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Wang Y, Chen X, Kong X, Chen Y, Xiang Z, Xiang Y, Hu Y, Hou Y, Zhou S, Shen C, Mu L, Su D, Zhang R. A unique mechanism of snRNP core assembly. Nat Commun 2025; 16:3166. [PMID: 40175367 PMCID: PMC11965559 DOI: 10.1038/s41467-025-58461-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Accepted: 03/19/2025] [Indexed: 04/04/2025] Open
Abstract
The assembly of most spliceosomal snRNP cores involves seven Sm proteins (D1/D2/F/E/G/D3/B) forming a ring around snRNA, typically requiring essential assembly chaperones like the SMN complex, associated with spinal muscular atrophy (SMA). Strikingly, in budding yeast, snRNP core assembly only involves Brr1, a nonessential homolog of Gemin2. Here, we reveal two distinct pathways in budding yeast: an inefficient chaperone-mediated pathway involving Brr1 and a novel factor, Lot5, and a direct pathway. Lot5 binds D1/D2/F/E/G to form a heterohexameric ring (6S). Brr1 binds D1/D2/F/E/G and 6S but cannot displace Lot5 to facilitate assembly. Disruption of BRR1 and LOT5 genes caused mild growth retardation, but LOT5 overexpression substantially impeded growth. The direct pathway uniquely involves F/E/G as a trimer and a stable D1/D2/F/E/G intermediate complex, explaining the non-essentiality of chaperones. These findings unveil a unique snRNP core assembly mechanism, illuminate the evolution of assembly chaperones, and suggest avenues for studying SMA pathophysiology.
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Affiliation(s)
- Yingzhi Wang
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, P R China
- State Key Laboratory of Biotherapy and Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, P R China
| | - Xiaoshuang Chen
- State Key Laboratory of Biotherapy and Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, P R China
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, P R China
| | - Xi Kong
- State Key Laboratory of Biotherapy and Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, P R China
- Laboratory of Neurological Diseases and Brain Function, the Affiliated Hospital, Southwest Medical University, Luzhou, P R China
| | - Yunfeng Chen
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, P R China
- State Key Laboratory of Biotherapy and Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, P R China
| | - Zixi Xiang
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, P R China
- State Key Laboratory of Biotherapy and Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, P R China
| | - Yue Xiang
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, P R China
- State Key Laboratory of Biotherapy and Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, P R China
| | - Yan Hu
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, P R China
- State Key Laboratory of Biotherapy and Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, P R China
| | - Yan Hou
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, P R China
- State Key Laboratory of Biotherapy and Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, P R China
| | - Shijie Zhou
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, P R China
- State Key Laboratory of Biotherapy and Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, P R China
| | - Congcong Shen
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, P R China
- State Key Laboratory of Biotherapy and Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, P R China
| | - Li Mu
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, P R China
- State Key Laboratory of Biotherapy and Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, P R China
| | - Dan Su
- State Key Laboratory of Biotherapy and Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, P R China
| | - Rundong Zhang
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, P R China.
- State Key Laboratory of Biotherapy and Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, P R China.
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2
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Maita H, Nakagawa S. Balancing RNA processing and innate immune response: Possible roles for SMN condensates in snRNP biogenesis. Biochim Biophys Acta Gen Subj 2025; 1869:130764. [PMID: 39826814 DOI: 10.1016/j.bbagen.2025.130764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 01/07/2025] [Accepted: 01/13/2025] [Indexed: 01/22/2025]
Abstract
Biomolecular condensates like U-bodies are specialized cellular structures formed through multivalent interactions among intrinsically disordered regions. U-bodies sequester small nuclear ribonucleoprotein complexes (snRNPs) in the cytoplasm, and their formation in mammalian cells depends on stress conditions. Because of their location adjacent to P-bodies, U-bodies have been considered potential sites for snRNP storage or turnover. SMN, a chaperone for snRNP biogenesis, forms condensates through its Tudor domain. In fly models, defects in SMN trigger innate immune responses similar to those observed with excess cytoplasmic snRNA during viral infection in mammalian cells. Additionally, spinal muscular atrophy (SMA), caused by SMN deficiency, is associated with inflammation. Therefore, SMN may help prevent innate immune aberrant activation due to defective snRNP biogenesis by forming U-bodies to sequester these molecules. Further studies on U-body functions may provide therapeutic insights for diseases related to RNA metabolism.
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Affiliation(s)
- Hiroshi Maita
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0812, Japan; Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan.
| | - Shinichi Nakagawa
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0812, Japan; Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
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3
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DeAngelo JD, Maron MI, Roth JS, Silverstein AM, Gupta V, Stransky S, Basken J, Azofeifa J, Sidoli S, Gamble MJ, Shechter D. Productive mRNA Chromatin Escape is Promoted by PRMT5 Methylation of SNRPB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.607355. [PMID: 39149374 PMCID: PMC11326253 DOI: 10.1101/2024.08.09.607355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Protein Arginine Methyltransferase 5 (PRMT5) regulates RNA splicing and transcription by symmetric dimethylation of arginine residues (Rme2s/SDMA) in many RNA binding proteins. However, the mechanism by which PRMT5 couples splicing to transcriptional output is unknown. Here, we demonstrate that a major function of PRMT5 activity is to promote chromatin escape of a novel, large class of mRNAs that we term Genomically Retained Incompletely Processed Polyadenylated Transcripts (GRIPPs). Using nascent and total transcriptomics, spike-in controlled fractionated cell transcriptomics, and total and fractionated cell proteomics, we show that PRMT5 inhibition and knockdown of the PRMT5 SNRP (Sm protein) adapter protein pICln (CLNS1A) -but not type I PRMT inhibition-leads to gross detention of mRNA, SNRPB, and SNRPD3 proteins on chromatin. Compared to most transcripts, these chromatin-trapped polyadenylated RNA transcripts have more introns, are spliced slower, and are enriched in detained introns. Using a combination of PRMT5 inhibition and inducible isogenic wildtype and arginine-mutant SNRPB, we show that arginine methylation of these snRNPs is critical for mediating their homeostatic chromatin and RNA interactions. Overall, we conclude that a major role for PRMT5 is in controlling transcript processing and splicing completion to promote chromatin escape and subsequent nuclear export.
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Affiliation(s)
- Joseph D. DeAngelo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
- Contributed equally
| | - Maxim I. Maron
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
- Contributed equally
- Current address: Department of Medicine, Weill Cornell Medical College, 1300 York Ave, New York, NY 10065
| | - Jacob S. Roth
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Aliza M. Silverstein
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Varun Gupta
- Department of Oncology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Joel Basken
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461
- Current address: Enveda Biosciences, Boulder, Colorado, 80301, United States
| | - Joey Azofeifa
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Matthew J. Gamble
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
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Agrofoglio YC, Iglesias MJ, Perez-Santángelo S, de Leone MJ, Koester T, Catalá R, Salinas J, Yanovsky MJ, Staiger D, Mateos JL. Arginine methylation of SM-LIKE PROTEIN 4 antagonistically affects alternative splicing during Arabidopsis stress responses. THE PLANT CELL 2024; 36:2219-2237. [PMID: 38518124 PMCID: PMC11132874 DOI: 10.1093/plcell/koae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/09/2024] [Indexed: 03/24/2024]
Abstract
Arabidopsis (Arabidopsis thaliana) PROTEIN ARGININE METHYLTRANSFERASE5 (PRMT5) post-translationally modifies RNA-binding proteins by arginine (R) methylation. However, the impact of this modification on the regulation of RNA processing is largely unknown. We used the spliceosome component, SM-LIKE PROTEIN 4 (LSM4), as a paradigm to study the role of R-methylation in RNA processing. We found that LSM4 regulates alternative splicing (AS) of a suite of its in vivo targets identified here. The lsm4 and prmt5 mutants show a considerable overlap of genes with altered AS raising the possibility that splicing of those genes could be regulated by PRMT5-dependent LSM4 methylation. Indeed, LSM4 methylation impacts AS, particularly of genes linked with stress response. Wild-type LSM4 and an unmethylable version complement the lsm4-1 mutant, suggesting that methylation is not critical for growth in normal environments. However, LSM4 methylation increases with abscisic acid and is necessary for plants to grow under abiotic stress. Conversely, bacterial infection reduces LSM4 methylation, and plants that express unmethylable-LSM4 are more resistant to Pseudomonas than those expressing wild-type LSM4. This tolerance correlates with decreased intron retention of immune-response genes upon infection. Taken together, this provides direct evidence that R-methylation adjusts LSM4 function on pre-mRNA splicing in an antagonistic manner in response to biotic and abiotic stress.
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Affiliation(s)
- Yamila Carla Agrofoglio
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EGA Buenos Aires, Argentina
| | - María José Iglesias
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EGA Buenos Aires, Argentina
| | - Soledad Perez-Santángelo
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - María José de Leone
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - Tino Koester
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Rafael Catalá
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Julio Salinas
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Marcelo J Yanovsky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Julieta L Mateos
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EGA Buenos Aires, Argentina
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
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5
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Garcia EL, Steiner RE, Raimer AC, Herring LE, Matera AG, Spring AM. Dysregulation of innate immune signaling in animal models of spinal muscular atrophy. BMC Biol 2024; 22:94. [PMID: 38664795 PMCID: PMC11044505 DOI: 10.1186/s12915-024-01888-z] [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: 10/28/2023] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is a devastating neuromuscular disease caused by hypomorphic loss of function in the survival motor neuron (SMN) protein. SMA presents across a broad spectrum of disease severity. Unfortunately, genetic models of intermediate SMA have been difficult to generate in vertebrates and are thus unable to address key aspects of disease etiology. To address these issues, we developed a Drosophila model system that recapitulates the full range of SMA severity, allowing studies of pre-onset biology as well as late-stage disease processes. RESULTS Here, we carried out transcriptomic and proteomic profiling of mild and intermediate Drosophila models of SMA to elucidate molecules and pathways that contribute to the disease. Using this approach, we elaborated a role for the SMN complex in the regulation of innate immune signaling. We find that mutation or tissue-specific depletion of SMN induces hyperactivation of the immune deficiency (IMD) and Toll pathways, leading to overexpression of antimicrobial peptides (AMPs) and ectopic formation of melanotic masses in the absence of an external challenge. Furthermore, the knockdown of downstream targets of these signaling pathways reduced melanotic mass formation caused by SMN loss. Importantly, we identify SMN as a negative regulator of a ubiquitylation complex that includes Traf6, Bendless, and Diap2 and plays a pivotal role in several signaling networks. CONCLUSIONS In alignment with recent research on other neurodegenerative diseases, these findings suggest that hyperactivation of innate immunity contributes to SMA pathology. This work not only provides compelling evidence that hyperactive innate immune signaling is a primary effect of SMN depletion, but it also suggests that the SMN complex plays a regulatory role in this process in vivo. In summary, immune dysfunction in SMA is a consequence of reduced SMN levels and is driven by cellular and molecular mechanisms that are conserved between insects and mammals.
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Affiliation(s)
- Eric L Garcia
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Rebecca E Steiner
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- RNA Discovery and Lineberger Comprehensive Cancer Centers, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA
- Present Address: Lake, Erie College of Osteopathic Medicine, Bradenton, FL, USA
| | - Amanda C Raimer
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA
- Present Address, Radford University, Radford, VA, USA
| | - Laura E Herring
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - A Gregory Matera
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA.
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA.
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA.
- RNA Discovery and Lineberger Comprehensive Cancer Centers, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA.
| | - Ashlyn M Spring
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, 27402, USA.
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6
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Garcia EL, Steiner RE, Raimer AC, Herring LE, Matera AG, Spring AM. Dysregulation of innate immune signaling in animal models of Spinal Muscular Atrophy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571739. [PMID: 38168196 PMCID: PMC10760185 DOI: 10.1101/2023.12.14.571739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Background Spinal Muscular Atrophy (SMA) is a devastating neuromuscular disease caused by hypomorphic loss of function in the Survival Motor Neuron (SMN) protein. SMA presents across broad spectrum of disease severity. Unfortunately, vertebrate models of intermediate SMA have been difficult to generate and are thus unable to address key aspects of disease etiology. To address these issues, we developed a Drosophila model system that recapitulates the full range of SMA severity, allowing studies of pre-onset biology as well as late-stage disease processes. Results Here, we carried out transcriptomic and proteomic profiling of mild and intermediate Drosophila models of SMA to elucidate molecules and pathways that contribute to the disease. Using this approach, we elaborated a role for the SMN complex in the regulation of innate immune signaling. We find that mutation or tissue-specific depletion of SMN induces hyperactivation of the Immune Deficiency (IMD) and Toll pathways, leading to overexpression of antimicrobial peptides (AMPs) and ectopic formation of melanotic masses in the absence of an external challenge. Furthermore, knockdown of downstream targets of these signaling pathways reduced melanotic mass formation caused by SMN loss. Importantly, we identify SMN as a negative regulator of an ubiquitylation complex that includes Traf6, Bendless and Diap2, and plays a pivotal role in several signaling networks. Conclusions In alignment with recent research on other neurodegenerative diseases, these findings suggest that hyperactivation of innate immunity contributes to SMA pathology. This work not only provides compelling evidence that hyperactive innate immune signaling is a primary effect of SMN depletion, but it also suggests that the SMN complex plays a regulatory role in this process in vivo. In summary, immune dysfunction in SMA is a consequence of reduced SMN levels and is driven by cellular and molecular mechanisms that are conserved between insects and mammals.
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Affiliation(s)
- Eric L. Garcia
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill NC, USA
- Department of Biology, University of Kentucky, Lexington KY, USA
| | - Rebecca E. Steiner
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill NC, USA
- Department of Biology, University of North Carolina at Chapel Hill
| | - Amanda C. Raimer
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill
| | - Laura E. Herring
- Department of Pharmacology, University of North Carolina at Chapel Hill
| | - A. Gregory Matera
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill
- Department of Biology, University of North Carolina at Chapel Hill
- Department of Genetics, University of North Carolina at Chapel Hill
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill
| | - Ashlyn M. Spring
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill NC, USA
- Department of Biology, University of North Carolina at Greensboro, Greensboro NC, USA
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7
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Hu Y, Hou Y, Zhou S, Wang Y, Shen C, Mu L, Su D, Zhang R. Mechanism of assembly of snRNP cores assisted by ICln and the SMN complex in fission yeast. iScience 2023; 26:107604. [PMID: 37664592 PMCID: PMC10470402 DOI: 10.1016/j.isci.2023.107604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/11/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023] Open
Abstract
The spliceosomal snRNP cores, each comprised of a snRNA and a seven-membered Sm ring (D1/D2/F/E/G/D3/B), are assembled by twelve chaperoning proteins in human. However, only six assembly-assisting proteins, ICln and the SMN complex (SMN/Gemin2/Gemin6-8), have been found in Schizosaccharomyces pombe (Sp). Here, we used recombinant proteins to reconstitute the chaperone machinery and investigated the roles of these proteins systematically. We found that, like the human system, the assembly in S. pombe requires ICln and the SMN complex sequentially. However, there are several significant differences. For instance, h_F/E/G forms heterohexamers and heterotrimers, while Sp_F/E/G only forms heterohexamers; h_Gemin2 alone can bind D1/D2/F/E/G, but Sp_Gemin2 cannot. Moreover, we found that Sp_Gemin2 is essential using genetic approaches. These mechanistic studies reveal that these six proteins are necessary and sufficient for Sm core assembly at the molecular level, and enrich our understanding of the chaperone systems in species variation and evolution.
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Affiliation(s)
- Yan Hu
- Department of Ophthalmology, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
| | - Yan Hou
- Department of Ophthalmology, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
| | - Shijie Zhou
- Department of Ophthalmology, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
| | - Yingzhi Wang
- Department of Ophthalmology, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
| | - Congcong Shen
- Department of Ophthalmology, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
| | - Li Mu
- Department of Ophthalmology, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
| | - Dan Su
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
| | - Rundong Zhang
- Department of Ophthalmology, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
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8
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Mateos JL, Sanchez SE, Legris M, Esteve-Bruna D, Torchio JC, Petrillo E, Goretti D, Blanco-Touriñán N, Seymour DK, Schmid M, Weigel D, Alabadí D, Yanovsky MJ. PICLN modulates alternative splicing and light/temperature responses in plants. PLANT PHYSIOLOGY 2023; 191:1036-1051. [PMID: 36423226 PMCID: PMC9922395 DOI: 10.1093/plphys/kiac527] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
Plants undergo transcriptome reprograming to adapt to daily and seasonal fluctuations in light and temperature conditions. While most efforts have focused on the role of master transcription factors, the importance of splicing factors modulating these processes is now emerging. Efficient pre-mRNA splicing depends on proper spliceosome assembly, which in plants and animals requires the methylosome complex. Ion Chloride nucleotide-sensitive protein (PICLN) is part of the methylosome complex in both humans and Arabidopsis (Arabidopsis thaliana), and we show here that the human PICLN ortholog rescues phenotypes of Arabidopsis picln mutants. Altered photomorphogenic and photoperiodic responses in Arabidopsis picln mutants are associated with changes in pre-mRNA splicing that partially overlap with those in PROTEIN ARGININE METHYL TRANSFERASE5 (prmt5) mutants. Mammalian PICLN also acts in concert with the Survival Motor Neuron (SMN) complex component GEMIN2 to modulate the late steps of UsnRNP assembly, and many alternative splicing events regulated by PICLN but not PRMT5, the main protein of the methylosome, are controlled by Arabidopsis GEMIN2. As with GEMIN2 and SM PROTEIN E1/PORCUPINE (SME1/PCP), low temperature, which increases PICLN expression, aggravates morphological and molecular defects of picln mutants. Taken together, these results establish a key role for PICLN in the regulation of pre-mRNA splicing and in mediating plant adaptation to daily and seasonal fluctuations in environmental conditions.
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Affiliation(s)
- Julieta L Mateos
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1405BWE, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EHA, Argentina
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Biele-feld 33615, Germany
| | - Sabrina E Sanchez
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1405BWE, Argentina
| | - Martina Legris
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1405BWE, Argentina
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen 72076, Germany
| | - David Esteve-Bruna
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politecnica de Valencia), Valencia 46022, Spain
| | - Jeanette C Torchio
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1405BWE, Argentina
| | - Ezequiel Petrillo
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EHA, Argentina
| | - Daniela Goretti
- Department of Plant Physiology, Umea Plant Science Centre, Umea University, Umea SE-901 87, Sweden
| | - Noel Blanco-Touriñán
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politecnica de Valencia), Valencia 46022, Spain
| | - Danelle K Seymour
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen 72076, Germany
| | - Markus Schmid
- Department of Plant Physiology, Umea Plant Science Centre, Umea University, Umea SE-901 87, Sweden
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen 72076, Germany
| | - David Alabadí
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politecnica de Valencia), Valencia 46022, Spain
| | - Marcelo J Yanovsky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1405BWE, Argentina
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9
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Raimer AC, Singh SS, Edula MR, Paris-Davila T, Vandadi V, Spring AM, Matera AG. Temperature-sensitive spinal muscular atrophy-causing point mutations lead to SMN instability, locomotor defects and premature lethality in Drosophila. Dis Model Mech 2020; 13:dmm043307. [PMID: 32501283 PMCID: PMC7325441 DOI: 10.1242/dmm.043307] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/18/2020] [Indexed: 12/15/2022] Open
Abstract
Spinal muscular atrophy (SMA) is the leading genetic cause of death in young children, arising from homozygous deletion or mutation of the survival motor neuron 1 (SMN1) gene. SMN protein expressed from a paralogous gene, SMN2, is the primary genetic modifier of SMA; small changes in overall SMN levels cause dramatic changes in disease severity. Thus, deeper insight into mechanisms that regulate SMN protein stability should lead to better therapeutic outcomes. Here, we show that SMA patient-derived missense mutations in the Drosophila SMN Tudor domain exhibit a pronounced temperature sensitivity that affects organismal viability, larval locomotor function and adult longevity. These disease-related phenotypes are domain specific and result from decreased SMN stability at elevated temperature. This system was utilized to manipulate SMN levels during various stages of Drosophila development. Owing to a large maternal contribution of mRNA and protein, Smn is not expressed zygotically during embryogenesis. Interestingly, we find that only baseline levels of SMN are required during larval stages, whereas high levels of the protein are required during pupation. This previously uncharacterized period of elevated SMN expression, during which the majority of adult tissues are formed and differentiated, could be an important and translationally relevant developmental stage in which to study SMN function. Taken together, these findings illustrate a novel in vivo role for the SMN Tudor domain in maintaining SMN homeostasis and highlight the necessity for high SMN levels at crucial developmental time points that are conserved from Drosophila to humans.
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Affiliation(s)
- Amanda C Raimer
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Suhana S Singh
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Maina R Edula
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Tamara Paris-Davila
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Vasudha Vandadi
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ashlyn M Spring
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - A Gregory Matera
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
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10
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Yu J, Luan X, Yan Y, Qiao C, Liu Y, Zhao D, Xie B, Zheng Q, Wang M, Chen W, Shen C, He Z, Hu X, Huang X, Li H, Chen B, Zheng B, Chen X, Fang J. Small ribonucleoprotein particle protein SmD3 governs the homeostasis of germline stem cells and the crosstalk between the spliceosome and ribosome signals in Drosophila. FASEB J 2019; 33:8125-8137. [PMID: 30921522 DOI: 10.1096/fj.201802536rr] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The ribonucleoprotein (RNP) spliceosome machinery triggers the precursor RNA splicing process in eukaryotes. Major spliceosome defects are implicated in male infertility; however, the underlying mechanistic links between the spliceosome and the ribosome in Drosophila testes remains largely unresolved. Small ribonucleoprotein particle protein SmD3 (SmD3) is a novel germline stem cell (GSC) regulatory gene identified in our previous screen of Drosophila testes. In the present study, using genetic manipulation in a Drosophila model, we demonstrated that SmD3 is required for the GSC niche and controls the self-renewal and differentiation of GSCs in the testis. Using in vitro assays in Schneider 2 cells, we showed that SmD3 also regulates the homeostasis of proliferation and apoptosis in Drosophila. Furthermore, using liquid chromatography-tandem mass spectrometry methods, SmD3 was identified as binding with ribosomal protein (Rp)L18, which is a key regulator of the large subunit in the ribosome. Moreover, SmD3 was observed to regulate spliceosome and ribosome subunit expression levels and controlled spliceosome and ribosome function via RpL18. Significantly, our findings revealed the genetic causes and molecular mechanisms underlying the stem cell niche and the crosstalk between the spliceosome and the ribosome.-Yu, J., Luan, X., Yan, Y., Qiao, C., Liu, Y., Zhao, D., Xie, B., Zheng, Q., Wang, M., Chen, W., Shen, C., He, Z., Hu, X., Huang, X., Li, H., Chen, B., Zheng, B., Chen, X., Fang, J. Small ribonucleoprotein particle protein SmD3 governs the homeostasis of germline stem cells and the crosstalk between the spliceosome and ribosome signals in Drosophila.
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Affiliation(s)
- Jun Yu
- Department of Gynecology, The Affiliated Hospital of Jiangsu University-Jiangsu University, Zhenjiang, China.,Reproductive Sciences Institute, Jiangsu University, Zhenjiang, China
| | - Xiaojin Luan
- Department of Gynecology, The Affiliated Hospital of Jiangsu University-Jiangsu University, Zhenjiang, China.,Reproductive Sciences Institute, Jiangsu University, Zhenjiang, China
| | - Yidan Yan
- Department of Gynecology, The Affiliated Hospital of Jiangsu University-Jiangsu University, Zhenjiang, China.,Reproductive Sciences Institute, Jiangsu University, Zhenjiang, China
| | - Chen Qiao
- Department of Clinical Pharmacy, The Affiliated Hospital of Jiangsu University-Jiangsu University, Zhenjiang, China
| | - Yuanyuan Liu
- Center for Reproduction and Genetics, Suzhou Municipal Hospital-The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Dan Zhao
- Reproductive Sciences Institute, Jiangsu University, Zhenjiang, China.,Center for Reproduction, The Fourth Affiliated Hospital of Jiangsu University-The Fourth People's Hospital of Zhenjiang, Zhenjiang, China
| | - Bing Xie
- Department of Obstetrics and Gynecology, The Fourth Affiliated Hospital of Jiangsu University-The Fourth People's Hospital of Zhenjiang, Zhenjiang, China
| | - Qianwen Zheng
- Department of Gynecology, The Affiliated Hospital of Jiangsu University-Jiangsu University, Zhenjiang, China.,Reproductive Sciences Institute, Jiangsu University, Zhenjiang, China
| | - Min Wang
- Department of Gynecology, The Affiliated Hospital of Jiangsu University-Jiangsu University, Zhenjiang, China
| | - Wanyin Chen
- Department of Gynecology, The Affiliated Hospital of Jiangsu University-Jiangsu University, Zhenjiang, China
| | - Cong Shen
- Center for Reproduction and Genetics, Suzhou Municipal Hospital-The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Zeyu He
- Department of Clinical Medicine, China Medical University, Shenyang, China
| | - Xing Hu
- Department of Gynecology, The Affiliated Hospital of Jiangsu University-Jiangsu University, Zhenjiang, China
| | - Xiaoyan Huang
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Hong Li
- Center for Reproduction and Genetics, Suzhou Municipal Hospital-The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Binghai Chen
- Department of Urology, The Affiliated Hospital of Jiangsu University
| | - Bo Zheng
- Center for Reproduction and Genetics, Suzhou Municipal Hospital-The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Xia Chen
- Department of Gynecology, The Affiliated Hospital of Jiangsu University-Jiangsu University, Zhenjiang, China.,Reproductive Sciences Institute, Jiangsu University, Zhenjiang, China
| | - Jie Fang
- Department of Gynecology, The Affiliated Hospital of Jiangsu University-Jiangsu University, Zhenjiang, China
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11
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Aquilina B, Cauchi RJ. Modelling motor neuron disease in fruit flies: Lessons from spinal muscular atrophy. J Neurosci Methods 2018; 310:3-11. [DOI: 10.1016/j.jneumeth.2018.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 04/06/2018] [Accepted: 04/07/2018] [Indexed: 12/25/2022]
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12
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Bonday ZQ, Cortez GS, Grogan MJ, Antonysamy S, Weichert K, Bocchinfuso WP, Li F, Kennedy S, Li B, Mader MM, Arrowsmith CH, Brown PJ, Eram MS, Szewczyk MM, Barsyte-Lovejoy D, Vedadi M, Guccione E, Campbell RM. LLY-283, a Potent and Selective Inhibitor of Arginine Methyltransferase 5, PRMT5, with Antitumor Activity. ACS Med Chem Lett 2018; 9:612-617. [PMID: 30034588 DOI: 10.1021/acsmedchemlett.8b00014] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/23/2018] [Indexed: 12/30/2022] Open
Abstract
Protein arginine methyltransferase 5 (PRMT5) is a type II arginine methyltransferase that catalyzes the formation of symmetric dimethylarginine in a number of nuclear and cytoplasmic proteins. Although the cellular functions of PRMT5 have not been fully unraveled, it has been implicated in a number of cellular processes like RNA processing, signal transduction, and transcriptional regulation. PRMT5 is ubiquitously expressed in most tissues and its expression has been shown to be elevated in several cancers including breast cancer, gastric cancer, glioblastoma, and lymphoma. Here, we describe the identification and characterization of a novel and selective PRMT5 inhibitor with potent in vitro and in vivo activity. Compound 1 (also called LLY-283) inhibited PRMT5 enzymatic activity in vitro and in cells with IC50 of 22 ± 3 and 25 ± 1 nM, respectively, while its diastereomer, compound 2 (also called LLY-284), was much less active. Compound 1 also showed antitumor activity in mouse xenografts when dosed orally and can serve as an excellent probe molecule for understanding the biological function of PRMT5 in normal and cancer cells.
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Affiliation(s)
- Zahid Q. Bonday
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Guillermo S. Cortez
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Michael J. Grogan
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Stephen Antonysamy
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Ken Weichert
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Wayne P. Bocchinfuso
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Steven Kennedy
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Binghui Li
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Mary M. Mader
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto and Princess Margaret Cancer Centre, 101 College Street, MaRS South Tower, Suite 707, Toronto, ON M5G 1L7, Canada
| | - Peter J. Brown
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Mohammad S. Eram
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | | | | | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Robert M. Campbell
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
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13
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Gruss OJ, Meduri R, Schilling M, Fischer U. UsnRNP biogenesis: mechanisms and regulation. Chromosoma 2017; 126:577-593. [PMID: 28766049 DOI: 10.1007/s00412-017-0637-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/14/2017] [Accepted: 07/14/2017] [Indexed: 12/24/2022]
Abstract
Macromolecular complexes composed of proteins or proteins and nucleic acids rather than individual macromolecules mediate many cellular activities. Maintenance of these activities is essential for cell viability and requires the coordinated production of the individual complex components as well as their faithful incorporation into functional entities. Failure of complex assembly may have fatal consequences and can cause severe diseases. While many macromolecular complexes can form spontaneously in vitro, they often require aid from assembly factors including assembly chaperones in the crowded cellular environment. The assembly of RNA protein complexes implicated in the maturation of pre-mRNAs (termed UsnRNPs) has proven to be a paradigm to understand the action of assembly factors and chaperones. UsnRNPs are assembled by factors united in protein arginine methyltransferase 5 (PRMT5)- and survival motor neuron (SMN)-complexes, which act sequentially in the UsnRNP production line. While the PRMT5-complex pre-arranges specific sets of proteins into stable intermediates, the SMN complex displaces assembly factors from these intermediates and unites them with UsnRNA to form the assembled RNP. Despite advanced mechanistic understanding of UsnRNP assembly, our knowledge of regulatory features of this essential and ubiquitous cellular function remains remarkably incomplete. One may argue that the process operates as a default biosynthesis pathway and does not require sophisticated regulatory cues. Simple theoretical considerations and a number of experimental data, however, indicate that regulation of UsnRNP assembly most likely happens at multiple levels. This review will not only summarize how individual components of this assembly line act mechanistically but also why, how, and when the UsnRNP workflow might be regulated by means of posttranslational modification in response to cellular signaling cues.
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Affiliation(s)
- Oliver J Gruss
- Department of Genetics, Rheinische Friedrich-Wilhelms-Universität Bonn, Karlrobert-Kreiten-Str. 13, 53115, Bonn, Germany.
| | - Rajyalakshmi Meduri
- Department of Biochemistry, University of Würzburg, Biozentrum, Am Hubland, D-97074, Würzburg, Germany
| | - Maximilian Schilling
- Department of Genetics, Rheinische Friedrich-Wilhelms-Universität Bonn, Karlrobert-Kreiten-Str. 13, 53115, Bonn, Germany
| | - Utz Fischer
- Department of Biochemistry, University of Würzburg, Biozentrum, Am Hubland, D-97074, Würzburg, Germany.
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14
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Tan QQ, Liu W, Zhu F, Lei CL, Hahn DA, Wang XP. Describing the Diapause-Preparatory Proteome of the Beetle Colaphellus bowringi and Identifying Candidates Affecting Lipid Accumulation Using Isobaric Tags for Mass Spectrometry-Based Proteome Quantification (iTRAQ). Front Physiol 2017; 8:251. [PMID: 28491041 PMCID: PMC5405119 DOI: 10.3389/fphys.2017.00251] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 04/10/2017] [Indexed: 11/23/2022] Open
Abstract
Prior to entering diapause, insects must prepare themselves physiologically to withstand the stresses of arresting their development for a lengthy period. While studies describing the biochemical and cellular milieu of the maintenance phase of diapause are accumulating, few studies have taken an “omics” approach to describing molecular events during the diapause preparatory phase. We used isobaric tags and mass spectrometry (iTRAQ) to quantitatively compare the expression profiles of proteins identified during the onset of diapause preparation phase in the heads of adult female cabbage beetles, Colaphellus bowringi. A total of 3,175 proteins were identified, 297 of which were differentially expressed between diapause-destined and non-diapause-destined female adults and could therefore be involved in diapause preparation in this species. Comparison of identified proteins with protein function databases shows that many of these differentially expressed proteins enhanced in diapause destined beetles are involved in energy production and conversion, carbohydrate metabolism and transport, and lipid metabolism. Further hand annotation of differentially abundant peptides nominates several associated with stress hardiness, including HSPs and antioxidants, as well as neural development. In contrast, non-diapause destined beetles show substantial increases in cuticle proteins, suggesting additional post-emergence growth. Using RNA interference to silence a fatty acid-binding protein (FABP) that was highly abundant in the head of diapause-destined females prevented the accumulation of lipids in the fat body, a common product of diapause preparation in this species and others. Surprisingly, RNAi against the FABP also affected the transcript abundance of several heat shock proteins. These results suggest that the identified differentially expressed proteins that play vital roles in lipid metabolism may also contribute somehow to enhanced hardiness to environmental stress that is characteristic of diapause.
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Affiliation(s)
- Qian-Qian Tan
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Wen Liu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Fen Zhu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Chao-Liang Lei
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Daniel A Hahn
- Department of Entomology and Nematology, University of FloridaGainesville, FL, USA
| | - Xiao-Ping Wang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
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15
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Neuenkirchen N, Englbrecht C, Ohmer J, Ziegenhals T, Chari A, Fischer U. Reconstitution of the human U snRNP assembly machinery reveals stepwise Sm protein organization. EMBO J 2015; 34:1925-41. [PMID: 26069323 DOI: 10.15252/embj.201490350] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 05/12/2015] [Indexed: 11/09/2022] Open
Abstract
The assembly of spliceosomal U snRNPs depends on the coordinated action of PRMT5 and SMN complexes in vivo. These trans-acting factors enable the faithful delivery of seven Sm proteins onto snRNA and the formation of the common core of snRNPs. To gain mechanistic insight into their mode of action, we reconstituted the assembly machinery from recombinant sources. We uncover a stepwise and ordered formation of distinct Sm protein complexes on the PRMT5 complex, which is facilitated by the assembly chaperone pICln. Upon completion, the formed pICln-Sm units are displaced by new pICln-Sm protein substrates and transferred onto the SMN complex. The latter acts as a Brownian machine that couples spontaneous conformational changes driven by thermal energy to prevent mis-assembly and to ensure the transfer of Sm proteins to cognate RNA. Investigation of mutant SMN complexes provided insight into the contribution of individual proteins to these activities. The biochemical reconstitution presented here provides a basis for a detailed molecular dissection of the U snRNP assembly reaction.
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Affiliation(s)
- Nils Neuenkirchen
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
| | - Clemens Englbrecht
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jürgen Ohmer
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
| | - Thomas Ziegenhals
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
| | - Ashwin Chari
- Research Group of 3D Electron Cryomicroscopy, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Utz Fischer
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany Department of Radiation Medicine and Applied Sciences, University of California, San Diego, San Diego, CA, USA
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16
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17
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Hao LT, Duy PQ, Jontes JD, Beattie CE. Motoneuron development influences dorsal root ganglia survival and Schwann cell development in a vertebrate model of spinal muscular atrophy. Hum Mol Genet 2014; 24:346-60. [PMID: 25180019 DOI: 10.1093/hmg/ddu447] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Low levels of the survival motor neuron protein (SMN) cause the disease spinal muscular atrophy. A primary characteristic of this disease is motoneuron dysfunction and paralysis. Understanding why motoneurons are affected by low levels of SMN will lend insight into this disease and to motoneuron biology in general. Motoneurons in zebrafish smn mutants develop abnormally; however, it is unclear where Smn is needed for motoneuron development since it is a ubiquitously expressed protein. We have addressed this issue by expressing human SMN in motoneurons in zebrafish maternal-zygotic (mz) smn mutants. First, we demonstrate that SMN is present in axons, but only during the period of robust motor axon outgrowth. We also conclusively demonstrate that SMN acts cell autonomously in motoneurons for proper motoneuron development. This includes the formation of both axonal and dendritic branches. Analysis of the peripheral nervous system revealed that Schwann cells and dorsal root ganglia (DRG) neurons developed abnormally in mz-smn mutants. Schwann cells did not wrap axons tightly and had expanded nodes of Ranvier. The majority of DRG neurons had abnormally short peripheral axons and later many of them failed to divide and died. Expressing SMN just in motoneurons rescued both of these cell types showing that their failure to develop was secondary to the developmental defects in motoneurons. Driving SMN just in motoneurons did not increase survival of the animal, suggesting that SMN is needed for motoneuron development and motor circuitry, but that SMN in other cells types factors into survival.
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Affiliation(s)
- Le Thi Hao
- Department of Neuroscience, The Ohio State University College of Medicine, 190 Rightmire Hall, 1060 Carmack Rd, Columbus, OH 43210, USA
| | - Phan Q Duy
- Department of Neuroscience, The Ohio State University College of Medicine, 190 Rightmire Hall, 1060 Carmack Rd, Columbus, OH 43210, USA
| | - James D Jontes
- Department of Neuroscience, The Ohio State University College of Medicine, 190 Rightmire Hall, 1060 Carmack Rd, Columbus, OH 43210, USA
| | - Christine E Beattie
- Department of Neuroscience, The Ohio State University College of Medicine, 190 Rightmire Hall, 1060 Carmack Rd, Columbus, OH 43210, USA
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18
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SMA-causing missense mutations in survival motor neuron (Smn) display a wide range of phenotypes when modeled in Drosophila. PLoS Genet 2014; 10:e1004489. [PMID: 25144193 PMCID: PMC4140637 DOI: 10.1371/journal.pgen.1004489] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 05/19/2014] [Indexed: 11/30/2022] Open
Abstract
Mutations in the human survival motor neuron 1 (SMN) gene are the primary cause of spinal muscular atrophy (SMA), a devastating neuromuscular disorder. SMN protein has a well-characterized role in the biogenesis of small nuclear ribonucleoproteins (snRNPs), core components of the spliceosome. Additional tissue-specific and global functions have been ascribed to SMN; however, their relevance to SMA pathology is poorly understood and controversial. Using Drosophila as a model system, we created an allelic series of twelve Smn missense mutations, originally identified in human SMA patients. We show that animals expressing these SMA-causing mutations display a broad range of phenotypic severities, similar to the human disease. Furthermore, specific interactions with other proteins known to be important for SMN's role in RNP assembly are conserved. Intragenic complementation analyses revealed that the three most severe mutations, all of which map to the YG box self-oligomerization domain of SMN, display a stronger phenotype than the null allele and behave in a dominant fashion. In support of this finding, the severe YG box mutants are defective in self-interaction assays, yet maintain their ability to heterodimerize with wild-type SMN. When expressed at high levels, wild-type SMN is able to suppress the activity of the mutant protein. These results suggest that certain SMN mutants can sequester the wild-type protein into inactive complexes. Molecular modeling of the SMN YG box dimer provides a structural basis for this dominant phenotype. These data demonstrate that important structural and functional features of the SMN YG box are conserved between vertebrates and invertebrates, emphasizing the importance of self-interaction to the proper functioning of SMN. Spinal Muscular Atrophy (SMA) is a prevalent childhood neuromuscular disease, which in its most common form causes death by the age of two. One in fifty Americans is a carrier for SMA, making this genetic disease a serious health concern. SMA is caused by loss of function mutations in the survival motor neuron 1 (SMN1) gene. SMN is an essential protein and has a well-characterized function in the assembly of small nuclear ribonucleoproteins (snRNPs), which are core components of the spliceosome. To elucidate the phenotypic consequences of disrupting specific SMN protein interactions, we have generated a series of SMA-causing point mutations, modeled in Drosophila melanogaster. Using this system, we have shown that key aspects of SMN structure and function are conserved between humans and flies. Intragenic complementation analyses reveal the potential for dominant negative interactions between wild-type and mutant SMN subunits, highlighting the essential nature of the YG box in formation of higher-order SMN multimers. These results provide a basis for future studies investigating therapy targeted at restoration of functional SMN oligomers.
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19
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Yao R, Jiang H, Ma Y, Wang L, Wang L, Du J, Hou P, Gao Y, Zhao L, Wang G, Zhang Y, Liu DX, Huang B, Lu J. PRMT7 induces epithelial-to-mesenchymal transition and promotes metastasis in breast cancer. Cancer Res 2014; 74:5656-67. [PMID: 25136067 DOI: 10.1158/0008-5472.can-14-0800] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Epithelial-to-mesenchymal transition (EMT) enables metastasis. E-cadherin loss is a hallmark of EMT, but there remains an incomplete understanding of the epigenetics of this process. The protein arginine methyltransferase PRMT7 functions in various physiologic processes, including mRNA splicing, DNA repair, and neural differentiation, but its possible roles in cancer and metastasis have not been explored. In this report, we show that PRMT7 is expressed at higher levels in breast carcinoma cells and that elevated PRMT7 mediates EMT and metastasis. PRMT7 could inhibit the expression of E-cadherin by binding to its proximal promoter in a manner associated with altered histone methylation, specifically with elevated H4R3me2s and reduced H3K4me3, H3Ac, and H4Ac, which occurred at the E-cadherin promoter upon EMT induction. Moreover, PRMT7 interacted with YY1 and HDAC3 and was essential to link these proteins to the E-cadherin promoter. Silencing PRMT7 restored E-cadherin expression by repressing H4R3me2s and by increasing H3K4me3 and H4Ac, attenuating cell migration and invasion in MDA-MB-231 breast cancer cells. Overall, our results define PRMT7 as an inducer of breast cancer metastasis and present the opportunity for applying PRMT7-targeted therapeutics to treat highly invasive breast cancers.
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Affiliation(s)
- Ruosi Yao
- The Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China
| | - Hao Jiang
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Yuhui Ma
- The Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China
| | - Liping Wang
- Department of Pathology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Lin Wang
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Juan Du
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Pingfu Hou
- The Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China
| | - Yanyan Gao
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Li Zhao
- The Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China
| | - Guannan Wang
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, China
| | - Yu Zhang
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Dong-Xu Liu
- The Liggins Institute, the University of Auckland, Auckland, New Zealand
| | - Baiqu Huang
- The Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China.
| | - Jun Lu
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China.
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20
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Cauchi RJ. Gem depletion: amyotrophic lateral sclerosis and spinal muscular atrophy crossover. CNS Neurosci Ther 2014; 20:574-81. [PMID: 24645792 DOI: 10.1111/cns.12242] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 01/25/2014] [Accepted: 01/27/2014] [Indexed: 12/22/2022] Open
Abstract
The determining factor of spinal muscular atrophy (SMA), the most common motor neuron degenerative disease of childhood, is the survival motor neuron (SMN) protein. SMN and its Gemin associates form a complex that is indispensible for the biogenesis of small nuclear ribonucleoproteins (snRNPs), which constitute the building blocks of spliceosomes. It is as yet unclear whether a decreased capacity of SMN in snRNP assembly, and, hence, transcriptome abnormalities, account for the specific neuromuscular phenotype in SMA. Across metazoa, the SMN-Gemins complex concentrates in multiple nuclear gems that frequently neighbour or overlap Cajal bodies. The number of gems has long been known to be a faithful indicator of SMN levels, which are linked to SMA severity. Intriguingly, a flurry of recent studies have revealed that depletion of this nuclear structure is also a signature feature of amyotrophic lateral sclerosis (ALS), the most common adult-onset motor neuron disease. This review discusses such a surprising crossover in addition to highlighting the most recent work on the intricate world of spliceosome building, which seems to be at the heart of motor neuron physiology and survival.
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Affiliation(s)
- Ruben J Cauchi
- Department of Physiology and Biochemistry, University of Malta, Msida 2080, Malta
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21
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Klusza S, Novak A, Figueroa S, Palmer W, Deng WM. Prp22 and spliceosome components regulate chromatin dynamics in germ-line polyploid cells. PLoS One 2013; 8:e79048. [PMID: 24244416 PMCID: PMC3820692 DOI: 10.1371/journal.pone.0079048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 09/18/2013] [Indexed: 12/15/2022] Open
Abstract
During Drosophila oogenesis, the endopolyploid nuclei of germ-line nurse cells undergo a dramatic shift in morphology as oogenesis progresses; the easily-visible chromosomes are initially polytenic during the early stages of oogenesis before they transiently condense into a distinct '5-blob' configuration, with subsequent dispersal into a diffuse state. Mutations in many genes, with diverse cellular functions, can affect the ability of nurse cells to fully decondense their chromatin, resulting in a '5-blob arrest' phenotype that is maintained throughout the later stages of oogenesis. However, the mechanisms and significance of nurse-cell (NC) chromatin dispersal remain poorly understood. Here, we report that a screen for modifiers of the 5-blob phenotype in the germ line isolated the spliceosomal gene peanuts, the Drosophila Prp22. We demonstrate that reduction of spliceosomal activity through loss of peanuts promotes decondensation defects in NC nuclei during mid-oogenesis. We also show that the Prp38 spliceosomal protein accumulates in the nucleoplasm of nurse cells with impaired peanuts function, suggesting that spliceosomal recycling is impaired. Finally, we reveal that loss of additional spliceosomal proteins impairs the full decondensation of NC chromatin during later stages of oogenesis, suggesting that individual spliceosomal subcomplexes modulate expression of the distinct subset of genes that are required for correct morphology in endopolyploid nurse cells.
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Affiliation(s)
- Stephen Klusza
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Amanda Novak
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Shirelle Figueroa
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - William Palmer
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
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22
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Bezzi M, Teo SX, Muller J, Mok WC, Sahu SK, Vardy LA, Bonday ZQ, Guccione E. Regulation of constitutive and alternative splicing by PRMT5 reveals a role for Mdm4 pre-mRNA in sensing defects in the spliceosomal machinery. Genes Dev 2013; 27:1903-16. [PMID: 24013503 PMCID: PMC3778243 DOI: 10.1101/gad.219899.113] [Citation(s) in RCA: 226] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 07/26/2013] [Indexed: 01/08/2023]
Abstract
The tight control of gene expression at the level of both transcription and post-transcriptional RNA processing is essential for mammalian development. We here investigate the role of protein arginine methyltransferase 5 (PRMT5), a putative splicing regulator and transcriptional cofactor, in mammalian development. We demonstrate that selective deletion of PRMT5 in neural stem/progenitor cells (NPCs) leads to postnatal death in mice. At the molecular level, the absence of PRMT5 results in reduced methylation of Sm proteins, aberrant constitutive splicing, and the alternative splicing of specific mRNAs with weak 5' donor sites. Intriguingly, the products of these mRNAs are, among others, several proteins regulating cell cycle progression. We identify Mdm4 as one of these key mRNAs that senses the defects in the spliceosomal machinery and transduces the signal to activate the p53 response, providing a mechanistic explanation of the phenotype observed in vivo. Our data demonstrate that PRMT5 is a master regulator of splicing in mammals and uncover a new role for the Mdm4 pre-mRNA, which could be exploited for anti-cancer therapy.
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Affiliation(s)
- Marco Bezzi
- Division of Cancer Genetics and Therapeutics, Laboratory of Chromatin, Epigenetics, and Differentiation, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore
| | - Shun Xie Teo
- Division of Cancer Genetics and Therapeutics, Laboratory of Chromatin, Epigenetics, and Differentiation, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore
| | - Julius Muller
- Division of Cancer Genetics and Therapeutics, Laboratory of Chromatin, Epigenetics, and Differentiation, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore
| | - Wei Chuen Mok
- Division of Cancer Genetics and Therapeutics, Laboratory of Chromatin, Epigenetics, and Differentiation, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore
| | - Sanjeeb Kumar Sahu
- Division of Cancer Genetics and Therapeutics, Laboratory of Chromatin, Epigenetics, and Differentiation, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore
| | - Leah A. Vardy
- Institute of Medical Biology (IMB), A*STAR, Singapore 138673, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Zahid Q. Bonday
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, USA
| | - Ernesto Guccione
- Division of Cancer Genetics and Therapeutics, Laboratory of Chromatin, Epigenetics, and Differentiation, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore
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23
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Wang YC, Li C. Evolutionarily conserved protein arginine methyltransferases in non-mammalian animal systems. FEBS J 2012; 279:932-45. [PMID: 22251447 DOI: 10.1111/j.1742-4658.2012.08490.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein arginine methylation is catalyzed by members of the protein arginine methyltransferase (PRMT) family. In the present review, nine PRMTs identified in mammals (human) were used as templates to survey homologous PRMTs in 10 animal species with a completed sequence available in non-mammalian vertebrates, invertebrate chordates, echinoderms, arthropods, nematodes and cnidarians. We show the conservation of the most typical type I PRMT1 and type II PRMT5 in all of the species examined, the wide yet different distribution of PRMT3, 4 and 7 in non-mammalian animals, the vertebrate-restricted distribution of PRMT8 and the special reptile/avian-deficient distribution of PRMT2 and 6. We summarize the basic functions of each PRMT and focus on the current investigations of PRMTs in the non-mammalian animal models, including Xenopus, fish (zebrafish, flounder and medaka), Drosophila and Caenorhabditis elegans. Studies in the model systems not only complement the understanding of the functions of PRMTs in mammals, but also provide valuable information about their evolution, as well as their critical roles and interplays.
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Affiliation(s)
- Yi-Chun Wang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
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24
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Blackwell E, Ceman S. Arginine methylation of RNA-binding proteins regulates cell function and differentiation. Mol Reprod Dev 2012; 79:163-75. [PMID: 22345066 DOI: 10.1002/mrd.22024] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 12/26/2011] [Indexed: 12/13/2022]
Abstract
Arginine methylation is a post-translational modification that regulates protein function. RNA-binding proteins are an important class of cell-function mediators, some of which are methylated on arginine. Early studies of RNA-binding proteins and arginine methylation are briefly introduced, and the enzymes that mediate this post-translational modification are described. We review the most common RNA-binding domains and briefly discuss how they associate with RNAs. We address the following groups of RNA-binding proteins: hnRNP, Sm, Piwi, Vasa, FMRP, and HuD. hnRNPs were the first RNA-binding proteins found to be methylated on arginine. The Sm proteins function in RNA processing and germ cell specification. The Piwi proteins are largely germ cell specific and are also required for germ cell production, as is Vasa. FMRP participates in germ cell formation in Drosophila, but is more widely known for its neuronal function. Similarly, HuD plays a role in nervous system development and function. We review the effects of arginine methylation on the function of each protein, then conclude by addressing remaining questions and future directions of arginine methylation as an important and emerging area of regulation.
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Affiliation(s)
- Ernest Blackwell
- Department of Cell and Developmental Biology, Neuroscience Program and College of Medicine, University of Illinois, Urbana-Champaign, Illlinois, USA
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25
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Zurita-Lopez CI, Sandberg T, Kelly R, Clarke SG. Human protein arginine methyltransferase 7 (PRMT7) is a type III enzyme forming ω-NG-monomethylated arginine residues. J Biol Chem 2012; 287:7859-70. [PMID: 22241471 DOI: 10.1074/jbc.m111.336271] [Citation(s) in RCA: 199] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Full-length human protein arginine methyltransferase 7 (PRMT7) expressed as a fusion protein in Escherichia coli was initially found to generate only ω-N(G)-monomethylated arginine residues in small peptides, suggesting that it is a type III enzyme. A later study, however, characterized fusion proteins of PRMT7 expressed in bacterial and mammalian cells as a type II/type I enzyme, capable of producing symmetrically dimethylated arginine (type II activity) as well as small amounts of asymmetric dimethylarginine (type I activity). We have sought to clarify the enzymatic activity of human PRMT7. We analyzed the in vitro methylation products of a glutathione S-transferase (GST)-PRMT7 fusion protein with robust activity using a variety of arginine-containing synthetic peptides and protein substrates, including a GST fusion with the N-terminal domain of fibrillarin (GST-GAR), myelin basic protein, and recombinant human histones H2A, H2B, H3, and H4. Regardless of the methylation reaction conditions (incubation time, reaction volume, and substrate concentration), we found that PRMT7 only produces ω-N(G)-monomethylarginine with these substrates. In control experiments, we showed that mammalian GST-PRMT1 and Myc-PRMT5 were, unlike PRMT7, able to dimethylate both peptide P-SmD3 and SmB/D3 to give the expected asymmetric and symmetric products, respectively. These experiments show that PRMT7 is indeed a type III human methyltransferase capable of forming only ω-N(G)-monomethylarginine, not asymmetric ω-N(G),N(G)-dimethylarginine or symmetric ω-N(G),N(G')-dimethylarginine, under the conditions tested.
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Affiliation(s)
- Cecilia I Zurita-Lopez
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, California 90095-1569, USA
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26
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Yu MC. The Role of Protein Arginine Methylation in mRNP Dynamics. Mol Biol Int 2011; 2011:163827. [PMID: 22091396 PMCID: PMC3195771 DOI: 10.4061/2011/163827] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 02/12/2011] [Indexed: 12/13/2022] Open
Abstract
In eukaryotes, messenger RNA biogenesis depends on the ordered and precise assembly of a nuclear messenger ribonucleoprotein particle (mRNP) during transcription. This process requires a well-orchestrated and dynamic sequence of molecular recognition events by specific RNA-binding proteins. Arginine methylation is a posttranslational modification found in a plethora of RNA-binding proteins responsible for mRNP biogenesis. These RNA-binding proteins include both heterogeneous nuclear ribonucleoproteins (hnRNPs) and serine/arginine-rich (SR) proteins. In this paper, I discuss the mechanisms of action by which arginine methylation modulates various facets of mRNP biogenesis, and how the collective consequences of this modification impart the specificity required to generate a mature, translational- and export-competent mRNP.
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Affiliation(s)
- Michael C Yu
- Department of Biological Sciences, State University of New York at Buffalo, 109 Cooke Hall, Buffalo, NY 14260, USA
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27
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Boyer JG, Bowerman M, Kothary R. The many faces of SMN: deciphering the function critical to spinal muscular atrophy pathogenesis. FUTURE NEUROLOGY 2010. [DOI: 10.2217/fnl.10.57] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Spinal muscular atrophy (SMA) is the leading genetic cause of infant death, affecting 1 in 6000–10,000 live births. SMA is an autosomal recessive disorder characterized by the degeneration of α-motor neurons, and lower limb and proximal muscle weakness and wasting. SMA is the result of the deletion of or mutations in the survival motor neuron (SMN)1 gene. Currently, our understanding of how loss of the widely expressed SMN leads to the selective pathogenesis observed in SMA is limited. Here, we discuss the known nuclear and cytoplasmic functions of the SMN protein and how they relate to the SMA pathology reported in motor neurons, striated muscle and at neuromuscular junctions. While a vast amount of work in various cell and animal models has increased our knowledge of the many functions of the SMN protein, we have yet to come to a full understanding of which role(s) are central to SMA pathogenesis.
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Affiliation(s)
- Justin G Boyer
- Ottawa Hospital Research Institute, Regenerative Medicine Program, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, ON, Canada
| | - Mélissa Bowerman
- Ottawa Hospital Research Institute, Regenerative Medicine Program, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, ON, Canada
| | - Rashmi Kothary
- Department of Medicine, University of Ottawa, ON, Canada
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28
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Sanchez SE, Petrillo E, Beckwith EJ, Zhang X, Rugnone ML, Hernando CE, Cuevas JC, Godoy Herz MA, Depetris-Chauvin A, Simpson CG, Brown JWS, Cerdán PD, Borevitz JO, Mas P, Ceriani MF, Kornblihtt AR, Yanovsky MJ. A methyl transferase links the circadian clock to the regulation of alternative splicing. Nature 2010; 468:112-6. [PMID: 20962777 DOI: 10.1038/nature09470] [Citation(s) in RCA: 232] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Accepted: 09/01/2010] [Indexed: 12/11/2022]
Abstract
Circadian rhythms allow organisms to time biological processes to the most appropriate phases of the day-night cycle. Post-transcriptional regulation is emerging as an important component of circadian networks, but the molecular mechanisms linking the circadian clock to the control of RNA processing are largely unknown. Here we show that PROTEIN ARGININE METHYL TRANSFERASE 5 (PRMT5), which transfers methyl groups to arginine residues present in histones and Sm spliceosomal proteins, links the circadian clock to the control of alternative splicing in plants. Mutations in PRMT5 impair several circadian rhythms in Arabidopsis thaliana and this phenotype is caused, at least in part, by a strong alteration in alternative splicing of the core-clock gene PSEUDO RESPONSE REGULATOR 9 (PRR9). Furthermore, genome-wide studies show that PRMT5 contributes to the regulation of many pre-messenger-RNA splicing events, probably by modulating 5'-splice-site recognition. PRMT5 expression shows daily and circadian oscillations, and this contributes to the mediation of the circadian regulation of expression and alternative splicing of a subset of genes. Circadian rhythms in locomotor activity are also disrupted in dart5-1, a mutant affected in the Drosophila melanogaster PRMT5 homologue, and this is associated with alterations in splicing of the core-clock gene period and several clock-associated genes. Our results demonstrate a key role for PRMT5 in the regulation of alternative splicing and indicate that the interplay between the circadian clock and the regulation of alternative splicing by PRMT5 constitutes a common mechanism that helps organisms to synchronize physiological processes with daily changes in environmental conditions.
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Affiliation(s)
- Sabrina E Sanchez
- IFEVA, Facultad de Agronomía, UBA-CONICET, C1417DSE Buenos Aires, Argentina
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29
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Anne J. Arginine methylation of SmB is required for Drosophila germ cell development. Development 2010; 137:2819-28. [PMID: 20659974 DOI: 10.1242/dev.052944] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Sm proteins constitute the common core of spliceosomal small nuclear ribonucleoproteins. Although Sm proteins are known to be methylated at specific arginine residues within the C-terminal arginine-glycine dipeptide (RG) repeats, the biological relevance of these modifications remains unknown. In this study, a tissue-specific function of arginine methylation of the SmB protein was identified in Drosophila. Analysis of the distribution of SmB during oogenesis revealed that this protein accumulates at the posterior pole of the oocyte, a cytoplasmic region containing the polar granules, which are necessary for the formation of primordial germ cells. The pole plasm localisation of SmB requires the methylation of arginine residues in its RG repeats by the Capsuléen-Valois methylosome complex. Functional studies showed that the methylation of these arginine residues is essential for distinct processes of the germline life cycle, including germ cell formation, migration and differentiation. In particular, the methylation of a subset of these arginine residues appears essential for the anchoring of the polar granules at the posterior cortex of the oocyte, whereas the methylation of another subset controls germ cell migration during embryogenesis. These results demonstrate a crucial role of arginine methylation in directing the subcellular localisation of SmB and that this modification contributes specifically to the establishment and development of germ cells.
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Affiliation(s)
- Joël Anne
- Department of Developmental Genetics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, Heidelberg, Germany.
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30
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Dafou D, Grun B, Sinclair J, Lawrenson K, Benjamin EC, Hogdall E, Kruger-Kjaer S, Christensen L, Sowter HM, Al-Attar A, Edmondson R, Darby S, Berchuck A, Laird PW, Pearce CL, Ramus SJ, Jacobs IJ, Gayther SA. Microcell-mediated chromosome transfer identifies EPB41L3 as a functional suppressor of epithelial ovarian cancers. Neoplasia 2010; 12:579-89. [PMID: 20651987 PMCID: PMC2907584 DOI: 10.1593/neo.10340] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2010] [Revised: 03/30/2010] [Accepted: 04/05/2010] [Indexed: 12/23/2022]
Abstract
We used a functional complementation approach to identify tumor-suppressor genes and putative therapeutic targets for ovarian cancer. Microcell-mediated transfer of chromosome 18 in the ovarian cancer cell line TOV21G induced in vitro and in vivo neoplastic suppression. Gene expression microarray profiling in TOV21G(+18) hybrids identified 14 candidate genes on chromosome 18 that were significantly overexpressed and therefore associated with neoplastic suppression. Further analysis of messenger RNA and protein expression for these genes in additional ovarian cancer cell lines indicated that EPB41L3 (erythrocyte membrane protein band 4.1-like 3, alternative names DAL-1 and 4.1B) was a candidate ovarian cancer-suppressor gene. Immunoblot analysis showed that EPB41L3 was activated in TOV21G(+18) hybrids, expressed in normal ovarian epithelial cell lines, but was absent in 15 (78%) of 19 ovarian cancer cell lines. Using immunohistochemistry, 66% of 794 invasive ovarian tumors showed no EPB41L3 expression compared with only 24% of benign ovarian tumors and 0% of normal ovarian epithelial tissues. EPB41L3 was extensively methylated in ovarian cancer cell lines and primary ovarian tumors compared with normal tissues (P = .00004), suggesting this may be the mechanism of gene inactivation in ovarian cancers. Constitutive reexpression of EPB41L3 in a three-dimensional multicellular spheroid model of ovarian cancer caused significant growth suppression and induced apoptosis. Transmission and scanning electron microscopy demonstrated many similarities between EPB41L3-expressing cells and chromosome 18 donor-recipient hybrids, suggesting that EPB41L3 is the gene responsible for neoplastic suppression after chromosome 18 transfer. Finally, an inducible model of EPB41L3 expression in three-dimensional spheroids confirmed that reexpression of EPB41L3 induces extensive apoptotic cell death in ovarian cancers.
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Affiliation(s)
- Dimitra Dafou
- EGA Institute for Women's Health, Gynaecological Cancer Research Laboratories, University College London, London, UK
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31
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Burghes AHM, Beattie CE. Spinal muscular atrophy: why do low levels of survival motor neuron protein make motor neurons sick? Nat Rev Neurosci 2009; 10:597-609. [PMID: 19584893 PMCID: PMC2853768 DOI: 10.1038/nrn2670] [Citation(s) in RCA: 562] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many neurogenetic disorders are caused by the mutation of ubiquitously expressed genes. One such disorder, spinal muscular atrophy, is caused by loss or mutation of the survival motor neuron1 gene (SMN1), leading to reduced SMN protein levels and a selective dysfunction of motor neurons. SMN, together with partner proteins, functions in the assembly of small nuclear ribonucleoproteins (snRNPs), which are important for pre-mRNA splicing. It has also been suggested that SMN might function in the assembly of other ribonucleoprotein complexes. Two hypotheses have been proposed to explain the molecular dysfunction that gives rise to spinal muscular atrophy (SMA) and its specificity to a particular group of neurons. The first hypothesis states that the loss of SMN's well-known function in snRNP assembly causes an alteration in the splicing of a specific gene (or genes). The second hypothesis proposes that SMN is crucial for the transport of mRNA in neurons and that disruption of this function results in SMA.
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Affiliation(s)
- Arthur H M Burghes
- Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA.
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32
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Palfi Z, Jaé N, Preusser C, Kaminska KH, Bujnicki JM, Lee JH, Günzl A, Kambach C, Urlaub H, Bindereif A. SMN-assisted assembly of snRNP-specific Sm cores in trypanosomes. Genes Dev 2009; 23:1650-64. [PMID: 19605687 DOI: 10.1101/gad.526109] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Spliceosomal small nuclear ribonucleoproteins (snRNPs) in trypanosomes contain either the canonical heptameric Sm ring (U1, U5, spliced leader snRNPs), or variant Sm cores with snRNA-specific Sm subunits (U2, U4 snRNPs). Searching for specificity factors, we identified SMN and Gemin2 proteins that are highly divergent from known orthologs. SMN is splicing-essential in trypanosomes and nuclear-localized, suggesting that Sm core assembly in trypanosomes is nuclear. We demonstrate in vitro that SMN is sufficient to confer specificity of canonical Sm core assembly and to discriminate against binding to nonspecific RNA and to U2 and U4 snRNAs. SMN interacts transiently with the SmD3B subcomplex, contacting specifically SmB. SMN remains associated throughout the assembly of the Sm heteroheptamer and dissociates only when a functional Sm site is incorporated. These data establish a novel role of SMN, mediating snRNP specificity in Sm core assembly, and yield new biochemical insight into the mechanism of SMN activity.
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Affiliation(s)
- Zsofia Palfi
- Institute of Biochemistry, Justus Liebig University of Giessen, Giessen, Germany
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33
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Kirino Y, Kim N, de Planell-Saguer M, Khandros E, Chiorean S, Klein PS, Rigoutsos I, Jongens TA, Mourelatos Z. Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability. Nat Cell Biol 2009; 11:652-8. [PMID: 19377467 PMCID: PMC2746449 DOI: 10.1038/ncb1872] [Citation(s) in RCA: 194] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Accepted: 01/30/2009] [Indexed: 11/09/2022]
Abstract
Piwi family proteins are essential for germline development and bind piwi-interacting RNAs (piRNAs). The grandchildless gene aub of Drosophila melanogaster encodes the piRNA-binding protein Aubergine (Aub), which is essential for formation of primordial germ cells (PGCs). Here we report that Piwi family proteins of mouse, Xenopus laevis and Drosophila contain symmetrical dimethylarginines (sDMAs). We found that Piwi proteins are expressed in Xenopus oocytes and we identified numerous Xenopus piRNAs. We report that the Drosophila homologue of protein methyltransferase 5 (dPRMT5, csul/dart5), which is also the product of a grandchildless gene, is required for arginine methylation of Drosophila Piwi, Ago3 and Aub proteins in vivo. Loss of dPRMT5 activity led to a reduction in the levels of piRNAs, Ago3 and Aub proteins, and accumulation of retrotransposons in the Drosophila ovary. Our studies explain the relationship between aub and dPRMT5 (csul/dart5) genes by demonstrating that dPRMT5 is the enzyme that methylates Aub. Our findings underscore the significance of sDMA modification of Piwi proteins in the germline and suggest an interacting pathway of genes that are required for piRNA function and PGC specification.
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Affiliation(s)
- Yohei Kirino
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Namwoo Kim
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Mariàngels de Planell-Saguer
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Eugene Khandros
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Stephanie Chiorean
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Peter S. Klein
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Isidore Rigoutsos
- Bioinformatics and Pattern Discovery Group, IBM TJ Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Thomas A. Jongens
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Zissimos Mourelatos
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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Patel SB, Bellini M. The assembly of a spliceosomal small nuclear ribonucleoprotein particle. Nucleic Acids Res 2008; 36:6482-93. [PMID: 18854356 PMCID: PMC2582628 DOI: 10.1093/nar/gkn658] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The U1, U2, U4, U5 and U6 small nuclear ribonucleoprotein particles (snRNPs) are essential elements of the spliceosome, the enzyme that catalyzes the excision of introns and the ligation of exons to form a mature mRNA. Since their discovery over a quarter century ago, the structure, assembly and function of spliceosomal snRNPs have been extensively studied. Accordingly, the functions of splicing snRNPs and the role of various nuclear organelles, such as Cajal bodies (CBs), in their nuclear maturation phase have already been excellently reviewed elsewhere. The aim of this review is, then, to briefly outline the structure of snRNPs and to synthesize new and exciting developments in the snRNP biogenesis pathways.
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Affiliation(s)
- Snehal Bhikhu Patel
- Biochemistry and College of Medicine and Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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