are critical to MN function and survival led to the study of dysregulated miRNAs in SMA pathogenesis. Circulating miRNAs have drawn attention as a readily available biomarker due to their property of being clinically detectable in numerous human biofluids through non-invasive approaches. As there are recent promising findings from novel miRNA-based medicines, this article presents an extensive review of the most up-to-date studies connecting specific miRNAs to SMA pathogenesis and the potential applications of miRNAs as biomarkers and therapeutic targets for SMA.
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Affiliation(s)
- Tai-Heng Chen
- Department of Pediatrics, Division of Pediatric Emergency, Kaohsiung Medical University Hospital, School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, No. 100, Tzyou 1st Road, Kaohsiung 80708, Taiwan
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18
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Fang S, Hou X, Qiu K, He R, Feng X, Liang X. The occurrence and function of alternative splicing in fungi. FUNGAL BIOL REV 2020. [DOI: 10.1016/j.fbr.2020.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Singh RN, Ottesen EW, Singh NN. The First Orally Deliverable Small Molecule for the Treatment of Spinal Muscular Atrophy. Neurosci Insights 2020; 15:2633105520973985. [PMID: 33283185 PMCID: PMC7691903 DOI: 10.1177/2633105520973985] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/27/2020] [Indexed: 12/12/2022] Open
Abstract
Spinal muscular atrophy (SMA) is 1 of the leading causes of infant mortality. SMA
is mostly caused by low levels of Survival Motor Neuron (SMN) protein due to
deletion of or mutation in the SMN1 gene. Its nearly identical
copy, SMN2, fails to compensate for the loss of
SMN1 due to predominant skipping of exon 7. Correction of
SMN2 exon 7 splicing by an antisense oligonucleotide (ASO),
nusinersen (Spinraza™), that targets the intronic splicing silencer N1 (ISS-N1)
became the first approved therapy for SMA. Restoration of SMN levels using gene
therapy was the next. Very recently, an orally deliverable small molecule,
risdiplam (Evrysdi™), became the third approved therapy for SMA. Here we discuss
how these therapies are positioned to meet the needs of the broad phenotypic
spectrum of SMA patients.
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Affiliation(s)
- Ravindra N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
| | - Eric W Ottesen
- Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
| | - Natalia N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
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20
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Rademacher S, Detering NT, Schüning T, Lindner R, Santonicola P, Wefel IM, Dehus J, Walter LM, Brinkmann H, Niewienda A, Janek K, Varela MA, Bowerman M, Di Schiavi E, Claus P. A Single Amino Acid Residue Regulates PTEN-Binding and Stability of the Spinal Muscular Atrophy Protein SMN. Cells 2020; 9:cells9112405. [PMID: 33153033 PMCID: PMC7692393 DOI: 10.3390/cells9112405] [Citation(s) in RCA: 3] [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: 06/02/2020] [Revised: 10/23/2020] [Accepted: 10/27/2020] [Indexed: 11/16/2022] Open
Abstract
Spinal Muscular Atrophy (SMA) is a neuromuscular disease caused by decreased levels of the survival of motoneuron (SMN) protein. Post-translational mechanisms for regulation of its stability are still elusive. Thus, we aimed to identify regulatory phosphorylation sites that modulate function and stability. Our results show that SMN residues S290 and S292 are phosphorylated, of which SMN pS290 has a detrimental effect on protein stability and nuclear localization. Furthermore, we propose that phosphatase and tensin homolog (PTEN), a novel phosphatase for SMN, counteracts this effect. In light of recent advancements in SMA therapies, a significant need for additional approaches has become apparent. Our study demonstrates S290 as a novel molecular target site to increase the stability of SMN. Characterization of relevant kinases and phosphatases provides not only a new understanding of SMN function, but also constitutes a novel strategy for combinatorial therapeutic approaches to increase the level of SMN in SMA.
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Affiliation(s)
- Sebastian Rademacher
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
| | - Nora T. Detering
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
- Center for Systems Neuroscience (ZSN), 30559 Hannover, Germany
| | - Tobias Schüning
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
- Center for Systems Neuroscience (ZSN), 30559 Hannover, Germany
| | - Robert Lindner
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
| | - Pamela Santonicola
- Institute of Biosciences and Bioresources, National Research Council of Italy, 80131 Naples, Italy; (P.S.); (E.D.S.)
| | - Inga-Maria Wefel
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
| | - Janina Dehus
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
| | - Lisa M. Walter
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
- Center for Systems Neuroscience (ZSN), 30559 Hannover, Germany
| | - Hella Brinkmann
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
| | - Agathe Niewienda
- Shared Facility for Mass Spectrometry, Institute of Biochemistry, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; (A.N.); (K.J.)
| | - Katharina Janek
- Shared Facility for Mass Spectrometry, Institute of Biochemistry, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; (A.N.); (K.J.)
| | - Miguel A. Varela
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK; (M.A.V.); (M.B.)
- Department of Paediatrics, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Melissa Bowerman
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK; (M.A.V.); (M.B.)
- School of Medicine, Keele University, Staffordshire ST5 5BG, UK
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10 7AG, UK
| | - Elia Di Schiavi
- Institute of Biosciences and Bioresources, National Research Council of Italy, 80131 Naples, Italy; (P.S.); (E.D.S.)
| | - Peter Claus
- Institute of Neuroanatomy and Cell Biology, Hannover Medical School, 30625 Hannover, Germany; (S.R.); (N.T.D.); (T.S.); (R.L.); (I.-M.W.); (J.D.); (L.M.W.); (H.B.)
- Center for Systems Neuroscience (ZSN), 30559 Hannover, Germany
- Correspondence:
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21
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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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22
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Clinical interpretation of variants identified in RNU4ATAC, a non-coding spliceosomal gene. PLoS One 2020; 15:e0235655. [PMID: 32628740 PMCID: PMC7337319 DOI: 10.1371/journal.pone.0235655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/19/2020] [Indexed: 12/16/2022] Open
Abstract
Biallelic variants in RNU4ATAC, a non-coding gene transcribed into the minor spliceosome component U4atac snRNA, are responsible for three rare recessive developmental diseases, namely Taybi-Linder/MOPD1, Roifman and Lowry-Wood syndromes. Next-generation sequencing of clinically heterogeneous cohorts (children with either a suspected genetic disorder or a congenital microcephaly) recently identified mutations in this gene, illustrating how profoundly these technologies are modifying genetic testing and assessment. As RNU4ATAC has a single non-coding exon, the bioinformatic prediction algorithms assessing the effect of sequence variants on splicing or protein function are irrelevant, which makes variant interpretation challenging to molecular diagnostic laboratories. In order to facilitate and improve clinical diagnostic assessment and genetic counseling, we present i) an update of the previously reported RNU4ATAC mutations and an analysis of the genetic variations affecting this gene using the Genome Aggregation Database (gnomAD) resource; ii) the pathogenicity prediction performances of scores computed based on an RNA structure prediction tool and of those produced by the Combined Annotation Dependent Depletion tool for the 285 RNU4ATAC variants identified in patients or in large-scale sequencing projects; iii) a method, based on a cellular assay, that allows to measure the effect of RNU4ATAC variants on splicing efficiency of a minor (U12-type) reporter intron. Lastly, the concordance of bioinformatic predictions and cellular assay results was investigated.
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Hasler D, Meister G, Fischer U. Stabilize and connect: the role of LARP7 in nuclear non-coding RNA metabolism. RNA Biol 2020; 18:290-303. [PMID: 32401147 DOI: 10.1080/15476286.2020.1767952] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
La and La-related proteins (LARPs) are characterized by a common RNA interaction platform termed the La module. This structural hallmark allows LARPs to pervade various aspects of RNA biology. The metazoan LARP7 protein binds to the 7SK RNA as part of a 7SK small nuclear ribonucleoprotein (7SK snRNP), which inhibits the transcriptional activity of RNA polymerase II (Pol II). Additionally, recent findings revealed unanticipated roles of LARP7 in the assembly of other RNPs, as well as in the modification, processing and cellular transport of RNA molecules. Reduced levels of functional LARP7 have been linked to cancer and Alazami syndrome, two seemingly unrelated human diseases characterized either by hyperproliferation or growth retardation. Here, we review the intricate regulatory networks centered on LARP7 and assess how malfunction of these networks may relate to the etiology of LARP7-linked diseases.
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Affiliation(s)
- Daniele Hasler
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
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24
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Maccallini P, Bavasso F, Scatolini L, Bucciarelli E, Noviello G, Lisi V, Palumbo V, D'Angeli S, Cacchione S, Cenci G, Ciapponi L, Wakefield JG, Gatti M, Raffa GD. Intimate functional interactions between TGS1 and the Smn complex revealed by an analysis of the Drosophila eye development. PLoS Genet 2020; 16:e1008815. [PMID: 32453722 PMCID: PMC7289441 DOI: 10.1371/journal.pgen.1008815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/11/2020] [Accepted: 04/30/2020] [Indexed: 11/27/2022] Open
Abstract
Trimethylguanosine synthase 1 (TGS1) is a conserved enzyme that mediates formation of the trimethylguanosine cap on several RNAs, including snRNAs and telomerase RNA. Previous studies have shown that TGS1 binds the Survival Motor Neuron (SMN) protein, whose deficiency causes spinal muscular atrophy (SMA). Here, we analyzed the roles of the Drosophila orthologs of the human TGS1 and SMN genes. We show that the Drosophila TGS1 protein (dTgs1) physically interacts with all subunits of the Drosophila Smn complex (Smn, Gem2, Gem3, Gem4 and Gem5), and that a human TGS1 transgene rescues the mutant phenotype caused by dTgs1 loss. We demonstrate that both dTgs1 and Smn are required for viability of retinal progenitor cells and that downregulation of these genes leads to a reduced eye size. Importantly, overexpression of dTgs1 partially rescues the eye defects caused by Smn depletion, and vice versa. These results suggest that the Drosophila eye model can be exploited for screens aimed at the identification of genes and drugs that modify the phenotypes elicited by Tgs1 and Smn deficiency. These modifiers could help to understand the molecular mechanisms underlying SMA pathogenesis and devise new therapies for this genetic disease. We explored the functional relationships between TGS1 and SMN using Drosophila as model organism. TGS1 is an enzyme that modifies the structure of the 5’-end of several RNAs, including telomerase RNA and the small nuclear RNAs (snRNAs) that are required for messenger RNA maturation. The SMN protein regulates snRNAs biogenesis and mutations in human SMN cause Spinal Muscular Atrophy (SMA), a devastating disorder characterized by neurodegeneration, progressive paralysis and death. We show that mutations in the Drosophila TGS1 (dTgs1) gene cause lethality, which is rescued by a human TGS1 transgene. We also show that the dTgs1 protein physically interacts with all subunits of the Smn complex, and that downregulation of either dTgs1 or Smn leads to a reduced Drosophila eye size. Notably, overexpression of dTgs1 partially rescues the eye defects caused by Smn knockdown, and vice versa, indicating that these genes cooperate in eye development. These results suggest that the eye model can be exploited for screens aimed at detection of chemical and genetic modifiers of the eye mutant phenotype elicited by dTgs1 and Smn deficiency, providing new clues about SMA pathogenesis and potential therapies.
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Affiliation(s)
- Paolo Maccallini
- Dipartimento di Biologia e Biotecnologie “C Darwin”, Sapienza University of Rome, Rome, Italy
| | - Francesca Bavasso
- Dipartimento di Biologia e Biotecnologie “C Darwin”, Sapienza University of Rome, Rome, Italy
| | - Livia Scatolini
- Dipartimento di Biologia e Biotecnologie “C Darwin”, Sapienza University of Rome, Rome, Italy
| | | | - Gemma Noviello
- Dipartimento di Biologia e Biotecnologie “C Darwin”, Sapienza University of Rome, Rome, Italy
| | - Veronica Lisi
- Dipartimento di Biologia e Biotecnologie “C Darwin”, Sapienza University of Rome, Rome, Italy
| | - Valeria Palumbo
- Dipartimento di Biologia e Biotecnologie “C Darwin”, Sapienza University of Rome, Rome, Italy
| | - Simone D'Angeli
- Dipartimento di Biologia Ambientale, Sapienza University of Rome, Rome, Italy
| | - Stefano Cacchione
- Dipartimento di Biologia e Biotecnologie “C Darwin”, Sapienza University of Rome, Rome, Italy
| | - Giovanni Cenci
- Dipartimento di Biologia e Biotecnologie “C Darwin”, Sapienza University of Rome, Rome, Italy
- Fondazione Cenci Bolognetti, Istituto Pasteur, Rome, Italy
| | - Laura Ciapponi
- Dipartimento di Biologia e Biotecnologie “C Darwin”, Sapienza University of Rome, Rome, Italy
| | - James G. Wakefield
- Biosciences/Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, United Kingdom
| | - Maurizio Gatti
- Dipartimento di Biologia e Biotecnologie “C Darwin”, Sapienza University of Rome, Rome, Italy
- Istituto di Biologia e Patologia Molecolari (IBPM) del CNR, Rome, Italy
- * E-mail: (MG); (GDR)
| | - Grazia Daniela Raffa
- Dipartimento di Biologia e Biotecnologie “C Darwin”, Sapienza University of Rome, Rome, Italy
- * E-mail: (MG); (GDR)
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25
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Rossi S, Rompietti V, Antonucci Y, Giovannini D, Scopa C, Scaricamazza S, Scardigli R, Cestra G, Serafino A, Carrì MT, D'Ambrosi N, Cozzolino M. UsnRNP trafficking is regulated by stress granules and compromised by mutant ALS proteins. Neurobiol Dis 2020; 138:104792. [PMID: 32027933 DOI: 10.1016/j.nbd.2020.104792] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 01/24/2020] [Accepted: 02/03/2020] [Indexed: 12/13/2022] Open
Abstract
Activation of the integrated stress response (ISR), alterations in nucleo-cytoplasmic (N/C) transport and changes in alternative splicing regulation are all common traits of the pathogenesis of Amyotrophic Lateral Sclerosis (ALS). However, whether these processes act independently from each other, or are part of a coordinated mechanism of gene expression regulation that is affected in pathogenic conditions, is still rather undefined. To answer these questions, in this work we set out to characterise the functional connections existing between ISR activation and nucleo-cytosol trafficking and nuclear localization of spliceosomal U-rich small nuclear ribonucleoproteins (UsnRNPs), the core constituents of the spliceosome, and to study how ALS-linked mutant proteins affect this interplay. Activation of the ISR induces a profound reorganization of nuclear Gems and Cajal bodies, the membrane-less particles that assist UsnRNP maturation and storage. This effect requires the cytoplasmic assembly of SGs and is associated to the disturbance of the nuclear import of UsnRNPs by the snurportin-1/importin-β1 system. Notably, these effects are reversed by both inhibiting the ISR or upregulating importin-β1. This indicates that SGs are major determinants of Cajal bodies assembly and that the modulation of N/C trafficking of UsnRNPs might control alternative splicing in response to stress. Importantly, the dismantling of nuclear Gems and Cajal bodies by ALS-linked mutant FUS or C9orf72-derived dipeptide repeat proteins is halted by overexpression of importin-β1, but not by inhibition of the ISR. This suggests that changes in the nuclear localization of the UsnRNP complexes induced by mutant ALS proteins are uncoupled from ISR activation, and that defects in the N/C trafficking of UsnRNPs might play a role in ALS pathogenesis.
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Affiliation(s)
- Simona Rossi
- Istituto di Farmacologia Traslazionale (IFT), CNR, 00133 Rome, Italy; Dipartimento di Biologia, Università di Roma "Tor Vergata", Rome, Italy.
| | | | - Ylenia Antonucci
- Istituto di Farmacologia Traslazionale (IFT), CNR, 00133 Rome, Italy
| | | | - Chiara Scopa
- European Brain Research Institute (EBRI), Rome, Italy
| | | | - Raffaella Scardigli
- Istituto di Farmacologia Traslazionale (IFT), CNR, 00133 Rome, Italy; European Brain Research Institute (EBRI), Rome, Italy
| | - Gianluca Cestra
- Istituto di Biologia e Patologia Molecolari (IBPM), CNR, Rome, Italy; Dipartimento di Biologia e Biotecnologia "Charles Darwin", Università di Roma "Sapienza", Rome, Italy
| | | | | | - Nadia D'Ambrosi
- Dipartimento di Biologia, Università di Roma "Tor Vergata", Rome, Italy
| | - Mauro Cozzolino
- Istituto di Farmacologia Traslazionale (IFT), CNR, 00133 Rome, Italy.
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26
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Li Z, Wu L, Wu H, Zhang X, Mei J, Zhou X, Wang GL, Liu W. Arginine methylation is required for remodelling pre-mRNA splicing and induction of autophagy in rice blast fungus. THE NEW PHYTOLOGIST 2020; 225:413-429. [PMID: 31478201 DOI: 10.1111/nph.16156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/18/2019] [Indexed: 06/10/2023]
Abstract
Protein arginine methyltransferases (PRMTs) regulate many physiological processes, including autophagy. However, the direct roles of the various PRMTs during autophagosome formation remain unclear. Here, we characterised the function of MoHMT1 in the rice blast fungus, Magnaporthe oryzae. Knockout of MoHMT1 results in inhibited growth and a decreased ability to cause disease lesions on rice seedlings. MoHMT1 catalyses the di-methylation of arginine 247, 251, 261 and 271 residues of MoSNP1, a U1 small nuclear ribonucleoprotein (snRNP) component, likely in a manner dependent on direct interaction. RNA-seq analysis revealed that alternative splicing of pre-mRNAs of 558 genes, including the autophagy-related (ATG) gene MoATG4, was altered in MoHMT1 deletion mutants, compared with wild-type strains under normal growth conditions. During light exposure or nitrogen starvation, MoHMT1 localises to autophagosomes and MoHMT1 mutants display defects in autophagy induction. Under nitrogen starvation, six additional MoATG genes were identified with retained introns in their mRNA transcripts, corresponding with a significant reduction in transcripts of intron-spliced isoforms in the MoHMT1 mutant strain. Our study shows that arginine methylation plays an essential role in accurate pre-mRNA splicing necessary for a range of developmental processes, including autophagosome formation.
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Affiliation(s)
- Zhiqiang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Liye Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hang Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xixi Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jie Mei
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Guo-Liang Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Department of Plant Pathology, Ohio State University, Columbus, OH, 43210, USA
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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27
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Spring AM, Raimer AC, Hamilton CD, Schillinger MJ, Matera AG. Comprehensive Modeling of Spinal Muscular Atrophy in Drosophila melanogaster. Front Mol Neurosci 2019; 12:113. [PMID: 31156382 PMCID: PMC6532329 DOI: 10.3389/fnmol.2019.00113] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 04/18/2019] [Indexed: 01/02/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a neurodegenerative disorder that affects motor neurons, primarily in young children. SMA is caused by mutations in the Survival Motor Neuron 1 (SMN1) gene. SMN functions in the assembly of spliceosomal RNPs and is well conserved in many model systems including mouse, zebrafish, fruit fly, nematode, and fission yeast. Work in Drosophila has focused on the loss of SMN function during larval stages, primarily using null alleles or strong hypomorphs. A systematic analysis of SMA-related phenotypes in the context of moderate alleles that more closely mimic the genetics of SMA has not been performed in the fly, leading to debate over the validity and translational value of this model. We, therefore, examined 14 Drosophila lines expressing SMA patient-derived missense mutations in Smn, with a focus on neuromuscular phenotypes in the adult stage. Animals were evaluated on the basis of organismal viability and longevity, locomotor function, neuromuscular junction structure, and muscle health. In all cases, we observed phenotypes similar to those of SMA patients, including progressive loss of adult motor function. The severity of these defects is variable and forms a broad spectrum across the 14 lines examined, recapitulating the full range of phenotypic severity observed in human SMA. This includes late-onset models of SMA, which have been difficult to produce in other model systems. The results provide direct evidence that SMA-related locomotor decline can be reproduced in the fly and support the use of patient-derived SMN missense mutations as a comprehensive system for modeling SMA.
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Affiliation(s)
- Ashlyn M. Spring
- Integrative Program in Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, United States
| | - Amanda C. Raimer
- Integrative Program in Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, United States
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, United States
| | - Christine D. Hamilton
- Integrative Program in Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, United States
| | | | - A. Gregory Matera
- Integrative Program in Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, United States
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, United States
- Department of Biology, University of North Carolina, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States
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28
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Massenet S. In vivo assembly of eukaryotic signal recognition particle: A still enigmatic process involving the SMN complex. Biochimie 2019; 164:99-104. [PMID: 30978374 DOI: 10.1016/j.biochi.2019.04.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/07/2019] [Indexed: 12/29/2022]
Abstract
The signal recognition particle (SRP) is a universally conserved non-coding ribonucleoprotein complex that is essential for targeting transmembrane and secretory proteins to the endoplasmic reticulum. Its composition and size varied during evolution. In mammals, SRP contains one RNA molecule, 7SL RNA, and six proteins: SRP9, 14, 19, 54, 68 and 72. Despite a very good understanding of the SRP structure and of the SRP assembly in vitro, how SRP is assembled in vivo remains largely enigmatic. Here we review current knowledge on how the 7SL RNA is assembled with core proteins to form functional RNP particles in cells. SRP biogenesis is believed to take place both in the nucleolus and in the cytoplasm and to rely on the survival of motor neuron complex, whose defect leads to spinal muscular atrophy.
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Affiliation(s)
- Séverine Massenet
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-University of Lorraine, Biopôle de l'Université de Lorraine, Campus Brabois-Santé, 9 avenue de la forêt de Haye, BP 20199, 54505 Vandoeuvre-les-Nancy, France.
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29
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Yu J, Yan Y, Luan X, Qiao C, Liu Y, Zhao D, Xie B, Zheng Q, Wang M, Chen W, Shen C, He Z, Hu X, Huang X, Li H, Shao Q, Chen X, Zheng B, Fang J. Srlp is crucial for the self-renewal and differentiation of germline stem cells via RpL6 signals in Drosophila testes. Cell Death Dis 2019; 10:294. [PMID: 30931935 PMCID: PMC6443671 DOI: 10.1038/s41419-019-1527-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 03/11/2019] [Accepted: 03/14/2019] [Indexed: 12/22/2022]
Abstract
Self-renewal and differentiation in germline stem cells (GSCs) are tightly regulated by the stem cell niche and via multiple approaches. In our previous study, we screened the novel GSC regulatory gene Srlp in Drosophila testes. However, the underlying mechanistic links between Srlp and the stem cell niche remain largely undetermined. Here, using genetic manipulation of the Drosophila model, we systematically analyze the function and mechanism of Srlp in vivo and in vitro. In Drosophila, Srlp is an essential gene that regulates the self-renewal and differentiation of GSCs in the testis. In the in vitro assay, Srlp is found to control the proliferation ability and cell death in S2 cells, which is consistent with the phenotype observed in Drosophila testis. Furthermore, results of the liquid chromatography-tandem mass spectrometry (LC-MS/MS) reveal that RpL6 binds to Srlp. Srlp also regulates the expression of spliceosome and ribosome subunits and controls spliceosome and ribosome function via RpL6 signals. Collectively, our findings uncover the genetic causes and molecular mechanisms underlying the stem cell niche. This study provides new insights for elucidating the pathogenic mechanism of male sterility and the formation of testicular germ cell tumor.
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Affiliation(s)
- Jun Yu
- Department of Gynecology, The Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang Jiangsu, 212001, China.,Reproductive Sciences Institute of Jiangsu University, Zhenjiang Jiangsu, 212001, China
| | - Yidan Yan
- Department of Gynecology, The Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang Jiangsu, 212001, China.,Reproductive Sciences Institute of Jiangsu University, Zhenjiang Jiangsu, 212001, China
| | - Xiaojin Luan
- Department of Gynecology, The Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang Jiangsu, 212001, China.,Reproductive Sciences Institute of Jiangsu University, Zhenjiang Jiangsu, 212001, China
| | - Chen Qiao
- Department of Clinical Pharmacy, the Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang Jiangsu, 212001, China
| | - Yuanyuan Liu
- Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Jiangsu, 215002, China
| | - Dan Zhao
- Reproductive Sciences Institute of Jiangsu University, Zhenjiang Jiangsu, 212001, China.,Center for Reproduction, The Fourth People's Hospital of Zhenjiang, Zhenjiang Jiangsu, 212013, China
| | - Bing Xie
- Department of Gynecology, The Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang Jiangsu, 212001, China
| | - Qianwen Zheng
- Department of Gynecology, The Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang Jiangsu, 212001, China.,Reproductive Sciences Institute of Jiangsu University, Zhenjiang Jiangsu, 212001, China
| | - Min Wang
- Department of Gynecology, The Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang Jiangsu, 212001, China
| | - Wanyin Chen
- Department of Gynecology, The Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang Jiangsu, 212001, China
| | - Cong Shen
- Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Jiangsu, 215002, China
| | - Zeyu He
- Department of Clinical Medicine, China Medical University, Shenyang Liaoning, 110001, China
| | - Xing Hu
- Department of Gynecology, The Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang Jiangsu, 212001, China
| | - Xiaoyan Huang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing Jiangsu, 211166, China
| | - Hong Li
- Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Jiangsu, 215002, China
| | - Qixiang Shao
- Reproductive Sciences Institute of Jiangsu University, Zhenjiang Jiangsu, 212001, China.,Department of Immunology and Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang Jiangsu, 212013, China
| | - Xia Chen
- Department of Gynecology, The Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang Jiangsu, 212001, China. .,Reproductive Sciences Institute of Jiangsu University, Zhenjiang Jiangsu, 212001, China.
| | - Bo Zheng
- Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Jiangsu, 215002, China.
| | - Jie Fang
- Department of Gynecology, The Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang Jiangsu, 212001, China.
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30
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Beattie CE, Kolb SJ. Spinal muscular atrophy: Selective motor neuron loss and global defect in the assembly of ribonucleoproteins. Brain Res 2018; 1693:92-97. [DOI: 10.1016/j.brainres.2018.02.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 02/10/2018] [Accepted: 02/15/2018] [Indexed: 12/13/2022]
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31
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Smigiel R, Landsberg G, Schilling M, Rydzanicz M, Pollak A, Walczak A, Stodolak A, Stawinski P, Mierzewska H, Sasiadek MM, Gruss OJ, Ploski R. Developmental epileptic encephalopathy with hypomyelination and brain atrophy associated with PTPN23 variants affecting the assembly of UsnRNPs. Eur J Hum Genet 2018; 26:1502-1511. [PMID: 29899372 DOI: 10.1038/s41431-018-0179-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/20/2018] [Accepted: 04/26/2018] [Indexed: 01/08/2023] Open
Abstract
PTPN23 encodes a ubiquitously expressed non-receptor type, catalytically inactive protein-tyrosine phosphatase found in all cells including neurons. Recently, we have identified PTPN23 in a cellular screen for the systematic identification of novel regulators of survival motor neuron (SMN) function in the assembly of splicing factors (Uridine-rich small nuclear ribonucleoproteins, UsnRNPs). Based on three families, recessive PTPN23 variants have been associated with human disease tentatively, without functional studies. Here, we describe a pediatric proband with severe developmental delay, epilepsy, cortical blindness, hypomyelination and brain atrophy on MRI. Whole exome sequencing and family study showed two novel PTPN23 variants, c.1902C>G (p.(Asn634Lys)) and c.2974delC (p.(Leu992Tyrfs*168)), in compound heterozygous state, which are predicted in silico to be damaging. When studying patient's fibroblasts we found similar expression of SMN but a dramatic reduction of cells displaying SMN accumulation in Cajal bodies (CB). SMN strongly accumulated in CB in more than 50% of unrelated control cell fibroblasts as well as in fibroblasts from the parent carrying only the c.2974delC (p.(Leu992Tyrfs*168)) variant (predicted to cause loss-of-function). In contrast, only 22% of cells showed respective SMN accumulations in patient fibroblasts (p = 1.9-2.5 × 10-7) while showing a higher level of nucleoplasmic SMN. Furthermore, the remaining accumulations in patient cells displayed weaker SMN signals than control or heterozygous wt/c.2974delC (p.(Leu992Tyrfs*168)) fibroblasts. Our report provides the first description of the clinical phenotype of recessive PTPN23 variants with pathogenicity substantiated by a functional study.
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Affiliation(s)
- Robert Smigiel
- Department of Paediatrics and Rare Disorders, Wroclaw Medical University, Wroclaw, Poland
| | - Gerd Landsberg
- Institute of Genetics, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Maximilian Schilling
- Institute of Genetics, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | | | - Agnieszka Pollak
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw, Poland
| | - Anna Walczak
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Anna Stodolak
- Department of Paediatrics and Rare Disorders, Wroclaw Medical University, Wroclaw, Poland
| | - Piotr Stawinski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland.,Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw, Poland
| | - Hanna Mierzewska
- Department of Child and Adolescent Neurology, Institute of Mother and Child, Warsaw, Poland
| | - Maria M Sasiadek
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
| | - Oliver J Gruss
- Institute of Genetics, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.
| | - Rafal Ploski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland.
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Roithová A, Klimešová K, Pánek J, Will CL, Lührmann R, Staněk D, Girard C. The Sm-core mediates the retention of partially-assembled spliceosomal snRNPs in Cajal bodies until their full maturation. Nucleic Acids Res 2018; 46:3774-3790. [PMID: 29415178 PMCID: PMC5909452 DOI: 10.1093/nar/gky070] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/19/2018] [Accepted: 01/25/2018] [Indexed: 01/23/2023] Open
Abstract
Cajal bodies (CBs) are nuclear non-membrane bound organelles where small nuclear ribonucleoprotein particles (snRNPs) undergo their final maturation and quality control before they are released to the nucleoplasm. However, the molecular mechanism how immature snRNPs are targeted and retained in CBs has yet to be described. Here, we microinjected and expressed various snRNA deletion mutants as well as chimeric 7SK, Alu or bacterial SRP non-coding RNAs and provide evidence that Sm and SMN binding sites are necessary and sufficient for CB localization of snRNAs. We further show that Sm proteins, and specifically their GR-rich domains, are important for accumulating snRNPs in CBs. Accordingly, core snRNPs containing the Sm proteins, but not naked snRNAs, restore the formation of CBs after their depletion. Finally, we show that immature but not fully assembled snRNPs are able to induce CB formation and that microinjection of an excess of U2 snRNP-specific proteins, which promotes U2 snRNP maturation, chases U2 snRNA from CBs. We propose that the accessibility of the Sm ring represents the molecular basis for the quality control of the final maturation of snRNPs and the sequestration of immature particles in CBs.
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Affiliation(s)
- Adriana Roithová
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Klára Klimešová
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Josef Pánek
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Cindy L Will
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | | | - David Staněk
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Cyrille Girard
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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Abstract
Gemin3, also known as DDX20 or DP103, is a DEAD-box RNA helicase which is involved in more than one cellular process. Though RNA unwinding has been determined in vitro, it is surprisingly not required for all of its activities in cellular metabolism. Gemin3 is an essential gene, present in Amoeba and Metazoa. The highly conserved N-terminus hosts the helicase core, formed of the helicase- and DEAD-domains, which, based on crystal structure determination, have key roles in RNA binding. The C-terminus of Gemin3 is highly divergent between species and serves as the interaction site for several accessory factors that could recruit Gemin3 to its target substrates and/or modulate its function. This review article focuses on the known roles of Gemin3, first as a core member of the survival motor neuron (SMN) complex, in small nuclear ribonucleoprotein biogenesis. Although mechanistic details are lacking, a critical function for Gemin3 in this pathway is supported by numerous in vitro and in vivo studies. Gene expression activities of Gemin3 are next underscored, mainly messenger ribonucleoprotein trafficking, gene silencing via microRNA processing, and transcriptional regulation. The involvement of Gemin3 in abnormal cell signal transduction pathways involving p53 and NF-κB is also highlighted. Finally, the clinical implications of Gemin3 deregulation are discussed including links to spinal muscular atrophy, poliomyelitis, amyotrophic lateral sclerosis, and cancer. Impressive progress made over the past two decades since the discovery of Gemin3 bodes well for further work that refines the mechanism(s) underpinning its multiple activities.
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Abstract
Spinal muscular atrophy (SMA) is a motor neuron disease caused by mutations/deletions within the survival of motor neuron 1 (SMN1) gene that lead to a pathological reduction of SMN protein levels. SMN is part of a multiprotein complex, functioning as a molecular chaperone that facilitates the assembly of spliceosomal small nuclear ribonucleoproteins (snRNP). In addition to its role in spliceosome formation, SMN has also been found to interact with mRNA-binding proteins (mRBPs), and facilitate their assembly into mRNP transport granules. The association of protein and RNA in RNP complexes plays an important role in an extensive and diverse set of cellular processes that regulate neuronal growth, differentiation, and the maturation and plasticity of synapses. This review discusses the role of SMN in RNP assembly and localization, focusing on molecular defects that affect mRNA processing and may contribute to SMA pathology.
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Tosolini AP, Sleigh JN. Motor Neuron Gene Therapy: Lessons from Spinal Muscular Atrophy for Amyotrophic Lateral Sclerosis. Front Mol Neurosci 2017; 10:405. [PMID: 29270111 PMCID: PMC5725447 DOI: 10.3389/fnmol.2017.00405] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/21/2017] [Indexed: 12/11/2022] Open
Abstract
Spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS) are severe nervous system diseases characterized by the degeneration of lower motor neurons. They share a number of additional pathological, cellular, and genetic parallels suggesting that mechanistic and clinical insights into one disorder may have value for the other. While there are currently no clinical ALS gene therapies, the splice-switching antisense oligonucleotide, nusinersen, was recently approved for SMA. This milestone was achieved through extensive pre-clinical research and patient trials, which together have spawned fundamental insights into motor neuron gene therapy. We have thus tried to distil key information garnered from SMA research, in the hope that it may stimulate a more directed approach to ALS gene therapy. Not only must the type of therapeutic (e.g., antisense oligonucleotide vs. viral vector) be sensibly selected, but considerable thought must be applied to the where, which, what, and when in order to enhance treatment benefit: to where (cell types and tissues) must the drug be delivered and how can this be best achieved? Which perturbed pathways must be corrected and can they be concurrently targeted? What dosing regime and concentration should be used? When should medication be administered? These questions are intuitive, but central to identifying and optimizing a successful gene therapy. Providing definitive solutions to these quandaries will be difficult, but clear thinking about therapeutic testing is necessary if we are to have the best chance of developing viable ALS gene therapies and improving upon early generation SMA treatments.
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Affiliation(s)
- Andrew P Tosolini
- Sobell Department of Motor Neuroscience and Movement Disorders, Institute of Neurology, University College London, London, United Kingdom
| | - James N Sleigh
- Sobell Department of Motor Neuroscience and Movement Disorders, Institute of Neurology, University College London, London, United Kingdom
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