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Sharma G, Paganin M, Lauria F, Perenthaler E, Viero G. The SMN-ribosome interplay: a new opportunity for Spinal Muscular Atrophy therapies. Biochem Soc Trans 2024; 52:465-479. [PMID: 38391004 PMCID: PMC10903476 DOI: 10.1042/bst20231116] [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: 12/22/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
The underlying cause of Spinal Muscular Atrophy (SMA) is in the reduction of survival motor neuron (SMN) protein levels due to mutations in the SMN1 gene. The specific effects of SMN protein loss and the resulting pathological alterations are not fully understood. Given the crucial roles of the SMN protein in snRNP biogenesis and its interactions with ribosomes and translation-related proteins and mRNAs, a decrease in SMN levels below a specific threshold in SMA is expected to affect translational control of gene expression. This review covers both direct and indirect SMN interactions across various translation-related cellular compartments and processes, spanning from ribosome biogenesis to local translation and beyond. Additionally, it aims to outline deficiencies and alterations in translation observed in SMA models and patients, while also discussing the implications of the relationship between SMN protein and the translation machinery within the context of current and future therapies.
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Musawi S, Donnio LM, Zhao Z, Magnani C, Rassinoux P, Binda O, Huang J, Jacquier A, Coudert L, Lomonte P, Martinat C, Schaeffer L, Mottet D, Côté J, Mari PO, Giglia-Mari G. Nucleolar reorganization after cellular stress is orchestrated by SMN shuttling between nuclear compartments. Nat Commun 2023; 14:7384. [PMID: 37968267 PMCID: PMC10652021 DOI: 10.1038/s41467-023-42390-4] [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: 10/13/2022] [Accepted: 10/10/2023] [Indexed: 11/17/2023] Open
Abstract
Spinal muscular atrophy is an autosomal recessive neuromuscular disease caused by mutations in the multifunctional protein Survival of Motor Neuron, or SMN. Within the nucleus, SMN localizes to Cajal bodies, which are associated with nucleoli, nuclear organelles dedicated to the first steps of ribosome biogenesis. The highly organized structure of the nucleolus can be dynamically altered by genotoxic agents. RNAP1, Fibrillarin, and nucleolar DNA are exported to the periphery of the nucleolus after genotoxic stress and, once DNA repair is fully completed, the organization of the nucleolus is restored. We find that SMN is required for the restoration of the nucleolar structure after genotoxic stress. During DNA repair, SMN shuttles from the Cajal bodies to the nucleolus. This shuttling is important for nucleolar homeostasis and relies on the presence of Coilin and the activity of PRMT1.
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Affiliation(s)
- Shaqraa Musawi
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Lise-Marie Donnio
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France.
| | - Zehui Zhao
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
| | - Charlène Magnani
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
| | - Phoebe Rassinoux
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
| | - Olivier Binda
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
- Faculty of Medicine, Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, K1H 8M5, Ontario, Canada
| | - Jianbo Huang
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
| | - Arnaud Jacquier
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
| | - Laurent Coudert
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
| | - Patrick Lomonte
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
| | - Cécile Martinat
- INSERM/UEPS UMR 861, Paris Saclay Université, I-STEM, 91100, Corbeil-Essonnes, France
| | - Laurent Schaeffer
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
| | - Denis Mottet
- GIGA-Molecular Biology of Diseases, Gene Expression and Cancer Laboratory, B34 + 1, University of Liege, Avenue de l'Hôpital 1, B-4000, Liège, Belgium
| | - Jocelyn Côté
- Faculty of Medicine, Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, K1H 8M5, Ontario, Canada
| | - Pierre-Olivier Mari
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France
| | - Giuseppina Giglia-Mari
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM), CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, 68008, Lyon, France.
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Wang YC, Chang CP, Lai YC, Chan CH, Ou SC, Wang SH, Li C. The conservation and diversity of the exons encoding the glycine and arginine rich domain of the fibrillarin gene in vertebrates, with special focus on reptiles and birds. Gene 2023; 866:147345. [PMID: 36893875 DOI: 10.1016/j.gene.2023.147345] [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: 09/05/2022] [Revised: 02/18/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
The nucleolar rRNA 2'-O-methyltransferase fibrillarin (FBL) contains a highly conserved methyltransferase domain at the C-terminus and a diverse glycine arginine-rich (GAR) domain at the N-terminus in eukaryotes. We found that a nine-exon configuration of fbl and exon 2-3 encoded GAR domain are conserved and specific in vertebrates. All internal exons except exon 2 and 3 are of the same lengths in different vertebrate lineages. The lengths of exon 2 and 3 vary in different vertebrate species but the ones with longer exon 2 usually have shorter exon 3 complementarily, limiting lengths of the GAR domain within a certain range. In tetrapods except for reptiles, exon 2 appears to be longer than exon 3. We specifically analyzed different lineages of reptiles for their GAR sequences and exon lengths. The lengths of exon 2 in reptiles are around 80-130-nt shorter and the lengths of exon 3 in reptiles are around 50-90 nt longer than those in other tetrapods, all in the GAR-coding regions. An FSPR sequence is present at the beginning of the GAR domain encoded by exon 2 in all vertebrates, and a specific FXSP/G element (X can be K, R, Q, N, and H) exist in the middle of GAR with phenylalanine as the 3rd exon 3-encoded amino acid residue starting from jawfish. Snakes, turtles, and songbirds contain shorter exon 2 compared with lizards, indicating continuous deletions in exon 2 and insertions/duplications in exon 3 in these lineages. Specifically, we confirmed the presence the fbl gene in chicken and validated the RNA expression. Our analyses of the GAR-encoding exons of fbl in vertebrates and reptiles should provide the basis for further evolutionary analyses of more GAR domain encoding proteins.
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Affiliation(s)
- Yi-Chun Wang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chien-Ping Chang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Yu-Chuan Lai
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Chi-Ho Chan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan; Department of Microbiology and Immunology, Chung Shan Medical University, Taichung, Taiwan
| | - Shan-Chia Ou
- Department of Veterinary Medicine, Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung, Taiwan
| | - Sue-Hong Wang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chuan Li
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan.
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Webster SF, Ghalei H. Maturation of small nucleolar RNAs: from production to function. RNA Biol 2023; 20:715-736. [PMID: 37796118 PMCID: PMC10557570 DOI: 10.1080/15476286.2023.2254540] [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] [Accepted: 08/28/2023] [Indexed: 10/06/2023] Open
Abstract
Small Nucleolar RNAs (snoRNAs) are an abundant group of non-coding RNAs with well-defined roles in ribosomal RNA processing, folding and chemical modification. Besides their classic roles in ribosome biogenesis, snoRNAs are also implicated in several other cellular activities including regulation of splicing, transcription, RNA editing, cellular trafficking, and miRNA-like functions. Mature snoRNAs must undergo a series of processing steps tightly regulated by transiently associating factors and coordinated with other cellular processes including transcription and splicing. In addition to their mature forms, snoRNAs can contribute to gene expression regulation through their derivatives and degradation products. Here, we review the current knowledge on mechanisms of snoRNA maturation, including the different pathways of processing, and the regulatory mechanisms that control snoRNA levels and complex assembly. We also discuss the significance of studying snoRNA maturation, highlight the gaps in the current knowledge and suggest directions for future research in this area.
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Affiliation(s)
- Sarah F. Webster
- Biochemistry, Cell, and Developmental Biology Graduate Program, Emory University, Atlanta, Georgia, USA
- Department of Biochemistry, Emory University, Atlanta, Georgia, USA
| | - Homa Ghalei
- Department of Biochemistry, Emory University, Atlanta, Georgia, USA
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Grice SJ, Liu JL. Motor defects in a Drosophila model for spinal muscular atrophy result from SMN depletion during early neurogenesis. PLoS Genet 2022; 18:e1010325. [PMID: 35877682 PMCID: PMC9352204 DOI: 10.1371/journal.pgen.1010325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 08/04/2022] [Accepted: 07/05/2022] [Indexed: 11/18/2022] Open
Abstract
Spinal muscular atrophy (SMA) is the most common autosomal recessive neurodegenerative disease, and is characterised by spinal motor neuron loss, impaired motor function and, often, premature death. Mutations and deletions in the widely expressed survival motor neuron 1 (SMN1) gene cause SMA; however, the mechanisms underlying the selectivity of motor neuron degeneration are not well understood. Although SMA is degenerative in nature, SMN function during embryonic and early postnatal development appears to be essential for motor neuron survival in animal models and humans. Notwithstanding, how developmental defects contribute to the subversion of postnatal and adult motor function remains elusive. Here, in a Drosophila SMA model, we show that neurodevelopmental defects precede gross locomotor dysfunction in larvae. Furthermore, to specifically address the relevance of SMN during neurogenesis and in neurogenic cell types, we show that SMN knockdown using neuroblast-specific and pan-neuronal drivers, but not differentiated neuron or glial cell drivers, impairs adult motor function. Using targeted knockdown, we further restricted SMN manipulation in neuroblasts to a defined time window. Our aim was to express specifically in the neuronal progenitor cell types that have not formed synapses, and thus a time that precedes neuromuscular junction formation and maturation. By restoring SMN levels in these distinct neuronal population, we partially rescue the larval locomotor defects of Smn mutants. Finally, combinatorial SMN knockdown in immature and mature neurons synergistically enhances the locomotor and survival phenotypes. Our in-vivo study is the first to directly rescue the motor defects of an SMA model by expressing Smn in an identifiable population of Drosophila neuroblasts and developing neurons, highlighting that neuronal sensitivity to SMN loss may arise before synapse establishment and nerve cell maturation. Spinal muscular atrophy (SMA) is the most common genetic cause of infant mortality and leads to the degeneration of the nerves that control muscle function. Loss-of-function mutations in the widely expressed survival motor neuron 1 (SMN1) gene cause SMA, but how low levels of SMN protein cause the neuronal dysfunction is not known. Although SMA is a disease of nerve degeneration, SMN function during nerve cell development may be important, particularly in severe forms of SMA. Nevertheless, how the defects during development and throughout early life contribute to the disease is not well understood. We have previously demonstrated that SMN protein becomes enriched in neuroblasts, which are the cells that divide to produce neurons. In the present study, motor defects observed in our fly model for SMA could be rescued by restoring SMN in neuroblasts alone. In addition, we show that knocking down SMN in healthy flies within the same cell type causes impaired motor function. The present study shows that the manipulation of SMN in a developmentally important cell type can cause motor defects, indicating that a period of abnormal neurodevelopment may contribute to SMA.
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Affiliation(s)
- Stuart J. Grice
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (SJG); , (J-LL)
| | - Ji-Long Liu
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- School of Life Science and Technology, Shanghai, Tech University, Shanghai, China
- * E-mail: (SJG); , (J-LL)
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Gabanella F, Barbato C, Fiore M, Petrella C, de Vincentiis M, Greco A, Minni A, Corbi N, Passananti C, Di Certo MG. Fine-Tuning of mTOR mRNA and Nucleolin Complexes by SMN. Cells 2021; 10:3015. [PMID: 34831238 PMCID: PMC8616268 DOI: 10.3390/cells10113015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 11/17/2022] Open
Abstract
Increasing evidence points to the Survival Motor Neuron (SMN) protein as a key determinant of translation pathway. Besides its role in RNA processing and sorting, several works support a critical implication of SMN in ribosome biogenesis. We previously showed that SMN binds ribosomal proteins (RPs) as well as their encoding transcripts, ensuring an appropriate level of locally synthesized RPs. SMN impacts the translation machinery in both neural and non-neural cells, in agreement with the concept that SMN is an essential protein in all cell types. Here, we further assessed the relationship between SMN and translation-related factors in immortalized human fibroblasts. We focused on SMN-nucleolin interaction, keeping in mind that nucleolin is an RNA-binding protein, highly abundant within the nucleolus, that exhibits a central role in ribosomes production. Nucleolin may also affects translation network by binding the mammalian target of rapamycin (mTOR) mRNA and promoting its local synthesis. In this regard, for the first time we provided evidence that SMN protein itself associates with mTOR transcript. Collectively, we found that: (1) SMN coexists with nucleolin-mTOR mRNA complexes at subcellular level; (2) SMN deficiency impairs nucleolar compartmentalization of nucleolin, and (3) this event correlates with the nuclear retention of mTOR mRNA. These findings suggest that SMN may regulate not only structural components of translation machinery, but also their upstream regulating factors.
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Affiliation(s)
- Francesca Gabanella
- CNR-Institute of Biochemistry and Cell Biology, Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155-00161 Rome, Italy; (C.B.); (M.F.); (C.P.)
- CNR-Institute of Molecular Biology and Pathology, Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena, 291-00161 Rome, Italy; (N.C.); (C.P.)
| | - Christian Barbato
- CNR-Institute of Biochemistry and Cell Biology, Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155-00161 Rome, Italy; (C.B.); (M.F.); (C.P.)
| | - Marco Fiore
- CNR-Institute of Biochemistry and Cell Biology, Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155-00161 Rome, Italy; (C.B.); (M.F.); (C.P.)
| | - Carla Petrella
- CNR-Institute of Biochemistry and Cell Biology, Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155-00161 Rome, Italy; (C.B.); (M.F.); (C.P.)
| | - Marco de Vincentiis
- Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155-00161 Rome, Italy; (M.d.V.); (A.G.); (A.M.)
| | - Antonio Greco
- Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155-00161 Rome, Italy; (M.d.V.); (A.G.); (A.M.)
| | - Antonio Minni
- Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155-00161 Rome, Italy; (M.d.V.); (A.G.); (A.M.)
| | - Nicoletta Corbi
- CNR-Institute of Molecular Biology and Pathology, Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena, 291-00161 Rome, Italy; (N.C.); (C.P.)
| | - Claudio Passananti
- CNR-Institute of Molecular Biology and Pathology, Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena, 291-00161 Rome, Italy; (N.C.); (C.P.)
| | - Maria Grazia Di Certo
- CNR-Institute of Biochemistry and Cell Biology, Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155-00161 Rome, Italy; (C.B.); (M.F.); (C.P.)
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7
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Wijaya YOS, Ar Rohmah M, Niba ETE, Morisada N, Noguchi Y, Hidaka Y, Ozasa S, Inoue T, Shimazu T, Takahashi Y, Tozawa T, Chiyonobu T, Inoue T, Shiroshita T, Yokoyama A, Okamoto K, Awano H, Takeshima Y, Saito T, Saito K, Nishio H, Shinohara M. Phenotypes of SMA patients retaining SMN1 with intragenic mutation. Brain Dev 2021; 43:745-758. [PMID: 33892995 DOI: 10.1016/j.braindev.2021.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/17/2021] [Accepted: 03/21/2021] [Indexed: 01/09/2023]
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder caused by homozygous deletion or intragenic mutation of the SMN1 gene. It is well-known that high copy number of its homologous gene, SMN2, modifies the phenotype of SMN1-deleted patients. However, in the patients with intragenic SMN1 mutation, the relationship between phenotype and SMN2 copy number remains unclear. METHODS We have analyzed a total of 515 Japanese patients with SMA-like symptoms (delayed developmental milestones, respiratory failures, muscle weakness etc.) from 1996 to 2019. SMN1 and SMN2 copy numbers were determined by quantitative polymerase chain reaction (PCR) method and/or multiplex ligation-dependent probe amplification (MLPA) method. Intragenic SMN1 mutations were identified through DNA and RNA analysis of the fresh blood samples. RESULTS A total of 241 patients were diagnosed as having SMA. The majority of SMA patients showed complete loss of SMN1 (n = 228, 95%), but some patients retained SMN1 and carried an intragenic mutation in the retaining SMN1 (n = 13, 5%). Ten different mutations were identified in these 13 patients, consisting of missense, nonsense, frameshift and splicing defect-causing mutations. The ten mutations were c.275G > C (p.Trp92Ser), c.819_820insT (p.Thr274Tyrfs*32), c.830A > G (p.Tyr277Cys), c.5C > T (p.Ala2Val), c.826 T > C (p.Tyr276His), c.79C > T (p.Gln27*), c.188C > A (p.Ser63*), c.422 T > C (p.Leu141Pro), c.835-2A > G (exon 7 skipping) and c.835-3C > A (exon 7 skipping). It should be noted here that some patients with milder phenotype carried only a single SMN2 copy (n = 3), while other patients with severe phenotype carried 3 SMN2 copies (n = 4). CONCLUSION Intragenic mutations in SMN1 may contribute more significantly to clinical severity than SMN2 copy numbers.
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Affiliation(s)
- Yogik Onky Silvana Wijaya
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan.
| | - Mawaddah Ar Rohmah
- Department of Neurology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - Emma Tabe Eko Niba
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan.
| | - Naoya Morisada
- Department of Clinical Genetics, Hyogo Prefectural Kobe Children's Hospital, Kobe, Japan.
| | - Yoriko Noguchi
- Department of Clinical Laboratory, Kobe University Hospital, Kobe, Japan.
| | - Yasufumi Hidaka
- Department of Pediatrics, Kitakyushu Municipal Medical Center, Kitakyushu, Japan.
| | - Shiro Ozasa
- Department of Pediatrics, Kumamoto University, Kumamoto, Japan.
| | - Takeshi Inoue
- Department of Neonatology, Kumamoto City Hospital, Kumamoto, Japan.
| | - Tomoyuki Shimazu
- Department of Pediatrics, National Hospital Organization Kumamoto Saishunso Hospital, Kumamoto, Japan.
| | - Yuya Takahashi
- Department of Pediatrics, Nagaoka Red Cross Hospital, Nagaoka, Japan.
| | - Takenori Tozawa
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan.
| | - Tomohiro Chiyonobu
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan.
| | - Takushi Inoue
- Department of Pediatrics, National Hospital Organization Okayama Medical Center, Okayama, Japan.
| | | | - Atsushi Yokoyama
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan.
| | - Kentaro Okamoto
- Department of Pediatrics, Ehime Prefectural Imabari Hospital, Imabari, Japan.
| | - Hiroyuki Awano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan.
| | - Yasuhiro Takeshima
- Department of Pediatrics, Hyogo College of Medicine, Nishinomiya, Japan.
| | - Toshio Saito
- Division of Child Neurology, Department of Neurology, National Hospital Organization Osaka Toneyama Medical Center, Toyonaka, Japan.
| | - Kayoko Saito
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan.
| | - Hisahide Nishio
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan; Faculty of Medical Rehabilitation, Kobe Gakuin University, Kobe, Japan.
| | - Masakazu Shinohara
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan.
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Lett KE, Logan MK, McLaurin DM, Hebert MD. Coilin enhances phosphorylation and stability of DGCR8 and promotes miRNA biogenesis. Mol Biol Cell 2021; 32:br4. [PMID: 34319763 PMCID: PMC8684749 DOI: 10.1091/mbc.e21-05-0225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
MicroRNAs (miRNAs) are ∼22 nt small noncoding RNAs that control gene expression at the posttranscriptional level through translational inhibition and destabilization of their target mRNAs. The biogenesis of miRNAs involves a series of processing steps beginning with cropping of the primary miRNA transcript by the Microprocessor complex, which is comprised of Drosha and DGCR8. Here we report a novel regulatory interaction between the Microprocessor components and coilin, the Cajal Body (CB) marker protein. Coilin knockdown causes alterations in the level of primary and mature miRNAs, let-7a and miR-34a, and their miRNA targets, HMGA2 and Notch1, respectively. We also found that coilin knockdown affects the levels of DGCR8 and Drosha in cells with (HeLa) and without (WI-38) CBs. To further explore the role of coilin in miRNA biogenesis, we conducted a series of co-immunoprecipitation experiments using coilin and DGCR8 constructs, which revealed that coilin and DGCR8 can form a complex. Additionally, our results indicate that phosphorylation of DGCR8, which has been shown to increase protein stability, is impacted by coilin knockdown. Collectively, our results implicate coilin as a member of the regulatory network governing miRNA biogenesis.
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Affiliation(s)
- Katheryn E Lett
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Madelyn K Logan
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Douglas M McLaurin
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Michael D Hebert
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
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9
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Logan MK, McLaurin DM, Hebert MD. Synergistic interactions between Cajal bodies and the miRNA processing machinery. Mol Biol Cell 2020; 31:1561-1569. [PMID: 32432989 PMCID: PMC7521794 DOI: 10.1091/mbc.e20-02-0144] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cajal bodies (CBs) are subnuclear domains involved in the formation of ribonucleoproteins (RNPs) including small nuclear RNPs (snRNPs). CBs associate with specific gene loci, which impacts expression and provides a platform for the biogenesis of the nascent transcripts emanating from these genes. Here we report that CBs can associate with the C19MC microRNA (miRNA) gene cluster, which suggests a role for CBs in the biogenesis of animal miRNAs. The machinery involved in the formation of miRNAs includes the Drosha/DGCR8 complex, which processes primary-miRNA to precursor miRNA. Further processing of precursor miRNA by Dicer and other components generates mature miRNA. To test if CBs influence the expression and formation of miRNAs, we examined two representative miRNAs (miR-520 h and let-7a) in conditions that disrupt CBs. CB disruption correlates with alterations in the level of primary and mature miRNA and the let-7a mRNA target, HMGA2. We have also found that the processing of some small CB-specific RNAs (scaRNAs) is directly mediated by the Drosha/DGCR8 complex. ScaRNAs form scaRNPs, which play an important role in snRNP formation. Collectively, our results demonstrate that CBs and the miRNA processing machinery functionally interact and together contribute to the biogenesis of miRNAs and snRNPs.
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Affiliation(s)
- Madelyn K Logan
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216
| | - Douglas M McLaurin
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216
| | - Michael D Hebert
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216
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10
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Sapaly D, Delers P, Coridon J, Salman B, Letourneur F, Dumont F, Lefebvre S. The Small-Molecule Flunarizine in Spinal Muscular Atrophy Patient Fibroblasts Impacts on the Gemin Components of the SMN Complex and TDP43, an RNA-Binding Protein Relevant to Motor Neuron Diseases. Front Mol Biosci 2020; 7:55. [PMID: 32363199 PMCID: PMC7181958 DOI: 10.3389/fmolb.2020.00055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/18/2020] [Indexed: 01/01/2023] Open
Abstract
The motor neurodegenerative disease spinal muscular atrophy (SMA) is caused by alterations of the survival motor neuron 1 (SMN1) gene involved in RNA metabolism. Although the disease mechanisms are not completely elucidated, SMN protein deficiency leads to abnormal small nuclear ribonucleoproteins (snRNPs) assembly responsible for widespread splicing defects. SMN protein localizes in nuclear bodies that are lost in SMA and adult onset amyotrophic lateral sclerosis (ALS) patient cells harboring TDP-43 or FUS/TLS mutations. We previously reported that flunarizine recruits SMN into nuclear bodies and improves the phenotype of an SMA mouse model. However, the precise mode of action remains elusive. Here, a marked reduction of the integral components of the SMN complex is observed in severe SMA patient fibroblast cells. We show that flunarizine increases the protein levels of a subset of components of the SMN-Gemins complex, Gemins2-4, and markedly reduces the RNA and protein levels of the pro-oxydant thioredoxin-interacting protein (TXNIP) encoded by an mRNA target of Gemin5. We further show that SMN deficiency causes a dissociation of the localization of the SMN complex components from the same nuclear bodies. The accumulation of TDP-43 in SMN-positive nuclear bodies is also perturbed in SMA cells. Notably, TDP-43 is found to co-localize with SMN in nuclear bodies of flunarizine-treated SMA cells. Our findings indicate that flunarizine reverses cellular changes caused by SMN deficiency in SMA cells and further support the view of a common pathway in RNA metabolism underlying infantile and adult motor neuron diseases.
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Affiliation(s)
- Delphine Sapaly
- INSERM UMR-S 1124, Toxicité Environnementale, Cibles Thérapeutiques, Signalisation Cellulaire et Biomarqueurs, Campus Saint-Germain-des-Prés, Université de Paris, Paris, France
| | - Perrine Delers
- INSERM UMR-S 1124, Toxicité Environnementale, Cibles Thérapeutiques, Signalisation Cellulaire et Biomarqueurs, Campus Saint-Germain-des-Prés, Université de Paris, Paris, France
| | - Jennifer Coridon
- BioMedTech Facilities INSERM US36 - CNRS UMS 2009, Campus Saint-Germain-des-Prés, Université de Paris, Paris, France
| | - Badih Salman
- INSERM UMR-S 1124, Toxicité Environnementale, Cibles Thérapeutiques, Signalisation Cellulaire et Biomarqueurs, Campus Saint-Germain-des-Prés, Université de Paris, Paris, France
| | | | - Florent Dumont
- Genom'ic Platform, INSERM U1016, Institut Cochin, Paris, France
| | - Suzie Lefebvre
- INSERM UMR-S 1124, Toxicité Environnementale, Cibles Thérapeutiques, Signalisation Cellulaire et Biomarqueurs, Campus Saint-Germain-des-Prés, Université de Paris, Paris, France
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11
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Lomonte P, Baklouti F, Binda O. The Biochemistry of Survival Motor Neuron Protein Is Paving the Way to Novel Therapies for Spinal Muscle Atrophy. Biochemistry 2020; 59:1391-1397. [PMID: 32227847 DOI: 10.1021/acs.biochem.9b01124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Spinal muscle atrophy (SMA) is the leading genetic cause of infant mortality. SMA originates from the loss of functional survival motor neuron (SMN) protein. In most SMA cases, the SMN1 gene is deleted. However, in some cases, SMN is mutated, impairing its biological functions. SMN mutants could provide clues about the biological functions of SMN and the specific impact on SMA, potentially leading to the identification of new pathways and thus providing novel treatment alternatives, and even personalized care. Here, we discuss the biochemistry of SMN and the most recent SMA treatment strategies.
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Affiliation(s)
- Patrick Lomonte
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène (INMG), 69008 Lyon, France
| | - Faouzi Baklouti
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène (INMG), 69008 Lyon, France
| | - Olivier Binda
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène (INMG), 69008 Lyon, France
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12
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Osman EY, Bolding MR, Villalón E, Kaifer KA, Lorson ZC, Tisdale S, Hao Y, Conant GC, Pires JC, Pellizzoni L, Lorson CL. Functional characterization of SMN evolution in mouse models of SMA. Sci Rep 2019; 9:9472. [PMID: 31263170 PMCID: PMC6603021 DOI: 10.1038/s41598-019-45822-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/11/2019] [Indexed: 12/13/2022] Open
Abstract
Spinal Muscular Atrophy (SMA) is a monogenic neurodegenerative disorder and the leading genetic cause of infantile mortality. While several functions have been ascribed to the SMN (survival motor neuron) protein, their specific contribution to the disease has yet to be fully elucidated. We hypothesized that some, but not all, SMN homologues would rescue the SMA phenotype in mouse models, thereby identifying disease-relevant domains. Using AAV9 to deliver Smn homologs to SMA mice, we identified a conservation threshold that marks the boundary at which homologs can rescue the SMA phenotype. Smn from Danio rerio and Xenopus laevis significantly prevent disease, whereas Smn from Drosophila melanogaster, Caenorhabditis elegans, and Schizosaccharomyces pombe was significantly less efficacious. This phenotypic rescue correlated with correction of RNA processing defects induced by SMN deficiency and neuromuscular junction pathology. Based upon the sequence conservation in the rescuing homologs, a minimal SMN construct was designed consisting of exons 2, 3, and 6, which showed a partial rescue of the SMA phenotype. While a significant extension in survival was observed, the absence of a complete rescue suggests that while the core conserved region is essential, additional sequences contribute to the overall ability of the SMN protein to rescue disease pathology.
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Affiliation(s)
- Erkan Y Osman
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Madeline R Bolding
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Eric Villalón
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Kevin A Kaifer
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Zachary C Lorson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Sarah Tisdale
- Center for Motor Neuron Biology and Disease, Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
| | - Yue Hao
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA.,Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.,Division of Biological Sciences, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - J Chris Pires
- Department of Biological Sciences, Program in Genetics, North Carolina State University, Raleigh, NC, 27695, USA
| | - Livio Pellizzoni
- Center for Motor Neuron Biology and Disease, Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
| | - Christian L Lorson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA. .,Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
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13
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Dimitrova DG, Teysset L, Carré C. RNA 2'-O-Methylation (Nm) Modification in Human Diseases. Genes (Basel) 2019; 10:E117. [PMID: 30764532 PMCID: PMC6409641 DOI: 10.3390/genes10020117] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 12/24/2022] Open
Abstract
Nm (2'-O-methylation) is one of the most common modifications in the RNA world. It has the potential to influence the RNA molecules in multiple ways, such as structure, stability, and interactions, and to play a role in various cellular processes from epigenetic gene regulation, through translation to self versus non-self recognition. Yet, building scientific knowledge on the Nm matter has been hampered for a long time by the challenges in detecting and mapping this modification. Today, with the latest advancements in the area, more and more Nm sites are discovered on RNAs (tRNA, rRNA, mRNA, and small non-coding RNA) and linked to normal or pathological conditions. This review aims to synthesize the Nm-associated human diseases known to date and to tackle potential indirect links to some other biological defects.
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Affiliation(s)
- Dilyana G Dimitrova
- Sorbonne Université, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Transgenerational Epigenetics & Small RNA Biology, Laboratoire de Biologie du Développement, 75005 Paris, France.
| | - Laure Teysset
- Sorbonne Université, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Transgenerational Epigenetics & Small RNA Biology, Laboratoire de Biologie du Développement, 75005 Paris, France.
| | - Clément Carré
- Sorbonne Université, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Transgenerational Epigenetics & Small RNA Biology, Laboratoire de Biologie du Développement, 75005 Paris, France.
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14
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Identification of Functional Domain(s) of Fibrillarin Interacted with p2 of Rice stripe virus. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2018; 2018:8402839. [PMID: 29736196 PMCID: PMC5875058 DOI: 10.1155/2018/8402839] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 12/06/2017] [Indexed: 11/30/2022]
Abstract
p2 of Rice stripe virus may promote virus systemic infection by interacting with the full length of fibrillarin from Nicotiana benthamiana (NbFib2) in the nucleolus and cajal body (CB). NbFib2 contains three functional domains. We used yeast two-hybrid, colocalization, and bimolecular fluorescence complementation (BiFC) assays to study the interactions between p2 and the three domains of NbFib2, namely, the N-terminal fragment containing a glycine and arginine-rich (GAR) domain, the central RNA-binding domain, and the C-terminal fragment containing an α-helical domain. The results show that the N-terminal domain is indispensable for NbFib2 to localize in the nucleolus and cajal body. p2 binds all three regions of NbFib2, and they target to the nucleus but fail to the nucleolus and cajal bodies (CBs).
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15
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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: 3.6] [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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16
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Love AJ, Yu C, Petukhova NV, Kalinina NO, Chen J, Taliansky ME. Cajal bodies and their role in plant stress and disease responses. RNA Biol 2017; 14:779-790. [PMID: 27726481 PMCID: PMC5519230 DOI: 10.1080/15476286.2016.1243650] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/19/2016] [Accepted: 09/27/2016] [Indexed: 12/11/2022] Open
Abstract
Cajal bodies (CBs) are distinct sub-nuclear structures that are present in eukaryotic living cells and are often associated with the nucleolus. CBs play important roles in RNA metabolism and formation of RNPs involved in transcription, splicing, ribosome biogenesis, and telomere maintenance. Besides these primary roles, CBs appear to be involved in additional functions that may not be directly related to RNA metabolism and RNP biogenesis. In this review, we assess possible roles of plant CBs in RNA regulatory pathways such as nonsense-mediated mRNA decay and RNA silencing. We also summarize recent progress and discuss new non-canonical functions of plant CBs in responses to stress and disease. It is hypothesized that CBs can regulate these responses via their interaction with poly(ADP ribose)polymerase (PARP), which is known to play an important role in various physiological processes including responses to biotic and abiotic stresses. It is suggested that CBs and their components modify PARP activities and functions.
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Affiliation(s)
- Andrew J. Love
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, UK
| | - Chulang Yu
- State Key Laboratory Breeding Base for Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | | | - Natalia O. Kalinina
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow, Russia
| | - Jianping Chen
- State Key Laboratory Breeding Base for Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Michael E. Taliansky
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, UK
- State Key Laboratory Breeding Base for Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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17
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Massenet S, Bertrand E, Verheggen C. Assembly and trafficking of box C/D and H/ACA snoRNPs. RNA Biol 2017; 14:680-692. [PMID: 27715451 PMCID: PMC5519232 DOI: 10.1080/15476286.2016.1243646] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/09/2016] [Accepted: 09/27/2016] [Indexed: 12/23/2022] Open
Abstract
Box C/D and box H/ACA snoRNAs are abundant non-coding RNAs that localize in the nucleolus and mostly function as guides for nucleotide modifications. While a large pool of snoRNAs modifies rRNAs, an increasing number of snoRNAs could also potentially target mRNAs. ScaRNAs belong to a family of specific RNAs that localize in Cajal bodies and that are structurally similar to snoRNAs. Most scaRNAs are involved in snRNA modification, while telomerase RNA, which contains H/ACA motifs, functions in telomeric DNA synthesis. In this review, we describe how box C/D and H/ACA snoRNAs are processed and assembled with core proteins to form functional RNP particles. Their biogenesis involve several transport factors that first direct pre-snoRNPs to Cajal bodies, where some processing steps are believed to take place, and then to nucleoli. Assembly of core proteins involves the HSP90/R2TP chaperone-cochaperone system for both box C/D and H/ACA RNAs, but also several factors specific for each family. These assembly factors chaperone unassembled core proteins, regulate the formation and disassembly of pre-snoRNP intermediates, and control the activity of immature particles. The AAA+ ATPase RUVBL1 and RUVBL2 belong to the R2TP co-chaperones and play essential roles in snoRNP biogenesis, as well as in the formation of other macro-molecular complexes. Despite intensive research, their mechanisms of action are still incompletely understood.
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Affiliation(s)
- Séverine Massenet
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS, 9 Avenue de la forêt de Haye, 54505 Vandoeuvre-les-Nancy Cedex, France, Université de Lorraine, Campus Biologie –Santé, CS 50184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France, Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Céline Verheggen
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France, Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
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18
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Singh RN, Howell MD, Ottesen EW, Singh NN. Diverse role of survival motor neuron protein. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2017; 1860:299-315. [PMID: 28095296 PMCID: PMC5325804 DOI: 10.1016/j.bbagrm.2016.12.008] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 12/23/2016] [Accepted: 12/30/2016] [Indexed: 02/07/2023]
Abstract
The multifunctional Survival Motor Neuron (SMN) protein is required for the survival of all organisms of the animal kingdom. SMN impacts various aspects of RNA metabolism through the formation and/or interaction with ribonucleoprotein (RNP) complexes. SMN regulates biogenesis of small nuclear RNPs, small nucleolar RNPs, small Cajal body-associated RNPs, signal recognition particles and telomerase. SMN also plays an important role in DNA repair, transcription, pre-mRNA splicing, histone mRNA processing, translation, selenoprotein synthesis, macromolecular trafficking, stress granule formation, cell signaling and cytoskeleton maintenance. The tissue-specific requirement of SMN is dictated by the variety and the abundance of its interacting partners. Reduced expression of SMN causes spinal muscular atrophy (SMA), a leading genetic cause of infant mortality. SMA displays a broad spectrum ranging from embryonic lethality to an adult onset. Aberrant expression and/or localization of SMN has also been associated with male infertility, inclusion body myositis, amyotrophic lateral sclerosis and osteoarthritis. This review provides a summary of various SMN functions with implications to a better understanding of SMA and other pathological conditions.
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Affiliation(s)
- Ravindra N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States.
| | - Matthew D Howell
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States
| | - Eric W Ottesen
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States
| | - Natalia N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States
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19
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Gama-Carvalho M, L Garcia-Vaquero M, R Pinto F, Besse F, Weis J, Voigt A, Schulz JB, De Las Rivas J. Linking amyotrophic lateral sclerosis and spinal muscular atrophy through RNA-transcriptome homeostasis: a genomics perspective. J Neurochem 2017; 141:12-30. [PMID: 28054357 DOI: 10.1111/jnc.13945] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/02/2016] [Accepted: 12/24/2016] [Indexed: 12/11/2022]
Abstract
In this review, we present our most recent understanding of key biomolecular processes that underlie two motor neuron degenerative disorders, amyotrophic lateral sclerosis, and spinal muscular atrophy. We focus on the role of four multifunctional proteins involved in RNA metabolism (TDP-43, FUS, SMN, and Senataxin) that play a causal role in these diseases. Recent results have led to a novel scenario of intricate connections between these four proteins, bringing transcriptome homeostasis into the spotlight as a common theme in motor neuron degeneration. We review reported functional and physical interactions between these four proteins, highlighting their common association with nuclear bodies and small nuclear ribonucleoprotein particle biogenesis and function. We discuss how these interactions are turning out to be particularly relevant for the control of transcription and chromatin homeostasis, including the recent identification of an association between SMN and Senataxin required to ensure the resolution of DNA-RNA hybrid formation and proper termination by RNA polymerase II. These connections strongly support the existence of common pathways underlying the spinal muscular atrophy and amyotrophic lateral sclerosis phenotype. We also discuss the potential of genome-wide expression profiling, in particular RNA sequencing derived data, to contribute to unravelling the underlying mechanisms. We provide a review of publicly available datasets that have addressed both diseases using these approaches, and highlight the value of investing in cross-disease studies to promote our understanding of the pathways leading to neurodegeneration.
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Affiliation(s)
- Margarida Gama-Carvalho
- Universidade de Lisboa, Faculdade de Ciências, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, 1749-016 Lisboa, Portugal
| | - Marina L Garcia-Vaquero
- Universidade de Lisboa, Faculdade de Ciências, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, 1749-016 Lisboa, Portugal
| | - Francisco R Pinto
- Universidade de Lisboa, Faculdade de Ciências, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, 1749-016 Lisboa, Portugal
| | | | - Joachim Weis
- Institute of Neuropathology, RWTH Aachen University, Aachen, Germany
| | - Aaron Voigt
- Department of Neurology, University Hospital, RWTH Aachen University, Aachen, Germany.,JARA-Institute Molecular Neuroscience and Neuroimaging, Forschungszentrum Jülich GmbH and RWTH Aachen University, Aachen, Germany
| | - Jörg B Schulz
- Department of Neurology, University Hospital, RWTH Aachen University, Aachen, Germany.,JARA-Institute Molecular Neuroscience and Neuroimaging, Forschungszentrum Jülich GmbH and RWTH Aachen University, Aachen, Germany
| | - Javier De Las Rivas
- Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), Salamanca, Spain
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20
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Hebert MD, Poole AR. Towards an understanding of regulating Cajal body activity by protein modification. RNA Biol 2016; 14:761-778. [PMID: 27819531 DOI: 10.1080/15476286.2016.1243649] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The biogenesis of small nuclear ribonucleoproteins (snRNPs), small Cajal body-specific RNPs (scaRNPs), small nucleolar RNPs (snoRNPs) and the telomerase RNP involves Cajal bodies (CBs). Although many components enriched in the CB contain post-translational modifications (PTMs), little is known about how these modifications impact individual protein function within the CB and, in concert with other modified factors, collectively regulate CB activity. Since all components of the CB also reside in other cellular locations, it is also important that we understand how PTMs affect the subcellular localization of CB components. In this review, we explore the current knowledge of PTMs on the activity of proteins known to enrich in CBs in an effort to highlight current progress as well as illuminate paths for future investigation.
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Affiliation(s)
- Michael D Hebert
- a Department of Biochemistry , The University of Mississippi Medical Center , Jackson , MS , USA
| | - Aaron R Poole
- a Department of Biochemistry , The University of Mississippi Medical Center , Jackson , MS , USA
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21
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Poole AR, Enwerem II, Vicino IA, Coole JB, Smith SV, Hebert MD. Identification of processing elements and interactors implicate SMN, coilin and the pseudogene-encoded coilp1 in telomerase and box C/D scaRNP biogenesis. RNA Biol 2016; 13:955-972. [PMID: 27419845 DOI: 10.1080/15476286.2016.1211224] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Many cellular functions, such as translation, require ribonucleoproteins (RNPs). The biogenesis of RNPs is a multi-step process that, depending on the RNP, can take place in many cellular compartments. Here we examine 2 different RNPs: telomerase and small Cajal body-specific RNPs (scaRNPs). Both of these RNPs are enriched in the Cajal body (CB), which is a subnuclear domain that also has high concentrations of another RNP, small nuclear RNPs (snRNPs). SnRNPs are essential components of the spliceosome, and scaRNPs modify the snRNA component of the snRNP. The CB contains many proteins, including WRAP53, SMN and coilin, the CB marker protein. We show here that coilin, SMN and coilp1, a newly identified protein encoded by a pseudogene in human, associate with telomerase RNA and a subset of scaRNAs. We also have identified a processing element within box C/D scaRNA. Our findings thus further strengthen the connection between the CB proteins coilin and SMN in the biogenesis of telomeras e and box C/D scaRNPs, and reveal a new player, coilp1, that likely participates in this process.
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Affiliation(s)
- Aaron R Poole
- a Department of Biochemistry , The University of Mississippi Medical Center , Jackson , MS , USA
| | - Isioma I Enwerem
- a Department of Biochemistry , The University of Mississippi Medical Center , Jackson , MS , USA
| | - Ian A Vicino
- a Department of Biochemistry , The University of Mississippi Medical Center , Jackson , MS , USA
| | - Jackson B Coole
- a Department of Biochemistry , The University of Mississippi Medical Center , Jackson , MS , USA
| | - Stanley V Smith
- b Department of Pharmacology and Toxicology , The University of Mississippi Medical Center , Jackson , MS , USA
| | - Michael D Hebert
- a Department of Biochemistry , The University of Mississippi Medical Center , Jackson , MS , USA
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22
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Tang AY. RNA processing-associated molecular mechanisms of neurodegenerative diseases. J Appl Genet 2015; 57:323-33. [DOI: 10.1007/s13353-015-0330-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/22/2015] [Accepted: 11/26/2015] [Indexed: 12/13/2022]
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Farooq F, MacKenzie AE. Current and emerging treatment options for spinal muscular atrophy. Degener Neurol Neuromuscul Dis 2015; 5:75-81. [PMID: 32669914 PMCID: PMC7337203 DOI: 10.2147/dnnd.s48420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 04/23/2015] [Indexed: 11/23/2022] Open
Abstract
Spinal muscular atrophy is one of the most common inherited neuromuscular conditions; our understanding of the genetic pathology and translational research coming from this insight has made significant progress over the past decade. This short review provides the background of the disease along with the bench to bedside progress of some promising treatment options to develop better understanding of the present state of the disease.
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Affiliation(s)
- Faraz Farooq
- Science Education Division, Emirates College for Advanced Education, Abu Dhabi, United Arab Emirates.,Children's Hospital of Eastern Ontario (CHEO) Research Institute, Ottawa, ON, Canada
| | - Alex E MacKenzie
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Ottawa, ON, Canada.,University of Ottawa, Ottawa, ON, Canada
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24
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Enwerem II, Wu G, Yu YT, Hebert MD. Cajal body proteins differentially affect the processing of box C/D scaRNPs. PLoS One 2015; 10:e0122348. [PMID: 25875178 PMCID: PMC4395269 DOI: 10.1371/journal.pone.0122348] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/13/2015] [Indexed: 11/19/2022] Open
Abstract
Small nuclear ribonucleoproteins (snRNPs), which are required for pre-mRNA splicing, contain extensively modified snRNA. Small Cajal body-specific ribonucleoproteins (scaRNPs) mediate these modifications. It is unknown how the box C/D class of scaRNPs localizes to Cajal Bodies (CBs). The processing of box C/D scaRNA is also unclear. Here, we explore the processing of box C/D scaRNA 2 and 9 by coilin. We also broaden our investigation to include WRAP53 and SMN, which accumulate in CBs, play a role in RNP biogenesis and associate with coilin. These studies demonstrate that the processing of an ectopically expressed scaRNA2 is altered upon the reduction of coilin, WRAP53 or SMN, but the extent and direction of this change varies depending on the protein reduced. We also show that box C/D scaRNP activity is reduced in a cell line derived from coilin knockout mice. Collectively, the findings presented here further implicate coilin as being a direct participant in the formation of box C/D scaRNPs, and demonstrate that WRAP53 and SMN may also play a role, but the activity of these proteins is divergent to coilin.
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Affiliation(s)
- Isioma I. Enwerem
- Department of Biochemistry, The University of Mississippi Medical Center, Jackson, Mississippi 39216–4505, United States of America
| | - Guowei Wu
- Department of Biochemistry and Biophysics, The University of Rochester Medical Center, Rochester, New York 14642, United States of America
| | - Yi Tao Yu
- Department of Biochemistry and Biophysics, The University of Rochester Medical Center, Rochester, New York 14642, United States of America
| | - Michael D. Hebert
- Department of Biochemistry, The University of Mississippi Medical Center, Jackson, Mississippi 39216–4505, United States of America
- * E-mail:
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25
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Piazzon N, Schlotter F, Lefebvre S, Dodré M, Méreau A, Soret J, Besse A, Barkats M, Bordonné R, Branlant C, Massenet S. Implication of the SMN complex in the biogenesis and steady state level of the signal recognition particle. Nucleic Acids Res 2012; 41:1255-72. [PMID: 23221635 PMCID: PMC3553995 DOI: 10.1093/nar/gks1224] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Spinal muscular atrophy is a severe motor neuron disease caused by reduced levels of the ubiquitous Survival of MotoNeurons (SMN) protein. SMN is part of a complex that is essential for spliceosomal UsnRNP biogenesis. Signal recognition particle (SRP) is a ribonucleoprotein particle crucial for co-translational targeting of secretory and membrane proteins to the endoplasmic reticulum. SRP biogenesis is a nucleo-cytoplasmic multistep process in which the protein components, except SRP54, assemble with 7S RNA in the nucleolus. Then, SRP54 is incorporated after export of the pre-particle into the cytoplasm. The assembly factors necessary for SRP biogenesis remain to be identified. Here, we show that 7S RNA binds to purified SMN complexes in vitro and that SMN complexes associate with SRP in cellular extracts. We identified the RNA determinants required. Moreover, we report a specific reduction of 7S RNA levels in the spinal cord of SMN-deficient mice, and in a Schizosaccharomyces pombe strain carrying a temperature-degron allele of SMN. Additionally, microinjected antibodies directed against SMN or Gemin2 interfere with the association of SRP54 with 7S RNA in Xenopus laevis oocytes. Our data show that reduced levels of the SMN protein lead to defect in SRP steady-state level and describe the SMN complex as the first identified cellular factor required for SRP biogenesis.
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Affiliation(s)
- Nathalie Piazzon
- Laboratoire ARN-RNP structure-fonction-maturation, Enzymologie Moléculaire et Structurale (AREMS), Nancy Université-CNRS, UMR 7214, FR 3209, Faculté de Médecine de Nancy, BP 184, 9 avenue de la forêt de Haye, 54506 Vandoeuvre-les-Nancy Cedex, France
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26
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Locatelli D, d'Errico P, Capra S, Finardi A, Colciaghi F, Setola V, Terao M, Garattini E, Battaglia G. Spinal muscular atrophy pathogenic mutations impair the axonogenic properties of axonal-survival of motor neuron. J Neurochem 2012; 121:465-74. [PMID: 22324632 DOI: 10.1111/j.1471-4159.2012.07689.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The axonal survival of motor neuron (a-SMN) protein is a truncated isoform of SMN1, the spinal muscular atrophy (SMA) disease gene. a-SMN is selectively localized in axons and endowed with remarkable axonogenic properties. At present, the role of a-SMN in SMA is unknown. As a first step to verify a link between a-SMN and SMA, we investigated by means of over-expression experiments in neuroblastoma-spinal cord hybrid cell line (NSC34) whether SMA pathogenic mutations located in the N-terminal part of the protein affected a-SMN function. We demonstrated here that either SMN1 missense mutations or small intragenic re-arrangements located in the Tudor domain consistently altered the a-SMN capability of inducing axonal elongation in vitro. Mutated human a-SMN proteins determined in almost all NSC34 motor neurons the growth of short axons with prominent morphologic abnormalities. Our data indicate that the Tudor domain is critical in dictating a-SMN function possibly because it is an association domain for proteins involved in axon growth. They also indicate that Tudor domain mutations are functionally relevant not only for FL-SMN but also for a-SMN, raising the possibility that also a-SMN loss of function may contribute to the pathogenic steps leading to SMA.
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Affiliation(s)
- Denise Locatelli
- Molecular Neuroanatomy and Pathogenesis Unit, Neurological Institute 'C. Besta', Milano, Italy
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27
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Workman E, Kolb SJ, Battle DJ. Spliceosomal small nuclear ribonucleoprotein biogenesis defects and motor neuron selectivity in spinal muscular atrophy. Brain Res 2012; 1462:93-9. [PMID: 22424789 DOI: 10.1016/j.brainres.2012.02.051] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 02/17/2012] [Accepted: 02/21/2012] [Indexed: 12/22/2022]
Abstract
The SMN protein is essential and participates in the assembly of macromolecular complexes of RNA and protein in all cells. The best-characterized function of SMN is as an assembler of spliceosomal small nuclear ribonucleoproteins (snRNPs). SMN performs this function as part of a complex with several other proteins called Gemins. snRNPs are assembled in the cytoplasm in a stepwise manner and then are imported to the nucleus where they participate globally in the splicing of pre-mRNA. Mutations in the SMN1 gene result in the motor neuron disease, spinal muscular atrophy (SMA). Most of these mutations result in a reduction in the expression levels of the SMN protein, which, in turn, results in a reduction in snRNP assembly capacity. This review highlights current studies that have investigated the mechanism of SMN-dependent snRNP assembly, as well as the downstream effects on pre-mRNA splicing that result from a decrease in SMN. This article is part of a Special Issue entitled "RNA-Binding Proteins".
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Affiliation(s)
- Eileen Workman
- Department of Molecular and Cellular Biochemistry, Wexner Medical Center at The Ohio State University, Columbus, OH 43210, USA
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28
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Farooq F, Molina FA, Hadwen J, MacKenzie D, Witherspoon L, Osmond M, Holcik M, MacKenzie A. Prolactin increases SMN expression and survival in a mouse model of severe spinal muscular atrophy via the STAT5 pathway. J Clin Invest 2011; 121:3042-50. [PMID: 21785216 DOI: 10.1172/jci46276] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2011] [Accepted: 06/01/2011] [Indexed: 12/13/2022] Open
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neurodegenerative disease that is characterized by the loss of motor neurons, resulting in progressive muscle atrophy. It is caused by the loss of functional survival motor neuron (SMN) protein due to mutations or deletion in the SMN1 gene. A potential treatment strategy for SMA is to upregulate levels of SMN protein. Several agents that activate STAT5 in human and mouse cell lines enhance SMN expression from the SMN2 gene and can compensate, at least in part, for the loss of production of a functional protein from SMN1. Here, we have shown that prolactin (PRL) increases SMN levels via activation of the STAT5 pathway. PRL increased SMN mRNA and protein levels in cultured human and mouse neuronal cells. Administration of STAT5-specific siRNA blocked the effects of PRL, indicating that the PRL-induced transcriptional upregulation of the SMN-encoding gene was mediated by activation of STAT5. Furthermore, systemic administration of PRL to WT mice induced SMN expression in the brain and spinal cord. Critically, PRL treatment increased SMN levels, improved motor function, and enhanced survival in a mouse model of severe SMA. Our results confirm earlier work suggesting STAT5 pathway activators as potential therapeutic compounds for the treatment of SMA and identify PRL as one such promising agent.
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29
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Rakitina DV, Taliansky M, Brown JWS, Kalinina NO. Two RNA-binding sites in plant fibrillarin provide interactions with various RNA substrates. Nucleic Acids Res 2011; 39:8869-80. [PMID: 21785141 PMCID: PMC3203579 DOI: 10.1093/nar/gkr594] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Fibrillarin, one of the major proteins of the nucleolus, plays several essential roles in ribosome biogenesis including pre-rRNA processing and 2′-O-ribose methylation of rRNA and snRNAs. Recently, it has been shown that fibrillarin plays a role in virus infections and is associated with viral RNPs. Here, we demonstrate the ability of recombinant fibrillarin 2 from Arabidopsis thaliana (AtFib2) to interact with RNAs of different lengths and types including rRNA, snoRNA, snRNA, siRNA and viral RNAs in vitro. Our data also indicate that AtFib2 possesses two RNA-binding sites in the central (138–179 amino acids) and C-terminal (225–281 amino acids) parts of the protein, respectively. The conserved GCVYAVEF octamer does not bind RNA directly as suggested earlier, but may assist with the proper folding of the central RNA-binding site.
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Affiliation(s)
- D. V. Rakitina
- Department of Virology and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119991, Russia, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK and Plant Sciences Division, University of Dundee, DD2 5DA, UK
| | - Michael Taliansky
- Department of Virology and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119991, Russia, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK and Plant Sciences Division, University of Dundee, DD2 5DA, UK
- *To whom correspondence should be addressed. Tel: +44(0)1382562731; Fax: +44 (0)1382 562426;
| | - J. W. S. Brown
- Department of Virology and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119991, Russia, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK and Plant Sciences Division, University of Dundee, DD2 5DA, UK
| | - N. O. Kalinina
- Department of Virology and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119991, Russia, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK and Plant Sciences Division, University of Dundee, DD2 5DA, UK
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30
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Fuentes JL, Strayer MS, Matera AG. Molecular determinants of survival motor neuron (SMN) protein cleavage by the calcium-activated protease, calpain. PLoS One 2010; 5:e15769. [PMID: 21209906 PMCID: PMC3012718 DOI: 10.1371/journal.pone.0015769] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 11/28/2010] [Indexed: 01/13/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a leading genetic cause of childhood mortality, caused by reduced levels of survival motor neuron (SMN) protein. SMN functions as part of a large complex in the biogenesis of small nuclear ribonucleoproteins (snRNPs). It is not clear if defects in snRNP biogenesis cause SMA or if loss of some tissue-specific function causes disease. We recently demonstrated that the SMN complex localizes to the Z-discs of skeletal and cardiac muscle sarcomeres, and that SMN is a proteolytic target of calpain. Calpains are implicated in muscle and neurodegenerative disorders, although their relationship to SMA is unclear. Using mass spectrometry, we identified two adjacent calpain cleavage sites in SMN, S192 and F193. Deletion of small motifs in the region surrounding these sites inhibited cleavage. Patient-derived SMA mutations within SMN reduced calpain cleavage. SMN(D44V), reported to impair Gemin2 binding and amino-terminal SMN association, drastically inhibited cleavage, suggesting a role for these interactions in regulating calpain cleavage. Deletion of A188, a residue mutated in SMA type I (A188S), abrogated calpain cleavage, highlighting the importance of this region. Conversely, SMA mutations that interfere with self-oligomerization of SMN, Y272C and SMNΔ7, had no effect on cleavage. Removal of the recently-identified SMN degron (Δ268-294) resulted in increased calpain sensitivity, suggesting that the C-terminus of SMN is important in dictating availability of the cleavage site. Investigation into the spatial determinants of SMN cleavage revealed that endogenous calpains can cleave cytosolic, but not nuclear, SMN. Collectively, the results provide insight into a novel aspect of the post-translation regulation of SMN.
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Affiliation(s)
- Jennifer L. Fuentes
- Program in Molecular Biology and Biotechnology, Departments of Biology and Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Molly S. Strayer
- Program in Molecular Biology and Biotechnology, Departments of Biology and Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - A. Gregory Matera
- Program in Molecular Biology and Biotechnology, Departments of Biology and Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
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31
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Taliansky ME, Brown JWS, Rajamäki ML, Valkonen JPT, Kalinina NO. Involvement of the plant nucleolus in virus and viroid infections: parallels with animal pathosystems. Adv Virus Res 2010; 77:119-58. [PMID: 20951872 PMCID: PMC7149663 DOI: 10.1016/b978-0-12-385034-8.00005-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The nucleolus is a dynamic subnuclear body with roles in ribosome subunit biogenesis, mediation of cell-stress responses, and regulation of cell growth. An increasing number of reports reveal that similar to the proteins of animal viruses, many plant virus proteins localize in the nucleolus to divert host nucleolar proteins from their natural functions in order to exert novel role(s) in the virus infection cycle. This chapter will highlight studies showing how plant viruses recruit nucleolar functions to facilitate virus translation and replication, virus movement and assembly of virus-specific ribonucleoprotein (RNP) particles, and to counteract plant host defense responses. Plant viruses also provide a valuable tool to gain new insights into novel nucleolar functions and processes. Investigating the interactions between plant viruses and the nucleolus will facilitate the design of novel strategies to control plant virus infections.
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Affiliation(s)
- M E Taliansky
- Scottish Crop Research Institute, Invergowrie, Dundee, United Kingdom
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32
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Hebert MD. Phosphorylation and the Cajal body: modification in search of function. Arch Biochem Biophys 2010; 496:69-76. [PMID: 20193656 PMCID: PMC2850958 DOI: 10.1016/j.abb.2010.02.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 02/24/2010] [Indexed: 12/25/2022]
Abstract
The Cajal body (CB) is a subnuclear domain that contains proteins and factors involved in a diverse range of activities including ribonucleoprotein maturation, histone gene transcription and telomerase assembly. Among these activities, the CBs' role in small nuclear ribonucleoprotein (snRNP) biogenesis is best characterized. Although CBs are found in plants, flies and mammals, not all cell types contain CBs. Rather, CBs are most prominent in transcriptionally active cells, such as cancer and neuronal cells. Many CB components, including the CB marker protein coilin, are phosphorylated in humans. The functional consequence of phosphorylation on CB assembly, activity and disassembly is largely unknown. Also unknown are the signaling pathways, kinases and phosphatases that act upon proteins which localize in the CB. The goal of this review is to demonstrate the need for a concerted effort towards elucidating the functional consequence of phosphorylation on CB formation and activity.
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Affiliation(s)
- Michael D Hebert
- Department of Biochemistry, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
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33
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Shafey D, Boyer JG, Bhanot K, Kothary R. Identification of novel interacting protein partners of SMN using tandem affinity purification. J Proteome Res 2010; 9:1659-69. [PMID: 20201562 DOI: 10.1021/pr9006987] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mutations in the survival motor neuron (SMN) gene cause spinal muscular atrophy (SMA), a neuromuscular disease associated with muscle weakness that progresses to paralysis, respiratory distress, and ultimately death. Both neurons and muscle are severely affected in this disease. Tandem affinity purification (TAP) has emerged as a useful tool for studying protein complexes in vitro. We have used this purification system to discover novel SMN interacting partners in C2C12 muscle and PC12 neuronal cells. To do so, we fused a TAP-tag, consisting of a HIS hexamer and FLAG epitope separated by the tobacco etch virus (TEV) protease cleavage site, to either the N- or C-terminal region of SMN. Interestingly, the profile of SMN interacting proteins varies depending on the cell type and stage. We have identified a number of novel SMN interacting proteins in both C2C12 and PC12 cells, and from among these we have validated Annexin II and myosin regulatory light chain (MRLC). The discovery of these proteins will lead to a better understanding of the mechanisms underlying the pathophysiology of SMA.
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Affiliation(s)
- Dina Shafey
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
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34
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Fuller HR, Man NT, Lam LT, Thanh LT, Keough RA, Asperger A, Gonda TJ, Morris GE. The SMN interactome includes Myb-binding protein 1a. J Proteome Res 2010; 9:556-63. [PMID: 19928837 DOI: 10.1021/pr900884g] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding networks of interacting proteins is a major goal in cell biology. The survival of motor neurons protein (SMN) interacts, directly or indirectly, with a large number of other proteins and reduced levels of SMN cause the inherited disorder spinal muscular atrophy (SMA). Some SMN interactions are stable and stoichiometric, such as those with gemins, while others are expected to be transient and substoichiometric, such as the functional interaction of SMN with coilin in Cajal bodies. This study set out to determine whether novel components of the extensive SMN interactome can be identified by a proteomic approach. SMN complexes were immuno-precipitated from HeLa nuclear extracts, using anti-SMN monoclonal antibody attached to magnetic beads, digested with trypsin, separated by capillary-liquid chromatography and analyzed by MALDI TOF/TOF mass spectrometry. One-hundred and one proteins were detected with a p value of <0.05, SMN, gemins and U snRNPs being the dominant "hits". Sixty-nine of these were rejected after MALDI analysis of two control pull-downs using antibodies against unrelated nuclear proteins. The proteins found only in anti-SMN pulldowns were either known SMN partners, and/or contained dimethylated RG domains involved in direct interaction with the SMN tudor domain, or they were known binding partners of such direct SMN interactors. Myb-binding protein 1a, identified as a novel candidate, is a mainly nucleolar protein of unknown function but it partially colocalized with SMN in Cajal bodies in HeLa cell nucleoplasm and, like SMN, was reduced in cells from an SMA patient.
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Affiliation(s)
- Heidi R Fuller
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10 7AG, United Kingdom
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Huen J, Kakihara Y, Ugwu F, Cheung KLY, Ortega J, Houry WA. Rvb1–Rvb2: essential ATP-dependent helicases for critical complexesThis paper is one of a selection of papers published in this special issue entitled 8th International Conference on AAA Proteins and has undergone the Journal's usual peer review process. Biochem Cell Biol 2010; 88:29-40. [DOI: 10.1139/o09-122] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Rvb1 and Rvb2 are highly conserved, essential AAA+ helicases found in a wide range of eukaryotes. The versatility of these helicases and their central role in the biology of the cell is evident from their involvement in a wide array of critical cellular complexes. Rvb1 and Rvb2 are components of the chromatin-remodeling complexes INO80, Swr-C, and BAF. They are also members of the histone acetyltransferase Tip60 complex, and the recently identified R2TP complex present in Saccharomyces cerevisiae and Homo sapiens; a complex that is involved in small nucleolar ribonucleoprotein (snoRNP) assembly. Furthermore, in humans, Rvb1 and Rvb2 have been identified in the URI prefoldin-like complex. In Drosophila, the Polycomb Repressive complex 1 contains Rvb2, but not Rvb1, and the Brahma complex contains Rvb1 and not Rvb2. Both of these complexes are involved in the regulation of growth and development genes in Drosophila. Rvbs are therefore crucial factors in various cellular processes. Their importance in chromatin remodeling, transcription regulation, DNA damage repair, telomerase assembly, mitotic spindle formation, and snoRNP biogenesis is discussed in this review.
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Affiliation(s)
- Jennifer Huen
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Yoshito Kakihara
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Francisca Ugwu
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Kevin L. Y. Cheung
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Joaquin Ortega
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
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Samaha H, Delorme V, Pontvianne F, Cooke R, Delalande F, Van Dorsselaer A, Echeverria M, Sáez-Vásquez J. Identification of protein factors and U3 snoRNAs from a Brassica oleracea RNP complex involved in the processing of pre-rRNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:383-398. [PMID: 19891704 DOI: 10.1111/j.1365-313x.2009.04061.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We report on the structural characterization of a functional U3 snoRNA ribonucleoprotein complex isolated from Brassica oleracea. The BoU3 snoRNP complex (formerly NF D) binds ribosomal DNA (rDNA), specifically cleaves pre-rRNA at the primary cleavage site in vitro and probably links transcription to early pre-rRNA processing in vivo. Using a proteomic approach we have identified 62 proteins in the purified BoU3 snoRNP fraction, including small RNA associated proteins (Fibrillarin, NOP5/Nop58p, Diskerin/Cbf5p, SUS2/PRP8 and CLO/GFA1/sn114p) and 40S ribosomal associated proteins (22 RPS and four ARCA-like proteins). Another major protein group is composed of chaperones/chaperonins (HSP81/TCP-1) and at least one proteasome subunit (RPN1a). Remarkably, RNA-dependent RNA polymerase (RdRP) and Tudor staphylococcal nuclease (TSN) proteins, which have RNA- and/or DNA-associated activities, were also revealed in the complex. Furthermore, three U3 snoRNA variants were identified in the BoU3 snoRNP fraction, notably an evolutionarily conserved and variable stem loop structure located just downstream from the C-box domain of the U3 sequence structures. We conclude that the BoU3 snoRNP complex is mainly required for 40S pre-ribosome synthesis. It is also expected that U3 snoRNA variants and interacting proteins might play a major role in BoU3 snoRNP complex assembly and/or function. This study provides a basis for further investigation of these novel ribonucleoprotein factors and their role in plant ribosome biogenesis.
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Affiliation(s)
- Hala Samaha
- Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS-IRD-UPVD, Perpignan France
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Abstract
AbstractReduced levels of the survival of motor neurons protein (SMN), cause the inherited neuromuscular disorder, spinal muscular atrophy (SMA). The majority of therapeutic approaches to date have been focused on finding ways to increase expression of functional SMN protein, though stabilization of SMN protein may also be an important consideration. SMN interacts, directly or indirectly, stably or transiently, with a large number of other proteins, some of which contribute to SMN stability and may therefore be potential targets for SMA therapy. We recently characterized the nuclear SMN interactome using LC-MALDI-TOF/TOF analysis of anti-SMN pull-downs and identified myb-binding protein-1a (Mybbp1a) as a novel partner. In light of interest in cytoplasm-specific roles of the SMN complex, we have applied the same approach to characterise the cytoplasmic SMN interactome. We now show that SMN complexes from HeLa cytoplasmic extracts differ significantly from those found in nuclear extracts, with gemin5, importinbeta and annexin A2 easily detected only in the cytoplasmic extracts, whereas interaction of SMN with Mybbp1a appears to occur only in the nucleus. SMN is ubiquitinylated and we also found proteins of the ubiquitin-proteasome system associated with SMN in the cytoplasm.
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Shin CJ, Davis MJ, Ragan MA. Towards the mammalian interactome: Inference of a core mammalian interaction set in mouse. Proteomics 2009; 9:5256-66. [DOI: 10.1002/pmic.200900262] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Farooq F, Balabanian S, Liu X, Holcik M, MacKenzie A. p38 Mitogen-activated protein kinase stabilizes SMN mRNA through RNA binding protein HuR. Hum Mol Genet 2009; 18:4035-45. [DOI: 10.1093/hmg/ddp352] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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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 DOI: 10.1038/nrn2670] [Citation(s) in RCA: 535] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [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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Adams-Cioaba MA, Min J. Structure and function of histone methylation binding proteins. Biochem Cell Biol 2009; 87:93-105. [PMID: 19234526 DOI: 10.1139/o08-129] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chromatin structure is regulated by chromatin remodeling factors, histone exchange, linker histone association, and histone modification. Covalent modification of histones is an important factor in the regulation of the associated processes. The implementation and removal of various histone modifications have been implicated in DNA replication, repair, recombination, and transcription, and in RNA processing. In recent years, histone methylation has emerged as one of the key modifications regulating chromatin function. However, the mechanisms involved are complex and not well understood. A large volume of structural and biochemical information has been recently amassed for the Tudor, plant homeodomain (PHD), and malignant brain tumor (MBT) protein families. This review summarizes current knowledge of the structures and modes of recognition employed by the PHD, Tudor, and MBT domains in their interactions with target histone peptides.
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Mtango NR, Potireddy S, Latham KE. Expression of microRNA processing machinery genes in rhesus monkey oocytes and embryos of different developmental potentials. Mol Reprod Dev 2009; 76:255-69. [PMID: 18646051 PMCID: PMC2631102 DOI: 10.1002/mrd.20950] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) are a class of small RNAs that silence gene expression. In animal cells, miRNAs bind to the 3' untranslated regions of specific mRNAs and inhibit their translation. The correct regulation of mRNA expression by miRNAs is believed to be important for oocyte maturation, early development and implantation. We examined the expression of 25 mRNAs involved in the microRNA processing pathway in a nonhuman primate oocyte and embryo model. We observed that mRNAs related to miRNA splicing are downregulated during oocyte maturation while those related to miRNA processing are upregulated, indicating that there may exist a temporal difference in their activities related to transcriptional activity in germinal vesicle stage oocytes. We also observed that the vast majority of mRNAs examined were insensitive to alpha-amanitin at the 8-16 cell stage. The expression data did not reveal a major impact of embryo culture, and hormonal stimulation protocol affected only a small number of mRNAs, suggesting that the components of the pathway may be accumulated in the oocyte during oogenesis and resistant to exogenous insults. In comparison to published mouse array data, we observed species differences and similarities in the temporal expression patterns of some genes, suggesting that miRNA processing may be regulated differently. These data extend our understanding of the potential roles of miRNA during primate embryogenesis.
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Affiliation(s)
- Namdori R Mtango
- The Fels Institute for Cancer Research and Molecular Biology, Temple University Medical School, Philadelphia, Pennsylvania 19140, USA
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Lechertier T, Grob A, Hernandez-Verdun D, Roussel P. Fibrillarin and Nop56 interact before being co-assembled in box C/D snoRNPs. Exp Cell Res 2009; 315:928-42. [PMID: 19331828 DOI: 10.1016/j.yexcr.2009.01.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Revised: 12/12/2008] [Accepted: 01/16/2009] [Indexed: 11/16/2022]
Abstract
Small nucleolar RNAs play crucial roles in ribosome biogenesis. They guide folding, site-specific nucleotide modifications and participate in cleavage of precursor ribosomal RNAs. To better understand how the biogenesis of the box C/D small nucleolar RNPs (snoRNPs) occur in a cellular context, we used a new approach based on the possibility of relocalizing a given nuclear complex by adding an affinity tag for B23 to one component of this complex. We selectively delocalized each core box C/D protein, namely 15.5kD, Nop56, Nop58 and fibrillarin, and analyzed the effect of such changes on other components of the box C/D snoRNPs. We show that modifying the localization and the mobility of core box C/D proteins impairs their association with box C/D snoRNPs. In addition, we demonstrate that fibrillarin and Nop56 directly interact in vivo. This interaction, indispensable for the association of both proteins with the box C/D snoRNPs, does not involve the glycine- and arginine-rich domain or the RNA-binding domain but the alpha-helix domain of fibrillarin. In addition, no RNA seems required to maintain fibrillarin-Nop56 interaction.
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Affiliation(s)
- Tanguy Lechertier
- Institut Jacques Monod, UMR 7592 CNRS/Universités Paris 6 et 7, 2 Place Jussieu, 75251 Paris Cedex 05, France
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Renvoisé B, Colasse S, Burlet P, Viollet L, Meier UT, Lefebvre S. The loss of the snoRNP chaperone Nopp140 from Cajal bodies of patient fibroblasts correlates with the severity of spinal muscular atrophy. Hum Mol Genet 2009; 18:1181-9. [PMID: 19129172 DOI: 10.1093/hmg/ddp009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a common autosomal recessive neurodegenerative disease caused by reduced survival motor neuron (SMN) levels. The assembly machinery containing SMN is implicated in the biogenesis of the spliceosomal small nuclear ribonucleoproteins (snRNPs). SMN is present in both the cytoplasm and nucleus, where it transiently accumulates in subnuclear domains named Cajal bodies (CBs) and functions in the maturation of snRNPs and small nucleolar (sno)RNPs. The impact of lowering SMN levels on the composition of CBs in SMA cells is still not completely understood. Here, we analyse the CB composition in immortalized and primary fibroblasts from SMA patients. We show that the U snRNA export factors PHAX and chromosome region maintenance 1 and the box C/D snoRNP core protein fibrillarin concentrate in CBs from SMA cells, whereas the box H/ACA core proteins GAR1 and NAP57/dyskerin show reduced CB localization. Remarkably, the functional deficiency in SMA cells is associated with decreased localization of the snoRNP chaperone Nopp140 in CBs that correlates with disease severity. Indeed, RNA interference knockdown experiments in control fibroblasts demonstrate that SMN is required for accumulation of Nopp140 in CBs. Conversely, overexpression of SMN in SMA cells restores the CB localization of Nopp140, whereas SMN mutants found in SMA patients are defective in promoting the association of Nopp140 with CBs. Taken together, we demonstrate that only a subset of CB functions (as indicated by the association of representative factors) are impaired in SMA cells and, importantly, we identify the decrease of Nopp140 localization in CBs as a phenotypic marker for SMA.
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Affiliation(s)
- Benoît Renvoisé
- Laboratoire de Biologie Cellulaire des Membranes, Department of Cell Biology, Institut Jacques Monod (IJM), UMR 7592 CNRS/Universités Paris 6 et 7, Paris Cedex 05, France
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Rossoll W, Bassell GJ. Spinal muscular atrophy and a model for survival of motor neuron protein function in axonal ribonucleoprotein complexes. Results Probl Cell Differ 2009; 48:289-326. [PMID: 19343312 PMCID: PMC3718852 DOI: 10.1007/400_2009_4] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Spinal muscular atrophy (SMA) is a neurodegenerative disease that results from loss of function of the SMN1 gene, encoding the ubiquitously expressed survival of motor neuron (SMN) protein, a protein best known for its housekeeping role in the SMN-Gemin multiprotein complex involved in spliceosomal small nuclear ribonucleoprotein (snRNP) assembly. However, numerous studies reveal that SMN has many interaction partners, including mRNA binding proteins and actin regulators, suggesting its diverse role as a molecular chaperone involved in mRNA metabolism. This review focuses on studies suggesting an important role of SMN in regulating the assembly, localization, or stability of axonal messenger ribonucleoprotein (mRNP) complexes. Various animal models for SMA are discussed, and phenotypes described that indicate a predominant function for SMN in neuronal development and synapse formation. These models have begun to be used to test different therapeutic strategies that have the potential to restore SMN function. Further work to elucidate SMN mechanisms within motor neurons and other cell types involved in neuromuscular circuitry hold promise for the potential treatment of SMA.
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Affiliation(s)
- Wilfried Rossoll
- Departments of Cell Biology and Neurology, Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322, USA.
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Trinkle-Mulcahy L, Boulon S, Lam YW, Urcia R, Boisvert FM, Vandermoere F, Morrice NA, Swift S, Rothbauer U, Leonhardt H, Lamond A. Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes. ACTA ACUST UNITED AC 2008; 183:223-39. [PMID: 18936248 PMCID: PMC2568020 DOI: 10.1083/jcb.200805092] [Citation(s) in RCA: 349] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The identification of interaction partners in protein complexes is a major goal in cell biology. Here we present a reliable affinity purification strategy to identify specific interactors that combines quantitative SILAC-based mass spectrometry with characterization of common contaminants binding to affinity matrices (bead proteomes). This strategy can be applied to affinity purification of either tagged fusion protein complexes or endogenous protein complexes, illustrated here using the well-characterized SMN complex as a model. GFP is used as the tag of choice because it shows minimal nonspecific binding to mammalian cell proteins, can be quantitatively depleted from cell extracts, and allows the integration of biochemical protein interaction data with in vivo measurements using fluorescence microscopy. Proteins binding nonspecifically to the most commonly used affinity matrices were determined using quantitative mass spectrometry, revealing important differences that affect experimental design. These data provide a specificity filter to distinguish specific protein binding partners in both quantitative and nonquantitative pull-down and immunoprecipitation experiments.
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Affiliation(s)
- Laura Trinkle-Mulcahy
- Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland, UK.
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Identification of genes that function in the biogenesis and localization of small nucleolar RNAs in Saccharomyces cerevisiae. Mol Cell Biol 2008; 28:3686-99. [PMID: 18378690 DOI: 10.1128/mcb.01115-07] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Small nucleolar RNAs (snoRNAs) orchestrate the modification and cleavage of pre-rRNA and are essential for ribosome biogenesis. Recent data suggest that after nucleoplasmic synthesis, snoRNAs transiently localize to the Cajal body (in plant and animal cells) or the homologous nucleolar body (in budding yeast) for maturation and assembly into snoRNPs prior to accumulation in their primary functional site, the nucleolus. However, little is known about the trans-acting factors important for the intranuclear trafficking and nucleolar localization of snoRNAs. Here, we describe a large-scale genetic screen to identify proteins important for snoRNA transport in Saccharomyces cerevisiae. We performed fluorescence in situ hybridization analysis to visualize U3 snoRNA localization in a collection of temperature-sensitive yeast mutants. We have identified Nop4, Prp21, Tao3, Sec14, and Htl1 as proteins important for the proper localization of U3 snoRNA. Mutations in genes encoding these proteins lead to specific defects in the targeting or retention of the snoRNA to either the nucleolar body or the nucleolus. Additional characterization of the mutants revealed impairment in specific steps of U3 snoRNA processing, demonstrating that snoRNA maturation and trafficking are linked processes.
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Neuenkirchen N, Chari A, Fischer U. Deciphering the assembly pathway of Sm-class U snRNPs. FEBS Lett 2008; 582:1997-2003. [DOI: 10.1016/j.febslet.2008.03.009] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Revised: 03/09/2008] [Accepted: 03/10/2008] [Indexed: 11/16/2022]
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Bertrand E, Bordonné R. Assembly and Traffic of Small Nuclear RNPs. RNA TRAFFICKING AND NUCLEAR STRUCTURE DYNAMICS 2008; 35:79-97. [PMID: 15113080 DOI: 10.1007/978-3-540-74266-1_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR 5535-IFR 122, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
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Canetta E, Kim SH, Kalinina NO, Shaw J, Adya AK, Gillespie T, Brown JWS, Taliansky M. A plant virus movement protein forms ringlike complexes with the major nucleolar protein, fibrillarin, in vitro. J Mol Biol 2007; 376:932-7. [PMID: 18199452 PMCID: PMC7126915 DOI: 10.1016/j.jmb.2007.12.039] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Revised: 12/17/2007] [Accepted: 12/18/2007] [Indexed: 12/21/2022]
Abstract
Fibrillarin, one of the major proteins of the nucleolus, has methyltransferase activity directing 2′-O-ribose methylation of rRNA and snRNAs and is required for rRNA processing. The ability of the plant umbravirus, groundnut rosette virus, to move long distances through the phloem, the specialized plant vascular system, has been shown to strictly depend on the interaction of one of its proteins, the ORF3 protein (protein encoded by open reading frame 3), with fibrillarin. This interaction is essential for several stages in the groundnut rosette virus life cycle such as nucleolar import of the ORF3 protein via Cajal bodies, relocalization of some fibrillarin from the nucleolus to cytoplasm, and assembly of cytoplasmic umbraviral ribonucleoprotein particles that are themselves required for the long-distance spread of the virus and systemic infection. Here, using atomic force microscopy, we determine the architecture of these complexes as single-layered ringlike structures with a diameter of 18–22 nm and a height of 2.0 ± 0.4 nm, which consist of several (n = 6–8) distinct protein granules. We also estimate the molar ratio of fibrillarin to ORF3 protein in the complexes as approximately 1:1. Based on these data, we propose a model of the structural organization of fibrillarin–ORF3 protein complexes and discuss potential mechanistic and functional implications that may also apply to other viruses.
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Affiliation(s)
- Elisabetta Canetta
- BIONTHE (Bio- and Nano-Technologies for Health & Environment) Centre, School of Contemporary Sciences, University of Abertay, Dundee, Bell Street, Dundee DD1 1HG, UK
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