1
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Ciocia A, Mestre-Farràs N, Vicent-Nacht I, Guitart T, Gebauer F. CSDE1: a versatile regulator of gene expression in cancer. NAR Cancer 2024; 6:zcae014. [PMID: 38600987 PMCID: PMC11005786 DOI: 10.1093/narcan/zcae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/13/2024] [Accepted: 03/10/2024] [Indexed: 04/12/2024] Open
Abstract
RNA-binding proteins (RBPs) have garnered significant attention in the field of cancer due to their ability to modulate diverse tumor traits. Once considered untargetable, RBPs have sparked renewed interest in drug development, particularly in the context of RNA-binding modulators of translation. This review focuses on one such modulator, the protein CSDE1, and its pivotal role in regulating cancer hallmarks. We discuss context-specific functions of CSDE1 in tumor development, its mechanisms of action, and highlight features that support its role as a molecular adaptor. Additionally, we discuss the regulation of CSDE1 itself and its potential value as biomarker and therapeutic target.
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Affiliation(s)
- Annagiulia Ciocia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
| | - Neus Mestre-Farràs
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Ignacio Vicent-Nacht
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
| | - Tanit Guitart
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Fátima Gebauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
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2
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Esser LM, Li Q, Jüdt M, Kähne T, Stork B, Grimmler M, Wesselborg S, Peter C. The Impact of p70S6 Kinase-Dependent Phosphorylation of Gemin2 in UsnRNP Biogenesis. Int J Mol Sci 2023; 24:15552. [PMID: 37958537 PMCID: PMC10649565 DOI: 10.3390/ijms242115552] [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: 09/22/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
The survival motor neuron (SMN) complex is a multi-megadalton complex involved in post-transcriptional gene expression in eukaryotes via promotion of the biogenesis of uridine-rich small nuclear ribonucleoproteins (UsnRNPs). The functional center of the complex is formed from the SMN/Gemin2 subunit. By binding the pentameric ring made up of the Sm proteins SmD1/D2/E/F/G and allowing for their transfer to a uridine-rich short nuclear RNA (UsnRNA), the Gemin2 protein in particular is crucial for the selectivity of the Sm core assembly. It is well established that post-translational modifications control UsnRNP biogenesis. In our work presented here, we emphasize the crucial role of Gemin2, showing that the phospho-status of Gemin2 influences the capacity of the SMN complex to condense in Cajal bodies (CBs) in vivo. Additionally, we define Gemin2 as a novel and particular binding partner and phosphorylation substrate of the mTOR pathway kinase ribosomal protein S6 kinase beta-1 (p70S6K). Experiments using size exclusion chromatography further demonstrated that the Gemin2 protein functions as a connecting element between the 6S complex and the SMN complex. As a result, p70S6K knockdown lowered the number of CBs, which in turn inhibited in vivo UsnRNP synthesis. In summary, these findings reveal a unique regulatory mechanism of UsnRNP biogenesis.
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Affiliation(s)
- Lea Marie Esser
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Qiaoping Li
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Maximilian Jüdt
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Thilo Kähne
- Institute of Experimental Internal Medicine, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Björn Stork
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Matthias Grimmler
- Institute for Biomolecular Research, Hochschule Fresenius gGmbH, University of Applied Sciences, 65510 Idstein, Germany
- DiaServe Laboratories GmbH, 82393 Iffeldorf, Germany
| | - Sebastian Wesselborg
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Christoph Peter
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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3
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Esser LM, Schmitz K, Hillebrand F, Erkelenz S, Schaal H, Stork B, Grimmler M, Wesselborg S, Peter C. Phosphorylation of pICln by the autophagy activating kinase ULK1 regulates snRNP biogenesis and splice activity of the cell. Comput Struct Biotechnol J 2023; 21:2100-2109. [PMID: 36968021 PMCID: PMC10034211 DOI: 10.1016/j.csbj.2023.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 03/10/2023] [Accepted: 03/11/2023] [Indexed: 03/18/2023] Open
Abstract
The spliceosome, responsible for all mature protein-coding transcripts of eukaryotic intron-containing genes, consists of small uridine-rich nuclear ribonucleoproteins (UsnRNPs). The assembly of UsnRNPs depends, on one hand, on the arginine methylation of Sm proteins catalyzed by the PRMT5 complex. On the other hand, it depends on the phosphorylation of the PRMT5 subunit pICln by the Uncoordinated Like Kinase 1 (ULK1). In consequence, phosphorylation of pICln affects the stability of the UsnRNP assembly intermediate, the so-called 6 S complex. The detailed mechanisms of phosphorylation-dependent integrity and subsequent UsnRNP assembly of the 6 S complex in vivo have not yet been analyzed. By using a phospho-specific antibody against ULK1-dependent phosphorylation sites of pICln, we visualize the intracellular distribution of phosphorylated pICln. Furthermore, we detect the colocaliphosphor-pICln1 with phospho-pICln by size-exclusion chromatography and immunofluorescence techniques. We also show that phosphorylated pICln is predominantly present in the 6 S complex. The addition of ULK1 to in vitro produced 6 S complex, as well as the reconstitution of ULK1 in ULK1-deficient cells, increases the efficiency of snRNP biogenesis. Accordingly, inhibition of ULK1 and the associated decreased pICln phosphorylation lead to accumulation of the 6 S complex and reduction in the spliceosomal activity of the cell.
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4
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Blatnik AJ, McGovern VL, Burghes AHM. What Genetics Has Told Us and How It Can Inform Future Experiments for Spinal Muscular Atrophy, a Perspective. Int J Mol Sci 2021; 22:8494. [PMID: 34445199 PMCID: PMC8395208 DOI: 10.3390/ijms22168494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/28/2021] [Accepted: 08/04/2021] [Indexed: 02/06/2023] Open
Abstract
Proximal spinal muscular atrophy (SMA) is an autosomal recessive neurodegenerative disorder characterized by motor neuron loss and subsequent atrophy of skeletal muscle. SMA is caused by deficiency of the essential survival motor neuron (SMN) protein, canonically responsible for the assembly of the spliceosomal small nuclear ribonucleoproteins (snRNPs). Therapeutics aimed at increasing SMN protein levels are efficacious in treating SMA. However, it remains unknown how deficiency of SMN results in motor neuron loss, resulting in many reported cellular functions of SMN and pathways affected in SMA. Herein is a perspective detailing what genetics and biochemistry have told us about SMA and SMN, from identifying the SMA determinant region of the genome, to the development of therapeutics. Furthermore, we will discuss how genetics and biochemistry have been used to understand SMN function and how we can determine which of these are critical to SMA moving forward.
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Affiliation(s)
| | | | - Arthur H. M. Burghes
- Department of Biological Chemistry & Pharmacology, The Ohio State University Wexner Medical Center, Rightmire Hall, Room 168, 1060 Carmack Road, Columbus, OH 43210, USA; (A.J.B.III); (V.L.M.)
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5
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Schmitz K, Cox J, Esser LM, Voss M, Sander K, Löffler A, Hillebrand F, Erkelenz S, Schaal H, Kähne T, Klinker S, Zhang T, Nagel-Steger L, Willbold D, Seggewiß S, Schlütermann D, Stork B, Grimmler M, Wesselborg S, Peter C. An essential role of the autophagy activating kinase ULK1 in snRNP biogenesis. Nucleic Acids Res 2021; 49:6437-6455. [PMID: 34096600 PMCID: PMC8216288 DOI: 10.1093/nar/gkab452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 01/31/2023] Open
Abstract
The biogenesis of small uridine-rich nuclear ribonucleoproteins (UsnRNPs) depends on the methylation of Sm proteins catalyzed by the methylosome and the subsequent action of the SMN complex, which assembles the heptameric Sm protein ring onto small nuclear RNAs (snRNAs). In this sophisticated process, the methylosome subunit pICln (chloride conductance regulatory protein) is attributed to an exceptional key position as an ‘assembly chaperone’ by building up a stable precursor Sm protein ring structure. Here, we show that—apart from its autophagic role—the Ser/Thr kinase ULK1 (Uncoordinated [unc-51] Like Kinase 1) functions as a novel key regulator in UsnRNP biogenesis by phosphorylation of the C-terminus of pICln. As a consequence, phosphorylated pICln is no longer capable to hold up the precursor Sm ring structure. Consequently, inhibition of ULK1 results in a reduction of efficient UsnRNP core assembly. Thus ULK1, depending on its complex formation, exerts different functions in autophagy or snRNP biosynthesis.
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Affiliation(s)
- Katharina Schmitz
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jan Cox
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lea Marie Esser
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Martin Voss
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Katja Sander
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Antje Löffler
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Frank Hillebrand
- Institute of Virology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Steffen Erkelenz
- Institute of Virology, University Hospital Düsseldorf, Düsseldorf, Germany.,Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Heiner Schaal
- Institute of Virology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Thilo Kähne
- Insitute of Experimental Internal Medicine, Otto von Guericke University, Magdeburg, Germany
| | - Stefan Klinker
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany
| | - Tao Zhang
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany.,Institute of Biological Information Processing (Structural Biochemistry: IBI-7), Forschungszentrum Jülich, Jülich, Germany
| | - Luitgard Nagel-Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany.,Institute of Biological Information Processing (Structural Biochemistry: IBI-7), Forschungszentrum Jülich, Jülich, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany.,Institute of Biological Information Processing (Structural Biochemistry: IBI-7), Forschungszentrum Jülich, Jülich, Germany
| | - Sabine Seggewiß
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - David Schlütermann
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Björn Stork
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Matthias Grimmler
- Hochschule Fresenius, Idstein, Germany.,DiaSys Diagnostic Systems GmbH, Alte Strasse 9, 65558 Holzheim, Germany
| | - Sebastian Wesselborg
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christoph Peter
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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6
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Jin L, Chen Y, Crossman DK, Datta A, Vu T, Mobley JA, Basu MK, Scarduzio M, Wang H, Chang C, Datta PK. STRAP regulates alternative splicing fidelity during lineage commitment of mouse embryonic stem cells. Nat Commun 2020; 11:5941. [PMID: 33230114 PMCID: PMC7684319 DOI: 10.1038/s41467-020-19698-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/05/2020] [Indexed: 12/15/2022] Open
Abstract
Alternative splicing (AS) is involved in cell fate decisions and embryonic development. However, regulation of these processes is poorly understood. Here, we have identified the serine threonine kinase receptor-associated protein (STRAP) as a putative spliceosome-associated factor. Upon Strap deletion, there are numerous AS events observed in mouse embryoid bodies (EBs) undergoing a neuroectoderm-like state. Global mapping of STRAP-RNA binding in mouse embryos by enhanced-CLIP sequencing (eCLIP-seq) reveals that STRAP preferably targets transcripts for nervous system development and regulates AS through preferred binding positions, as demonstrated for two neuronal-specific genes, Nnat and Mark3. We have found that STRAP involves in the assembly of 17S U2 snRNP proteins. Moreover, in Xenopus, loss of Strap leads to impeded lineage differentiation in embryos, delayed neural tube closure, and altered exon skipping. Collectively, our findings reveal a previously unknown function of STRAP in mediating the splicing networks of lineage commitment, alteration of which may be involved in early embryonic lethality in mice.
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Affiliation(s)
- Lin Jin
- Division of Hematology and Oncology, Department of Medicine, UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- Birmingham Veterans Affairs Medical Center, Birmingham, AL, 35233, USA
| | - Yunjia Chen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - David K Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Arunima Datta
- Division of Hematology and Oncology, Department of Medicine, UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- Birmingham Veterans Affairs Medical Center, Birmingham, AL, 35233, USA
| | - Trung Vu
- Division of Hematology and Oncology, Department of Medicine, UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- Birmingham Veterans Affairs Medical Center, Birmingham, AL, 35233, USA
| | - James A Mobley
- Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Malay Kumar Basu
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Mariangela Scarduzio
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutic, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Hengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Chenbei Chang
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Pran K Datta
- Division of Hematology and Oncology, Department of Medicine, UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
- Birmingham Veterans Affairs Medical Center, Birmingham, AL, 35233, USA.
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7
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Guo AX, Cui JJ, Wang LY, Yin JY. The role of CSDE1 in translational reprogramming and human diseases. Cell Commun Signal 2020; 18:14. [PMID: 31987048 PMCID: PMC6986143 DOI: 10.1186/s12964-019-0496-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/16/2019] [Indexed: 02/06/2023] Open
Abstract
Abstract CSDE1 (cold shock domain containing E1) plays a key role in translational reprogramming, which determines the fate of a number of RNAs during biological processes. Interestingly, the role of CSDE1 is bidirectional. It not only promotes and represses the translation of RNAs but also increases and decreases the abundance of RNAs. However, the mechanisms underlying this phenomenon are still unknown. In this review, we propose a “protein-RNA connector” model to explain this bidirectional role and depict its three versions: sequential connection, mutual connection and facilitating connection. As described in this molecular model, CSDE1 binds to RNAs and cooperates with other protein regulators. CSDE1 connects with different RNAs and their regulators for different purposes. The triple complex of CSDE1, a regulator and an RNA reprograms translation in different directions for each transcript. Meanwhile, a number of recent studies have found important roles for CSDE1 in human diseases. This model will help us to understand the role of CSDE1 in translational reprogramming and human diseases. Video Abstract
Graphical abstract ![]()
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Affiliation(s)
- Ao-Xiang Guo
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Jia-Jia Cui
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Lei-Yun Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China. .,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China. .,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China. .,Hunan Provincial Gynecological Cancer Diagnosis and Treatment Engineering Research Center, Changsha, 410078, People's Republic of China. .,Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumor, Changsha, 410078, People's Republic of China.
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8
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Song M, Yang X, Ren X, Maliskova L, Li B, Jones IR, Wang C, Jacob F, Wu K, Traglia M, Tam TW, Jamieson K, Lu SY, Ming GL, Li Y, Yao J, Weiss LA, Dixon JR, Judge LM, Conklin BR, Song H, Gan L, Shen Y. Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes. Nat Genet 2019; 51:1252-1262. [PMID: 31367015 PMCID: PMC6677164 DOI: 10.1038/s41588-019-0472-1] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 06/21/2019] [Indexed: 12/13/2022]
Abstract
Mutations in gene regulatory elements have been associated with a wide range of complex neuropsychiatric disorders. However, due to their cell-type specificity and difficulties in characterizing their regulatory targets, the ability to identify causal genetic variants has remained limited. To address these constraints, we perform an integrative analysis of chromatin interactions, open chromatin regions and transcriptomes using promoter capture Hi-C, assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and RNA sequencing, respectively, in four functionally distinct neural cell types: induced pluripotent stem cell (iPSC)-induced excitatory neurons and lower motor neurons, iPSC-derived hippocampal dentate gyrus-like neurons and primary astrocytes. We identify hundreds of thousands of long-range cis-interactions between promoters and distal promoter-interacting regions, enabling us to link regulatory elements to their target genes and reveal putative processes that are dysregulated in disease. Finally, we validate several promoter-interacting regions by using clustered regularly interspaced short palindromic repeats (CRISPR) techniques in human excitatory neurons, demonstrating that CDK5RAP3, STRAP and DRD2 are transcriptionally regulated by physically linked enhancers.
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Affiliation(s)
- Michael Song
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, CA, USA
| | - Xiaoyu Yang
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Xingjie Ren
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Lenka Maliskova
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Bingkun Li
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Ian R Jones
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Chao Wang
- Gladstone Institute of Neurological Disease, University of California, San Francisco, CA, USA
| | - Fadi Jacob
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth Wu
- Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, CA, USA
| | - Michela Traglia
- Department of Psychiatry, University of California, San Francisco, CA, USA
| | - Tsz Wai Tam
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Kirsty Jamieson
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Si-Yao Lu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
| | - Guo-Li Ming
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - Jun Yao
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
| | - Lauren A Weiss
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Psychiatry, University of California, San Francisco, CA, USA
| | - Jesse R Dixon
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Luke M Judge
- Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, CA, USA
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Bruce R Conklin
- Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Hongjun Song
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Li Gan
- Gladstone Institute of Neurological Disease, University of California, San Francisco, CA, USA
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Yin Shen
- Institute for Human Genetics, University of California, San Francisco, CA, USA.
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, CA, USA.
- Department of Neurology, University of California, San Francisco, CA, USA.
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9
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Booy EP, McRae EK, Ezzati P, Choi T, Gussakovsky D, McKenna SA. Comprehensive analysis of the BC200 ribonucleoprotein reveals a reciprocal regulatory function with CSDE1/UNR. Nucleic Acids Res 2019; 46:11575-11591. [PMID: 30247708 PMCID: PMC6265466 DOI: 10.1093/nar/gky860] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 09/12/2018] [Indexed: 12/11/2022] Open
Abstract
BC200 is a long non-coding RNA primarily expressed in brain but aberrantly expressed in various cancers. To gain a further understanding of the function of BC200, we performed proteomic analyses of the BC200 ribonucleoprotein (RNP) by transfection of 3′ DIG-labelled BC200. Protein binding partners of the functionally related murine RNA BC1 as well as a scrambled BC200 RNA were also assessed in both human and mouse cell lines. Stringent validation of proteins identified by mass spectrometry confirmed 14 of 84 protein binding partners and excluded eight proteins that did not appreciably bind BC200 in reverse experiments. Gene ontology analyses revealed general roles in RNA metabolic processes, RNA processing and splicing. Protein/RNA interaction sites were mapped with a series of RNA truncations revealing three distinct modes of interaction involving either the 5′ Alu-domain, 3′ A-rich or 3′ C-rich regions. Due to their high enrichment values in reverse experiments, CSDE1 and STRAP were further analyzed demonstrating a direct interaction between CSDE1 and BC200 and indirect binding of STRAP to BC200 via heterodimerization with CSDE1. Knock-down studies identified a reciprocal regulatory relationship between CSDE1 and BC200 and immunofluorescence analysis of BC200 knock-down cells demonstrated a dramatic reorganization of CSDE1 into distinct nuclear foci.
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Affiliation(s)
- Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ewan Ks McRae
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Peyman Ezzati
- Manitoba Centre for Proteomics and Systems Biology, Section of Biomedical Proteomics, Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba and Health Sciences Centre, Winnipeg, Manitoba, Canada
| | - Taegi Choi
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Daniel Gussakovsky
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
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10
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Composition of the Survival Motor Neuron (SMN) Complex in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2019; 9:491-503. [PMID: 30563832 PMCID: PMC6385987 DOI: 10.1534/g3.118.200874] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Spinal Muscular Atrophy (SMA) is caused by homozygous mutations in the human survival motor neuron 1 (SMN1) gene. SMN protein has a well-characterized role in the biogenesis of small nuclear ribonucleoproteins (snRNPs), core components of the spliceosome. SMN is part of an oligomeric complex with core binding partners, collectively called Gemins. Biochemical and cell biological studies demonstrate that certain Gemins are required for proper snRNP assembly and transport. However, the precise functions of most Gemins are unknown. To gain a deeper understanding of the SMN complex in the context of metazoan evolution, we investigated its composition in Drosophila melanogaster Using transgenic flies that exclusively express Flag-tagged SMN from its native promoter, we previously found that Gemin2, Gemin3, Gemin5, and all nine classical Sm proteins, including Lsm10 and Lsm11, co-purify with SMN. Here, we show that CG2941 is also highly enriched in the pulldown. Reciprocal co-immunoprecipitation reveals that epitope-tagged CG2941 interacts with endogenous SMN in Schneider2 cells. Bioinformatic comparisons show that CG2941 shares sequence and structural similarity with metazoan Gemin4. Additional analysis shows that three other genes (CG14164, CG31950 and CG2371) are not orthologous to Gemins 6-7-8, respectively, as previously suggested. In D.melanogaster, CG2941 is located within an evolutionarily recent genomic triplication with two other nearly identical paralogous genes (CG32783 and CG32786). RNAi-mediated knockdown of CG2941 and its two close paralogs reveals that Gemin4 is essential for organismal viability.
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11
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Moore KS, Yagci N, van Alphen F, Meijer AB, ‘t Hoen PAC, von Lindern M. Strap associates with Csde1 and affects expression of select Csde1-bound transcripts. PLoS One 2018; 13:e0201690. [PMID: 30138317 PMCID: PMC6107111 DOI: 10.1371/journal.pone.0201690] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 07/22/2018] [Indexed: 02/06/2023] Open
Abstract
Erythropoiesis is regulated at many levels, including control of mRNA translation. Changing environmental conditions, such as hypoxia or the availability of nutrients and growth factors, require a rapid response enacted by the enhanced or repressed translation of existing transcripts. Cold shock domain protein e1 (Csde1/Unr) is an RNA-binding protein required for erythropoiesis and strongly upregulated in erythroblasts relative to other hematopoietic progenitors. The aim of this study is to identify the Csde1-containing protein complexes and investigate their role in post-transcriptional expression control of Csde1-bound transcripts. We show that Serine/Threonine kinase receptor-associated protein (Strap/Unrip), was the protein most strongly associated with Csde1 in erythroblasts. Strap is a WD40 protein involved in signaling and RNA splicing, but its role when associated with Csde1 is unknown. Reduced expression of Strap did not alter the pool of transcripts bound by Csde1. Instead, it altered the mRNA and/or protein expression of several Csde1-bound transcripts that encode for proteins essential for translational regulation during hypoxia, such as Hmbs, eIF4g3 and Pabpc4. Also affected by Strap knockdown were Vim, a Gata-1 target crucial for erythrocyte enucleation, and Elavl1, which stabilizes Gata-1 mRNA. The major cellular processes affected by both Csde1 and Strap were ribosome function and cell cycle control.
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Affiliation(s)
- Kat S. Moore
- Sanquin Research, Department of Hematopoiesis, and Landsteiner Laboratory Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Nurcan Yagci
- Sanquin Research, Department of Hematopoiesis, and Landsteiner Laboratory Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Floris van Alphen
- Sanquin Research, Department of Research Facilities, Amsterdam, The Netherlands
| | - Alexander B. Meijer
- Sanquin Research, Department of Research Facilities, Amsterdam, The Netherlands
- Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Peter A. C. ‘t Hoen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marieke von Lindern
- Sanquin Research, Department of Hematopoiesis, and Landsteiner Laboratory Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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12
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Jha NN, Kim JK, Monani UR. Motor neuron biology and disease: A current perspective on infantile-onset spinal muscular atrophy. FUTURE NEUROLOGY 2018; 13:161-172. [PMID: 31396020 DOI: 10.2217/fnl-2018-0008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Infantile-onset spinal muscular atrophy (SMA) is a prototypical disease in which to investigate selective neurodegenerative phenotypes. Caused by low levels of the ubiquitously expressed Survival Motor Neuron (SMN) protein, the disease mainly targets the spinal motor neurons. This selective phenotype remains largely unexplained, but has not hindered the development of SMN repletion as a means to a treatment. Here we chronicle recent advances in the area of SMA biology. We provide a brief background to the disease, highlight major advances that have shaped our current understanding of SMA, trace efforts to treat the condition, discuss the outcome of two promising new therapies and conclude by considering contemporary as well as new challenges stemming from recent successes within the field.
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Affiliation(s)
- Narendra N Jha
- Department of Pathology & Cell Biology, 630 W. 168 St., Columbia University Medical Center, New York, NY 10032.,Center for Motor Neuron Biology & Disease, 630 W. 168 St., Columbia University Medical Center, New York, NY 10032
| | - Jeong-Ki Kim
- Department of Pathology & Cell Biology, 630 W. 168 St., Columbia University Medical Center, New York, NY 10032.,Center for Motor Neuron Biology & Disease, 630 W. 168 St., Columbia University Medical Center, New York, NY 10032
| | - Umrao R Monani
- Department of Pathology & Cell Biology, 630 W. 168 St., Columbia University Medical Center, New York, NY 10032.,Department of Neurology, 630 W. 168 St., Columbia University Medical Center, New York, NY 10032.,Center for Motor Neuron Biology & Disease, 630 W. 168 St., Columbia University Medical Center, New York, NY 10032
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13
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Lanfranco M, Cacciottolo R, Borg RM, Vassallo N, Juge F, Bordonné R, Cauchi RJ. Novel interactors of the Drosophila
Survival Motor Neuron (SMN) Complex suggest its full conservation. FEBS Lett 2017; 591:3600-3614. [DOI: 10.1002/1873-3468.12853] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/14/2017] [Accepted: 09/14/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Maia Lanfranco
- Institut de Génétique Moléculaire de Montpellier; CNRS-UMR 5535; Université de Montpellier; France
- Department of Physiology and Biochemistry; Faculty of Medicine and Surgery; University of Malta; Msida Malta
- Centre for Molecular Medicine and Biobanking; University of Malta; Msida Malta
| | - Rebecca Cacciottolo
- Department of Physiology and Biochemistry; Faculty of Medicine and Surgery; University of Malta; Msida Malta
- Centre for Molecular Medicine and Biobanking; University of Malta; Msida Malta
| | - Rebecca M. Borg
- Institut de Génétique Moléculaire de Montpellier; CNRS-UMR 5535; Université de Montpellier; France
- Department of Physiology and Biochemistry; Faculty of Medicine and Surgery; University of Malta; Msida Malta
- Centre for Molecular Medicine and Biobanking; University of Malta; Msida Malta
| | - Neville Vassallo
- Department of Physiology and Biochemistry; Faculty of Medicine and Surgery; University of Malta; Msida Malta
- Centre for Molecular Medicine and Biobanking; University of Malta; Msida Malta
| | - François Juge
- Institut de Génétique Moléculaire de Montpellier; CNRS-UMR 5535; Université de Montpellier; France
| | - Rémy Bordonné
- Institut de Génétique Moléculaire de Montpellier; CNRS-UMR 5535; Université de Montpellier; France
| | - Ruben J. Cauchi
- Department of Physiology and Biochemistry; Faculty of Medicine and Surgery; University of Malta; Msida Malta
- Centre for Molecular Medicine and Biobanking; University of Malta; Msida Malta
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14
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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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15
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Lanfranco M, Vassallo N, Cauchi RJ. Spinal Muscular Atrophy: From Defective Chaperoning of snRNP Assembly to Neuromuscular Dysfunction. Front Mol Biosci 2017. [PMID: 28642865 PMCID: PMC5463183 DOI: 10.3389/fmolb.2017.00041] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Spinal Muscular Atrophy (SMA) is a neuromuscular disorder that results from decreased levels of the survival motor neuron (SMN) protein. SMN is part of a multiprotein complex that also includes Gemins 2–8 and Unrip. The SMN-Gemins complex cooperates with the protein arginine methyltransferase 5 (PRMT5) complex, whose constituents include WD45, PRMT5 and pICln. Both complexes function as molecular chaperones, interacting with and assisting in the assembly of an Sm protein core onto small nuclear RNAs (snRNAs) to generate small nuclear ribonucleoproteins (snRNPs), which are the operating components of the spliceosome. Molecular and structural studies have refined our knowledge of the key events taking place within the crowded environment of cells and the numerous precautions undertaken to ensure the faithful assembly of snRNPs. Nonetheless, it remains unclear whether a loss of chaperoning in snRNP assembly, considered as a “housekeeping” activity, is responsible for the selective neuromuscular phenotype in SMA. This review thus shines light on in vivo studies that point toward disturbances in snRNP assembly and the consequential transcriptome abnormalities as the primary drivers of the progressive neuromuscular degeneration underpinning the disease. Disruption of U1 snRNP or snRNP assembly factors other than SMN induces phenotypes that mirror aspects of SMN deficiency, and splicing defects, described in numerous SMA models, can lead to a DNA damage and stress response that compromises the survival of the motor system. Restoring the correct chaperoning of snRNP assembly is therefore predicted to enhance the benefit of SMA therapeutic modalities based on augmenting SMN expression.
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Affiliation(s)
- Maia Lanfranco
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of MaltaMsida, Malta.,Center for Molecular Medicine and Biobanking, University of MaltaMsida, Malta.,Institut de Génétique Moléculaire de Montpellier, Center National de la Recherche Scientifique-UMR 5535, Université de MontpellierMontpellier, France
| | - Neville Vassallo
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of MaltaMsida, Malta.,Center for Molecular Medicine and Biobanking, University of MaltaMsida, Malta
| | - Ruben J Cauchi
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of MaltaMsida, Malta.,Center for Molecular Medicine and Biobanking, University of MaltaMsida, Malta
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16
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Yip BH, Steeples V, Repapi E, Armstrong RN, Llorian M, Roy S, Shaw J, Dolatshad H, Taylor S, Verma A, Bartenstein M, Vyas P, Cross NC, Malcovati L, Cazzola M, Hellström-Lindberg E, Ogawa S, Smith CW, Pellagatti A, Boultwood J. The U2AF1S34F mutation induces lineage-specific splicing alterations in myelodysplastic syndromes. J Clin Invest 2017; 127:2206-2221. [PMID: 28436936 PMCID: PMC5451246 DOI: 10.1172/jci91363] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/21/2017] [Indexed: 12/23/2022] Open
Abstract
Mutations of the splicing factor–encoding gene U2AF1 are frequent in the myelodysplastic syndromes (MDS), a myeloid malignancy, and other cancers. Patients with MDS suffer from peripheral blood cytopenias, including anemia, and an increasing percentage of bone marrow myeloblasts. We studied the impact of the common U2AF1S34F mutation on cellular function and mRNA splicing in the main cell lineages affected in MDS. We demonstrated that U2AF1S34F expression in human hematopoietic progenitors impairs erythroid differentiation and skews granulomonocytic differentiation toward granulocytes. RNA sequencing of erythroid and granulomonocytic colonies revealed that U2AF1S34F induced a higher number of cassette exon splicing events in granulomonocytic cells than in erythroid cells. U2AF1S34F altered mRNA splicing of many transcripts that were expressed in both cell types in a lineage-specific manner. In hematopoietic progenitors, the introduction of isoform changes identified in the U2AF1S34F target genes H2AFY, encoding an H2A histone variant, and STRAP, encoding serine/threonine kinase receptor–associated protein, recapitulated phenotypes associated with U2AF1S34F expression in erythroid and granulomonocytic cells, suggesting a causal link. Furthermore, we showed that isoform modulation of H2AFY and STRAP rescues the erythroid differentiation defect in U2AF1S34F MDS cells, suggesting that splicing modulators could be used therapeutically. These data have critical implications for understanding MDS phenotypic heterogeneity and support the development of therapies targeting splicing abnormalities.
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Affiliation(s)
- Bon Ham Yip
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Violetta Steeples
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Emmanouela Repapi
- The Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Richard N Armstrong
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Miriam Llorian
- Department of Biochemistry, Downing Site, University of Cambridge, Cambridge, United Kingdom
| | - Swagata Roy
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Jacqueline Shaw
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Hamid Dolatshad
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Stephen Taylor
- The Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Amit Verma
- Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Paresh Vyas
- Medical Research Council, Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, and Department of Hematology, Oxford University Hospital National Health Service Trust, Oxford, United Kingdom
| | - Nicholas Cp Cross
- Faculty of Medicine, University of Southampton, Southampton, and National Genetics Reference Laboratory (Wessex), Salisbury, United Kingdom
| | - Luca Malcovati
- Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Mario Cazzola
- Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Eva Hellström-Lindberg
- Center for Hematology and Regenerative Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Christopher Wj Smith
- Department of Biochemistry, Downing Site, University of Cambridge, Cambridge, United Kingdom
| | - Andrea Pellagatti
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
| | - Jacqueline Boultwood
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and BRC Blood Theme, National Institute for Health Research (NIHR) Oxford Biomedical Centre, Oxford University Hospital, Oxford, United Kingdom
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17
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Kamenska A, Simpson C, Vindry C, Broomhead H, Bénard M, Ernoult-Lange M, Lee BP, Harries LW, Weil D, Standart N. The DDX6-4E-T interaction mediates translational repression and P-body assembly. Nucleic Acids Res 2016; 44:6318-34. [PMID: 27342281 PMCID: PMC5291280 DOI: 10.1093/nar/gkw565] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/10/2016] [Accepted: 06/14/2016] [Indexed: 12/13/2022] Open
Abstract
4E-Transporter binds eIF4E via its consensus sequence YXXXXLΦ, shared with eIF4G, and is a nucleocytoplasmic shuttling protein found enriched in P-(rocessing) bodies. 4E-T inhibits general protein synthesis by reducing available eIF4E levels. Recently, we showed that 4E-T bound to mRNA however represses its translation in an eIF4E-independent manner, and contributes to silencing of mRNAs targeted by miRNAs. Here, we address further the mechanism of translational repression by 4E-T by first identifying and delineating the interacting sites of its major partners by mass spectrometry and western blotting, including DDX6, UNR, unrip, PAT1B, LSM14A and CNOT4. Furthermore, we document novel binding between 4E-T partners including UNR-CNOT4 and unrip-LSM14A, altogether suggesting 4E-T nucleates a complex network of RNA-binding protein interactions. In functional assays, we demonstrate that joint deletion of two short conserved motifs that bind UNR and DDX6 relieves repression of 4E-T-bound mRNA, in part reliant on the 4E-T-DDX6-CNOT1 axis. We also show that the DDX6-4E-T interaction mediates miRNA-dependent translational repression and de novo P-body assembly, implying that translational repression and formation of new P-bodies are coupled processes. Altogether these findings considerably extend our understanding of the role of 4E-T in gene regulation, important in development and neurogenesis.
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Affiliation(s)
- Anastasiia Kamenska
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK
| | - Clare Simpson
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK
| | - Caroline Vindry
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK
| | - Helen Broomhead
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK
| | - Marianne Bénard
- Sorbonne Universités, UPMC, CNRS, IBPS, Developmental Biology Laboratory, 75005 Paris, France
| | - Michèle Ernoult-Lange
- Sorbonne Universités, UPMC, CNRS, IBPS, Developmental Biology Laboratory, 75005 Paris, France
| | - Benjamin P Lee
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter EX2 5DW
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter EX2 5DW
| | - Dominique Weil
- Sorbonne Universités, UPMC, CNRS, IBPS, Developmental Biology Laboratory, 75005 Paris, France
| | - Nancy Standart
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK
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18
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Borg RM, Fenech Salerno B, Vassallo N, Bordonne R, Cauchi RJ. Disruption of snRNP biogenesis factors Tgs1 and pICln induces phenotypes that mirror aspects of SMN-Gemins complex perturbation in Drosophila, providing new insights into spinal muscular atrophy. Neurobiol Dis 2016; 94:245-58. [PMID: 27388936 DOI: 10.1016/j.nbd.2016.06.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 06/20/2016] [Accepted: 06/27/2016] [Indexed: 01/27/2023] Open
Abstract
The neuromuscular disorder, spinal muscular atrophy (SMA), results from insufficient levels of the survival motor neuron (SMN) protein. Together with Gemins 2-8 and Unrip, SMN forms the large macromolecular SMN-Gemins complex, which is known to be indispensable for chaperoning the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). It remains unclear whether disruption of this function is responsible for the selective neuromuscular degeneration in SMA. In the present study, we first show that loss of wmd, the Drosophila Unrip orthologue, has a negative impact on the motor system. However, due to lack of a functional relationship between wmd/Unrip and Gemin3, it is likely that Unrip joined the SMN-Gemins complex only recently in evolution. Second, we uncover that disruption of either Tgs1 or pICln, two cardinal players in snRNP biogenesis, results in viability and motor phenotypes that closely resemble those previously uncovered on loss of the constituent members of the SMN-Gemins complex. Interestingly, overexpression of both factors leads to motor dysfunction in Drosophila, a situation analogous to that of Gemin2. Toxicity is conserved in the yeast S. pombe where pICln overexpression induces a surplus of Sm proteins in the cytoplasm, indicating that a block in snRNP biogenesis is partly responsible for this phenotype. Importantly, we show a strong functional relationship and a physical interaction between Gemin3 and either Tgs1 or pICln. We propose that snRNP biogenesis is the pathway connecting the SMN-Gemins complex to a functional neuromuscular system, and its disturbance most likely leads to the motor dysfunction that is typical in SMA.
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Affiliation(s)
- Rebecca M Borg
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta; Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta; Institut de Génétique Moléculaire de Montpellier, CNRS-UMR5535, Université Montpellier 1 and 2, Montpellier, France
| | - Benji Fenech Salerno
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta; Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta
| | - Neville Vassallo
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta; Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta
| | - Rémy Bordonne
- Institut de Génétique Moléculaire de Montpellier, CNRS-UMR5535, Université Montpellier 1 and 2, Montpellier, France
| | - Ruben J Cauchi
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta; Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta.
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19
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Burns JK, Kothary R, Parks RJ. Opening the window: The case for carrier and perinatal screening for spinal muscular atrophy. Neuromuscul Disord 2016; 26:551-9. [PMID: 27460292 DOI: 10.1016/j.nmd.2016.06.459] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 11/26/2022]
Abstract
Spinal muscular atrophy (SMA) is the most common genetically inherited neurodegenerative disease that leads to infant mortality worldwide. SMA is caused by genetic deletion or mutation in the survival of motor neuron 1 (SMN1) gene, which results in a deficiency in SMN protein. For reasons that are still unclear, SMN protein deficiency predominantly affects α-motor neurons, resulting in their degeneration and subsequent paralysis of limb and trunk muscles, progressing to death in severe cases. Emerging evidence suggests that SMN protein deficiency also affects the heart, autonomic nervous system, skeletal muscle, liver, pancreas and perhaps many other organs. Currently, there is no cure for SMA. Patient treatment includes respiratory care, physiotherapy, and nutritional management, which can somewhat ameliorate disease symptoms and increase life span. Fortunately, several novel therapies have advanced to human clinical trials. However, data from studies in animal models of SMA indicate that the greatest therapeutic benefit is achieved through initiating treatment as early as possible, before widespread loss of motor neurons has occurred. In this review, we discuss the merit of carrier and perinatal patient screening for SMA considering the efficacy of emerging therapeutics and the physical, emotional and financial burden of the disease on affected families and society.
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Affiliation(s)
- Joseph K Burns
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Canada; Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Canada; University of Ottawa Centre for Neuromuscular Disease, Ottawa, Canada
| | - Rashmi Kothary
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Canada; University of Ottawa Centre for Neuromuscular Disease, Ottawa, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada; Department of Medicine, University of Ottawa, Ottawa, Canada
| | - Robin J Parks
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Canada; Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Canada; University of Ottawa Centre for Neuromuscular Disease, Ottawa, Canada; Department of Medicine, University of Ottawa, Ottawa, Canada.
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20
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Donlin-Asp PG, Bassell GJ, Rossoll W. A role for the survival of motor neuron protein in mRNP assembly and transport. Curr Opin Neurobiol 2016; 39:53-61. [PMID: 27131421 DOI: 10.1016/j.conb.2016.04.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/27/2016] [Accepted: 04/13/2016] [Indexed: 02/08/2023]
Abstract
Localization and local translation of mRNA plays a key role in neuronal development and function. While studies in various systems have provided insights into molecular mechanisms of mRNA transport and local protein synthesis, the factors that control the assembly of mRNAs and mRNA binding proteins into messenger ribonucleoprotein (mRNP) transport granules remain largely unknown. In this review we will discuss how insights on a motor neuron disease, spinal muscular atrophy (SMA), is advancing our understanding of regulated assembly of transport competent mRNPs and how defects in their assembly and delivery may contribute to the degeneration of motor neurons observed in SMA and other neurological disorders.
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Affiliation(s)
- Paul G Donlin-Asp
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
| | - Wilfried Rossoll
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA.
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21
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Stoehr A, Yang Y, Patel S, Evangelista AM, Aponte A, Wang G, Liu P, Boylston J, Kloner PH, Lin Y, Gucek M, Zhu J, Murphy E. Prolyl hydroxylation regulates protein degradation, synthesis, and splicing in human induced pluripotent stem cell-derived cardiomyocytes. Cardiovasc Res 2016; 110:346-58. [PMID: 27095734 DOI: 10.1093/cvr/cvw081] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/12/2016] [Indexed: 12/12/2022] Open
Abstract
AIMS Protein hydroxylases are oxygen- and α-ketoglutarate-dependent enzymes that catalyse hydroxylation of amino acids such as proline, thus linking oxygen and metabolism to enzymatic activity. Prolyl hydroxylation is a dynamic post-translational modification that regulates protein stability and protein-protein interactions; however, the extent of this modification is largely uncharacterized. The goals of this study are to investigate the biological consequences of prolyl hydroxylation and to identify new targets that undergo prolyl hydroxylation in human cardiomyocytes. METHODS AND RESULTS We used human induced pluripotent stem cell-derived cardiomyocytes in combination with pulse-chase amino acid labelling and proteomics to analyse the effects of prolyl hydroxylation on protein degradation and synthesis. We identified 167 proteins that exhibit differences in degradation with inhibition of prolyl hydroxylation by dimethyloxalylglycine (DMOG); 164 were stabilized. Proteins involved in RNA splicing such as serine/arginine-rich splicing factor 2 (SRSF2) and splicing factor and proline- and glutamine-rich (SFPQ) were stabilized with DMOG. DMOG also decreased protein translation of cytoskeletal and sarcomeric proteins such as α-cardiac actin. We searched the mass spectrometry data for proline hydroxylation and identified 134 high confidence peptides mapping to 78 unique proteins. We identified SRSF2, SFPQ, α-cardiac actin, and cardiac titin as prolyl hydroxylated. We identified 29 prolyl hydroxylated proteins that showed a significant difference in either protein degradation or synthesis. Additionally, we performed next-generation RNA sequencing and showed that the observed decrease in protein synthesis was not due to changes in mRNA levels. Because RNA splicing factors were prolyl hydroxylated, we investigated splicing ± inhibition of prolyl hydroxylation and detected 369 alternative splicing events, with a preponderance of exon skipping. CONCLUSIONS This study provides the first extensive characterization of the cardiac prolyl hydroxylome and demonstrates that inhibition of α-ketoglutarate hydroxylases alters protein stability, translation, and splicing.
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Affiliation(s)
- Andrea Stoehr
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yanqin Yang
- DNA Sequencing and Genomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sajni Patel
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alicia M Evangelista
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Angel Aponte
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Guanghui Wang
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Poching Liu
- DNA Sequencing and Genomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer Boylston
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Philip H Kloner
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yongshun Lin
- iPS Cell Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marjan Gucek
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jun Zhu
- DNA Sequencing and Genomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth Murphy
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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22
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Young PA, Leonard S, Martin DSD, Findlay JBC. Analysis of the effect of a novel therapeutic for type 2 diabetes on the proteome of a muscle cell line. Proteomics 2015; 16:70-9. [PMID: 26573124 DOI: 10.1002/pmic.201500050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 09/05/2015] [Accepted: 11/11/2015] [Indexed: 01/18/2023]
Abstract
Elevated serum retinol-binding protein (RBP) concentration has been implicated in the development of insulin resistance and type 2 diabetes. Two series of small molecules have been designed to lower serum levels by reducing secretion of the transthyretin-RBP complex from the liver and enhancing RBP clearance through the kidney. These small molecules were seen to improve glucose and insulin tolerance tests and to reduce body weight gain in mice rendered diabetic through a high fat diet. A proteomics study was conducted to better understand the effects of these compounds in muscle cells, muscle being the primary site for energy expenditure. One lead compound, RTC-15, is seen to have a significant effect on proteins involved in fat and glucose metabolism. This could indicate that the compound is having a direct effect on muscle tissue to improve energy homeostasis as well as a whole body effect on circulating RBP levels. This newly characterized group of antidiabetic compounds may prove useful in the treatment and prevention of insulin resistance and obesity.
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Affiliation(s)
- Pamela A Young
- Marie Curie Laboratory for Membrane Proteins, Department of Biology, Maynooth University, Maynooth, Ireland
| | - Siobhán Leonard
- Marie Curie Laboratory for Membrane Proteins, Department of Biology, Maynooth University, Maynooth, Ireland
| | - Darren S D Martin
- Marie Curie Laboratory for Membrane Proteins, Department of Biology, Maynooth University, Maynooth, Ireland
| | - John B C Findlay
- Marie Curie Laboratory for Membrane Proteins, Department of Biology, Maynooth University, Maynooth, Ireland
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23
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Bizarro J, Dodré M, Huttin A, Charpentier B, Schlotter F, Branlant C, Verheggen C, Massenet S, Bertrand E. NUFIP and the HSP90/R2TP chaperone bind the SMN complex and facilitate assembly of U4-specific proteins. Nucleic Acids Res 2015; 43:8973-89. [PMID: 26275778 PMCID: PMC4605303 DOI: 10.1093/nar/gkv809] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/27/2015] [Indexed: 12/17/2022] Open
Abstract
The Sm proteins are loaded on snRNAs by the SMN complex, but how snRNP-specific proteins are assembled remains poorly characterized. U4 snRNP and box C/D snoRNPs have structural similarities. They both contain the 15.5K and proteins with NOP domains (PRP31 for U4, NOP56/58 for snoRNPs). Biogenesis of box C/D snoRNPs involves NUFIP and the HSP90/R2TP chaperone system and here, we explore the function of this machinery in U4 RNP assembly. We show that yeast Prp31 interacts with several components of the NUFIP/R2TP machinery, and that these interactions are separable from each other. In human cells, PRP31 mutants that fail to stably associate with U4 snRNA still interact with components of the NUFIP/R2TP system, indicating that these interactions precede binding of PRP31 to U4 snRNA. Knock-down of NUFIP leads to mislocalization of PRP31 and decreased association with U4. Moreover, NUFIP is associated with the SMN complex through direct interactions with Gemin3 and Gemin6. Altogether, our data suggest a model in which the NUFIP/R2TP system is connected with the SMN complex and facilitates assembly of U4 snRNP-specific proteins.
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Affiliation(s)
- Jonathan Bizarro
- Equipe labélisée Ligue contre le Cancer, Institut de Génétique Moléculaire de Montpellier, IGMM-UMR 5535 du CNRS-Université de Montpellier, 1919, route de Mende, 34293 Montpellier Cedex 5, France
| | - Maxime Dodré
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Alexandra Huttin
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Bruno Charpentier
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Florence Schlotter
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Christiane Branlant
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Céline Verheggen
- Equipe labélisée Ligue contre le Cancer, Institut de Génétique Moléculaire de Montpellier, IGMM-UMR 5535 du CNRS-Université de Montpellier, 1919, route de Mende, 34293 Montpellier Cedex 5, France
| | - Séverine Massenet
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Edouard Bertrand
- Equipe labélisée Ligue contre le Cancer, Institut de Génétique Moléculaire de Montpellier, IGMM-UMR 5535 du CNRS-Université de Montpellier, 1919, route de Mende, 34293 Montpellier Cedex 5, France
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24
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Targeting the eIF4A RNA helicase as an anti-neoplastic approach. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:781-91. [DOI: 10.1016/j.bbagrm.2014.09.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 09/03/2014] [Indexed: 01/22/2023]
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25
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Neuenkirchen N, Englbrecht C, Ohmer J, Ziegenhals T, Chari A, Fischer U. Reconstitution of the human U snRNP assembly machinery reveals stepwise Sm protein organization. EMBO J 2015; 34:1925-41. [PMID: 26069323 DOI: 10.15252/embj.201490350] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 05/12/2015] [Indexed: 11/09/2022] Open
Abstract
The assembly of spliceosomal U snRNPs depends on the coordinated action of PRMT5 and SMN complexes in vivo. These trans-acting factors enable the faithful delivery of seven Sm proteins onto snRNA and the formation of the common core of snRNPs. To gain mechanistic insight into their mode of action, we reconstituted the assembly machinery from recombinant sources. We uncover a stepwise and ordered formation of distinct Sm protein complexes on the PRMT5 complex, which is facilitated by the assembly chaperone pICln. Upon completion, the formed pICln-Sm units are displaced by new pICln-Sm protein substrates and transferred onto the SMN complex. The latter acts as a Brownian machine that couples spontaneous conformational changes driven by thermal energy to prevent mis-assembly and to ensure the transfer of Sm proteins to cognate RNA. Investigation of mutant SMN complexes provided insight into the contribution of individual proteins to these activities. The biochemical reconstitution presented here provides a basis for a detailed molecular dissection of the U snRNP assembly reaction.
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Affiliation(s)
- Nils Neuenkirchen
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
| | - Clemens Englbrecht
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jürgen Ohmer
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
| | - Thomas Ziegenhals
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
| | - Ashwin Chari
- Research Group of 3D Electron Cryomicroscopy, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Utz Fischer
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany Department of Radiation Medicine and Applied Sciences, University of California, San Diego, San Diego, CA, USA
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26
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Piñeiro D, Fernandez-Chamorro J, Francisco-Velilla R, Martinez-Salas E. Gemin5: A Multitasking RNA-Binding Protein Involved in Translation Control. Biomolecules 2015; 5:528-44. [PMID: 25898402 PMCID: PMC4496684 DOI: 10.3390/biom5020528] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 04/01/2015] [Accepted: 04/09/2015] [Indexed: 12/31/2022] Open
Abstract
Gemin5 is a RNA-binding protein (RBP) that was first identified as a peripheral component of the survival of motor neurons (SMN) complex. This predominantly cytoplasmic protein recognises the small nuclear RNAs (snRNAs) through its WD repeat domains, allowing assembly of the SMN complex into small nuclear ribonucleoproteins (snRNPs). Additionally, the amino-terminal end of the protein has been reported to possess cap-binding capacity and to interact with the eukaryotic initiation factor 4E (eIF4E). Gemin5 was also shown to downregulate translation, to be a substrate of the picornavirus L protease and to interact with viral internal ribosome entry site (IRES) elements via a bipartite non-canonical RNA-binding site located at its carboxy-terminal end. These features link Gemin5 with translation control events. Thus, beyond its role in snRNPs biogenesis, Gemin5 appears to be a multitasking protein cooperating in various RNA-guided processes. In this review, we will summarise current knowledge of Gemin5 functions. We will discuss the involvement of the protein on translation control and propose a model to explain how the proteolysis fragments of this RBP in picornavirus-infected cells could modulate protein synthesis.
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Affiliation(s)
- David Piñeiro
- Medical Research Council Toxicology Unit, Lancaster Rd, Leicester LE1 9HN, UK.
| | - Javier Fernandez-Chamorro
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Nicolas Cabrera 1, Madrid 28049, Spain.
| | - Rosario Francisco-Velilla
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Nicolas Cabrera 1, Madrid 28049, Spain.
| | - Encarna Martinez-Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Nicolas Cabrera 1, Madrid 28049, Spain.
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27
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Chen YC, Chang JG, Jong YJ, Liu TY, Yuo CY. High expression level of Tra2-β1 is responsible for increased SMN2 exon 7 inclusion in the testis of SMA mice. PLoS One 2015; 10:e0120721. [PMID: 25781985 PMCID: PMC4363149 DOI: 10.1371/journal.pone.0120721] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 01/26/2015] [Indexed: 01/06/2023] Open
Abstract
Spinal muscular atrophy (SMA) is an inherited neuromuscular disease caused by deletion or mutation of SMN1 gene. All SMA patients carry a nearly identical SMN2 gene, which produces low level of SMN protein due to mRNA exon 7 exclusion. Previously, we found that the testis of SMA mice (smn−/− SMN2) expresses high level of SMN2 full-length mRNA, indicating a testis-specific mechanism for SMN2 exon 7 inclusion. To elucidate the underlying mechanism, we established primary cultures of testis cells from SMA mice and analyzed them for SMN2 exon 7 splicing. We found that primary testis cells after a 2-hour culture still expressed high level of SMN2 full-length mRNA, but the level decreased after longer cultures. We then compared the protein levels of relevant splicing factors, and found that the level of Tra2-β1 also decreased during testis cell culture, correlated with SMN2 full-length mRNA downregulation. In addition, the testis of SMA mice expressed the highest level of Tra2-β1 among the many tissues examined. Furthermore, overexpression of Tra2-β1, but not ASF/SF2, increased SMN2 minigene exon 7 inclusion in primary testis cells and spinal cord neurons, whereas knockdown of Tra2-β1 decreased SMN2 exon 7 inclusion in primary testis cells of SMA mice. Therefore, our results indicate that high expression level of Tra2-β1 is responsible for increased SMN2 exon 7 inclusion in the testis of SMA mice. This study also suggests that the expression level of Tra2-β1 may be a modifying factor of SMA disease and a potential target for SMA treatment.
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Affiliation(s)
- Yu-Chia Chen
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jan-Gowth Chang
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Yuh-Jyh Jong
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Departments of Pediatrics and Clinical Laboratory, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Ting-Yuan Liu
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chung-Yee Yuo
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
- * E-mail:
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28
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Presynaptic localization of Smn and hnRNP R in axon terminals of embryonic and postnatal mouse motoneurons. PLoS One 2014; 9:e110846. [PMID: 25338097 PMCID: PMC4206449 DOI: 10.1371/journal.pone.0110846] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 09/23/2014] [Indexed: 11/19/2022] Open
Abstract
Spinal muscular atrophy (SMA) is caused by deficiency of the ubiquitously expressed survival motoneuron (SMN) protein. SMN is crucial component of a complex for the assembly of spliceosomal small nuclear ribonucleoprotein (snRNP) particles. Other cellular functions of SMN are less characterized so far. SMA predominantly affects lower motoneurons, but the cellular basis for this relative specificity is still unknown. In contrast to nonneuronal cells where the protein is mainly localized in perinuclear regions and the nucleus, Smn is also present in dendrites, axons and axonal growth cones of isolated motoneurons invitro. However, this distribution has not been shown invivo and it is not clear whether Smn and hnRNP R are also present in presynaptic axon terminals of motoneurons in postnatal mice. Smn also associates with components not included in the classical SMN complex like RNA-binding proteins FUS, TDP43, HuD and hnRNP R which are involved in RNA processing, subcellular localization and translation. We show here that Smn and hnRNP R are present in presynaptic compartments at neuromuscular endplates of embryonic and postnatal mice. Smn and hnRNP R are localized in close proximity to each other in axons and axon terminals both invitro and invivo. We also provide new evidence for a direct interaction of Smn and hnRNP R invitro and invivo, particularly in the cytosol of motoneurons. These data point to functions of SMN beyond snRNP assembly which could be crucial for recruitment and transport of RNA particles into axons and axon terminals, a mechanism which may contribute to SMA pathogenesis.
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29
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Stejskalová E, Staněk D. The splicing factor U1-70K interacts with the SMN complex and is required for nuclear gem integrity. J Cell Sci 2014; 127:3909-15. [PMID: 25052091 DOI: 10.1242/jcs.155838] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The nuclear SMN complex localizes to specific structures called nuclear gems. The loss of gems is a cellular marker for several neurodegenerative diseases. Here, we identify that the U1-snRNP-specific protein U1-70K localizes to nuclear gems, and we show that U1-70K is necessary for gem integrity. Furthermore, we show that the interaction between U1-70K and the SMN complex is RNA independent, and we map the SMN complex binding site to the unstructured N-terminal tail of U1-70K. Consistent with these results, the expression of the U1-70K N-terminal tail rescues gem formation. These findings show that U1-70K is an SMN-complex-associating protein, and they suggest a new function for U1-70K in the formation of nuclear gems.
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Affiliation(s)
- Eva Stejskalová
- Department of RNA Biology, Institute of Molecular Genetics AS CR, 142 20 Prague, Czech Republic Faculty of Science, Charles University in Prague, 128 43 Prague, Czech Republic
| | - David Staněk
- Department of RNA Biology, Institute of Molecular Genetics AS CR, 142 20 Prague, Czech Republic
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30
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Flury V, Restuccia U, Bachi A, Mühlemann O. Characterization of phosphorylation- and RNA-dependent UPF1 interactors by quantitative proteomics. J Proteome Res 2014; 13:3038-53. [PMID: 24762188 DOI: 10.1021/pr5002143] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human up-frameshift 1 (UPF1) is an ATP-dependent RNA helicase and phosphoprotein implicated in several biological processes but is best known for its key function in nonsense-mediated mRNA decay (NMD). Here we employed a combination of stable isotope labeling of amino acids in cell culture experiments to determine by quantitative proteomics UPF1 interactors. We used this approach to distinguish between RNA-mediated and protein-mediated UPF1 interactors and to determine proteins that preferentially bind the hypo- or the hyper-phosphorylated form of UPF1. Confirming and expanding previous studies, we identified the eukaryotic initiation factor 3 (eIF3) as a prominent protein-mediated interactor of UPF1. However, unlike previously reported, eIF3 binds to UPF1 independently of UPF1's phosphorylation state. Furthermore, our data revealed many nucleus-associated RNA-binding proteins that preferentially associate with hyper-phosphorylated UPF1 in an RNase-sensitive manner, suggesting that UPF1 gets recruited to mRNA and becomes phosphorylated before being exported to the cytoplasm as part of the mRNP.
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Affiliation(s)
- Valentin Flury
- Department of Chemistry and Biochemistry, University of Bern , Freiestr. 3, Bern 3012, Switzerland
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31
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Cauchi RJ. Gem depletion: amyotrophic lateral sclerosis and spinal muscular atrophy crossover. CNS Neurosci Ther 2014; 20:574-81. [PMID: 24645792 DOI: 10.1111/cns.12242] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 01/25/2014] [Accepted: 01/27/2014] [Indexed: 12/22/2022] Open
Abstract
The determining factor of spinal muscular atrophy (SMA), the most common motor neuron degenerative disease of childhood, is the survival motor neuron (SMN) protein. SMN and its Gemin associates form a complex that is indispensible for the biogenesis of small nuclear ribonucleoproteins (snRNPs), which constitute the building blocks of spliceosomes. It is as yet unclear whether a decreased capacity of SMN in snRNP assembly, and, hence, transcriptome abnormalities, account for the specific neuromuscular phenotype in SMA. Across metazoa, the SMN-Gemins complex concentrates in multiple nuclear gems that frequently neighbour or overlap Cajal bodies. The number of gems has long been known to be a faithful indicator of SMN levels, which are linked to SMA severity. Intriguingly, a flurry of recent studies have revealed that depletion of this nuclear structure is also a signature feature of amyotrophic lateral sclerosis (ALS), the most common adult-onset motor neuron disease. This review discusses such a surprising crossover in addition to highlighting the most recent work on the intricate world of spliceosome building, which seems to be at the heart of motor neuron physiology and survival.
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Affiliation(s)
- Ruben J Cauchi
- Department of Physiology and Biochemistry, University of Malta, Msida 2080, Malta
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32
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The Gemin associates of survival motor neuron are required for motor function in Drosophila. PLoS One 2013; 8:e83878. [PMID: 24391840 PMCID: PMC3877121 DOI: 10.1371/journal.pone.0083878] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 11/09/2013] [Indexed: 12/13/2022] Open
Abstract
Membership of the survival motor neuron (SMN) complex extends to nine factors, including the SMN protein, the product of the spinal muscular atrophy (SMA) disease gene, Gemins 2-8 and Unrip. The best-characterised function of this macromolecular machine is the assembly of the Sm-class of uridine-rich small nuclear ribonucleoprotein (snRNP) particles and each SMN complex member has a key role during this process. So far, however, only little is known about the function of the individual Gemin components in vivo. Here, we make use of the Drosophila model organism to uncover loss-of-function phenotypes of Gemin2, Gemin3 and Gemin5, which together with SMN form the minimalistic fly SMN complex. We show that ectopic overexpression of the dead helicase Gem3(ΔN) mutant or knockdown of Gemin3 result in similar motor phenotypes, when restricted to muscle, and in combination cause lethality, hence suggesting that Gem3(ΔN) overexpression mimics a loss-of-function. Based on the localisation pattern of Gem3(ΔN), we predict that the nucleus is the primary site of the antimorphic or dominant-negative mechanism of Gem3(ΔN)-mediated interference. Interestingly, phenotypes induced by human SMN overexpression in Drosophila exhibit similarities to those induced by overexpression of Gem3(ΔN). Through enhanced knockdown we also uncover a requirement of Gemin2, Gemin3 and Gemin5 for viability and motor behaviour, including locomotion as well as flight, in muscle. Notably, in the case of Gemin3 and Gemin5, such function also depends on adequate levels of the respective protein in neurons. Overall, these findings lead us to speculate that absence of any one member is sufficient to arrest the SMN-Gemins complex function in a nucleocentric pathway, which is critical for motor function in vivo.
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Low WK, Li J, Zhu M, Kommaraju SS, Shah-Mittal J, Hull K, Liu JO, Romo D. Second-generation derivatives of the eukaryotic translation initiation inhibitor pateamine A targeting eIF4A as potential anticancer agents. Bioorg Med Chem 2013; 22:116-25. [PMID: 24359706 DOI: 10.1016/j.bmc.2013.11.046] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/15/2013] [Accepted: 11/23/2013] [Indexed: 02/06/2023]
Abstract
A series of pateamine A (1) derivatives were synthesized for structure/activity relationship (SAR) studies and a selection of previous generation analogs were re-evaluated based on current information regarding the mechanism of action of these translation inhibitors. Structural modifications in the new generation of derivatives focused on alterations to the C19-C22 Z,E-diene and the trienyl side chain of the previously described simplified, des-methyl, des-amino pateamine A (DMDAPatA, 2). Derivatives were tested for anti-proliferative activity in cell culture and for inhibition of mammalian cap-dependent translation in vitro. Activity was highly dependent on the rigidity and conformation of the macrolide and the functionality of the side chain. The only well tolerated substitutions were replacement of the N,N-dimethyl amino group found on the side chain of 2 with other tertiary amine groups. SAR reported here suggests that this site may be modified in future studies to improve serum stability, cell-type specificity, and/or specificity towards rapidly proliferating cells.
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Affiliation(s)
- Woon-Kai Low
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA.
| | - Jing Li
- Natural Product LINCHPIN Laboratory, Department of Chemistry, Texas A&M University, P.O. Box 300012, College Station, TX 77842-3012, USA
| | - Mingzhao Zhu
- Natural Product LINCHPIN Laboratory, Department of Chemistry, Texas A&M University, P.O. Box 300012, College Station, TX 77842-3012, USA
| | - Sai Shilpa Kommaraju
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Janki Shah-Mittal
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Ken Hull
- Natural Product LINCHPIN Laboratory, Department of Chemistry, Texas A&M University, P.O. Box 300012, College Station, TX 77842-3012, USA
| | - Jun O Liu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, 725 North Wolfe St., Baltimore, MD 21205, USA
| | - Daniel Romo
- Natural Product LINCHPIN Laboratory, Department of Chemistry, Texas A&M University, P.O. Box 300012, College Station, TX 77842-3012, USA; Department of Chemistry, Texas A&M University, P.O. Box 300012, College Station, TX 77842-3012, USA.
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Vukmirovic M, Manojlovic Z, Stefanovic B. Serine-threonine kinase receptor-associated protein (STRAP) regulates translation of type I collagen mRNAs. Mol Cell Biol 2013; 33:3893-906. [PMID: 23918805 PMCID: PMC3811873 DOI: 10.1128/mcb.00195-13] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 07/08/2013] [Indexed: 11/20/2022] Open
Abstract
Type I collagen is the most abundant protein in the human body and is composed of two α1(I) and one α2(I) polypeptides which assemble into a triple helix. For the proper assembly of the collagen triple helix, the individual polypeptides must be translated in coordination. Here, we show that serine-threonine kinase receptor-associated protein (STRAP) is tethered to collagen mRNAs by interaction with LARP6. LARP6 is a protein which directly binds the 5' stem-loop (5'SL) present in collagen α1(I) and α2(I) mRNAs, but it interacts with STRAP with its C-terminal domain, which is not involved in binding 5'SL. Being tethered to collagen mRNAs, STRAP prevents unrestricted translation, primarily that of collagen α2(I) mRNAs, by interacting with eukaryotic translation initiation factor 4A (eIF4A). In the absence of STRAP, more collagen α2(I) mRNA can be pulled down with eIF4A, and collagen α2(I) mRNA is unrestrictedly loaded onto the polysomes. This results in an imbalance of synthesis of α1(I) and α2(I) polypeptides, in hypermodifications of α1(I) polypeptide, and in inefficient assembly of the polypeptides into a collagen trimer and their secretion as monomers. These defects can be partially restored by supplementing STRAP. Thus, we discovered STRAP as a novel regulator of the coordinated translation of collagen mRNAs.
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Affiliation(s)
- Milica Vukmirovic
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, USA
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Frohn A, Eberl HC, Stöhr J, Glasmacher E, Rüdel S, Heissmeyer V, Mann M, Meister G. Dicer-dependent and -independent Argonaute2 protein interaction networks in mammalian cells. Mol Cell Proteomics 2012; 11:1442-56. [PMID: 22918229 DOI: 10.1074/mcp.m112.017756] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Argonaute (Ago) proteins interact with small regulatory RNAs such as microRNAs (miRNAs) and facilitate gene-silencing processes. miRNAs guide Ago proteins to specific mRNAs leading to translational silencing or mRNA decay. In order to understand the mechanistic details of miRNA function, it is important to characterize Ago protein interactors. Although several proteomic studies have been performed, it is not clear how the Ago interactome changes on miRNA or mRNA binding. Here, we report the analysis of Ago protein interactions in miRNA-containing and miRNA-depleted cells. Using stable isotope labeling in cell culture in conjunction with Dicer knock out mouse embryonic fibroblasts, we identify proteins that interact with Ago2 in the presence or the absence of Dicer. In contrast to our current view, we find that Ago-mRNA interactions can also take place in the absence of miRNAs. Our proteomics approach provides a rich resource for further functional studies on the cellular roles of Ago proteins.
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Affiliation(s)
- Anne Frohn
- Laboratory of RNA Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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36
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Renvoisé B, Quérol G, Verrier ER, Burlet P, Lefebvre S. A role for protein phosphatase PP1γ in SMN complex formation and subnuclear localization to Cajal bodies. J Cell Sci 2012; 125:2862-74. [PMID: 22454514 DOI: 10.1242/jcs.096255] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The spinal muscular atrophy (SMA) gene product SMN forms with gem-associated protein 2-8 (Gemin2-8) and unrip (also known as STRAP) the ubiquitous survival motor neuron (SMN) complex, which is required for the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs), their nuclear import and their localization to subnuclear domain Cajal bodies (CBs). The concentration of the SMN complex and snRNPs in CBs is reduced upon SMN deficiency in SMA cells. Subcellular localization of the SMN complex is regulated in a phosphorylation-dependent manner and the precise mechanisms remain poorly understood. Using co-immunoprecipitation in HeLa cell extracts and in vitro protein binding assays, we show here that the SMN complex and its component Gemin8 interact directly with protein phosphatase PP1γ. Overexpression of Gemin8 in cells increases the number of CBs and results in targeting of PP1γ to CBs. Moreover, depletion of PP1γ by RNA interference enhances the localization of the SMN complex and snRNPs to CBs. Consequently, the interaction between SMN and Gemin8 increases in cytoplasmic and nuclear extracts of PP1γ-depleted cells. Two-dimensional protein gel electrophoresis revealed that SMN is hyperphosphorylated in nuclear extracts of PP1γ-depleted cells and expression of PP1γ restores these isoforms. Notably, SMN deficiency in SMA leads to the aberrant subcellular localization of Gemin8 and PP1γ in the atrophic skeletal muscles, suggesting that the function of PP1γ is likely to be affected in disease. Our findings reveal a role of PP1γ in the formation of the SMN complex and the maintenance of CB integrity. Finally, we propose Gemin8 interaction with PP1γ as a target for therapeutic intervention in SMA.
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Affiliation(s)
- Benoît Renvoisé
- Laboratoire de Biologie Cellulaire des Membranes, Programme de Biologie Cellulaire, Institut Jacques-Monod, UMR 7592 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Hélène Brion, 75205 Paris cedex 13, France
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Fallini C, Bassell GJ, Rossoll W. Spinal muscular atrophy: the role of SMN in axonal mRNA regulation. Brain Res 2012; 1462:81-92. [PMID: 22330725 DOI: 10.1016/j.brainres.2012.01.044] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Accepted: 01/19/2012] [Indexed: 01/15/2023]
Abstract
Spinal muscular atrophy (SMA) is a neurodegenerative disease caused by homozygous mutations or deletions in the survival of motor neuron (SMN1) gene, encoding the ubiquitously expressed SMN protein. SMN associates with different proteins (Gemins 2-8, Unrip) to form a multimeric complex involved in the assembly of small nuclear ribonucleoprotein complexes (snRNPs). Since this activity is essential for the survival of all cell types, it still remains unclear why motor neurons are selectively vulnerable to low levels of SMN protein. Aside from its housekeeping role in the assembly of snRNPs, additional functions of SMN have been proposed. The well-documented localization of SMN in axonal transport granules and its interaction with numerous mRNA-binding proteins not involved in splicing regulation suggest a role in axonal RNA metabolism. This review will focus on the neuropathological and experimental evidence supporting a role for SMN in regulating the assembly, localization, or stability of axonal messenger ribonucleoprotein complexes (mRNPs). Furthermore, how defects in this non-canonical SMN function may contribute to the motor neuron pathology observed in SMA will be discussed. This article is part of a Special Issue entitled RNA-Binding Proteins.
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Affiliation(s)
- Claudia Fallini
- Department of Cell Biology, School of Medicine, Emory University School of Medicine, Atlanta 30322, USA
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Zhang R, So BR, Li P, Yong J, Glisovic T, Wan L, Dreyfuss G. Structure of a key intermediate of the SMN complex reveals Gemin2's crucial function in snRNP assembly. Cell 2011; 146:384-95. [PMID: 21816274 PMCID: PMC3160754 DOI: 10.1016/j.cell.2011.06.043] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2011] [Revised: 05/10/2011] [Accepted: 06/27/2011] [Indexed: 01/10/2023]
Abstract
The SMN complex mediates the assembly of heptameric Sm protein rings on small nuclear RNAs (snRNAs), which are essential for snRNP function. Specific Sm core assembly depends on Sm proteins and snRNA recognition by SMN/Gemin2- and Gemin5-containing subunits, respectively. The mechanism by which the Sm proteins are gathered while preventing illicit Sm assembly on non-snRNAs is unknown. Here, we describe the 2.5 Å crystal structure of Gemin2 bound to SmD1/D2/F/E/G pentamer and SMN's Gemin2-binding domain, a key assembly intermediate. Remarkably, through its extended conformation, Gemin2 wraps around the crescent-shaped pentamer, interacting with all five Sm proteins, and gripping its bottom and top sides and outer perimeter. Gemin2 reaches into the RNA-binding pocket, preventing RNA binding. Interestingly, SMN-Gemin2 interaction is abrogated by a spinal muscular atrophy (SMA)-causing mutation in an SMN helix that mediates Gemin2 binding. These findings provide insight into SMN complex assembly and specificity, linking snRNP biogenesis and SMA pathogenesis.
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Affiliation(s)
- Rundong Zhang
- Howard Hughes Medical Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6148, USA
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The survival of motor neuron (SMN) protein interacts with the mRNA-binding protein HuD and regulates localization of poly(A) mRNA in primary motor neuron axons. J Neurosci 2011; 31:3914-25. [PMID: 21389246 DOI: 10.1523/jneurosci.3631-10.2011] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Spinal muscular atrophy (SMA) results from reduced levels of the survival of motor neuron (SMN) protein, which has a well characterized function in spliceosomal small nuclear ribonucleoprotein assembly. Currently, it is not understood how deficiency of a housekeeping protein leads to the selective degeneration of spinal cord motor neurons. Numerous studies have shown that SMN is present in neuronal processes and has many interaction partners, including mRNA-binding proteins, suggesting a potential noncanonical role in axonal mRNA metabolism. In this study, we have established a novel technological approach using bimolecular fluorescence complementation (BiFC) and quantitative image analysis to characterize SMN-protein interactions in primary motor neurons. Consistent with biochemical studies on the SMN complex, BiFC analysis revealed that SMN dimerizes and interacts with Gemin2 in nuclear gems and axonal granules. In addition, using pull down assays, immunofluorescence, cell transfection, and BiFC, we characterized a novel interaction between SMN and the neuronal mRNA-binding protein HuD, which was dependent on the Tudor domain of SMN. A missense mutation in the SMN Tudor domain, which is known to cause SMA, impaired the interaction with HuD, but did not affect SMN axonal localization or self-association. Furthermore, time-lapse microscopy revealed SMN cotransport with HuD in live motor neurons. Importantly, SMN knockdown in primary motor neurons resulted in a specific reduction of both HuD protein and poly(A) mRNA levels in the axonal compartment. These findings reveal a noncanonical role for SMN whereby its interaction with mRNA-binding proteins may facilitate the localization of associated poly(A) mRNAs into axons.
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40
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Reiner JE, Datta PK. TGF-beta-dependent and -independent roles of STRAP in cancer. Front Biosci (Landmark Ed) 2011; 16:105-15. [PMID: 21196161 DOI: 10.2741/3678] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The serine-threonine kinase receptor-associated protein (STRAP) was initially identified as a putative inhibitor of the canonical TGF-beta signaling pathway. Because the Smad-dependent TGF-beta pathway negatively regulates cellular growth, early functional studies suggested that STRAP behaves as an oncogene. Indeed, a correlation between STRAP overexpression and various cancers has been identified. With the emergence of new studies on the biological function of STRAP, it is becoming clear that STRAP regulates several distinct cellular processes and modulates multiple signaling pathways. While STRAP itself does not possess enzymatic activity, it appears that STRAP influences biological processes through associations with cellular proteins. In this review, we will describe the TGF-beta-dependent and -independent functions of STRAP and provide a context for the significance of STRAP activity in the development of cancer.
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Affiliation(s)
- Jennifer Elisabeth Reiner
- Cancer Biology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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41
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Guderian G, Peter C, Wiesner J, Sickmann A, Schulze-Osthoff K, Fischer U, Grimmler M. RioK1, a new interactor of protein arginine methyltransferase 5 (PRMT5), competes with pICln for binding and modulates PRMT5 complex composition and substrate specificity. J Biol Chem 2010; 286:1976-86. [PMID: 21081503 DOI: 10.1074/jbc.m110.148486] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein arginine methylation plays a critical role in differential gene expression through modulating protein-protein and protein-DNA/RNA interactions. Although numerous proteins undergo arginine methylation, only limited information is available on how protein arginine methyltransferases (PRMTs) identify their substrates. The human PRMT5 complex consists of PRMT5, WD45/MEP50 (WD repeat domain 45/methylosome protein 50), and pICln and catalyzes the symmetrical arginine dimethylation of its substrate proteins. pICln recruits the spliceosomal Sm proteins to the PRMT5 complex for methylation, which allows their subsequent loading onto snRNA to form small nuclear ribonucleoproteins. To understand how the PRMT5 complex is regulated, we investigated its biochemical composition and identified RioK1 as a novel, stoichiometric component of the PRMT5 complex. We show that RioK1 and pICln bind to PRMT5 in a mutually exclusive fashion. This results in a PRMT5-WD45/MEP50 core structure that either associates with pICln or RioK1 in distinct complexes. Furthermore, we show that RioK1 functions in analogy to pICln as an adapter protein by recruiting the RNA-binding protein nucleolin to the PRMT5 complex for its symmetrical methylation. The exclusive interaction of PRMT5 with either pICln or RioK1 thus provides the first mechanistic insight into how a methyltransferase can distinguish between its substrate proteins.
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Affiliation(s)
- Gernot Guderian
- Department of Biochemistry, Biocenter of the University of Würzburg, D-97074 Würzburg, Germany
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42
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Gemin5 delivers snRNA precursors to the SMN complex for snRNP biogenesis. Mol Cell 2010; 38:551-62. [PMID: 20513430 PMCID: PMC2901871 DOI: 10.1016/j.molcel.2010.03.014] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Revised: 02/16/2010] [Accepted: 03/26/2010] [Indexed: 12/26/2022]
Abstract
The SMN complex assembles Sm cores on snRNAs, a key step in the biogenesis of snRNPs, the spliceosome's major components. Here, using SMN complex inhibitors identified by high-throughput screening and a ribo-proteomic strategy on formaldehyde crosslinked RNPs, we dissected this pathway in cells. We show that protein synthesis inhibition impairs the SMN complex, revealing discrete SMN and Gemin subunits and accumulating an snRNA precursor (pre-snRNA)-Gemin5 intermediate. By high-throughput sequencing of this transient intermediate's RNAs, we discovered the previously undetectable precursors of all the snRNAs and identified their Gemin5-binding sites. We demonstrate that pre-snRNA 3' sequences function to enhance snRNP biogenesis. The SMN complex is also inhibited by oxidation, and we show that it stalls an inventory-complete SMN complex containing pre-snRNAs. We propose a stepwise pathway of SMN complex formation and snRNP biogenesis, highlighting Gemin5's function in delivering pre-snRNAs as substrates for Sm core assembly and processing.
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Kashikar ND, Reiner J, Datta A, Datta PK. Serine threonine receptor-associated protein (STRAP) plays a role in the maintenance of mesenchymal morphology. Cell Signal 2009; 22:138-49. [PMID: 19781628 DOI: 10.1016/j.cellsig.2009.09.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 09/14/2009] [Indexed: 12/20/2022]
Abstract
The stromal tissue, made of extracellular matrix and mesenchymal cells, is vital for the functional design of all complex tissues. Fibroblasts are key components of stromal tissue and play a crucial role during organ development, wound repair, angiogenesis and fibrosis. We have previously reported the identification of a novel WD-domain protein, STRAP(1) that inhibits transforming growth factor-beta (TGF-beta) signaling and enhances tumorigenicity via TGF-beta-dependent and TGF-beta-independent mechanisms. Here, we report, for the first time, that deletion of STRAP from Mouse Embryonic Fibroblasts (MEFs) results in a loss of mesenchymal morphology. These cells lose their spindle shape and exhibit features of an epithelial morphology. Gene expression profiling has confirmed that deletion of STRAP affects expression of sets of genes important for diverse functions including cell-cell adhesion and cell polarization, and upregulates E-cadherin expression leading to the formation of adherens junctions, subsequent localization of beta-catenin to the cell membrane and downregulation of the mesenchymal markers like LEF1 (lymphoid enhancer-binding factor 1). Upregulation of WT1 (Wilms tumor homolog 1) in STRAP null MEFs plays a role in E-cadherin induction. Finally, stable expression of STRAP in these cells results in a loss of WT1 and E-cadherin expressions, and a reversal from epithelial to the mesenchymal morphology. Thus, these results provide a novel TGF-beta-independent function of STRAP and describe a mechanism for the role of STRAP in the maintenance of mesenchymal morphology.
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Affiliation(s)
- Nilesh D Kashikar
- Department of Surgery and Cancer Biology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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45
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Ogawa C, Usui K, Ito F, Itoh M, Hayashizaki Y, Suzuki H. Role of survival motor neuron complex components in small nuclear ribonucleoprotein assembly. J Biol Chem 2009; 284:14609-17. [PMID: 19321448 PMCID: PMC2682908 DOI: 10.1074/jbc.m809031200] [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: 12/01/2008] [Revised: 03/19/2009] [Indexed: 11/06/2022] Open
Abstract
Survival motor neuron (SMN) complex is essential for the biogenesis of the small nuclear ribonucleoprotein (snRNP) complex, although the complete role of each SMN complex component for the snRNP synthesis is largely unclear. We have identified an interaction between the two components Gemin2-Gemin7 using the mammalian two-hybrid system. In vitro stability assay revealed that the known SMN-Gemin7 interaction becomes stable in the presence of Gemin2 possibly via the identified Gemin2-Gemin7 interaction. Gemin7 knockdown revealed a decrease in snRNP assembly activity and a decrease in SmE protein, a component of snRNP, in the SMN complex, which was consistent with a previous discussion that the Gemin6-Gemin7 heterodimer may serve as a surrogate for the SmD3-SmB particle in forming a subcore, the intermediate complex for snRNP. Interestingly, we found that Unrip, but not Gemin8, can remove Gemin7 from the stable SMN-Gemin2-Gemin7 ternary complex. In an in vitro snRNP assembly assay using the Unrip knockdown and the untreated cell lysates, we revealed that there was a decrease in Gemin7 and increase in SmB/B' in the SMN complex observed in untreated cells during the assay, suggesting that the Gemin6-Gemin7 heterodimer in the subcore is exchanged by the SmD3-SmB particle to form snRNP. Surprisingly, these changes were not observed in the assay using the Unrip knockdown cell extracts, indicating the importance of Unrip in the formation of snRNP likely via removal of the Gemin6-Gemin7 from the SMN complex. Taken together, these results indicate that snRNP is synthesized by harmonization of the SMN complex components.
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Affiliation(s)
- Chihiro Ogawa
- RIKEN Omics Sciences Center, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Japan
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46
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Shpargel KB, Praveen K, Rajendra TK, Matera AG. Gemin3 is an essential gene required for larval motor function and pupation in Drosophila. Mol Biol Cell 2008; 20:90-101. [PMID: 18923150 DOI: 10.1091/mbc.e08-01-0024] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The assembly of metazoan Sm-class small nuclear ribonucleoproteins (snRNPs) is an elaborate, step-wise process that takes place in multiple subcellular compartments. The initial steps, including formation of the core RNP, are mediated by the survival motor neuron (SMN) protein complex. Loss-of-function mutations in human SMN1 result in a neuromuscular disease called spinal muscular atrophy. The SMN complex is comprised of SMN and a number of tightly associated proteins, collectively called Gemins. In this report, we identify and characterize the fruitfly ortholog of the DEAD box protein, Gemin3. Drosophila Gemin3 (dGem3) colocalizes and interacts with dSMN in vitro and in vivo. RNA interference for dGem3 codepletes dSMN and inhibits efficient Sm core assembly in vitro. Transposon insertion mutations in Gemin3 are larval lethals and also codeplete dSMN. Transgenic overexpression of dGem3 rescues lethality, but overexpression of dSMN does not, indicating that loss of dSMN is not the primary cause of death. Gemin3 mutant larvae exhibit motor defects similar to previously characterized Smn alleles. Remarkably, appreciable numbers of Gemin3 mutants (along with one previously undescribed Smn allele) survive as larvae for several weeks without pupating. Our results demonstrate the conservation of Gemin3 protein function in metazoan snRNP assembly and reveal that loss of either Smn or Gemin3 can contribute to neuromuscular dysfunction.
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Affiliation(s)
- Karl B Shpargel
- Department of Genetics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4955, USA
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47
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Walker MP, Rajendra TK, Saieva L, Fuentes JL, Pellizzoni L, Matera AG. SMN complex localizes to the sarcomeric Z-disc and is a proteolytic target of calpain. Hum Mol Genet 2008; 17:3399-410. [PMID: 18689355 DOI: 10.1093/hmg/ddn234] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a recessive neuromuscular disease caused by mutations in the human survival motor neuron 1 (SMN1) gene. The human SMN protein is part of a large macromolecular complex involved in the biogenesis of small ribonucleoproteins. Previously, we showed that SMN is a sarcomeric protein in flies and mice. In this report, we show that the entire mouse Smn complex localizes to the sarcomeric Z-disc. Smn colocalizes with alpha-actinin, a Z-disc marker protein, in both skeletal and cardiac myofibrils. Furthermore, this localization is both calcium- and calpain-dependent. Calpains are known to release proteins from various regions of the sarcomere as a part of the normal functioning of the muscle; however, this removal can be either direct or indirect. Using mammalian cell lysates, purified native SMN complexes, as well as recombinant SMN protein, we show that SMN is a direct target of calpain cleavage. Finally, myofibers from a mouse model of severe SMA, but not controls, display morphological defects that are consistent with a Z-disc deficiency. These results support the view that the SMN complex performs a muscle-specific function at the Z-discs.
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Affiliation(s)
- Michael P Walker
- Department of Genetics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4955, USA
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48
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Morris GE. The Cajal body. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2008; 1783:2108-15. [PMID: 18755223 DOI: 10.1016/j.bbamcr.2008.07.016] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Revised: 07/21/2008] [Accepted: 07/23/2008] [Indexed: 12/30/2022]
Abstract
The Cajal body, originally identified over 100 years ago as a nucleolar accessory body in neurons, has come to be identified with nucleoplasmic structures, often quite tiny, that contain coiled threads of the marker protein, coilin. The interaction of coilin with other proteins appears to increase the efficiency of several nuclear processes by concentrating their components in the Cajal body. The best-known of these processes is the modification and assembly of U snRNPs, some of which eventually form the RNA splicing machinery, or spliceosome. Over the last 10 years, research into the function of Cajal bodies has been greatly stimulated by the discovery that SMN, the protein deficient in the inherited neuromuscular disease, spinal muscular atrophy, is a Cajal body component and has an essential role in the assembly of spliceosomal U snRNPs in the cytoplasm and their delivery to the Cajal body in the nucleus.
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Affiliation(s)
- Glenn E Morris
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, OSWESTRY, SY10 7AG, UK.
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49
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Evolution of an RNP assembly system: a minimal SMN complex facilitates formation of UsnRNPs in Drosophila melanogaster. Proc Natl Acad Sci U S A 2008; 105:10045-50. [PMID: 18621711 DOI: 10.1073/pnas.0802287105] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In vertebrates, assembly of spliceosomal uridine-rich small nuclear ribonucleoproteins (UsnRNPs) is mediated by the SMN complex, a macromolecular entity composed of the proteins SMN and Gemins 2-8. Here we have studied the evolution of this machinery using complete genome assemblies of multiple model organisms. The SMN complex has gained complexity in evolution by a blockwise addition of Gemins onto an ancestral core complex composed of SMN and Gemin2. In contrast to this overall evolutionary trend to more complexity in metazoans, orthologs of most Gemins are missing in dipterans. In accordance with these bioinformatic data a previously undescribed biochemical purification strategy elucidated that the dipteran Drosophila melanogaster contains an SMN complex of remarkable simplicity. Surprisingly, this minimal complex not only mediates the assembly reaction in a manner very similar to its vertebrate counterpart, but also prevents misassembly onto nontarget RNAs. Our data suggest that only a minority of Gemins are required for the assembly reaction per se, whereas others may serve additional functions in the context of UsnRNP biogenesis. The evolution of the SMN complex is an interesting example of how the simplification of a biochemical process contributes to genome compaction.
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Piazzon N, Rage F, Schlotter F, Moine H, Branlant C, Massenet S. In vitro and in cellulo evidences for association of the survival of motor neuron complex with the fragile X mental retardation protein. J Biol Chem 2007; 283:5598-610. [PMID: 18093976 DOI: 10.1074/jbc.m707304200] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Spinal muscular atrophy (SMA) is caused by reduced levels of the survival of motor neuron (SMN) protein. Although the SMN complex is essential for assembly of spliceosomal U small nuclear RNPs, it is still not understood why reduced levels of the SMN protein specifically cause motor neuron degeneration. SMN was recently proposed to have specific functions in mRNA transport and translation regulation in neuronal processes. The defective protein in Fragile X mental retardation syndrome (FMRP) also plays a role in transport of mRNPs and in their translation. Therefore, we examined possible relationships of SMN with FMRP. We observed granules containing both transiently expressed red fluorescent protein(RFP)-tagged SMN and green fluorescent protein(GFP)-tagged FMRP in cell bodies and processes of rat primary neurons of hypothalamus in culture. By immunoprecipitation experiments, we detected an association of FMRP with the SMN complex in human neuroblastoma SH-SY5Y cells and in murine motor neuron MN-1 cells. Then, by in vitro experiments, we demonstrated that the SMN protein is essential for this association. We showed that the COOH-terminal region of FMRP, as well as the conserved YG box and the region encoded by exon 7 of SMN, are required for the interaction. Our findings suggest a link between the SMN complex and FMRP in neuronal cells.
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Affiliation(s)
- Nathalie Piazzon
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR 7567 CNRS-UHP Nancy I, Faculté des Sciences, BP 239, 54506 Vandoeuvre-les-Nancy Cedex
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