1
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Poulis P, Peske F, Rodnina MV. The many faces of ribosome translocation along the mRNA: reading frame maintenance, ribosome frameshifting and translational bypassing. Biol Chem 2023; 404:755-767. [PMID: 37077160 DOI: 10.1515/hsz-2023-0142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/22/2023] [Indexed: 04/21/2023]
Abstract
In each round of translation elongation, the ribosome translocates along the mRNA by precisely one codon. Translocation is promoted by elongation factor G (EF-G) in bacteria (eEF2 in eukaryotes) and entails a number of precisely-timed large-scale structural rearrangements. As a rule, the movements of the ribosome, tRNAs, mRNA and EF-G are orchestrated to maintain the exact codon-wise step size. However, signals in the mRNA, as well as environmental cues, can change the timing and dynamics of the key rearrangements leading to recoding of the mRNA into production of trans-frame peptides from the same mRNA. In this review, we discuss recent advances on the mechanics of translocation and reading frame maintenance. Furthermore, we describe the mechanisms and biological relevance of non-canonical translocation pathways, such as hungry and programmed frameshifting and translational bypassing, and their link to disease and infection.
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Affiliation(s)
- Panagiotis Poulis
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
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2
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Wright SE, Todd PK. Native functions of short tandem repeats. eLife 2023; 12:e84043. [PMID: 36940239 PMCID: PMC10027321 DOI: 10.7554/elife.84043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/08/2023] [Indexed: 03/21/2023] Open
Abstract
Over a third of the human genome is comprised of repetitive sequences, including more than a million short tandem repeats (STRs). While studies of the pathologic consequences of repeat expansions that cause syndromic human diseases are extensive, the potential native functions of STRs are often ignored. Here, we summarize a growing body of research into the normal biological functions for repetitive elements across the genome, with a particular focus on the roles of STRs in regulating gene expression. We propose reconceptualizing the pathogenic consequences of repeat expansions as aberrancies in normal gene regulation. From this altered viewpoint, we predict that future work will reveal broader roles for STRs in neuronal function and as risk alleles for more common human neurological diseases.
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Affiliation(s)
- Shannon E Wright
- Department of Neurology, University of Michigan–Ann ArborAnn ArborUnited States
- Neuroscience Graduate Program, University of Michigan–Ann ArborAnn ArborUnited States
- Department of Neuroscience, Picower InstituteCambridgeUnited States
| | - Peter K Todd
- Department of Neurology, University of Michigan–Ann ArborAnn ArborUnited States
- VA Ann Arbor Healthcare SystemAnn ArborUnited States
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3
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Wright SE, Rodriguez CM, Monroe J, Xing J, Krans A, Flores BN, Barsur V, Ivanova MI, Koutmou KS, Barmada SJ, Todd PK. CGG repeats trigger translational frameshifts that generate aggregation-prone chimeric proteins. Nucleic Acids Res 2022; 50:8674-8689. [PMID: 35904811 PMCID: PMC9410890 DOI: 10.1093/nar/gkac626] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/13/2022] [Indexed: 11/25/2022] Open
Abstract
CGG repeat expansions in the FMR1 5’UTR cause the neurodegenerative disease Fragile X-associated tremor/ataxia syndrome (FXTAS). These repeats form stable RNA secondary structures that support aberrant translation in the absence of an AUG start codon (RAN translation), producing aggregate-prone peptides that accumulate within intranuclear neuronal inclusions and contribute to neurotoxicity. Here, we show that the most abundant RAN translation product, FMRpolyG, is markedly less toxic when generated from a construct with a non-repetitive alternating codon sequence in place of the CGG repeat. While exploring the mechanism of this differential toxicity, we observed a +1 translational frameshift within the CGG repeat from the arginine to glycine reading frame. Frameshifts occurred within the first few translated repeats and were triggered predominantly by RNA sequence and structural features. Short chimeric R/G peptides form aggregates distinct from those formed by either pure arginine or glycine, and these chimeras induce toxicity in cultured rodent neurons. Together, this work suggests that CGG repeats support translational frameshifting and that chimeric RAN translated peptides may contribute to CGG repeat-associated toxicity in FXTAS and related disorders.
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Affiliation(s)
- Shannon E Wright
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA.,Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Caitlin M Rodriguez
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA.,Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA 84305, USA
| | - Jeremy Monroe
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jiazheng Xing
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amy Krans
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA.,VA Ann Arbor Healthcare System, Ann Arbor, MI 48105, USA
| | - Brittany N Flores
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA.,Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Venkatesha Barsur
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Magdalena I Ivanova
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA.,Biophysics Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kristin S Koutmou
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sami J Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA.,VA Ann Arbor Healthcare System, Ann Arbor, MI 48105, USA
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4
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Johnson SL, Prifti MV, Sujkowski A, Libohova K, Blount JR, Hong L, Tsou WL, Todi SV. Drosophila as a Model of Unconventional Translation in Spinocerebellar Ataxia Type 3. Cells 2022; 11:cells11071223. [PMID: 35406787 PMCID: PMC8997593 DOI: 10.3390/cells11071223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 12/21/2022] Open
Abstract
RNA toxicity contributes to diseases caused by anomalous nucleotide repeat expansions. Recent work demonstrated RNA-based toxicity from repeat-associated, non-AUG-initiated translation (RAN translation). RAN translation occurs around long nucleotide repeats that form hairpin loops, allowing for translation initiation in the absence of a start codon that results in potentially toxic, poly-amino acid repeat-containing proteins. Discovered in Spinocerebellar Ataxia Type (SCA) 8, RAN translation has been documented in several repeat-expansion diseases, including in the CAG repeat-dependent polyglutamine (polyQ) disorders. The ATXN3 gene, which causes SCA3, also known as Machado–Joseph Disease (MJD), contains a CAG repeat that is expanded in disease. ATXN3 mRNA possesses features linked to RAN translation. In this paper, we examined the potential contribution of RAN translation to SCA3/MJD in Drosophila by using isogenic lines that contain homomeric or interrupted CAG repeats. We did not observe unconventional translation in fly neurons or glia. However, our investigations indicate differential toxicity from ATXN3 protein-encoding mRNA that contains pure versus interrupted CAG repeats. Additional work suggests that this difference may be due in part to toxicity from homomeric CAG mRNA. We conclude that Drosophila is not suitable to model RAN translation for SCA3/MJD, but offers clues into the potential pathogenesis stemming from CAG repeat-containing mRNA in this disorder.
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Affiliation(s)
- Sean L. Johnson
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (S.L.J.); (M.V.P.); (A.S.); (K.L.); (J.R.B.); (L.H.); (W.-L.T.)
| | - Matthew V. Prifti
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (S.L.J.); (M.V.P.); (A.S.); (K.L.); (J.R.B.); (L.H.); (W.-L.T.)
| | - Alyson Sujkowski
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (S.L.J.); (M.V.P.); (A.S.); (K.L.); (J.R.B.); (L.H.); (W.-L.T.)
| | - Kozeta Libohova
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (S.L.J.); (M.V.P.); (A.S.); (K.L.); (J.R.B.); (L.H.); (W.-L.T.)
| | - Jessica R. Blount
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (S.L.J.); (M.V.P.); (A.S.); (K.L.); (J.R.B.); (L.H.); (W.-L.T.)
| | - Luke Hong
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (S.L.J.); (M.V.P.); (A.S.); (K.L.); (J.R.B.); (L.H.); (W.-L.T.)
- Department of Neurology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Wei-Ling Tsou
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (S.L.J.); (M.V.P.); (A.S.); (K.L.); (J.R.B.); (L.H.); (W.-L.T.)
| | - Sokol V. Todi
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (S.L.J.); (M.V.P.); (A.S.); (K.L.); (J.R.B.); (L.H.); (W.-L.T.)
- Department of Neurology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Correspondence:
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5
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Koehorst E, Núñez-Manchón J, Ballester-López A, Almendrote M, Lucente G, Arbex A, Chojnacki J, Vázquez-Manrique RP, Gómez-Escribano AP, Pintos-Morell G, Coll-Cantí J, Ramos-Fransi A, Martínez-Piñeiro A, Suelves M, Nogales-Gadea G. Characterization of RAN Translation and Antisense Transcription in Primary Cell Cultures of Patients with Myotonic Dystrophy Type 1. J Clin Med 2021; 10:jcm10235520. [PMID: 34884222 PMCID: PMC8658563 DOI: 10.3390/jcm10235520] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
Myotonic Dystrophy type 1 (DM1) is a muscular dystrophy with a multi-systemic nature. It was one of the first diseases in which repeat associated non-ATG (RAN) translation was described in 2011, but has not been further explored since. In order to enhance our knowledge of RAN translation in DM1, we decided to study the presence of DM1 antisense (DM1-AS) transcripts (the origin of the polyglutamine (polyGln) RAN protein) using RT-PCR and FISH, and that of RAN translation via immunoblotting and immunofluorescence in distinct DM1 primary cell cultures, e.g., myoblasts, skin fibroblasts and lymphoblastoids, from ten patients. DM1-AS transcripts were found in all DM1 cells, with a lower expression in patients compared to controls. Antisense RNA foci were found in the nuclei and cytoplasm of a subset of DM1 cells. The polyGln RAN protein was undetectable in all three cell types with both approaches. Immunoblots revealed a 42 kD polyGln containing protein, which was most likely the TATA-box-binding protein. Immunofluorescence revealed a cytoplasmic aggregate, which co-localized with the Golgi apparatus. Taken together, DM1-AS transcript levels were lower in patients compared to controls and a small portion of the transcripts included the expanded repeat. However, RAN translation was not present in patient-derived DM1 cells, or was in undetectable quantities for the available methods.
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Affiliation(s)
- Emma Koehorst
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
| | - Judit Núñez-Manchón
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
| | - Alfonsina Ballester-López
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain; (R.P.V.-M.); (A.P.G.-E.)
| | - Miriam Almendrote
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Giuseppe Lucente
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Andrea Arbex
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | | | - Rafael P. Vázquez-Manrique
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain; (R.P.V.-M.); (A.P.G.-E.)
- Laboratory of Molecular, Cellular and Genomic Biomedicine, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain
- Joint Unit for Rare Diseases IIS La Fe-CIPF, 46012 Valencia, Spain
| | - Ana Pilar Gómez-Escribano
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain; (R.P.V.-M.); (A.P.G.-E.)
- Laboratory of Molecular, Cellular and Genomic Biomedicine, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain
- Joint Unit for Rare Diseases IIS La Fe-CIPF, 46012 Valencia, Spain
| | - Guillem Pintos-Morell
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
- Reference Unit for Hereditary Metabolic Disorders (MetabERN), Vall d’Hebron University Hospital, 08035 Barcelona, Spain
| | - Jaume Coll-Cantí
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Alba Ramos-Fransi
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Alicia Martínez-Piñeiro
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Mònica Suelves
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
| | - Gisela Nogales-Gadea
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain; (R.P.V.-M.); (A.P.G.-E.)
- Correspondence: ; Tel.: +34-930330530
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6
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McGurk L, Rifai OM, Shcherbakova O, Perlegos AE, Byrns CN, Carranza FR, Zhou HW, Kim HJ, Zhu Y, Bonini NM. Toxicity of pathogenic ataxin-2 in Drosophila shows dependence on a pure CAG repeat sequence. Hum Mol Genet 2021; 30:1797-1810. [PMID: 34077532 PMCID: PMC8444453 DOI: 10.1093/hmg/ddab148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/12/2021] [Accepted: 05/24/2021] [Indexed: 12/31/2022] Open
Abstract
Spinocerebellar ataxia type 2 is a polyglutamine (polyQ) disease associated with an expanded polyQ domain within the protein product of the ATXN2 gene. Interestingly, polyQ repeat expansions in ATXN2 are also associated with amyotrophic lateral sclerosis (ALS) and parkinsonism depending upon the length of the polyQ repeat expansion. The sequence encoding the polyQ repeat also varies with disease presentation: a pure CAG repeat is associated with SCA2, whereas the CAG repeat in ALS and parkinsonism is typically interrupted with the glutamine encoding CAA codon. Here, we asked if the purity of the CAG sequence encoding the polyQ repeat in ATXN2 could impact the toxicity of the ataxin-2 protein in vivo in Drosophila. We found that ataxin-2 encoded by a pure CAG repeat conferred toxicity in the retina and nervous system, whereas ataxin-2 encoded by a CAA-interrupted repeat or CAA-only repeat failed to confer toxicity, despite expression of the protein at similar levels. Furthermore, the CAG-encoded ataxin-2 protein aggregated in the fly eye, while ataxin-2 encoded by either a CAA/G or CAA repeat remained diffuse. The toxicity of the CAG-encoded ataxin-2 protein was also sensitive to the translation factor eIF4H, a known modifier of the toxic GGGGCC repeat in flies. These data indicate that ataxin-2 encoded by a pure CAG versus interrupted CAA/G polyQ repeat domain is associated with differential toxicity, indicating that mechanisms associated with the purity of the sequence of the polyQ domain contribute to disease.
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Affiliation(s)
- Leeanne McGurk
- Division of Cell & Developmental Biology, School of Life Sciences, University of Dundee, Dundee, UK
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Olivia M Rifai
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - China N Byrns
- Neurosciences Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
- Medical Sciences Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Faith R Carranza
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Henry W Zhou
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Hyung-Jun Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Yongqing Zhu
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Nancy M Bonini
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
- Neurosciences Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
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7
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Malik I, Kelley CP, Wang ET, Todd PK. Molecular mechanisms underlying nucleotide repeat expansion disorders. Nat Rev Mol Cell Biol 2021; 22:589-607. [PMID: 34140671 PMCID: PMC9612635 DOI: 10.1038/s41580-021-00382-6] [Citation(s) in RCA: 141] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 02/05/2023]
Abstract
The human genome contains over one million short tandem repeats. Expansion of a subset of these repeat tracts underlies over fifty human disorders, including common genetic causes of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (C9orf72), polyglutamine-associated ataxias and Huntington disease, myotonic dystrophy, and intellectual disability disorders such as Fragile X syndrome. In this Review, we discuss the four major mechanisms by which expansion of short tandem repeats causes disease: loss of function through transcription repression, RNA-mediated gain of function through gelation and sequestration of RNA-binding proteins, gain of function of canonically translated repeat-harbouring proteins, and repeat-associated non-AUG translation of toxic repeat peptides. Somatic repeat instability amplifies these mechanisms and influences both disease age of onset and tissue specificity of pathogenic features. We focus on the crosstalk between these disease mechanisms, and argue that they often synergize to drive pathogenesis. We also discuss the emerging native functions of repeat elements and how their dynamics might contribute to disease at a larger scale than currently appreciated. Lastly, we propose that lynchpins tying these disease mechanisms and native functions together offer promising therapeutic targets with potential shared applications across this class of human disorders.
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Affiliation(s)
- Indranil Malik
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Chase P Kelley
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
- Genetics and Genomics Graduate Program, University of Florida, Gainesville, FL, USA
| | - Eric T Wang
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL, USA.
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA.
- VA Ann Arbor Healthcare System, Ann Arbor, MI, USA.
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8
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Mechanisms of repeat-associated non-AUG translation in neurological microsatellite expansion disorders. Biochem Soc Trans 2021; 49:775-792. [PMID: 33729487 PMCID: PMC8106499 DOI: 10.1042/bst20200690] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/20/2021] [Accepted: 02/23/2021] [Indexed: 02/08/2023]
Abstract
Repeat-associated non-AUG (RAN) translation was discovered in 2011 in spinocerebellar ataxia type 8 (SCA8) and myotonic dystrophy type 1 (DM1). This non-canonical form of translation occurs in all reading frames from both coding and non-coding regions of sense and antisense transcripts carrying expansions of trinucleotide to hexanucleotide repeat sequences. RAN translation has since been reported in 7 of the 53 known microsatellite expansion disorders which mainly present with neurodegenerative features. RAN translation leads to the biosynthesis of low-complexity polymeric repeat proteins with aggregating and cytotoxic properties. However, the molecular mechanisms and protein factors involved in assembling functional ribosomes in absence of canonical AUG start codons remain poorly characterised while secondary repeat RNA structures play key roles in initiating RAN translation. Here, we briefly review the repeat expansion disorders, their complex pathogenesis and the mechanisms of physiological translation initiation together with the known factors involved in RAN translation. Finally, we discuss research challenges surrounding the understanding of pathogenesis and future directions that may provide opportunities for the development of novel therapeutic approaches for this group of incurable neurodegenerative diseases.
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9
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Jazurek-Ciesiolka M, Ciesiolka A, Komur AA, Urbanek-Trzeciak MO, Krzyzosiak WJ, Fiszer A. RAN Translation of the Expanded CAG Repeats in the SCA3 Disease Context. J Mol Biol 2020; 432:166699. [PMID: 33157084 DOI: 10.1016/j.jmb.2020.10.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 01/08/2023]
Abstract
Spinocerebellar ataxia type 3 (SCA3) is a progressive neurodegenerative disorder caused by a CAG repeat expansion in the ATXN3 gene encoding the ataxin-3 protein. Despite extensive research the exact pathogenic mechanisms of SCA3 are still not understood in depth. In the present study, to gain insight into the toxicity induced by the expanded CAG repeats in SCA3, we comprehensively investigated repeat-associated non-ATG (RAN) translation in various cellular models expressing translated or non-canonically translated ATXN3 sequences with an increasing number of CAG repeats. We demonstrate that two SCA3 RAN proteins, polyglutamine (polyQ) and polyalanine (polyA), are found only in the case of CAG repeats of pathogenic length. Despite having distinct cellular localization, RAN polyQ and RAN polyA proteins are very often coexpressed in the same cell, impairing nuclear integrity and inducing apoptosis. We provide for the first time mechanistic insights into SCA3 RAN translation indicating that ATXN3 sequences surrounding the repeat region have an impact on SCA3 RAN translation initiation and efficiency. We revealed that RAN translation of polyQ proteins starts at non-cognate codons upstream of the CAG repeats, whereas RAN polyA proteins are likely translated within repeats. Furthermore, integrated stress response activation enhances SCA3 RAN translation. Our findings suggest that the ATXN3 sequence context plays an important role in triggering SCA3 RAN translation and that SCA3 RAN proteins may cause cellular toxicity.
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Affiliation(s)
- Magdalena Jazurek-Ciesiolka
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Adam Ciesiolka
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Alicja A Komur
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Martyna O Urbanek-Trzeciak
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Agnieszka Fiszer
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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10
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Molecular Dynamics Simulations Suggest a Non-Doublet Decoding Model of -1 Frameshifting by tRNA Ser3. Biomolecules 2019; 9:biom9110745. [PMID: 31752208 PMCID: PMC6920855 DOI: 10.3390/biom9110745] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/14/2019] [Accepted: 11/14/2019] [Indexed: 12/28/2022] Open
Abstract
In-frame decoding in the ribosome occurs through canonical or wobble Watson-Crick pairing of three mRNA codon bases (a triplet) with a triplet of anticodon bases in tRNA. Departures from the triplet-triplet interaction can result in frameshifting, meaning downstream mRNA codons are then read in a different register. There are many mechanisms to induce frameshifting, and most are insufficiently understood. One previously proposed mechanism is doublet decoding, in which only codon bases 1 and 2 are read by anticodon bases 34 and 35, which would lead to -1 frameshifting. In E. coli, tRNASer3GCU can induce -1 frameshifting at alanine (GCA) codons. The logic of the doublet decoding model is that the Ala codon's GC could pair with the tRNASer3's GC, leaving the third anticodon residue U36 making no interactions with mRNA. Under that model, a U36C mutation would still induce -1 frameshifting, but experiments refute this. We perform all-atom simulations of wild-type tRNASer3, as well as a U36C mutant. Our simulations revealed a hydrogen bond between U36 of the anticodon and G1 of the codon. The U36C mutant cannot make this interaction, as it lacks the hydrogen-bond-donating H3. The simulation thus suggests a novel, non-doublet decoding mechanism for -1 frameshifting by tRNASer3 at Ala codons.
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11
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Rodriguez CM, Todd PK. New pathologic mechanisms in nucleotide repeat expansion disorders. Neurobiol Dis 2019; 130:104515. [PMID: 31229686 DOI: 10.1016/j.nbd.2019.104515] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/07/2019] [Accepted: 06/19/2019] [Indexed: 12/14/2022] Open
Abstract
Tandem microsatellite repeats are common throughout the human genome and intrinsically unstable, exhibiting expansions and contractions both somatically and across generations. Instability in a small subset of these repeats are currently linked to human disease, although recent findings suggest more disease-causing repeats await discovery. These nucleotide repeat expansion disorders (NREDs) primarily affect the nervous system and commonly lead to neurodegeneration through toxic protein gain-of-function, protein loss-of-function, and toxic RNA gain-of-function mechanisms. However, the lines between these categories have blurred with recent findings of unconventional Repeat Associated Non-AUG (RAN) translation from putatively non-coding regions of the genome. Here we review two emerging topics in NREDs: 1) The mechanisms by which RAN translation occurs and its role in disease pathogenesis and 2) How nucleotide repeats as RNA and translated proteins influence liquid-liquid phase separation, membraneless organelle dynamics, and nucleocytoplasmic transport. We examine these topics with a particular eye on two repeats: the CGG repeat expansion responsible for Fragile X syndrome and Fragile X-associated Tremor Ataxia Syndrome (FXTAS) and the intronic GGGGCC repeat expansion in C9orf72, the most common inherited cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Our thesis is that these emerging disease mechanisms can inform a broader understanding of the native roles of microsatellites in cellular function and that aberrations in these native processes provide clues to novel therapeutic strategies for these currently untreatable disorders.
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Affiliation(s)
- C M Rodriguez
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA; Department of Genetics, Stanford University, Stanford, CA, USA
| | - P K Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA; VA Ann Arbor Healthcare System, Ann Arbor, MI, USA.
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12
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Adamla F, Rollins J, Newsom M, Snow S, Schosserer M, Heissenberger C, Horrocks J, Rogers AN, Ignatova Z. A Novel Caenorhabditis Elegans Proteinopathy Model Shows Changes in mRNA Translational Frameshifting During Aging. Cell Physiol Biochem 2019; 52:970-983. [PMID: 30977983 DOI: 10.33594/000000067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/26/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND/AIMS Regulation of mRNA translation is central to protein homeostasis and is optimized for speed and accuracy. Spontaneous recoding events occur virtually at any codon but at very low frequency and are commonly assumed to increase as the cell ages. METHODS Here, we leveraged the polyglutamine(polyQ)-frameshifting model of huntingtin exon 1 with CAG repeat length in the pathological range (Htt51Q), which undergoes enhanced non-programmed translational -1 frameshifting. RESULTS In body muscle cells of Caenorhabditis elegans, -1 frameshifting occured at the onset of expression of the zero-frame product, correlated with mRNA level of the non-frameshifted expression and formed aggregates correlated with reduced motility in C. elegans. Spontaneous frameshifting was modulated by IFG-1, the homologue of the nutrient-responsive eukaryotic initiation factor 4G (eIF4G), under normal growth conditions and NSUN-5, a conserved ribosomal RNA methyltransferase, under osmotic stress. CONCLUSION Our results suggest that frameshifting and aggregation occur at even early stages of development and, because of their intrinsic stability, may persist and accelerate the onset of age-related proteinopathies.
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Affiliation(s)
- Frauke Adamla
- Department of Chemistry and Biochemistry, University of Hamburg, Hamburg, Germany
| | - Jarod Rollins
- MDI Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME, USA
| | - Matthew Newsom
- MDI Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME, USA
| | - Santina Snow
- MDI Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME, USA
| | - Markus Schosserer
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Clemens Heissenberger
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Jordan Horrocks
- MDI Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME, USA
| | - Aric N Rogers
- MDI Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME, USA,
| | - Zoya Ignatova
- Department of Chemistry and Biochemistry, University of Hamburg, Hamburg, Germany,
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13
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mRNA-Mediated Duplexes Play Dual Roles in the Regulation of Bidirectional Ribosomal Frameshifting. Int J Mol Sci 2018; 19:ijms19123867. [PMID: 30518074 PMCID: PMC6321510 DOI: 10.3390/ijms19123867] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 11/26/2018] [Accepted: 11/30/2018] [Indexed: 11/17/2022] Open
Abstract
In contrast to -1 programmed ribosomal frameshifting (PRF) stimulation by an RNA pseudoknot downstream of frameshifting sites, a refolding upstream RNA hairpin juxtaposing the frameshifting sites attenuates -1 PRF in human cells and stimulates +1 frameshifting in yeast. This eukaryotic functional mimicry of the internal Shine-Dalgarno (SD) sequence-mediated duplex was confirmed directly in the 70S translation system, indicating that both frameshifting regulation activities of upstream hairpin are conserved between 70S and 80S ribosomes. Unexpectedly, a downstream pseudoknot also possessed two opposing hungry codon-mediated frameshifting regulation activities: attenuation of +1 frameshifting and stimulation of a non-canonical -1 frameshifting within the +1 frameshift-prone CUUUGA frameshifting site in the absence of release factor 2 (RF2) in vitro. However, the -1 frameshifting activity of the downstream pseudoknot is not coupled with its +1 frameshifting attenuation ability. Similarly, the +1 frameshifting activity of the upstream hairpin is not required for its -1 frameshifting attenuation function Thus, each of the mRNA duplexes flanking the two ends of a ribosomal mRNA-binding channel possesses two functions in bi-directional ribosomal frameshifting regulation: frameshifting stimulation and counteracting the frameshifting activity of each other.
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14
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Gao FB, Richter JD, Cleveland DW. Rethinking Unconventional Translation in Neurodegeneration. Cell 2017; 171:994-1000. [PMID: 29149615 DOI: 10.1016/j.cell.2017.10.042] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/16/2017] [Accepted: 10/25/2017] [Indexed: 11/27/2022]
Abstract
Eukaryotic translation is tightly regulated to ensure that protein production occurs at the right time and place. Recent studies on abnormal repeat proteins, especially in age-dependent neurodegenerative diseases caused by nucleotide repeat expansion, have highlighted or identified two forms of unconventional translation initiation: usage of AUG-like sites (near cognates) or repeat-associated non-AUG (RAN) translation. We discuss how repeat proteins may differ due to not just unconventional initiation, but also ribosomal frameshifting and/or imperfect repeat DNA replication, expansion, and repair, and we highlight how research on translation of repeats may uncover insights into the biology of translation and its contribution to disease.
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Affiliation(s)
- Fen-Biao Gao
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Joel D Richter
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605 USA.
| | - Don W Cleveland
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA 92093, USA; Department of Neurosciences, University of California at San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA.
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15
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Kapur M, Monaghan CE, Ackerman SL. Regulation of mRNA Translation in Neurons-A Matter of Life and Death. Neuron 2017; 96:616-637. [PMID: 29096076 DOI: 10.1016/j.neuron.2017.09.057] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 09/20/2017] [Accepted: 09/28/2017] [Indexed: 12/14/2022]
Abstract
Dynamic regulation of mRNA translation initiation and elongation is essential for the survival and function of neural cells. Global reductions in translation initiation resulting from mutations in the translational machinery or inappropriate activation of the integrated stress response may contribute to pathogenesis in a subset of neurodegenerative disorders. Aberrant proteins generated by non-canonical translation initiation may be a factor in the neuron death observed in the nucleotide repeat expansion diseases. Dysfunction of central components of the elongation machinery, such as the tRNAs and their associated enzymes, can cause translational infidelity and ribosome stalling, resulting in neurodegeneration. Taken together, dysregulation of mRNA translation is emerging as a unifying mechanism underlying the pathogenesis of many neurodegenerative disorders.
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Affiliation(s)
- Mridu Kapur
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Caitlin E Monaghan
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA.
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16
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Escalona-Rayo O, Fuentes-Vázquez P, Leyva-Gómez G, Cisneros B, Villalobos R, Magaña JJ, Quintanar-Guerrero D. Nanoparticulate strategies for the treatment of polyglutamine diseases by halting the protein aggregation process. Drug Dev Ind Pharm 2017; 43:871-888. [PMID: 28142290 DOI: 10.1080/03639045.2017.1281949] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Polyglutamine (polyQ) diseases are a class of neurodegenerative disorders that cause cellular dysfunction and, eventually, neuronal death in specific regions of the brain. Neurodegeneration is linked to the misfolding and aggregation of expanded polyQ-containing proteins, and their inhibition is one of major therapeutic strategies used commonly. However, successful treatment has been limited to date because of the intrinsic properties of therapeutic agents (poor water solubility, low bioavailability, poor pharmacokinetic properties), and difficulty in crossing physiological barriers, including the blood-brain barrier (BBB). In order to solve these problems, nanoparticulate systems with dimensions of 1-1000 nm able to incorporate small and macromolecules with therapeutic value, to protect and deliver them directly to the brain, have recently been developed, but their use for targeting polyQ disease-mediated protein misfolding and aggregation remains scarce. This review provides an update of the polyQ protein aggregation process and the development of therapeutic strategies for halting it. The main features that a nanoparticulate system should possess in order to enhance brain delivery are discussed, as well as the different types of materials utilized to produce them. The final part of this review focuses on the potential application of nanoparticulate system strategies to improve the specific and efficient delivery of therapeutic agents to the brain for the treatment of polyQ diseases.
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Affiliation(s)
- Oscar Escalona-Rayo
- a Laboratorio de Investigación y Posgrado en Tecnología Farmacéutica, Facultad de Estudios Superiores Cuautitlán , Universidad Nacional Autónoma de México (UNAM) , Cuautitlán Izcalli , Mexico
| | - Paulina Fuentes-Vázquez
- a Laboratorio de Investigación y Posgrado en Tecnología Farmacéutica, Facultad de Estudios Superiores Cuautitlán , Universidad Nacional Autónoma de México (UNAM) , Cuautitlán Izcalli , Mexico
| | - Gerardo Leyva-Gómez
- b Laboratory of Connective Tissue , CENIAQ, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra , Mexico City , Mexico
| | - Bulmaro Cisneros
- c Department of Genetics and Molecular Biology , CINVESTAV-IPN , Mexico City , Mexico
| | - Rafael Villalobos
- d División de Estudios de Posgrado (Tecnología Farmacéutica), Facultad de Estudios Superiores Cuautitlán , Universidad Nacional Autónoma de México (UNAM) , Cuautitlán Izcalli , Mexico
| | - Jonathan J Magaña
- e Laboratory of Genomic Medicine, Department of Genetics , Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra , Mexico City , Mexico
| | - David Quintanar-Guerrero
- a Laboratorio de Investigación y Posgrado en Tecnología Farmacéutica, Facultad de Estudios Superiores Cuautitlán , Universidad Nacional Autónoma de México (UNAM) , Cuautitlán Izcalli , Mexico
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17
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Griesche N, Schilling J, Weber S, Rohm M, Pesch V, Matthes F, Auburger G, Krauss S. Regulation of mRNA Translation by MID1: A Common Mechanism of Expanded CAG Repeat RNAs. Front Cell Neurosci 2016; 10:226. [PMID: 27774050 PMCID: PMC5054010 DOI: 10.3389/fncel.2016.00226] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 09/20/2016] [Indexed: 12/28/2022] Open
Abstract
Expansion of CAG repeats, which code for the disease-causing polyglutamine protein, is a common feature in polyglutamine diseases. RNA-mediated mechanisms that contribute to neuropathology in polyglutamine diseases are important. RNA-toxicity describes a phenomenon by which the mutant CAG repeat RNA recruits RNA-binding proteins, thereby leading to aberrant function. For example the MID1 protein binds to mutant huntingtin (HTT) RNA, which is linked to Huntington's disease (HD), at its CAG repeat region and induces protein synthesis of mutant protein. But is this mechanism specific to HD or is it a common mechanism in CAG repeat expansion disorders? To answer this question, we have analyzed the interaction between MID1 and three other CAG repeat mRNAs, Ataxin2 (ATXN2), Ataxin3 (ATXN3), and Ataxin7 (ATXN7), that all differ in the sequence flanking the CAG repeat. We show that ATXN2, ATXN3, and ATXN7 bind to MID1 in a CAG repeat length-dependent manner. Furthermore, we show that functionally, in line with what we have previously observed for HTT, the binding of MID1 to ATXN2, ATXN3, and ATXN7 mRNA induces protein synthesis in a repeat length-dependent manner. Our data suggest that regulation of protein translation by the MID1 complex is a common mechanism for CAG repeat containing mRNAs.
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Affiliation(s)
| | | | | | - Marlena Rohm
- German Center for Neurodegenerative Diseases Bonn, Germany
| | - Verena Pesch
- German Center for Neurodegenerative Diseases Bonn, Germany
| | - Frank Matthes
- German Center for Neurodegenerative Diseases Bonn, Germany
| | - Georg Auburger
- Experimental Neurology, Goethe University Medical School Frankfurt, Germany
| | - Sybille Krauss
- German Center for Neurodegenerative Diseases Bonn, Germany
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18
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Atkins JF, Loughran G, Bhatt PR, Firth AE, Baranov PV. Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use. Nucleic Acids Res 2016; 44:7007-78. [PMID: 27436286 PMCID: PMC5009743 DOI: 10.1093/nar/gkw530] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/26/2016] [Indexed: 12/15/2022] Open
Abstract
Genetic decoding is not ‘frozen’ as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational ‘correction’ of problem or ‘savior’ indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5′ or 3′ of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3′ from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression.
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Affiliation(s)
- John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland School of Microbiology, University College Cork, Cork, Ireland Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pramod R Bhatt
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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19
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Saffert P, Adamla F, Schieweck R, Atkins JF, Ignatova Z. An Expanded CAG Repeat in Huntingtin Causes +1 Frameshifting. J Biol Chem 2016; 291:18505-13. [PMID: 27382061 DOI: 10.1074/jbc.m116.744326] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Indexed: 01/08/2023] Open
Abstract
Maintenance of triplet decoding is crucial for the expression of functional protein because deviations either into the -1 or +1 reading frames are often non-functional. We report here that expression of huntingtin (Htt) exon 1 with expanded CAG repeats, implicated in Huntington pathology, undergoes a sporadic +1 frameshift to generate from the CAG repeat a trans-frame AGC repeat-encoded product. This +1 recoding is exclusively detected in pathological Htt variants, i.e. those with expanded repeats with more than 35 consecutive CAG codons. An atypical +1 shift site, UUC C at the 5' end of CAG repeats, which has some resemblance to the influenza A virus shift site, triggers the +1 frameshifting and is enhanced by the increased propensity of the expanded CAG repeats to form a stem-loop structure. The +1 trans-frame-encoded product can directly influence the aggregation of the parental Htt exon 1.
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Affiliation(s)
- Paul Saffert
- From the Institute of Biochemistry, University of Potsdam, 14467 Potsdam, Germany
| | - Frauke Adamla
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Rico Schieweck
- From the Institute of Biochemistry, University of Potsdam, 14467 Potsdam, Germany
| | - John F Atkins
- the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland, and the Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112
| | - Zoya Ignatova
- From the Institute of Biochemistry, University of Potsdam, 14467 Potsdam, Germany, Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany,
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20
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The expanding biology of the C9orf72 nucleotide repeat expansion in neurodegenerative disease. Nat Rev Neurosci 2016; 17:383-95. [PMID: 27150398 DOI: 10.1038/nrn.2016.38] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A nucleotide repeat expansion (NRE) within the chromosome 9 open reading frame 72 (C9orf72) gene was the first of this type of mutation to be linked to multiple neurological conditions, including amyotrophic lateral sclerosis and frontotemporal dementia. The pathogenic mechanisms through which the C9orf72 NRE contributes to these disorders include loss of C9orf72 function and gain-of-function mechanisms of C9orf72 driven by toxic RNA and protein species encoded by the NRE. These mechanisms have been linked to several cellular defects - including nucleocytoplasmic trafficking deficits and nuclear stress - that have been observed in both patients and animal models.
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21
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Green KM, Linsalata AE, Todd PK. RAN translation-What makes it run? Brain Res 2016; 1647:30-42. [PMID: 27060770 DOI: 10.1016/j.brainres.2016.04.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/24/2016] [Accepted: 04/01/2016] [Indexed: 12/14/2022]
Abstract
Nucleotide-repeat expansions underlie a heterogeneous group of neurodegenerative and neuromuscular disorders for which there are currently no effective therapies. Recently, it was discovered that such repetitive RNA motifs can support translation initiation in the absence of an AUG start codon across a wide variety of sequence contexts, and that the products of these atypical translation initiation events contribute to neuronal toxicity. This review examines what we currently know and do not know about repeat associated non-AUG (RAN) translation in the context of established canonical and non-canonical mechanisms of translation initiation. We highlight recent findings related to RAN translation in three repeat expansion disorders: CGG repeats in fragile X-associated tremor ataxia syndrome (FXTAS), GGGGCC repeats in C9orf72 associated amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) and CAG repeats in Huntington disease. These studies suggest that mechanistic differences may exist for RAN translation dependent on repeat type, repeat reading frame, and the surrounding sequence context, but that for at least some repeats, RAN translation retains a dependence on some of the canonical translational initiation machinery. This article is part of a Special Issue entitled SI:RNA Metabolism in Disease.
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Affiliation(s)
- Katelyn M Green
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, United States; Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Alexander E Linsalata
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, United States; Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Peter K Todd
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, United States; Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI, United States; Veterans Affairs Medical Center, Ann Arbor, MI, United States.
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22
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Bañez-Coronel M, Ayhan F, Tarabochia AD, Zu T, Perez BA, Tusi SK, Pletnikova O, Borchelt DR, Ross CA, Margolis RL, Yachnis AT, Troncoso JC, Ranum LPW. RAN Translation in Huntington Disease. Neuron 2016; 88:667-77. [PMID: 26590344 DOI: 10.1016/j.neuron.2015.10.038] [Citation(s) in RCA: 252] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 09/05/2015] [Accepted: 10/15/2015] [Indexed: 11/30/2022]
Abstract
Huntington disease (HD) is caused by a CAG ⋅ CTG expansion in the huntingtin (HTT) gene. While most research has focused on the HTT polyGln-expansion protein, we demonstrate that four additional, novel, homopolymeric expansion proteins (polyAla, polySer, polyLeu, and polyCys) accumulate in HD human brains. These sense and antisense repeat-associated non-ATG (RAN) translation proteins accumulate most abundantly in brain regions with neuronal loss, microglial activation and apoptosis, including caudate/putamen, white matter, and, in juvenile-onset cases, also the cerebellum. RAN protein accumulation and aggregation are length dependent, and individual RAN proteins are toxic to neural cells independent of RNA effects. These data suggest RAN proteins contribute to HD and that therapeutic strategies targeting both sense and antisense genes may be required for efficacy in HD patients. This is the first demonstration that RAN proteins are expressed across an expansion located in an open reading frame and suggests RAN translation may also contribute to other polyglutamine diseases.
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Affiliation(s)
- Monica Bañez-Coronel
- Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Fatma Ayhan
- Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Alex D Tarabochia
- Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Tao Zu
- Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Barbara A Perez
- Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Solaleh Khoramian Tusi
- Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Olga Pletnikova
- Department of Pathology, The John Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David R Borchelt
- Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA; Department of Neuroscience, University of Florida, Gainesville, FL 32610, USA
| | - Christopher A Ross
- Division of Neurobiology, The John Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Psychiatry, The John Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, The John Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pharmacology, The John Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neuroscience, The John Hopkins University School of Medicine, Baltimore, MD 21205, USA; Program in Cellular and Molecular Medicine, The John Hopkins University School of Medicine, Baltimore, MD 21205, USA; Baltimore Huntington's Disease Center, The John Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Russell L Margolis
- Division of Neurobiology, The John Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Psychiatry, The John Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, The John Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neuroscience, The John Hopkins University School of Medicine, Baltimore, MD 21205, USA; Baltimore Huntington's Disease Center, The John Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Anthony T Yachnis
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Juan C Troncoso
- Department of Pathology, The John Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, The John Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Laura P W Ranum
- Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA; Department of Neurology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
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Baranov PV, Atkins JF, Yordanova MM. Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning. Nat Rev Genet 2015; 16:517-29. [PMID: 26260261 DOI: 10.1038/nrg3963] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The non-universality of the genetic code is now widely appreciated. Codes differ between organisms, and certain genes are known to alter the decoding rules in a site-specific manner. Recently discovered examples of decoding plasticity are particularly spectacular. These examples include organisms and organelles with disruptions of triplet continuity during the translation of many genes, viruses that alter the entire genetic code of their hosts and organisms that adjust their genetic code in response to changing environments. In this Review, we outline various modes of alternative genetic decoding and expand existing terminology to accommodate recently discovered manifestations of this seemingly sophisticated phenomenon.
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Affiliation(s)
- Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Ireland
| | - John F Atkins
- 1] School of Biochemistry and Cell Biology, University College Cork, Ireland. [2] Department of Human Genetics, University of Utah, 15 N 2030 E Rm. 7410, Salt Lake City, Utah 84112-5330, USA
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Scoles DR, Ho MHT, Dansithong W, Pflieger LT, Petersen LW, Thai KK, Pulst SM. Repeat Associated Non-AUG Translation (RAN Translation) Dependent on Sequence Downstream of the ATXN2 CAG Repeat. PLoS One 2015; 10:e0128769. [PMID: 26086378 PMCID: PMC4472729 DOI: 10.1371/journal.pone.0128769] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 05/01/2015] [Indexed: 11/18/2022] Open
Abstract
Spinocerebellar ataxia type 2 (SCA2) is a progressive autosomal dominant disorder caused by the expansion of a CAG tract in the ATXN2 gene. The SCA2 disease phenotype is characterized by cerebellar atrophy, gait ataxia, and slow saccades. ATXN2 mutation causes gains of toxic and normal functions of the ATXN2 gene product, ataxin-2, and abnormally slow Purkinje cell firing frequency. Previously we investigated features of ATXN2 controlling expression and noted expression differences for ATXN2 constructs with varying CAG lengths, suggestive of repeat associated non-AUG translation (RAN translation). To determine whether RAN translation occurs for ATXN2 we assembled various ATXN2 constructs with ATXN2 tagged by luciferase, HA or FLAG tags, driven by the CMV promoter or the ATXN2 promoter. Luciferase expression from ATXN2-luciferase constructs lacking the ATXN2 start codon was weak vs AUG translation, regardless of promoter type, and did not increase with longer CAG repeat lengths. RAN translation was detected on western blots by the anti-polyglutamine antibody 1C2 for constructs driven by the CMV promoter but not the ATXN2 promoter, and was weaker than AUG translation. Strong RAN translation was also observed when driving the ATXN2 sequence with the CMV promoter with ATXN2 sequence downstream of the CAG repeat truncated to 18 bp in the polyglutamine frame but not in the polyserine or polyalanine frames. Our data demonstrate that ATXN2 RAN translation is weak compared to AUG translation and is dependent on ATXN2 sequences flanking the CAG repeat.
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Affiliation(s)
- Daniel R. Scoles
- Department of Neurology, University of Utah, 175 North Medical Drive East, 5th Floor, Salt Lake City, Utah, 84132, United States of America
- * E-mail:
| | - Mi H. T. Ho
- Department of Neurology, University of Utah, 175 North Medical Drive East, 5th Floor, Salt Lake City, Utah, 84132, United States of America
| | - Warunee Dansithong
- Department of Neurology, University of Utah, 175 North Medical Drive East, 5th Floor, Salt Lake City, Utah, 84132, United States of America
| | - Lance T. Pflieger
- Department of Neurology, University of Utah, 175 North Medical Drive East, 5th Floor, Salt Lake City, Utah, 84132, United States of America
| | - Lance W. Petersen
- Department of Neurology, University of Utah, 175 North Medical Drive East, 5th Floor, Salt Lake City, Utah, 84132, United States of America
| | - Khanh K. Thai
- Department of Neurology, University of Utah, 175 North Medical Drive East, 5th Floor, Salt Lake City, Utah, 84132, United States of America
| | - Stefan M. Pulst
- Department of Neurology, University of Utah, 175 North Medical Drive East, 5th Floor, Salt Lake City, Utah, 84132, United States of America
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25
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Uversky VN. The intrinsic disorder alphabet. III. Dual personality of serine. INTRINSICALLY DISORDERED PROTEINS 2015; 3:e1027032. [PMID: 28232888 DOI: 10.1080/21690707.2015.1027032] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 02/16/2015] [Accepted: 03/02/2015] [Indexed: 12/23/2022]
Abstract
Proteins are natural polypeptides consisting of 20 major amino acid residues, content and order of which in a given amino acid sequence defines the ability of a related protein to fold into unique functional state or to stay intrinsically disordered. Amino acid sequences code for both foldable (ordered) proteins/domains and for intrinsically disordered proteins (IDPs) and IDP regions (IDPRs), but these sequence codes are dramatically different. This difference starts with a very general property of the corresponding amino acid sequences, namely, their compositions. IDPs/IDPRs are enriched in specific disorder-promoting residues, whereas amino acid sequences of ordered proteins/domains typically contain more order-promoting residues. Therefore, the relative abundances of various amino acids in ordered and disordered proteins can be used to scale amino acids according to their disorder promoting potentials. This review continues a series of publications on the roles of different amino acids in defining the phenomenon of protein intrinsic disorder and represents serine, which is the third most disorder-promoting residue. Similar to previous publications, this review represents some physico-chemical properties of serine and the roles of this residue in structures and functions of ordered proteins, describes major posttranslational modifications tailored to serine, and finally gives an overview of roles of serine in structure and functions of intrinsically disordered proteins.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer Research Institute; Morsani College of Medicine, University of South Florida; Tampa, FL USA; Biology Department; Faculty of Science, King Abdulaziz University; Jeddah, Kingdom of Saudi Arabia; Institute for Biological Instrumentation, Russian Academy of Sciences; Pushchino, Moscow Region, Russia; Laboratory of Structural Dynamics, Stability and Folding of Proteins; Institute of Cytology, Russian Academy of Sciences; St. Petersburg, Russia
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26
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Wojciechowska M, Olejniczak M, Galka-Marciniak P, Jazurek M, Krzyzosiak WJ. RAN translation and frameshifting as translational challenges at simple repeats of human neurodegenerative disorders. Nucleic Acids Res 2014; 42:11849-64. [PMID: 25217582 PMCID: PMC4231732 DOI: 10.1093/nar/gku794] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Repeat-associated disorders caused by expansions of short sequences have been classified as coding and noncoding and are thought to be caused by protein gain-of-function and RNA gain-of-function mechanisms, respectively. The boundary between such classifications has recently been blurred by the discovery of repeat-associated non-AUG (RAN) translation reported in spinocerebellar ataxia type 8, myotonic dystrophy type 1, fragile X tremor/ataxia syndrome and C9ORF72 amyotrophic lateral sclerosis and frontotemporal dementia. This noncanonical translation requires no AUG start codon and can initiate in multiple frames of CAG, CGG and GGGGCC repeats of the sense and antisense strands of disease-relevant transcripts. RNA structures formed by the repeats have been suggested as possible triggers; however, the precise mechanism of the translation initiation remains elusive. Templates containing expansions of microsatellites have also been shown to challenge translation elongation, as frameshifting has been recognized across CAG repeats in spinocerebellar ataxia type 3 and Huntington's disease. Determining the critical requirements for RAN translation and frameshifting is essential to decipher the mechanisms that govern these processes. The contribution of unusual translation products to pathogenesis needs to be better understood. In this review, we present current knowledge regarding RAN translation and frameshifting and discuss the proposed mechanisms of translational challenges imposed by simple repeat expansions.
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Affiliation(s)
- Marzena Wojciechowska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Marta Olejniczak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Paulina Galka-Marciniak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Magdalena Jazurek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
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Fiszer A, Krzyzosiak WJ. Oligonucleotide-based strategies to combat polyglutamine diseases. Nucleic Acids Res 2014; 42:6787-810. [PMID: 24848018 PMCID: PMC4066792 DOI: 10.1093/nar/gku385] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Considerable advances have been recently made in understanding the molecular aspects of pathogenesis and in developing therapeutic approaches for polyglutamine (polyQ) diseases. Studies on pathogenic mechanisms have extended our knowledge of mutant protein toxicity, confirmed the toxicity of mutant transcript and identified other toxic RNA and protein entities. One very promising therapeutic strategy is targeting the causative gene expression with oligonucleotide (ON) based tools. This straightforward approach aimed at halting the early steps in the cascade of pathogenic events has been widely tested for Huntington's disease and spinocerebellar ataxia type 3. In this review, we gather information on the use of antisense oligonucleotides and RNA interference triggers for the experimental treatment of polyQ diseases in cellular and animal models. We present studies testing non-allele-selective and allele-selective gene silencing strategies. The latter include targeting SNP variants associated with mutations or targeting the pathologically expanded CAG repeat directly. We compare gene silencing effectors of various types in a number of aspects, including their design, efficiency in cell culture experiments and pre-clinical testing. We discuss advantages, current limitations and perspectives of various ON-based strategies used to treat polyQ diseases.
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Affiliation(s)
- Agnieszka Fiszer
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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Abstract
Well-established rules of translational initiation have been used as a cornerstone in molecular biology to understand gene expression and to frame fundamental questions on what proteins a cell synthesizes, how proteins work and to predict the consequences of mutations. For a group of neurological diseases caused by the abnormal expansion of short segments of DNA (e.g. CAG•CTG repeats), mutations within or outside of predicted coding and non-coding regions are thought to cause disease by protein gain- or loss-of-function or RNA gain-of-function mechanisms. In contrast to these predictions, the recent discovery of repeat-associated non-ATG (RAN) translation showed expansion mutations can express homopolymeric expansion proteins in all three reading frames without an AUG start codon. This unanticipated, non-canonical type of protein translation is length-and hairpin-dependent, takes place without frameshifting or RNA editing and occurs across a variety of repeat motifs. To date, RAN proteins have been reported in spinocerebellar ataxia type 8 (SCA8), myotonic dystrophy type 1 (DM1), fragile X tremor ataxia syndrome (FXTAS) and C9ORF72 amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD). In this article, we review what is currently known about RAN translation and recent progress toward understanding its contribution to disease.
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Affiliation(s)
| | - Laura P.W. Ranum
- To whom correspondence should be addressed at: Director, Center for NeuroGenetics, Professor of Molecular Genetics and Microbiology, College of Medicine, University of Florida, 2033 Mowry Road, PO Box 103610, Gainesville, FL 32610-3610, USA. Tel: +1-3522945209; Fax: +1-3522738284;
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29
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Depletion of cognate charged transfer RNA causes translational frameshifting within the expanded CAG stretch in huntingtin. Cell Rep 2013; 3:148-59. [PMID: 23352662 DOI: 10.1016/j.celrep.2012.12.019] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Revised: 10/17/2012] [Accepted: 12/28/2012] [Indexed: 11/20/2022] Open
Abstract
Huntington disease (HD), a dominantly inherited neurodegenerative disorder caused by the expansion of a CAG-encoded polyglutamine (polyQ) repeat in huntingtin (Htt), displays a highly heterogeneous etiopathology and disease onset. Here, we show that the translation of expanded CAG repeats in mutant Htt exon 1 leads to a depletion of charged glutaminyl-transfer RNA (tRNA)(Gln-CUG) that pairs exclusively to the CAG codon. This results in translational frameshifting and the generation of various transframe-encoded species that differently modulate the conformational switch to nucleate fibrillization of the parental polyQ protein. Intriguingly, the frameshifting frequency varies strongly among different cell lines and is higher in cells with intrinsically lower concentrations of tRNA(Gln-CUG). The concentration of tRNA(Gln-CUG) also differs among different brain areas in the mouse. We propose that translational frameshifting may act as a significant disease modifier that contributes to the cell-selective neurotoxicity and disease course heterogeneity of HD on both cellular and individual levels.
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Abstract
Frameshifting results from two main mechanisms: genomic insertions or deletions (indels) or programmed ribosomal frameshifting. Whereas indels can disrupt normal protein function, programmed ribosomal frameshifting can result in dual-coding genes, each of which can produce multiple functional products. Here, I summarize technical advances that have made it possible to identify programmed ribosomal frameshifting events in a systematic way. The results of these studies suggest that such frameshifting occurs in all genomes, and I will discuss methods that could help characterize the resulting alternative proteomes.
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Affiliation(s)
- Robin Ketteler
- MRC Laboratory for Molecular Cell Biology, Translational Research Resource Centre, University College London London, UK
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31
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Stochmanski SJ, Therrien M, Laganière J, Rochefort D, Laurent S, Karemera L, Gaudet R, Vyboh K, Van Meyel DJ, Di Cristo G, Dion PA, Gaspar C, Rouleau GA. Expanded ATXN3 frameshifting events are toxic in Drosophila and mammalian neuron models. Hum Mol Genet 2012; 21:2211-8. [PMID: 22337953 DOI: 10.1093/hmg/dds036] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Spinocerebellar ataxia type 3 is caused by the expansion of the coding CAG repeat in the ATXN3 gene. Interestingly, a -1 bp frameshift occurring within an (exp)CAG repeat would henceforth lead to translation from a GCA frame, generating polyalanine stretches instead of polyglutamine. Our results show that transgenic expression of (exp)CAG ATXN3 led to -1 frameshifting events, which have deleterious effects in Drosophila and mammalian neurons. Conversely, transgenic expression of polyglutamine-encoding (exp)CAA ATXN3 was not toxic. Furthermore, (exp)CAG ATXN3 mRNA does not contribute per se to the toxicity observed in our models. Our observations indicate that expanded polyglutamine tracts in Drosophila and mouse neurons are insufficient for the development of a phenotype. Hence, we propose that -1 ribosomal frameshifting contributes to the toxicity associated with (exp)CAG repeats.
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Affiliation(s)
- Shawn J Stochmanski
- Center of Excellence in Neuroscience of the Université de Montréal (CENUM), Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
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Abstract
Machado-Joseph disease (MJD), also known as spinocerebellar ataxia type 3 (SCA3), may be the most common dominantly inherited ataxia in the world. Here I will review historical, clinical, neuropathological, genetic, and pathogenic features of MJD, and finish with a brief discussion of present, and possible future, treatment for this currently incurable disorder. Like many other dominantly inherited ataxias, MJD/SCA3 shows remarkable clinical heterogeneity, reflecting the underlying genetic defect: an unstable CAG trinucleotide repeat that varies in size among affected persons. This pathogenic repeat in MJD/SCA3 encodes an expanded tract of the amino acid glutamine in the disease protein, which is known as ataxin-3. MJD/SCA3 is one of nine identified polyglutamine neurodegenerative diseases which share features of pathogenesis centered on protein misfolding and accumulation. The specific properties of MJD/SCA3 and its disease protein are discussed in light of what is known about the entire class of polyglutamine diseases.
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Affiliation(s)
- Henry Paulson
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200, USA.
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34
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van Eyk CL, McLeod CJ, O'Keefe LV, Richards RI. Comparative toxicity of polyglutamine, polyalanine and polyleucine tracts in Drosophila models of expanded repeat disease. Hum Mol Genet 2011; 21:536-47. [PMID: 22021427 DOI: 10.1093/hmg/ddr487] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Homopolymeric amino acid repeat sequences in proteins are of particular interest due to the discovery that expanded copy numbers of these repeats are the molecular basis for a growing list of human genetic diseases. Repeat copy numbers above a typical normal range of polyglutamine repeats have been found to be the principal pathogenic agents in a number of these diseases, including Huntington's disease. There is emerging evidence that expansions of amino acids encoded by other reading frames of CAG/CUG repeats, including polyalanine and polyleucine, could contribute to toxicity in the 'polyglutamine' diseases. We have therefore used the Drosophila model system to investigate effects of ectopic expression of polyglutamine, polyleucine and polyalanine repeats in vivo to assess their relative toxicities and the common and distinct characteristics of the pathogenesis that they cause. We find that these homopolymeric sequences all exhibit toxicity and are able to form aggregates in Drosophila, although there are marked differences in the degree of toxicity dependent upon the tissue in which they are expressed.
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Affiliation(s)
- Clare L van Eyk
- Discipline of Genetics, School of Molecular & Biomedical Science and ARC Special Research Centre for the Molecular Genetics of Development, The University of Adelaide, Adelaide, South Australia 5005, Australia
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35
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Singhal E, Sen P. Hepatocyte growth factor-induced c-Src-phosphatidylinositol 3-kinase-AKT-mammalian target of rapamycin pathway inhibits dendritic cell activation by blocking IκB kinase activity. Int J Biochem Cell Biol 2011; 43:1134-46. [PMID: 21536148 DOI: 10.1016/j.biocel.2011.04.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 03/23/2011] [Accepted: 04/12/2011] [Indexed: 01/11/2023]
Abstract
Hepatocyte growth factor modulates activation and antigen-presenting cell function of dendritic cells. However, the molecular basis for immunoregulation of dendritic cells by hepatocyte growth factor is undefined. In the current study, we demonstrate that hepatocyte growth factor exhibits inhibitory effect on dendritic cell activation by blocking IκB kinase activity and subsequent nuclear factor-κB activation. Inhibition of IκB kinase is mediated by hepatocyte growth factor-induced activation of c-Src. Proximal signaling events induced in dendritic cells by hepatocyte growth factor include a physical association of c-Src with the hepatocyte growth factor receptor c-MET and concomitant activation of c-Src. Activation of c-Src in turn establishes a complex consisting of phosphatidylinositol 3-kinase and c-MET, and promotes downstream activation of the phosphatidylinositol 3-kinase/AKT pathway and mammalian target of rapamycin. Blocking activation of c-Src, phosphatidylinositol 3-kinase and mammalian target of rapamycin prevents hepatocyte growth factor-induced inhibition of IκB kinase, nuclear factor-κB and dendritic cell activation. Notably, hepatocyte growth factor-stimulated c-Src activation results in induction of phosphatidylinositol 3-kinase complexes p85α/p110α and p85α/p110δ, which is required for activation of mammalian target of rapamycin, and consequent inhibition of IκB kinase and nuclear factor-κB activation. Our findings, for the first time, have identified the c-Src-phosphatidylinositol 3-kinase-AKT-mammalian target of rapamycin pathway that plays a pivotal role in mediating the inhibitory effects of hepatocyte growth factor on dendritic cell activation by blocking nuclear factor-κB signaling.
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Affiliation(s)
- Eshu Singhal
- Division of Cell Biology and Immunology, Institute of Microbial Technology, Council of Scientific and Industrial Research, Sector 39A, Chandigarh 160036, India
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36
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Abstract
Trinucleotide expansions cause disease by both protein- and RNA-mediated mechanisms. Unexpectedly, we discovered that CAG expansion constructs express homopolymeric polyglutamine, polyalanine, and polyserine proteins in the absence of an ATG start codon. This repeat-associated non-ATG translation (RAN translation) occurs across long, hairpin-forming repeats in transfected cells or when expansion constructs are integrated into the genome in lentiviral-transduced cells and brains. Additionally, we show that RAN translation across human spinocerebellar ataxia type 8 (SCA8) and myotonic dystrophy type 1 (DM1) CAG expansion transcripts results in the accumulation of SCA8 polyalanine and DM1 polyglutamine expansion proteins in previously established SCA8 and DM1 mouse models and human tissue. These results have implications for understanding fundamental mechanisms of gene expression. Moreover, these toxic, unexpected, homopolymeric proteins now should be considered in pathogenic models of microsatellite disorders.
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37
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Bettencourt C, Santos C, Montiel R, Costa MDC, Cruz-Morales P, Santos LR, Simões N, Kay T, Vasconcelos J, Maciel P, Lima M. Increased transcript diversity: novel splicing variants of Machado-Joseph disease gene (ATXN3). Neurogenetics 2009; 11:193-202. [PMID: 19714377 DOI: 10.1007/s10048-009-0216-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Accepted: 08/10/2009] [Indexed: 01/14/2023]
Abstract
Machado-Joseph disease (MJD) is a late-onset neurodegenerative disorder that presents clinical heterogeneity not completely explained by its causative mutation. MJD is caused by an expansion of a CAG tract at exon 10 of the ATXN3 gene (14q32.1), which encodes for ataxin-3. The main goal of this study was to analyze the occurrence of alternative splicing at the ATXN3 gene, by sequencing a total of 415 cDNAs clones (from 20 MJD patients and 14 controls). Two novel exons are described for the ATXN3 gene. Fifty-six alternative splicing variants, generated by four types of splicing events, were observed. From those variants, 50 were not previously described, and 26 were only found in MJD patients samples. Most of the variants (85.7%) present frameshift, which leads to the appearance of premature stop codons. Thirty-seven of the observed variants constitute good targets to nonsense-mediated decay, the remaining are likely to be translated into at least 20 different isoforms. The presence of ataxin-3 domains was assessed, and consequences of domain disruption are discussed. The present study demonstrates high variability in the ATXN3 gene transcripts, providing a basis for further investigation on the contribution of alternative splicing to the MJD pathogenic process, as well as to the larger group of the polyglutamine disorders.
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Affiliation(s)
- Conceição Bettencourt
- Center of Research in Natural Resources (CIRN), University of the Azores, Ponta Delgada, Portugal.
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Atkins JF, Björk GR. A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment. Microbiol Mol Biol Rev 2009; 73:178-210. [PMID: 19258537 PMCID: PMC2650885 DOI: 10.1128/mmbr.00010-08] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutants of translation components which compensate for both -1 and +1 frameshift mutations showed the first evidence for framing malleability. Those compensatory mutants isolated in bacteria and yeast with altered tRNA or protein factors are reviewed here and are considered to primarily cause altered P-site realignment and not altered translocation. Though the first sequenced tRNA mutant which suppressed a +1 frameshift mutation had an extra base in its anticodon loop and led to a textbook "yardstick" model in which the number of anticodon bases determines codon size, this model has long been discounted, although not by all. Accordingly, the reviewed data suggest that reading frame maintenance and translocation are two distinct features of the ribosome. None of the -1 tRNA suppressors have anticodon loops with fewer than the standard seven nucleotides. Many of the tRNA mutants potentially affect tRNA bending and/or stability and can be used for functional assays, and one has the conserved C74 of the 3' CCA substituted. The effect of tRNA modification deficiencies on framing has been particularly informative. The properties of some mutants suggest the use of alternative tRNA anticodon loop stack conformations by individual tRNAs in one translation cycle. The mutant proteins range from defective release factors with delayed decoding of A-site stop codons facilitating P-site frameshifting to altered EF-Tu/EF1alpha to mutant ribosomal large- and small-subunit proteins L9 and S9. Their study is revealing how mRNA slippage is restrained except where it is programmed to occur and be utilized.
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Affiliation(s)
- John F Atkins
- BioSciences Institute, University College, Cork, Ireland.
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Richard GF, Kerrest A, Dujon B. Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol Mol Biol Rev 2008; 72:686-727. [PMID: 19052325 PMCID: PMC2593564 DOI: 10.1128/mmbr.00011-08] [Citation(s) in RCA: 335] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Repeated elements can be widely abundant in eukaryotic genomes, composing more than 50% of the human genome, for example. It is possible to classify repeated sequences into two large families, "tandem repeats" and "dispersed repeats." Each of these two families can be itself divided into subfamilies. Dispersed repeats contain transposons, tRNA genes, and gene paralogues, whereas tandem repeats contain gene tandems, ribosomal DNA repeat arrays, and satellite DNA, itself subdivided into satellites, minisatellites, and microsatellites. Remarkably, the molecular mechanisms that create and propagate dispersed and tandem repeats are specific to each class and usually do not overlap. In the present review, we have chosen in the first section to describe the nature and distribution of dispersed and tandem repeats in eukaryotic genomes in the light of complete (or nearly complete) available genome sequences. In the second part, we focus on the molecular mechanisms responsible for the fast evolution of two specific classes of tandem repeats: minisatellites and microsatellites. Given that a growing number of human neurological disorders involve the expansion of a particular class of microsatellites, called trinucleotide repeats, a large part of the recent experimental work on microsatellites has focused on these particular repeats, and thus we also review the current knowledge in this area. Finally, we propose a unified definition for mini- and microsatellites that takes into account their biological properties and try to point out new directions that should be explored in a near future on our road to understanding the genetics of repeated sequences.
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Affiliation(s)
- Guy-Franck Richard
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS, URA2171, Université Pierre et Marie Curie, UFR927, 25 rue du Dr. Roux, F-75015, Paris, France.
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Abu-Baker A, Rouleau GA. Oculopharyngeal muscular dystrophy: Recent advances in the understanding of the molecular pathogenic mechanisms and treatment strategies. Biochim Biophys Acta Mol Basis Dis 2007; 1772:173-85. [PMID: 17110089 DOI: 10.1016/j.bbadis.2006.10.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2006] [Revised: 10/05/2006] [Accepted: 10/06/2006] [Indexed: 12/24/2022]
Abstract
Oculopharyngeal muscular dystrophy (OPMD) is an adult-onset disorder characterized by progressive eyelid drooping, swallowing difficulties and proximal limb weakness. OPMD is caused by a small expansion of a short polyalanine tract in the poly (A) binding protein nuclear 1 protein (PABPN1). The mechanism by which the polyalanine expansion mutation in PABPN1 causes disease is unclear. PABPN1 is a nuclear multi-functional protein which is involved in pre-mRNA polyadenylation, transcription regulation, and mRNA nucleocytoplasmic transport. The distinct pathological hallmark of OPMD is the presence of filamentous intranuclear inclusions (INIs) in patient's skeletal muscle cells. The exact relationship between mutant PABPN1 intranuclear aggregates and pathology is not clear. OPMD is a unique disease sharing common pathogenic features with other polyalanine disorders, as well as with polyglutamine and dystrophic disorders. This chapter aims to review the rapidly growing body of knowledge concerning OPMD. First, we outline the background of OPMD. Second, we compare OPMD with other trinucleotide repeat disorders. Third, we discuss the recent advances in the understanding of the molecular mechanisms underlying OPMD pathogenesis. Finally, we review recent therapeutic strategies for OPMD.
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Affiliation(s)
- Aida Abu-Baker
- Center for the Study of Brain Diseases, CHUM Research Center-Notre Dame Hospital, J.A. de Sève Pavillion, Room Y-3633, 1560, Sherbrooke Street East, Montreal, QC, Canada H2L 4M1
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Heir R, Ablasou C, Dumontier E, Elliott M, Fagotto-Kaufmann C, Bedford FK. The UBL domain of PLIC-1 regulates aggresome formation. EMBO Rep 2006; 7:1252-8. [PMID: 17082820 PMCID: PMC1794689 DOI: 10.1038/sj.embor.7400823] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2005] [Revised: 09/04/2006] [Accepted: 09/04/2006] [Indexed: 12/25/2022] Open
Abstract
Defects in protein folding and the proteasomal pathway have been linked with many neurodegenerative diseases. PLIC-1 (protein linking IAP to the cytoskeleton) is a ubiquitin-like protein that binds to the ubiquitin-interacting motif (UIM) of the proteasomal subunit S5a. Here, we show that PLIC-1 also binds to the UIM proteins ataxin 3--a deubiquitinating enzyme--HSJ1a--a co-chaperone--and EPS15 (epidermal growth factor substrate 15)--an endocytic protein. Using a polyglutamine (polyQ) disease model, we found that both endogenous PLIC-1 and EPS15 localize to perinuclear aggresomes, and that polyQ enhances their in vivo interaction. We show that knockdown of PLIC-1 and EPS15 by RNA interference reduces aggresome formation. In addition, PLIC-1(DeltaUBL) functions as a dominant-negative mutant, blocking both polyQ transport to aggresomes and the association of EPS15 with dispersed aggregates. We also show that PLIC-1 is upregulated by arsenite-induced protein misfolding. These results indicate a role for PLIC-1 in the protein aggregation-stress pathway, and we propose a novel function for the ubiquitin-like (UBL) domain--by means of UBL-UIM interactions--in transport to aggresomes.
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Affiliation(s)
- Renu Heir
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec H3A2B2, Canada
| | - Celine Ablasou
- Laboratoire d'Immunologie Equipe d'Accueil 2686, Faculte de Medecine, Pole Recherche, 1 Place de Verdun, 59045 Lille, France
| | - Emilie Dumontier
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec H3A2B2, Canada
| | - Meghan Elliott
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec H3A2B2, Canada
| | - Christine Fagotto-Kaufmann
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec H3A2B2, Canada
| | - Fiona K Bedford
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec H3A2B2, Canada
- Tel: +1 514 398 1426; Fax: +1 514 398 5047; E-mail:
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Wills NM, Atkins JF. The potential role of ribosomal frameshifting in generating aberrant proteins implicated in neurodegenerative diseases. RNA (NEW YORK, N.Y.) 2006; 12:1149-53. [PMID: 16714280 PMCID: PMC1484430 DOI: 10.1261/rna.84406] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Aberrant forms of proteins ubiquitin B and beta-amyloid precusor protein, UBB+1 and APP+1, are implicated in human neurodegenerative diseases. They have their carboxyl-terminal regions derived from an alternative reading frame. Transcription slippage has been invoked to explain the production of these proteins from abnormal mRNA. However, ribosomal frameshifting on wild-type mRNA may account for the great majority of the aberrant protein. Ribosomal frameshifting may also be involved in the progression of triplet expansion diseases such as Huntington's and spinocerebellar ataxias. In a particular spinocerebellar ataxia, SCA3, Toulouse and colleagues recently discovered -1 frameshifting in a transcript containing an expanded CAG-repeat. Antibiotics that affect mammalian ribosomes may have complex effects on frameshifting and disease progression.
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Affiliation(s)
- Norma M Wills
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
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Abstract
Codon reiteration disorders are caused by abnormal expansions of either polyglutamine or polyalanine tracts within the coding region of a protein. These mutations impair normal protein folding, resulting in aggregate formation in the affected tissues. Huntington's disease is the most common of the nine disorders caused by polyglutamine expansion mutations. The most extensively studied polyalanine expansion disorder is oculopharyngeal muscular dystrophy. There may be a link between diseases caused by polyglutamine and polyalanine expansion mutations as it has been shown that the expanded CAG/polyglutamine tract within the SCA3 gene can shift to the GCA[corrected]/polyalanine frame. Here, we show that this frameshifting phenomenon is more widespread and occurs in Huntington's disease. We have shown both +1 frameshift and +2 frameshift products (which may contain polyalanine or polyserine tracts, respectively) in human postmortem Huntington's disease brains and in a transgenic mouse model of Huntington's disease. Our data suggest that +1 and +2 frameshift products are generated at low levels. This may be relevant to the pathogenesis of human Huntington's disease, as we have previously shown that both polyserine and polyalanine-containing proteins are modifiers of mutant huntingtin toxicity, with low expression levels of polyalanine-containing proteins having a protective effect.
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Wills NM, Moore B, Hammer A, Gesteland RF, Atkins JF. A functional -1 ribosomal frameshift signal in the human paraneoplastic Ma3 gene. J Biol Chem 2006; 281:7082-8. [PMID: 16407312 DOI: 10.1074/jbc.m511629200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A bioinformatics approach to finding new cases of -1 frameshifting in the expression of human genes revealed a classical retrovirus-like heptanucleotide shift site followed by a potential structural stimulator in the paraneoplastic antigen Ma3 and Ma5 genes. Analysis of the sequence 3' of the shift site demonstrated that an RNA pseudoknot in Ma3 is important for promoting efficient -1 frame-shifting. Ma3 is a member of a family of six genes in humans whose protein products contain homology to retroviral Gag proteins. The -1 frameshift site and pseudoknot structure are conserved in other mammals, but there are some sequence differences. Although the functions of the Ma genes are unknown, the serious neurological effects of ectopic expression in tumor cells indicate their importance in the brain.
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Affiliation(s)
- Norma M Wills
- Department of Human Genetics, 15 N. 2030 E., Bldg. 533, University of Utah, Salt Lake City, UT 84112, USA
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Berger Z, Davies JE, Luo S, Pasco MY, Majoul I, O'Kane CJ, Rubinsztein DC. Deleterious and protective properties of an aggregate-prone protein with a polyalanine expansion. Hum Mol Genet 2005; 15:453-65. [PMID: 16371423 DOI: 10.1093/hmg/ddi460] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many aggregate-prone proteins, including proteins with long polyglutamine or polyalanine tracts, cause human diseases. Polyalanine proteins may also be present in the tissue of polyglutamine diseases as a result of frameshifting of the primary polyglutamine-encoding (CAG)n repeat mutation. We have generated a Drosophila model expressing green fluorescent protein tagged to 37 alanines that manifests both toxicity and inclusion formation in various tissues. Surprisingly, we show that this aggregate-prone protein with a polyalanine expansion can also protect against polyglutamine toxicity, which can be explained by induction of heat-shock response. A heat-shock response was also seen in an oculopharyngeal muscular dystrophy mouse model expressing an authentic polyalanine-expanded protein. We also show that long polyalanines can protect against a pro-apoptotic stimulus or the toxicity caused by the long polyalanines themselves. Thus, overexpression of an aggregate-prone protein without any normal functions can result in both pathogenic and protective effects in cell culture and in vivo.
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Affiliation(s)
- Zdenek Berger
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
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Latouche M, Fragner P, Martin E, El Hachimi KH, Zander C, Sittler A, Ruberg M, Brice A, Stevanin G. Polyglutamine and polyalanine expansions in ataxin7 result in different types of aggregation and levels of toxicity. Mol Cell Neurosci 2005; 31:438-45. [PMID: 16325416 DOI: 10.1016/j.mcn.2005.10.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2005] [Revised: 10/14/2005] [Accepted: 10/24/2005] [Indexed: 10/25/2022] Open
Abstract
Spinocerebellar ataxia type 7 (SCA7) is caused by expansion of a (CAG)n repeat in the ataxin7 gene, resulting in an abnormally long polyglutamine polyQ tract in the translated protein that aggregates in the form of neuronal intranuclear inclusions. Polyalanine (polyA) stretches, implicated in several genetic disorders, also appear to aggregate. To investigate the role of the aggregates in the pathologies, we compared the effects of ataxin7 containing a polyA (ataxin7 - 90A) or polyQ (ataxin7 - 100Q) expansion in HEK 293 cells and in primary cultures of rat mesencephalon. Both proteins formed nuclear and perinuclear aggregates that contained molecular chaperones and components of the ubiquitin-proteasome system, suggesting that they were abnormally folded. Ataxin-90A aggregates differed morphologically from ataxin7 - 100Q aggregates, consisted of small and amorphous rather than fibrillar inclusions and were more toxic to mesencephalic neurons, suggesting that toxicity was determined by the type of aggregate rather than the cellular misfolding response.
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Affiliation(s)
- Morwena Latouche
- INSERM U679 (former U289), Neurologie et Thérapeutique Expérimentale, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
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