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Liu H, Pillai M, Leung AKL. PARPs and ADP-ribosylation-mediated biomolecular condensates: determinants, dynamics, and disease implications. Trends Biochem Sci 2025:S0968-0004(24)00304-9. [PMID: 39922741 DOI: 10.1016/j.tibs.2024.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2024] [Revised: 12/17/2024] [Accepted: 12/20/2024] [Indexed: 02/10/2025]
Abstract
Biomolecular condensates are cellular compartments that selectively enrich proteins and other macromolecules despite lacking enveloping membranes. These compartments often form through phase separation triggered by multivalent nucleic acids. Emerging data have revealed that poly(ADP-ribose) (PAR), a nucleic acid-based protein modification catalyzed by ADP-ribosyltransferases (commonly known as PARPs), plays a crucial role in this process. This review focuses on the role of PARPs and ADP-ribosylation, and explores the principles and mechanisms by which PAR regulates condensate formation, dissolution, and dynamics. Future studies with advanced tools to examine PAR binding sites, substrate interactions, PAR length and structure, and transitions from condensates to aggregates will be key to unraveling the complexity of ADP-ribosylation in health and disease, including cancer, viral infection, and neurodegeneration.
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Affiliation(s)
- Hongrui Liu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Cross-Disciplinary Graduate Program in Biomedical Sciences (XDBio), School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Meenakshi Pillai
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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2
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Kuznetsov AV. Simulating the Growth of TATA-Box Binding Protein-Associated Factor 15 Inclusions in Neuron Soma. J Biomech Eng 2024; 146:121010. [PMID: 39222014 DOI: 10.1115/1.4066386] [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: 07/14/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
To the best of the author's knowledge, this paper presents the first attempt to develop a mathematical model of the formation and growth of inclusions containing misfolded TATA-box binding protein associated factor 15 (TAF15). It has recently been shown that TAF15 inclusions are involved in approximately 10% of cases of frontotemporal lobar degeneration (FTLD). FTLD is the second most common neurodegenerative disease after Alzheimer's disease (AD). It is characterized by a progressive loss of personality, behavioral changes, and a decline in language skills due to the degeneration of the frontal and anterior temporal lobes. The model simulates TAF15 monomer production, nucleation and autocatalytic growth of free TAF15 aggregates, and their deposition into TAF15 inclusions. The accuracy of the numerical solution of the model equations is validated by comparing it with analytical solutions available for limiting cases. Physiologically relevant parameter values were used to predict TAF15 inclusion growth. It is shown that the growth of TAF15 inclusions is influenced by two opposing mechanisms: the rate at which free TAF15 aggregates are deposited into inclusions and the rate of autocatalytic production of free TAF15 aggregates from monomers. A low deposition rate slows inclusion growth, while a high deposition rate hinders the autocatalytic production of new aggregates, thus also slowing inclusion growth. Consequently, the rate of inclusion growth is maximized at an intermediate deposition rate of free TAF15 aggregates into TAF15 inclusions.
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Affiliation(s)
- Andrey V Kuznetsov
- Department of Mechanical and Aerospace Engineering, North Carolina State University, Raleigh, NC 27695-7910
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3
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Feichtner A, Enzler F, Kugler V, Hoppe K, Mair S, Kremser L, Lindner H, Huber RG, Stelzl U, Stefan E, Torres-Quesada O. Phosphorylation of the compartmentalized PKA substrate TAF15 regulates RNA-protein interactions. Cell Mol Life Sci 2024; 81:162. [PMID: 38568213 PMCID: PMC10991009 DOI: 10.1007/s00018-024-05204-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 03/08/2024] [Accepted: 03/09/2024] [Indexed: 04/05/2024]
Abstract
Spatiotemporal-controlled second messengers alter molecular interactions of central signaling nodes for ensuring physiological signal transmission. One prototypical second messenger molecule which modulates kinase signal transmission is the cyclic-adenosine monophosphate (cAMP). The main proteinogenic cellular effectors of cAMP are compartmentalized protein kinase A (PKA) complexes. Their cell-type specific compositions precisely coordinate substrate phosphorylation and proper signal propagation which is indispensable for numerous cell-type specific functions. Here we present evidence that TAF15, which is implicated in the etiology of amyotrophic lateral sclerosis, represents a novel nuclear PKA substrate. In cross-linking and immunoprecipitation experiments (iCLIP) we showed that TAF15 phosphorylation alters the binding to target transcripts related to mRNA maturation, splicing and protein-binding related functions. TAF15 appears to be one of multiple PKA substrates that undergo RNA-binding dynamics upon phosphorylation. We observed that the activation of the cAMP-PKA signaling axis caused a change in the composition of a collection of RNA species that interact with TAF15. This observation appears to be a broader principle in the regulation of molecular interactions, as we identified a significant enrichment of RNA-binding proteins within endogenous PKA complexes. We assume that phosphorylation of RNA-binding domains adds another layer of regulation to binary protein-RNAs interactions with consequences to RNA features including binding specificities, localization, abundance and composition.
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Affiliation(s)
- Andreas Feichtner
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Florian Enzler
- Daniel Swarovski Research Laboratory, Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, Innrain 66/66a, 6020, Innsbruck, Austria
| | - Valentina Kugler
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Katharina Hoppe
- Institute of Developmental Immunology, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Sophia Mair
- Department of Cardiac Surgery, Medical University of Innsbruck, Innrain 66/66a, 6020, Innsbruck, Austria
- Vascage, Center of Clinical Stroke Research, 6020, Innsbruck, Austria
| | - Leopold Kremser
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Roland G Huber
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore, 138671, Singapore
| | - Ulrich Stelzl
- Institute of Pharmaceutical Sciences, University of Graz, Schubertstrasse 1, 8010, Graz, Austria
| | - Eduard Stefan
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria.
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
| | - Omar Torres-Quesada
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria.
- Division of Medical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
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4
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Guo CM, Tang L, Li X, Huang LY. TATA-box-binding protein-associated factor 15 is a novel biomarker that promotes cell proliferation and migration in gastrointestinal stromal tumor. World J Gastroenterol 2023; 29:2932-2949. [PMID: 37274797 PMCID: PMC10237090 DOI: 10.3748/wjg.v29.i19.2932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/06/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
BACKGROUND Gastrointestinal stromal tumor (GIST) is a common neoplasm with high rates of recurrence and metastasis, and its therapeutic efficacy is still not ideal. There is an unmet need to find new molecular therapeutic targets for GIST. TATA-box-binding protein-associated factor 15 (TAF15) contributes to the progress of various tumors, while the role and molecular mechanism of TAF15 in GIST progression are still unknown.
AIM To explore new molecular therapeutic targets for GIST and understand the biological role and underlying mechanisms of TAF15 in GIST progression.
METHODS Proteomic analysis was performed to explore the differentially expressed proteins in GIST. Western blotting and immunohistochemical analysis were used to verify the expression level of TAF15 in GIST tissues and cell lines. Cell counting kit-8, colony formation, wound-healing and transwell assay were executed to detect the ability of TAF15 on cell proliferation, migration and invasion. A xenograft mouse model was applied to explore the role of TAF15 in the progression of GIST. Western blotting was used to detect the phosphorylation level and total level of RAF1, MEK and ERK1/2.
RESULTS A total of 1669 proteins were identified as differentially expressed proteins with 762 upregulated and 907 downregulated in GIST. TAF15 was selected for the further study because of its important role in cell proliferation and migration. TAF15 was significantly over expressed in GIST tissues and cell lines. Overexpression of TAF15 was associated with larger tumor size and higher risk stage of GIST. TAF15 knockdown significantly inhibited the cell proliferation and migration of GIST in vitro and suppressed tumor growth in vivo. Moreover, the inhibition of TAF15 expression significantly decreased the phosphorylation level of RAF1, MEK and ERK1/2 in GIST cells and xenograft tissues, while the total RAF1, MEK and ERK1/2 had no significant change.
CONCLUSION TAF15 is over expressed in GIST tissues and cell lines. Overexpression of TAF15 was associated with a poor prognosis of GIST patients. TAF15 promotes cell proliferation and migration in GIST via the activation of the RAF1/MEK/ERK signaling pathway. Thus, TAF15 is expected to be a novel latent molecular biomarker or therapeutic target of GIST.
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Affiliation(s)
- Cheng-Ming Guo
- Department of Gastroenterology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai 264000, Shandong Province, China
| | - Li Tang
- Department of Gastroenterology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai 264000, Shandong Province, China
| | - Xu Li
- Department of Gastroenterology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai 264000, Shandong Province, China
| | - Liu-Ye Huang
- Department of Gastroenterology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai 264000, Shandong Province, China
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5
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Tang L, Guo C, Li X, Zhang B, Huang L. TAF15 promotes cell proliferation, migration and invasion of gastric cancer via activation of the RAF1/MEK/ERK signalling pathway. Sci Rep 2023; 13:5846. [PMID: 37037864 PMCID: PMC10086039 DOI: 10.1038/s41598-023-31959-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/20/2023] [Indexed: 04/12/2023] Open
Abstract
TATA-box-binding protein-associated Factor 15 (TAF15), a member of the FUS/EWS/TAF15 (FET) family, contributes to the progression of various tumours. However, the role and molecular mechanism of TAF15 in gastric cancer (GC) progression are still unknown. In this study, we found that TAF15 was significantly upregulated in GC tumour tissues and cell lines. Overexpression of TAF15 was associated with a larger tumour size, high pathologic stage and high T stage of GC. TAF15 knockdown suppressed the proliferation, migration and invasion of GC cells in vitro and inhibited the tumour growth in vivo. Additionally, TAF15 knockdown led to the significant reductions in the phosphorylation levels of RAF1, MEK and ERK1/2, while total RAF1, MEK and ERK1/2 exhibited no significant change in GC cell lines. In summary, TAF15 is overexpressed in GC tumour tissues and cell lines, and promotes cell proliferation, migration and invasion in GC via the RAF1/MEK/ERK signaling pathway, which suggests that TAF15 might be a potential molecular diagnostic marker or therapeutic target for GC.
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Affiliation(s)
- Li Tang
- Department of Gastroenterology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, People's Republic of China
| | - Chengming Guo
- Department of Gastroenterology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, People's Republic of China
| | - Xu Li
- Department of Gastroenterology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, People's Republic of China
| | - Bo Zhang
- Department of Gastroenterology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, People's Republic of China
| | - Liuye Huang
- Department of Gastroenterology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, People's Republic of China.
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6
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Lambert-Smith IA, Saunders DN, Yerbury JJ. Progress in biophysics and molecular biology proteostasis impairment and ALS. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 174:3-27. [PMID: 35716729 DOI: 10.1016/j.pbiomolbio.2022.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 05/19/2022] [Accepted: 06/09/2022] [Indexed: 12/11/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a rapidly progressive and fatal neurodegenerative disease that results from the loss of both upper and lower motor neurons. It is the most common motor neuron disease and currently has no effective treatment. There is mounting evidence to suggest that disturbances in proteostasis play a significant role in ALS pathogenesis. Proteostasis is the maintenance of the proteome at the right level, conformation and location to allow a cell to perform its intended function. In this review, we present a thorough synthesis of the literature that provides evidence that genetic mutations associated with ALS cause imbalance to a proteome that is vulnerable to such pressure due to its metastable nature. We propose that the mechanism underlying motor neuron death caused by defects in mRNA metabolism and protein degradation pathways converges on proteostasis dysfunction. We propose that the proteostasis network may provide an effective target for therapeutic development in ALS.
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Affiliation(s)
- Isabella A Lambert-Smith
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia; Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Darren N Saunders
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Justin J Yerbury
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia; Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.
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7
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Fortuna TR, Kour S, Anderson EN, Ward C, Rajasundaram D, Donnelly CJ, Hermann A, Wyne H, Shewmaker F, Pandey UB. DDX17 is involved in DNA damage repair and modifies FUS toxicity in an RGG-domain dependent manner. Acta Neuropathol 2021; 142:515-536. [PMID: 34061233 DOI: 10.1007/s00401-021-02333-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/07/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022]
Abstract
Mutations in the RNA binding protein, Fused in Sarcoma (FUS), lead to amyotrophic lateral sclerosis (ALS), the most frequent form of motor neuron disease. Cytoplasmic aggregation and defective DNA repair machinery are etiologically linked to mutant FUS-associated ALS. Although FUS is involved in numerous aspects of RNA processing, little is understood about the pathophysiological mechanisms of mutant FUS. Here, we employed RNA-sequencing technology in Drosophila brains expressing FUS to identify significantly altered genes and pathways involved in FUS-mediated neurodegeneration. We observed the expression levels of DEAD-Box Helicase 17 (DDX17) to be significantly downregulated in response to mutant FUS in Drosophila and human cell lines. Mutant FUS recruits nuclear DDX17 into cytoplasmic stress granules and physically interacts with DDX17 through the RGG1 domain of FUS. Ectopic expression of DDX17 reduces cytoplasmic mislocalization and sequestration of mutant FUS into cytoplasmic stress granules. We identified DDX17 as a novel regulator of the DNA damage response pathway whose upregulation repairs defective DNA damage repair machinery caused by mutant neuronal FUS ALS. In addition, we show DDX17 is a novel modifier of FUS-mediated neurodegeneration in vivo. Our findings indicate DDX17 is downregulated in response to mutant FUS, and restoration of DDX17 levels suppresses FUS-mediated neuropathogenesis and toxicity in vivo.
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8
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Tessier TM, MacNeil KM, Mymryk JS. Piggybacking on Classical Import and Other Non-Classical Mechanisms of Nuclear Import Appear Highly Prevalent within the Human Proteome. BIOLOGY 2020; 9:biology9080188. [PMID: 32718019 PMCID: PMC7463951 DOI: 10.3390/biology9080188] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/23/2022]
Abstract
One of the most conserved cellular pathways among eukaryotes is the extensively studied classical protein nuclear import pathway mediated by importin-α. Classical nuclear localization signals (cNLSs) are recognized by importin-α and are highly predictable due to their abundance of basic amino acids. However, various studies in model organisms have repeatedly demonstrated that only a fraction of nuclear proteins contain identifiable cNLSs, including those that directly interact with importin-α. Using data from the Human Protein Atlas and the Human Reference Interactome, and proteomic data from BioID/protein-proximity labeling studies using multiple human importin-α proteins, we determine that nearly 50% of the human nuclear proteome does not have a predictable cNLS. Surprisingly, between 25% and 50% of previously identified human importin-α cargoes do not have predictable cNLS. Analysis of importin-α cargo without a cNLS identified an alternative basic rich motif that does not resemble a cNLS. Furthermore, several previously suspected piggybacking proteins were identified, such as those belonging to the RNA polymerase II and transcription factor II D complexes. Additionally, many components of the mediator complex interact with at least one importin-α, yet do not have a predictable cNLS, suggesting that many of the subunits may enter the nucleus through an importin-α-dependent piggybacking mechanism.
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Affiliation(s)
- Tanner M. Tessier
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada; (T.M.T.); (K.M.M.)
| | - Katelyn M. MacNeil
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada; (T.M.T.); (K.M.M.)
| | - Joe S. Mymryk
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada; (T.M.T.); (K.M.M.)
- Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON N6A 3K7, Canada
- Department of Oncology, The University of Western Ontario, London, ON N6A 3K7, Canada
- London Regional Cancer Program, Lawson Health Research Institute, London, ON N6A 5W9, Canada
- Correspondence: ; Tel.: +1-519-685-8600 (ext. 53012)
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9
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Singh AK, Kapoor V, Thotala D, Hallahan DE. TAF15 contributes to the radiation-inducible stress response in cancer. Oncotarget 2020; 11:2647-2659. [PMID: 32676166 PMCID: PMC7343639 DOI: 10.18632/oncotarget.27663] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/15/2020] [Indexed: 12/28/2022] Open
Abstract
Resistance to radiation therapy is a significant problem in the treatment of non-small cell lung cancer (NSCLC). There is an unmet need to discover new molecular targets for drug development in combination with standard of care cancer therapy. We found that TAF15 was radiation-inducible using phage-displayed peptide libraries. In this study, we report that overexpression of TAF15 is correlated with worsened survival in NSCLC patients. Radiation treatment led to surface induction of TAF15 in vitro and in vivo. We genetically silenced TAF15 which led to a significant reduction in proliferation of NSCLC cells. Cells depleted of TAF15 exhibited cell cycle arrest and enhanced apoptosis through activation and accumulation of p53. In combination with radiation, TAF15 knockdown led to a significant reduction in the surviving fraction of NSCLC cell lines. To determine the importance of TAF15 surface expression, we targeted TAF15 with an antibody. In combination with radiation, the anti-TAF15 antibody led to a reduction in the surviving fraction of cancer cells. These studies show that TAF15 is a radiation-inducible molecular target that is accessible to anti-cancer antibodies and enhances cell viability in response to radiation.
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Affiliation(s)
- Abhay Kumar Singh
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Vaishali Kapoor
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Dinesh Thotala
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,Siteman Cancer Center, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Dennis E Hallahan
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,Siteman Cancer Center, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
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Quintero-Cadena P, Lenstra TL, Sternberg PW. RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting. Mol Cell 2020; 79:207-220.e8. [DOI: 10.1016/j.molcel.2020.05.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 04/09/2020] [Accepted: 05/19/2020] [Indexed: 12/15/2022]
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11
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Xue YC, Ng CS, Xiang P, Liu H, Zhang K, Mohamud Y, Luo H. Dysregulation of RNA-Binding Proteins in Amyotrophic Lateral Sclerosis. Front Mol Neurosci 2020; 13:78. [PMID: 32547363 PMCID: PMC7273501 DOI: 10.3389/fnmol.2020.00078] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/22/2020] [Indexed: 12/11/2022] Open
Abstract
Genetic analyses of patients with amyotrophic lateral sclerosis (ALS) have revealed a strong association between mutations in genes encoding many RNA-binding proteins (RBPs), including TARDBP, FUS, hnRNPA1, hnRNPA2B1, MATR3, ATXN2, TAF15, TIA-1, and EWSR1, and disease onset/progression. RBPs are a group of evolutionally conserved proteins that participate in multiple steps of RNA metabolism, including splicing, polyadenylation, mRNA stability, localization, and translation. Dysregulation of RBPs, as a consequence of gene mutations, impaired nucleocytoplasmic trafficking, posttranslational modification (PTM), aggregation, and sequestration by abnormal RNA foci, has been shown to be involved in neurodegeneration and the development of ALS. While the exact mechanism by which dysregulated RBPs contribute to ALS remains elusive, emerging evidence supports the notion that both a loss of function and/or a gain of toxic function of these ALS-linked RBPs play a significant role in disease pathogenesis through facilitating abnormal protein interaction, causing aberrant RNA metabolism, and by disturbing ribonucleoprotein granule dynamics and phase transition. In this review article, we summarize the current knowledge on the molecular mechanism by which RBPs are dysregulated and the influence of defective RBPs on cellular homeostasis during the development of ALS. The strategies of ongoing clinical trials targeting RBPs and/or relevant processes are also discussed in the present review.
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Affiliation(s)
- Yuan Chao Xue
- Centre for Heart and Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Chen Seng Ng
- Centre for Heart and Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Pinhao Xiang
- Centre for Heart and Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Huitao Liu
- Centre for Heart and Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Experimental Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kevin Zhang
- Centre for Heart and Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Yasir Mohamud
- Centre for Heart and Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Honglin Luo
- Centre for Heart and Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
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Abstract
The specific interaction of importins with nuclear localization signals (NLSs) of cargo proteins not only mediates nuclear import but also, prevents their aberrant phase separation and stress granule recruitment in the cytoplasm. The importin Transportin-1 (TNPO1) plays a key role in the (patho-)physiology of both processes. Here, we report that both TNPO1 and Transportin-3 (TNPO3) recognize two nonclassical NLSs within the cold-inducible RNA-binding protein (CIRBP). Our biophysical investigations show that TNPO1 recognizes an arginine-glycine(-glycine) (RG/RGG)-rich region, whereas TNPO3 recognizes a region rich in arginine-serine-tyrosine (RSY) residues. These interactions regulate nuclear localization, phase separation, and stress granule recruitment of CIRBP in cells. The presence of both RG/RGG and RSY regions in numerous other RNA-binding proteins suggests that the interaction of TNPO1 and TNPO3 with these nonclassical NLSs may regulate the formation of membraneless organelles and subcellular localization of numerous proteins.
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Gipson AB, Giloteaux L, Hanson MR, Bentolila S. Arabidopsis RanBP2-Type Zinc Finger Proteins Related to Chloroplast RNA Editing Factor OZ1. PLANTS 2020; 9:plants9030307. [PMID: 32121603 PMCID: PMC7154859 DOI: 10.3390/plants9030307] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 01/01/2023]
Abstract
OZ1, an RNA editing factor that controls the editing of 14 cytidine targets in Arabidopsis chloroplasts, contains two RanBP2-type zinc finger (Znf) domains. The RanBP2 Znf is a C4-type member of the broader zinc finger family with unique functions and an unusually diverse distribution in plants. The domain can mediate interactions with proteins or RNA and appears in protein types such as proteases, RNA editing factors, and chromatin modifiers; however, few characterized Arabidopsis proteins containing RanBP2 Znfs have been studied specifically with the domain in mind. In humans, RanBP2 Znf-containing proteins are involved in RNA splicing, transport, or transcription initiation. We present a phylogenetic overview of Arabidopsis RanBP2 Znf proteins and the functional niches that these proteins occupy in plants. OZ1 and its four-member family represent a branch of this family with major impact on the RNA biology of chloroplasts and mitochondria in Arabidopsis. We discuss what is known about other plant proteins carrying the RanBP2 Znf domain and point out how phylogenetic information can provide clues to functions of uncharacterized Znf proteins.
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14
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Batlle C, Yang P, Coughlin M, Messing J, Pesarrodona M, Szulc E, Salvatella X, Kim HJ, Taylor JP, Ventura S. hnRNPDL Phase Separation Is Regulated by Alternative Splicing and Disease-Causing Mutations Accelerate Its Aggregation. Cell Rep 2020; 30:1117-1128.e5. [PMID: 31995753 PMCID: PMC6996132 DOI: 10.1016/j.celrep.2019.12.080] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/12/2019] [Accepted: 12/19/2019] [Indexed: 12/14/2022] Open
Abstract
Prion-like proteins form multivalent assemblies and phase separate into membraneless organelles. Heterogeneous ribonucleoprotein D-like (hnRNPDL) is a RNA-processing prion-like protein with three alternative splicing (AS) isoforms, which lack none, one, or both of its two disordered domains. It has been suggested that AS might regulate the assembly properties of RNA-processing proteins by controlling the incorporation of multivalent disordered regions in the isoforms. This, in turn, would modulate their activity in the downstream splicing program. Here, we demonstrate that AS controls the phase separation of hnRNPDL, as well as the size and dynamics of its nuclear complexes, its nucleus-cytoplasm shuttling, and amyloidogenicity. Mutation of the highly conserved D378 in the disordered C-terminal prion-like domain of hnRNPDL causes limb-girdle muscular dystrophy 1G. We show that D378H/N disease mutations impact hnRNPDL assembly properties, accelerating aggregation and dramatically reducing the protein solubility in the muscle of Drosophila, suggesting a genetic loss-of-function mechanism for this muscular disorder.
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Affiliation(s)
- Cristina Batlle
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra 08193, Spain
| | - Peiguo Yang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Maura Coughlin
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - James Messing
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Chevy Chase, MD 201815, USA
| | - Mireia Pesarrodona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Joint BSC-IRB Research Programme in Computational Biology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Elzbieta Szulc
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Joint BSC-IRB Research Programme in Computational Biology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Joint BSC-IRB Research Programme in Computational Biology, Baldiri Reixac 10, 08028 Barcelona, Spain; ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Hong Joo Kim
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - J Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Chevy Chase, MD 201815, USA.
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra 08193, Spain.
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15
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Baradaran-Heravi Y, Van Broeckhoven C, van der Zee J. Stress granule mediated protein aggregation and underlying gene defects in the FTD-ALS spectrum. Neurobiol Dis 2019; 134:104639. [PMID: 31626953 DOI: 10.1016/j.nbd.2019.104639] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 09/12/2019] [Accepted: 10/11/2019] [Indexed: 12/12/2022] Open
Abstract
Stress granules (SGs) are dynamic membraneless compartments composed out of RNA-binding proteins (RBPs) and RNA molecules that assemble temporarily to allow the cell to cope with cellular stress by stalling mRNA translation and moving synthesis towards cytoprotective proteins. Aberrant SGs have become prime suspects in the nucleation of toxic protein aggregation in frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). Perturbed SG dynamics appears to be mediated by alterations in RNA binding proteins (RBP). Indeed, a growing number of FTD and/or ALS related RBPs coding genes (TDP43, FUS, EWSR1, TAF15, hnRNPA1, hnRNPA2B1, ATXN2, TIA1) have been identified to interfere with SG formation through mutation of their low-complexity domain (LCD), and thereby cause or influence disease. Interestingly, disease pathways associated to the C9orf72 repeat expansion, the leading genetic cause of the FTD-ALS spectrum, intersect with SG-mediated protein aggregate formation. In this review, we provide a comprehensive overview of known SG proteins and their genetic contribution to the FTD-ALS spectrum. Importantly, multiple LCD-baring RBPs have already been identified in FTD-ALS that have not yet been genetically linked to disease. These should be considered candidate genes and offer opportunities for gene prioritization when mining sequencing data of unresolved FTD and ALS. Further, we zoom into the current understanding of the molecular processes of perturbed RBP function leading to disturbed SG dynamics, RNA metabolism, and pathological inclusions. Finally, we indicate how these gained insights open new avenues for therapeutic strategies targeting phase separation and SG dynamics to reverse pathological protein aggregation and protect against toxicity.
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Affiliation(s)
- Yalda Baradaran-Heravi
- Neurodegenerative Brain Diseases group, Center for Molecular Neurology, VIB, Antwerp, Belgium; Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases group, Center for Molecular Neurology, VIB, Antwerp, Belgium; Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.
| | - Julie van der Zee
- Neurodegenerative Brain Diseases group, Center for Molecular Neurology, VIB, Antwerp, Belgium; Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.
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16
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Genetic activation of parkin rescues TAF15-induced neurotoxicity in a Drosophila model of amyotrophic lateral sclerosis. Neurobiol Aging 2019; 73:68-73. [DOI: 10.1016/j.neurobiolaging.2018.09.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 08/09/2018] [Accepted: 09/14/2018] [Indexed: 12/14/2022]
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17
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Zhao M, Kim JR, van Bruggen R, Park J. RNA-Binding Proteins in Amyotrophic Lateral Sclerosis. Mol Cells 2018; 41:818-829. [PMID: 30157547 PMCID: PMC6182225 DOI: 10.14348/molcells.2018.0243] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/23/2018] [Accepted: 08/10/2018] [Indexed: 12/11/2022] Open
Abstract
Significant research efforts are ongoing to elucidate the complex molecular mechanisms underlying amyotrophic lateral sclerosis (ALS), which may in turn pinpoint potential therapeutic targets for treatment. The ALS research field has evolved with recent discoveries of numerous genetic mutations in ALS patients, many of which are in genes encoding RNA binding proteins (RBPs), including TDP-43, FUS, ATXN2, TAF15, EWSR1, hnRNPA1, hnRNPA2/B1, MATR3 and TIA1. Accumulating evidence from studies on these ALS-linked RBPs suggests that dysregulation of RNA metabolism, cytoplasmic mislocalization of RBPs, dysfunction in stress granule dynamics of RBPs and increased propensity of mutant RBPs to aggregate may lead to ALS pathogenesis. Here, we review current knowledge of the biological function of these RBPs and the contributions of ALS-linked mutations to disease pathogenesis.
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Affiliation(s)
- Melody Zhao
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto,
Canada
- Department of Molecular Genetics, University of Toronto, Toronto,
Canada
| | - Jihye Rachel Kim
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto,
Canada
- Department of Molecular Genetics, University of Toronto, Toronto,
Canada
| | - Rebekah van Bruggen
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto,
Canada
| | - Jeehye Park
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto,
Canada
- Department of Molecular Genetics, University of Toronto, Toronto,
Canada
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18
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Ravanidis S, Kattan FG, Doxakis E. Unraveling the Pathways to Neuronal Homeostasis and Disease: Mechanistic Insights into the Role of RNA-Binding Proteins and Associated Factors. Int J Mol Sci 2018; 19:ijms19082280. [PMID: 30081499 PMCID: PMC6121432 DOI: 10.3390/ijms19082280] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 07/26/2018] [Accepted: 07/31/2018] [Indexed: 12/13/2022] Open
Abstract
The timing, dosage and location of gene expression are fundamental determinants of brain architectural complexity. In neurons, this is, primarily, achieved by specific sets of trans-acting RNA-binding proteins (RBPs) and their associated factors that bind to specific cis elements throughout the RNA sequence to regulate splicing, polyadenylation, stability, transport and localized translation at both axons and dendrites. Not surprisingly, misregulation of RBP expression or disruption of its function due to mutations or sequestration into nuclear or cytoplasmic inclusions have been linked to the pathogenesis of several neuropsychiatric and neurodegenerative disorders such as fragile-X syndrome, autism spectrum disorders, spinal muscular atrophy, amyotrophic lateral sclerosis and frontotemporal dementia. This review discusses the roles of Pumilio, Staufen, IGF2BP, FMRP, Sam68, CPEB, NOVA, ELAVL, SMN, TDP43, FUS, TAF15, and TIA1/TIAR in RNA metabolism by analyzing their specific molecular and cellular function, the neurological symptoms associated with their perturbation, and their axodendritic transport/localization along with their target mRNAs as part of larger macromolecular complexes termed ribonucleoprotein (RNP) granules.
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Affiliation(s)
- Stylianos Ravanidis
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
| | - Fedon-Giasin Kattan
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
| | - Epaminondas Doxakis
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
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19
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Eom H, Park SJ, Kim MK, Kim H, Kang H, Lee I. TAF15b, involved in the autonomous pathway for flowering, represses transcription of FLOWERING LOCUS C. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:79-91. [PMID: 29086456 DOI: 10.1111/tpj.13758] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/26/2017] [Accepted: 10/25/2017] [Indexed: 05/03/2023]
Abstract
TATA-binding protein-associated factors (TAFs) are general transcription factors within the transcription factor IID (TFIID) complex, which recognizes the core promoter of genes. In addition to their biochemical function, it is known that several TAFs are involved in the regulation of developmental processes. In this study, we found that TAF15b affects flowering time, especially through the autonomous pathway (AP) in Arabidopsis. The mutant taf15b shows late flowering compared with the wild type plant during both long and short days, and vernalization accelerates the flowering time of taf15b. In addition, taf15b shows strong upregulation of FLOWERING LOCUS C (FLC), a flowering repressor in Arabidopsis, and the flc taf15b double mutant completely offsets the late flowering of taf15b, indicating that TAF15b is a typical AP gene. The taf15b mutant also shows increased transcript levels of COOLAIR, an antisense transcript of FLC. Consistently, chromatin immunoprecipitation (ChIP) analyses showed that the TAF15b protein is enriched around both sense and antisense transcription start sites of the FLC locus. In addition, co-immunoprecipitation showed that TAF15b interacts with RNA polymerase II (Pol II), while ChIP showed increased enrichment of the phosphorylated forms, both serine 2 (Ser2) and Ser5, of the C-terminal domain of Pol II at the FLC locus, which is indicative of transcriptional elongation. Finally, taf15b showed higher enrichment of the active histone marker, H3K4me3, on FLC chromatin. Taken together, our results suggest that TAF15b affects flowering time through transcriptional repression of FLC in Arabidopsis.
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Affiliation(s)
- Hyunjoo Eom
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
- Center for RNA Research, Institute for Basic Science, Seoul, 08826, Korea
| | - Su Jung Park
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Min Kyung Kim
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Hoyeun Kim
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Hunseung Kang
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Ilha Lee
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
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20
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RNA-binding proteins with prion-like domains in health and disease. Biochem J 2017; 474:1417-1438. [PMID: 28389532 DOI: 10.1042/bcj20160499] [Citation(s) in RCA: 312] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/06/2017] [Accepted: 02/09/2017] [Indexed: 02/07/2023]
Abstract
Approximately 70 human RNA-binding proteins (RBPs) contain a prion-like domain (PrLD). PrLDs are low-complexity domains that possess a similar amino acid composition to prion domains in yeast, which enable several proteins, including Sup35 and Rnq1, to form infectious conformers, termed prions. In humans, PrLDs contribute to RBP function and enable RBPs to undergo liquid-liquid phase transitions that underlie the biogenesis of various membraneless organelles. However, this activity appears to render RBPs prone to misfolding and aggregation connected to neurodegenerative disease. Indeed, numerous RBPs with PrLDs, including TDP-43 (transactivation response element DNA-binding protein 43), FUS (fused in sarcoma), TAF15 (TATA-binding protein-associated factor 15), EWSR1 (Ewing sarcoma breakpoint region 1), and heterogeneous nuclear ribonucleoproteins A1 and A2 (hnRNPA1 and hnRNPA2), have now been connected via pathology and genetics to the etiology of several neurodegenerative diseases, including amyotrophic lateral sclerosis, frontotemporal dementia, and multisystem proteinopathy. Here, we review the physiological and pathological roles of the most prominent RBPs with PrLDs. We also highlight the potential of protein disaggregases, including Hsp104, as a therapeutic strategy to combat the aberrant phase transitions of RBPs with PrLDs that likely underpin neurodegeneration.
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21
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Prpar Mihevc S, Darovic S, Kovanda A, Bajc Česnik A, Župunski V, Rogelj B. Nuclear trafficking in amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Brain 2016; 140:13-26. [PMID: 27497493 DOI: 10.1093/brain/aww197] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/14/2016] [Accepted: 06/16/2016] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis and frontotemporal lobar degeneration are two ends of a phenotypic spectrum of disabling, relentlessly progressive and ultimately fatal diseases. A key characteristic of both conditions is the presence of TDP-43 (encoded by TARDBP) or FUS immunoreactive cytoplasmic inclusions in neuronal and glial cells. This cytoplasmic mislocalization of otherwise predominantly nuclear RNA binding proteins implies a perturbation of the nucleocytoplasmic shuttling as a possible event in the pathogenesis. Compromised nucleocytoplasmic shuttling has recently also been associated with a hexanucleotide repeat expansion mutation in C9orf72, which is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal lobar degeneration, and leads to accumulation of cytoplasmic TDP-43 inclusions. Mutation in C9orf72 may disrupt nucleocytoplasmic shuttling on the level of C9ORF72 protein, the transcribed hexanucleotide repeat RNA, and/or dipeptide repeat proteins translated form the hexanucleotide repeat RNA. These defects of nucleocytoplasmic shuttling may therefore, constitute the common ground of the underlying disease mechanisms in different molecular subtypes of amyotrophic lateral sclerosis and frontotemporal lobar degeneration.
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Affiliation(s)
- Sonja Prpar Mihevc
- 1 Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Simona Darovic
- 1 Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Anja Kovanda
- 1 Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Ana Bajc Česnik
- 1 Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Vera Župunski
- 2 Faculty of Chemistry and Chemical Technology, Večna pot 113, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Boris Rogelj
- 1 Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia .,2 Faculty of Chemistry and Chemical Technology, Večna pot 113, University of Ljubljana, SI-1000 Ljubljana, Slovenia.,3 Biomedical Research Institute BRIS, Puhova 10, SI-1000 Ljubljana, Slovenia
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22
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Abstract
Neurodegenerative disorders such as Alzheimer disease (AD), frontotemporal dementia (FTD), amyotrophic lateral sclerosis (ALS), Parkinson disease (PD), Huntington's disease (HD), and multiple sclerosis (MS) affect different neuronal cells, and have a variable age of onset, clinical symptoms, and pathological features. Despite the great progress in understanding the etiology of these disorders, the underlying mechanisms remain largely unclear. Among the processes affected in neurodegenerative diseases, alteration in RNA metabolism is emerging as a crucial player. RNA-binding proteins (RBPs) are involved at all stages of RNA metabolism and display a broad range of functions, including modulation of mRNA transcription, splicing, editing, export, stability, translation and localization and miRNA biogenesis, thus enormously impacting regulation of gene expression. On the other hand, aberrant regulation of RBP expression or activity can contribute to disease onset and progression. Recent reports identified mutations causative of neurological disorders in the genes encoding a family of RBPs named FET (FUS/TLS, EWS and TAF15). This review summarizes recent works documenting the involvement of FET proteins in the pathology of ALS, FTLD, essential tremor (ET) and other neurodegenerative diseases. Moreover, clinical implications of recent advances in FET research are critically discussed.
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Affiliation(s)
- Francesca Svetoni
- a University of Rome "Foro Italico," , Rome , Italy.,b Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia , Rome , Italy
| | - Paola Frisone
- b Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia , Rome , Italy
| | - Maria Paola Paronetto
- a University of Rome "Foro Italico," , Rome , Italy.,b Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia , Rome , Italy
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23
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Dong OX, Meteignier LV, Plourde MB, Ahmed B, Wang M, Jensen C, Jin H, Moffett P, Li X, Germain H. Arabidopsis TAF15b Localizes to RNA Processing Bodies and Contributes to snc1-Mediated Autoimmunity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:247-57. [PMID: 26713351 DOI: 10.1094/mpmi-11-15-0246-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In both animals and plants, messenger (m)RNA export has been shown to contribute to immune response regulation. The Arabidopsis nuclear protein MOS11, along with the nucleoporins MOS3/Nup96/SAR3 and Nup160/SAR1 are components of the mRNA export machinery and contribute to immunity mediated by nucleotide binding leucine-rich repeat immune receptors (NLR). The human MOS11 ortholog CIP29 is part of a small protein complex with three additional members: the RNA helicase DDX39, ALY, and TAF15b. We systematically assessed the biological roles of the Arabidopsis homologs of these proteins in toll interleukin 1 receptor-type NLR (TNL)-mediated immunity using reverse genetics. Although mutations in ALY and DDX39 did not result in obvious defects, taf15b mutation partially suppressed the autoimmune phenotypes of a gain-of-function TNL mutant, snc1. An additive effect on snc1 suppression was observed in mos11-1 taf15b snc1 triple mutant plants, suggesting that MOS11 and TAF15b have independent functions. TAF15b-GFP fusion protein, which fully complemented taf15b mutant phenotypes, localized to nuclei similarly to MOS11. However, it was also targeted to cytosolic granules identified as processing bodies. In addition, we observed no change in SNC1 mRNA levels, whereas less SNC1 protein accumulated in taf15b mutant, suggesting that TAF15b contributes to SNC1 homeostasis through posttranscriptional mechanisms. In summary, this study highlights the importance of posttranscriptional RNA processing mediated by TAF15b in the regulation of TNL-mediated immunity.
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Affiliation(s)
- Oliver X Dong
- 1 Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- 2 Michael Smith Laboratories, University of British Columbia
| | | | - Melodie B Plourde
- 4 Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, QC, G9A 5H7, Canada
- 5 Groupe de Recherche en Biologie Végétale (GRBV), Université du Québec à Trois-Rivières; and
| | - Bulbul Ahmed
- 4 Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, QC, G9A 5H7, Canada
- 5 Groupe de Recherche en Biologie Végétale (GRBV), Université du Québec à Trois-Rivières; and
| | - Ming Wang
- 6 Department of Plant Pathology and Microbiology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, U.S.A
| | | | - Hailing Jin
- 6 Department of Plant Pathology and Microbiology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, U.S.A
| | - Peter Moffett
- 3 Department of Biology, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Xin Li
- 1 Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- 2 Michael Smith Laboratories, University of British Columbia
| | - Hugo Germain
- 4 Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, QC, G9A 5H7, Canada
- 5 Groupe de Recherche en Biologie Végétale (GRBV), Université du Québec à Trois-Rivières; and
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24
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Gtf2ird1-Dependent Mohawk Expression Regulates Mechanosensing Properties of the Tendon. Mol Cell Biol 2016; 36:1297-309. [PMID: 26884464 PMCID: PMC4836271 DOI: 10.1128/mcb.00950-15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/08/2016] [Indexed: 11/20/2022] Open
Abstract
Mechanoforces experienced by an organ are translated into biological information for cellular sensing and response. In mammals, the tendon connective tissue experiences and resists physical forces, with tendon-specific mesenchymal cells called tenocytes orchestrating extracellular matrix (ECM) turnover. We show that Mohawk (Mkx), a tendon-specific transcription factor, is essential in mechanoresponsive tenogenesis through regulation of its downstream ECM genes such as type I collagens and proteoglycans such as fibromodulin both in vivo and in vitro Wild-type (WT) mice demonstrated an increase in collagen fiber diameter and density in response to physical treadmill exercise, whereas in Mkx(-/-) mice, tendons failed to respond to the same mechanical stimulation. Furthermore, functional screening of the Mkx promoter region identified several upstream transcription factors that regulate Mkx In particular, general transcription factor II-I repeat domain-containing protein 1 (Gtf2ird1) that is expressed in the cytoplasm of unstressed tenocytes translocated into the nucleus upon mechanical stretching to activate the Mkx promoter through chromatin regulation. Here, we demonstrate that Gtf2ird1 is essential for Mkx transcription, while also linking mechanical forces to Mkx-mediated tendon homeostasis and regeneration.
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25
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Kashyap M, Ganguly AK, Bhavesh NS. Structural delineation of stem-loop RNA binding by human TAF15 protein. Sci Rep 2015; 5:17298. [PMID: 26612539 PMCID: PMC4661536 DOI: 10.1038/srep17298] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/28/2015] [Indexed: 11/09/2022] Open
Abstract
Human TATA binding protein associated factor 2 N (TAF15) and Fused in sarcoma (FUS) are nucleic acid binding proteins belonging to the conserved FET family of proteins. They are involved in diverse processes such as pre-mRNA splicing, mRNA transport, and DNA binding. The absence of information regarding the structural mechanism employed by the FET family in recognizing and discriminating their cognate and non-cognate RNA targets has hampered the attainment of consensus on modes of protein-RNA binding for this family. Our study provides a molecular basis of this RNA recognition using a combination of solution-state NMR spectroscopy, calorimetry, docking and molecular dynamics simulation. Analysis of TAF15-RRM solution structure and its binding with stem-loop RNA has yielded conclusive evidence of a non-canonical mode of RNA recognition. Rather than classical stacking interactions that occur across nitrogen bases and aromatic amino acids on ribonucleoprotein sites, moderate-affinity hydrogen bonding network between the nitrogen bases in the stem-loop RNA and a concave face on the RRM surface primarily mediate TAF15-RRM RNA interaction. We have compared the binding affinities across a set of single-stranded RNA oligonucleotides to conclusively establish that RNA binding is dependent upon structural elements in the RNA rather than sequence.
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Affiliation(s)
- Maruthi Kashyap
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, 110 067, New Delhi, India
| | - Akshay Kumar Ganguly
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, 110 067, New Delhi, India
| | - Neel Sarovar Bhavesh
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, 110 067, New Delhi, India
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26
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Darovic S, Prpar Mihevc S, Župunski V, Gunčar G, Štalekar M, Lee YB, Shaw CE, Rogelj B. Phosphorylation of C-terminal tyrosine residue 526 in FUS impairs its nuclear import. J Cell Sci 2015; 128:4151-9. [PMID: 26403203 DOI: 10.1242/jcs.176602] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/17/2015] [Indexed: 12/13/2022] Open
Abstract
Aberrant cytoplasmic aggregation of FUS, which is caused by mutations primarily in the C-terminal nuclear localisation signal, is associated with 3% of cases of familial amyotrophic lateral sclerosis (ALS). FUS aggregates are also pathognomonic for 10% of all frontotemporal lobar degeneration (FTLD) cases; however, these cases are not associated with mutations in the gene encoding FUS. This suggests that there are differences in the mechanisms that drive inclusion formation of FUS in ALS and FTLD. Here, we show that the C-terminal tyrosine residue at position 526 of FUS is crucial for normal nuclear import. This tyrosine is subjected to phosphorylation, which reduces interaction with transportin 1 and might consequentially affect the transport of FUS into the nucleus. Furthermore, we show that this phosphorylation can occur through the activity of the Src family of kinases. Our study implicates phosphorylation as an additional mechanism by which nuclear transport of FUS might be regulated and potentially perturbed in ALS and FTLD.
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Affiliation(s)
- Simona Darovic
- Jožef Stefan Institute, Department of Biotechnology, Jamova 39, Ljubljana 1000, Slovenia
| | - Sonja Prpar Mihevc
- Jožef Stefan Institute, Department of Biotechnology, Jamova 39, Ljubljana 1000, Slovenia
| | - Vera Župunski
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Gregor Gunčar
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Maja Štalekar
- Jožef Stefan Institute, Department of Biotechnology, Jamova 39, Ljubljana 1000, Slovenia
| | - Youn-Bok Lee
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, King's College London, London SE5 9RT, UK
| | - Christopher E Shaw
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, King's College London, London SE5 9RT, UK
| | - Boris Rogelj
- Jožef Stefan Institute, Department of Biotechnology, Jamova 39, Ljubljana 1000, Slovenia Biomedical Research Institute BRIS, Puhova 10, Ljubljana 1000, Slovenia
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27
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The function of RNA-binding proteins at the synapse: implications for neurodegeneration. Cell Mol Life Sci 2015; 72:3621-35. [PMID: 26047658 PMCID: PMC4565867 DOI: 10.1007/s00018-015-1943-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 05/18/2015] [Accepted: 05/28/2015] [Indexed: 12/13/2022]
Abstract
The loss of synapses is a central event in
neurodegenerative diseases. Synaptic proteins are often associated with disease neuropathology, but their role in synaptic loss is not fully understood. Of the many processes involved in sustaining the integrity of synapses, local protein translation can directly impact synaptic formation, communication, and maintenance. RNA-binding proteins and their association with RNA granules serve to regulate mRNA transportation and translation at synapses and in turn regulate the synapse. Genetic mutations in RNA-binding proteins FUS and TDP-43 have been linked with causing neurodegenerative diseases: amyotrophic lateral sclerosis and frontotemporal dementia. The observation that mutations in FUS and TDP-43 coincide with changes in RNA granules provides evidence that dysfunction of RNA metabolism may underlie the mechanism of synaptic loss in these diseases. However, we do not know how mutations in RNA-binding proteins would affect RNA granule dynamics and local translation, or if these alterations would cause neurodegeneration. Further investigation into this area will lead to important insights into how disruption of RNA metabolism and local translation at synapses can cause neurodegenerative diseases.
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Izhar L, Adamson B, Ciccia A, Lewis J, Pontano-Vaites L, Leng Y, Liang AC, Westbrook TF, Harper JW, Elledge SJ. A Systematic Analysis of Factors Localized to Damaged Chromatin Reveals PARP-Dependent Recruitment of Transcription Factors. Cell Rep 2015; 11:1486-500. [PMID: 26004182 DOI: 10.1016/j.celrep.2015.04.053] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/16/2015] [Accepted: 04/25/2015] [Indexed: 01/09/2023] Open
Abstract
Localization to sites of DNA damage is a hallmark of DNA damage response (DDR) proteins. To identify DDR factors, we screened epitope-tagged proteins for localization to sites of chromatin damaged by UV laser microirradiation and found >120 proteins that localize to damaged chromatin. These include the BAF tumor suppressor complex and the amyotrophic lateral sclerosis (ALS) candidate protein TAF15. TAF15 contains multiple domains that bind damaged chromatin in a poly-(ADP-ribose) polymerase (PARP)-dependent manner, suggesting a possible role as glue that tethers multiple PAR chains together. Many positives were transcription factors; > 70% of randomly tested transcription factors localized to sites of DNA damage, and of these, ∼90% were PARP dependent for localization. Mutational analyses showed that localization to damaged chromatin is DNA-binding-domain dependent. By examining Hoechst staining patterns at damage sites, we see evidence of chromatin decompaction that is PARP dependent. We propose that PARP-regulated chromatin remodeling at sites of damage allows transient accessibility of DNA-binding proteins.
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Affiliation(s)
- Lior Izhar
- Department of Genetics, Harvard University Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Britt Adamson
- Department of Genetics, Harvard University Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alberto Ciccia
- Department of Genetics, Harvard University Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Jedd Lewis
- Department of Genetics, Harvard University Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Laura Pontano-Vaites
- Department of Cell Biology, Harvard University Medical School, Boston, MA 02115, USA
| | - Yumei Leng
- Department of Genetics, Harvard University Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Anthony C Liang
- Department of Genetics, Harvard University Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Thomas F Westbrook
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Human Genetics, and Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard University Medical School, Boston, MA 02115, USA
| | - Stephen J Elledge
- Department of Genetics, Harvard University Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA.
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29
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Shelkovnikova TA, Robinson HK, Southcombe JA, Ninkina N, Buchman VL. Multistep process of FUS aggregation in the cell cytoplasm involves RNA-dependent and RNA-independent mechanisms. Hum Mol Genet 2014; 23:5211-26. [PMID: 24842888 PMCID: PMC4159159 DOI: 10.1093/hmg/ddu243] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Fused in sarcoma (FUS) is an RNA-binding protein involved in pathogenesis of several neurodegenerative diseases. Aggregation of mislocalized FUS into non-amyloid inclusions is believed to be pivotal in the development of cell dysfunction, but the mechanism of their formation is unclear. Using transient expression of a panel of deletion and chimeric FUS variants in various cultured cells, we demonstrated that FUS accumulating in the cytoplasm nucleates a novel type of RNA granules, FUS granules (FGs), that are structurally similar but not identical to physiological RNA transport granules. Formation of FGs requires FUS N-terminal prion-like domain and the ability to bind specific RNAs. Clustering of FGs coupled with further recruitment of RNA and proteins produce larger structures, FUS aggregates (FAs), that resemble but are clearly distinct from stress granules. In conditions of attenuated transcription, FAs lose RNA and dissociate into RNA-free FUS complexes that become precursors of large aggresome-like structures. We propose a model of multistep FUS aggregation involving RNA-dependent and RNA-independent stages. This model can be extrapolated to formation of pathological inclusions in human FUSopathies.
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Affiliation(s)
- Tatyana A Shelkovnikova
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK, Institute of Physiologically Active Compounds Russian Academy of Sciences, 1 Severniy proezd, Chernogolovka 142432, Moscow Region, Russian Federation and
| | - Hannah K Robinson
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK
| | - Joshua A Southcombe
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK
| | - Natalia Ninkina
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK, Institute of General Pathology and Pathophysiology of Russian Academy of Medical Science, 8 Baltijskaya str, Moscow 125315, Russian Federation
| | - Vladimir L Buchman
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK,
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30
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hCLE/C14orf166 associates with DDX1-HSPC117-FAM98B in a novel transcription-dependent shuttling RNA-transporting complex. PLoS One 2014; 9:e90957. [PMID: 24608264 PMCID: PMC3946611 DOI: 10.1371/journal.pone.0090957] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 02/05/2014] [Indexed: 02/05/2023] Open
Abstract
hCLE/C14orf166 is a nuclear and cytoplasmic protein that interacts with the RNAP II, modulates nuclear RNA metabolism and is present in cytoplasmic RNA granules involved in localized translation. Here we have studied whether hCLE shares common interactors in the nucleus and the cytosol, which could shed light on its participation in the sequential phases of RNA metabolism. Nuclear and cytoplasmic purified hCLE-associated factors were identified and proteins involved in mRNA metabolism, motor-related proteins, cytoskeletal and translation-related factors were found. Purified hCLE complexes also contain RNAs and as expected some hCLE-interacting proteins (DDX1, HSPC117, FAM98B) were found both in the nucleus and the cytoplasm. Moreover, endogenous hCLE fractionates in protein complexes together with DDX1, HSPC117 and FAM98B and silencing of hCLE down-regulates their nuclear and cytosolic accumulation levels. Using a photoactivatable hCLE-GFP protein, nuclear import and export of hCLE was observed indicating that hCLE is a shuttling protein. Interestingly, hCLE nuclear import required active transcription, as did the import of DDX1, HSPC117 and FAM98B proteins. The data indicate that hCLE probably as a complex with DDX1, HSPC117 and FAM98B shuttles between the nucleus and the cytoplasm transporting RNAs suggesting that this complex has a prominent role on nuclear and cytoplasmic RNA fate.
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31
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Droppelmann CA, Campos-Melo D, Ishtiaq M, Volkening K, Strong MJ. RNA metabolism in ALS: When normal processes become pathological. Amyotroph Lateral Scler Frontotemporal Degener 2014; 15:321-36. [DOI: 10.3109/21678421.2014.881377] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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32
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Marko M, Leichter M, Patrinou-Georgoula M, Guialis A. Selective interactions of hnRNP M isoforms with the TET proteins TAF15 and TLS/FUS. Mol Biol Rep 2014; 41:2687-95. [PMID: 24474660 DOI: 10.1007/s11033-014-3128-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 01/11/2014] [Indexed: 11/26/2022]
Abstract
The molecular composition of macromolecular assemblies engaged in transcription and splicing influences biogenesis of mRNA transcripts. Preference for one over the other interactive protein partner within those complexes is expected to change the gene expression pattern and to affect subsequent cellular events. We report here the novel and selective associations between RNA-binding proteins, namely the hnRNP M1-4 isoforms-involved in early spliceosome assembly and alternative splicing-and the transcription factors TAF15 and TLS/FUS. In immunoprecipitation studies on HeLa nuclear extracts, TAF15 co-immunoprecipitates preferably with the higher molecular weight hnRNP M3/4 isoforms, opposite to TLS/FUS that associates with the lower molecular weight hnRNP M1/2 species. We demonstrate that these associations can be mediated through direct protein-protein interactions via the amino-termini of the TET proteins, independently of RNA. Finally, we show partial co-localization of TAF15 and TLS/FUS with hnRNP M proteins in HeLa nuclei, supporting the biochemically obtained data. The participation of hnRNP M in an expanding network of protein-protein interactions suggests its important functioning in the coordination of transcriptional and post-transcriptional events.
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Affiliation(s)
- Marija Marko
- Medical Faculty, Institute for Biochemistry I, University of Cologne, Joseph-Stelzmann-Str. 52, 50931, Cologne, Germany,
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33
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Abstract
Motifs rich in arginines and glycines were recognized several decades ago to play functional roles and were termed glycine-arginine-rich (GAR) domains and/or RGG boxes. We review here the evolving functions of the RGG box along with several sequence variations that we collectively term the RGG/RG motif. Greater than 1,000 human proteins harbor the RGG/RG motif, and these proteins influence numerous physiological processes such as transcription, pre-mRNA splicing, DNA damage signaling, mRNA translation, and the regulation of apoptosis. In particular, we discuss the role of the RGG/RG motif in mediating nucleic acid and protein interactions, a function that is often regulated by arginine methylation and partner-binding proteins. The physiological relevance of the RGG/RG motif is highlighted by its association with several diseases including neurological and neuromuscular diseases and cancer. Herein, we discuss the evidence for the emerging diverse functionality of this important motif.
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Affiliation(s)
- Palaniraja Thandapani
- Terry Fox Molecular Oncology Group and Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research and Departments of Oncology and Medicine, McGill University, Montreal, Quebec H3T 1E2, Canada
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34
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Bentmann E, Haass C, Dormann D. Stress granules in neurodegeneration - lessons learnt from TAR DNA binding protein of 43 kDa and fused in sarcoma. FEBS J 2013; 280:4348-70. [DOI: 10.1111/febs.12287] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 03/28/2013] [Accepted: 04/08/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Eva Bentmann
- Adolf Butenandt Institute; Department of Biochemistry; Ludwig Maximilians University; Munich Germany
| | - Christian Haass
- Adolf Butenandt Institute; Department of Biochemistry; Ludwig Maximilians University; Munich Germany
- German Center for Neurodegenerative Diseases (DZNE); Munich Germany
- Munich Cluster for Systems Neurology (SyNergy); Munich Germany
| | - Dorothee Dormann
- Adolf Butenandt Institute; Department of Biochemistry; Ludwig Maximilians University; Munich Germany
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35
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Dormann D, Haass C. Fused in sarcoma (FUS): an oncogene goes awry in neurodegeneration. Mol Cell Neurosci 2013; 56:475-86. [PMID: 23557964 DOI: 10.1016/j.mcn.2013.03.006] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 03/21/2013] [Accepted: 03/22/2013] [Indexed: 12/13/2022] Open
Abstract
Fused in sarcoma (FUS) is a nuclear DNA/RNA binding protein that regulates different steps of gene expression, including transcription, splicing and mRNA transport. FUS has been implicated in neurodegeneration, since mutations in FUS cause familial amyotrophic lateral sclerosis (ALS-FUS) and lead to the cytosolic deposition of FUS in the brain and spinal cord of ALS-FUS patients. Moreover, FUS and two related proteins of the same protein family (FET family) are co-deposited in cytoplasmic inclusions in a subset of patients with frontotemporal lobar degeneration (FTLD-FUS). Cytosolic deposition of these otherwise nuclear proteins most likely causes the loss of a yet unknown essential nuclear function and/or the gain of a toxic function in the cytosol. Here we summarize what is known about the physiological functions of the FET proteins in the nucleus and cytoplasm and review the distinctive pathomechanisms that lead to the deposition of only FUS in ALS-FUS, but all three FET proteins in FTLD-FUS. We suggest that ALS-FUS is caused by a selective dysfunction of FUS, while FTLD-FUS may be caused by a dysfunction of the entire FET family. This article is part of a Special Issue entitled 'RNA and splicing regulation in neurodegeneration'.
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Affiliation(s)
- Dorothee Dormann
- Adolf-Butenandt-Institute, Biochemistry, Ludwig-Maximilians-University, Schillerstr. 44, Munich 80336, Germany.
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