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Moldovean-Cioroianu NS. Reviewing the Structure-Function Paradigm in Polyglutamine Disorders: A Synergistic Perspective on Theoretical and Experimental Approaches. Int J Mol Sci 2024; 25:6789. [PMID: 38928495 PMCID: PMC11204371 DOI: 10.3390/ijms25126789] [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: 05/16/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Polyglutamine (polyQ) disorders are a group of neurodegenerative diseases characterized by the excessive expansion of CAG (cytosine, adenine, guanine) repeats within host proteins. The quest to unravel the complex diseases mechanism has led researchers to adopt both theoretical and experimental methods, each offering unique insights into the underlying pathogenesis. This review emphasizes the significance of combining multiple approaches in the study of polyQ disorders, focusing on the structure-function correlations and the relevance of polyQ-related protein dynamics in neurodegeneration. By integrating computational/theoretical predictions with experimental observations, one can establish robust structure-function correlations, aiding in the identification of key molecular targets for therapeutic interventions. PolyQ proteins' dynamics, influenced by their length and interactions with other molecular partners, play a pivotal role in the polyQ-related pathogenic cascade. Moreover, conformational dynamics of polyQ proteins can trigger aggregation, leading to toxic assembles that hinder proper cellular homeostasis. Understanding these intricacies offers new avenues for therapeutic strategies by fine-tuning polyQ kinetics, in order to prevent and control disease progression. Last but not least, this review highlights the importance of integrating multidisciplinary efforts to advancing research in this field, bringing us closer to the ultimate goal of finding effective treatments against polyQ disorders.
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Affiliation(s)
- Nastasia Sanda Moldovean-Cioroianu
- Institute of Materials Science, Bioinspired Materials and Biosensor Technologies, Kiel University, Kaiserstraße 2, 24143 Kiel, Germany;
- Faculty of Physics, Babeș-Bolyai University, Kogălniceanu 1, RO-400084 Cluj-Napoca, Romania
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2
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Mier P, Andrade-Navarro MA, Morett E. Homorepeat variability within the human population. NAR Genom Bioinform 2024; 6:lqae053. [PMID: 38774515 PMCID: PMC11106027 DOI: 10.1093/nargab/lqae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/12/2024] [Accepted: 05/08/2024] [Indexed: 05/24/2024] Open
Abstract
Genetic variation within populations plays a crucial role in driving evolution. Unlike the average protein sequence, the evolution of homorepeats can be influenced by DNA replication slippage, when DNA polymerases either add or skip repeats of nucleotides. While there are some diseases known to be caused by abnormal changes in the length of amino acid homorepeats, naturally occurring variations in homorepeat length remain relatively unexplored. In our study, we examined the variation in amino acid homorepeat length of human individuals by analyzing 125 748 exomes, as well as 15 708 whole genomes. Our analyses revealed significant variability in homorepeat length across the human population, indicating that these motifs are prone to mutations at higher rates than non repeat sequences. We focused our study on glutamine homorepeats, also known as polyQ sequences, and found that shorter polyQ sequences tend to exhibit greater length variation, while longer ones primarily undergo deletions. Notably, polyQ sequencesthat are more conserved across primates tend to show less variation within the human population, indicating stronger selective pressure to maintain their length. Overall, our results demonstrate that there is large natural variation in the length of homorepeats within the human population, with no apparent impact on observable traits.
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Affiliation(s)
- Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Miguel A Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Enrique Morett
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 2001, Cuernavaca, Morelos 62210, Mexico
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3
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Chuang CN, Liu HC, Woo TT, Chao JL, Chen CY, Hu HT, Hsueh YP, Wang TF. Noncanonical usage of stop codons in ciliates expands proteins with structurally flexible Q-rich motifs. eLife 2024; 12:RP91405. [PMID: 38393970 PMCID: PMC10942620 DOI: 10.7554/elife.91405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024] Open
Abstract
Serine(S)/threonine(T)-glutamine(Q) cluster domains (SCDs), polyglutamine (polyQ) tracts and polyglutamine/asparagine (polyQ/N) tracts are Q-rich motifs found in many proteins. SCDs often are intrinsically disordered regions that mediate protein phosphorylation and protein-protein interactions. PolyQ and polyQ/N tracts are structurally flexible sequences that trigger protein aggregation. We report that due to their high percentages of STQ or STQN amino acid content, four SCDs and three prion-causing Q/N-rich motifs of yeast proteins possess autonomous protein expression-enhancing activities. Since these Q-rich motifs can endow proteins with structural and functional plasticity, we suggest that they represent useful toolkits for evolutionary novelty. Comparative Gene Ontology (GO) analyses of the near-complete proteomes of 26 representative model eukaryotes reveal that Q-rich motifs prevail in proteins involved in specialized biological processes, including Saccharomyces cerevisiae RNA-mediated transposition and pseudohyphal growth, Candida albicans filamentous growth, ciliate peptidyl-glutamic acid modification and microtubule-based movement, Tetrahymena thermophila xylan catabolism and meiosis, Dictyostelium discoideum development and sexual cycles, Plasmodium falciparum infection, and the nervous systems of Drosophila melanogaster, Mus musculus and Homo sapiens. We also show that Q-rich-motif proteins are expanded massively in 10 ciliates with reassigned TAAQ and TAGQ codons. Notably, the usage frequency of CAGQ is much lower in ciliates with reassigned TAAQ and TAGQ codons than in organisms with expanded and unstable Q runs (e.g. D. melanogaster and H. sapiens), indicating that the use of noncanonical stop codons in ciliates may have coevolved with codon usage biases to avoid triplet repeat disorders mediated by CAG/GTC replication slippage.
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Affiliation(s)
| | - Hou-Cheng Liu
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
| | - Tai-Ting Woo
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
| | - Ju-Lan Chao
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
| | - Chiung-Ya Chen
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
| | - Hisao-Tang Hu
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
| | - Yi-Ping Hsueh
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
- Department of Biochemical Science and Technology, National Chiayi UniversityChiayiTaiwan
| | - Ting-Fang Wang
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
- Department of Biochemical Science and Technology, National Chiayi UniversityChiayiTaiwan
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4
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Geijtenbeek KW, Aranda AS, Sanz AS, Janzen J, Bury AE, Kors S, Al Amery N, Schmitz NCM, Reits EAJ, Schipper-Krom S. Insulin-Degrading Enzyme Efficiently Degrades polyQ Peptides but not Expanded polyQ Huntingtin Fragments. J Huntingtons Dis 2024; 13:201-214. [PMID: 38640164 DOI: 10.3233/jhd-230583] [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] [Indexed: 04/21/2024]
Abstract
Background Huntington's disease is an inheritable autosomal dominant disorder caused by an expanded CAG trinucleotide repeat within the Huntingtin gene, leading to a polyglutamine (polyQ) expansion in the mutant protein. Objective A potential therapeutic approach for delaying or preventing the onset of the disease involves enhancing the degradation of the aggregation-prone polyQ-expanded N-terminal mutant huntingtin (mHTT) exon1 fragment. A few proteases and peptidases have been identified that are able to cleave polyQ fragments with low efficiency. This study aims to identify a potent polyQ-degrading endopeptidase. Methods Here we used quenched polyQ peptides to identify a polyQ-degrading endopeptidase. Next we investigated its role on HTT turnover, using purified polyQ-expanded HTT fragments and striatal cells expressing mHTT exon1 peptides. Results We identified insulin-degrading enzyme (IDE) as a novel endopeptidase for degrading polyQ peptides. IDE was, however, ineffective in reducing purified polyQ-expanded HTT fragments. Similarly, in striatal cells expressing mHTT exon1 peptides, IDE did not enhance mHTT turnover. Conclusions This study shows that despite IDE's efficiency in degrading polyQ peptides, it does not contribute to the direct degradation of polyQ-expanded mHTT fragments.
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Affiliation(s)
- Karlijne W Geijtenbeek
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Angela Santiago Aranda
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Alicia Sanz Sanz
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Jolien Janzen
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Aleksandra E Bury
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Suzan Kors
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | | | - Nina C M Schmitz
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Eric A J Reits
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Sabine Schipper-Krom
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
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5
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Mier P, Andrade-Navarro MA. The nucleotide landscape of polyXY regions. Comput Struct Biotechnol J 2023; 21:5408-5412. [PMID: 38022702 PMCID: PMC10652141 DOI: 10.1016/j.csbj.2023.10.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023] Open
Abstract
PolyXY regions are compositionally biased regions composed of two different amino acids. They are classified according to the arrangement of the two amino acid types 'X' and 'Y' into direpeats (composed of alternating amino acids, e.g. 'XYXYXY'), joined (composed of two consecutive stretches of each amino acid, e.g. 'XXXYYY') and shuffled (other arrangements, e.g., 'XYXXYY'). They have been characterized at the amino acid level in all domains of life, and are described as often found within intrinsically disordered regions. Since DNA replication slippage has been proposed as a driver of repeat variation, and given that some polyXY have a repetitive nature, we hypothesized that characterizing the nucleotide coding of various types of polyXY could give hints about their origin and evolution. To test this, we obtained all polyXY regions in the human transcriptome, categorized them, and studied their coding nucleotide sequences. We observed that polyXY exacerbates the codon biases, and that the similarity between the X and Y codons is higher than in the background proteome. Our results support a general mechanism of emergence and evolution of polyXY from single-codon polyX. PolyXY are revealed as hotspots for replication slippage, particularly those composed of repeats: joined and direpeat polyXY. Inter-conversion to shuffled polyXY disrupts nucleotide repeats and restricts further evolution by replication slippage, a mechanism that we previously observed in polyX. Our results shed light on polyXY composition and should simplify the determination of their functions.
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Affiliation(s)
- Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Miguel A. Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
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6
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Koppenol R, Conceição A, Afonso IT, Afonso-Reis R, Costa RG, Tomé S, Teixeira D, da Silva JP, Côdesso JM, Brito DVC, Mendonça L, Marcelo A, Pereira de Almeida L, Matos CA, Nóbrega C. The stress granule protein G3BP1 alleviates spinocerebellar ataxia-associated deficits. Brain 2023; 146:2346-2363. [PMID: 36511898 PMCID: PMC10232246 DOI: 10.1093/brain/awac473] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 11/04/2022] [Accepted: 11/25/2022] [Indexed: 09/09/2023] Open
Abstract
Polyglutamine diseases are a group of neurodegenerative disorders caused by an abnormal expansion of CAG repeat tracts in the codifying regions of nine, otherwise unrelated, genes. While the protein products of these genes are suggested to play diverse cellular roles, the pathogenic mutant proteins bearing an expanded polyglutamine sequence share a tendency to self-assemble, aggregate and engage in abnormal molecular interactions. Understanding the shared paths that link polyglutamine protein expansion to the nervous system dysfunction and the degeneration that takes place in these disorders is instrumental to the identification of targets for therapeutic intervention. Among polyglutamine diseases, spinocerebellar ataxias (SCAs) share many common aspects, including the fact that they involve dysfunction of the cerebellum, resulting in ataxia. Our work aimed at exploring a putative new therapeutic target for the two forms of SCA with higher worldwide prevalence, SCA type 2 (SCA2) and type 3 (SCA3), which are caused by expanded forms of ataxin-2 (ATXN2) and ataxin-3 (ATXN3), respectively. The pathophysiology of polyglutamine diseases has been described to involve an inability to properly respond to cell stress. We evaluated the ability of GTPase-activating protein-binding protein 1 (G3BP1), an RNA-binding protein involved in RNA metabolism regulation and stress responses, to counteract SCA2 and SCA3 pathology, using both in vitro and in vivo disease models. Our results indicate that G3BP1 overexpression in cell models leads to a reduction of ATXN2 and ATXN3 aggregation, associated with a decrease in protein expression. This protective effect of G3BP1 against polyglutamine protein aggregation was reinforced by the fact that silencing G3bp1 in the mouse brain increases human expanded ATXN2 and ATXN3 aggregation. Moreover, a decrease of G3BP1 levels was detected in cells derived from patients with SCA2 and SCA3, suggesting that G3BP1 function is compromised in the context of these diseases. In lentiviral mouse models of SCA2 and SCA3, G3BP1 overexpression not only decreased protein aggregation but also contributed to the preservation of neuronal cells. Finally, in an SCA3 transgenic mouse model with a severe ataxic phenotype, G3BP1 lentiviral delivery to the cerebellum led to amelioration of several motor behavioural deficits. Overall, our results indicate that a decrease in G3BP1 levels may be a contributing factor to SCA2 and SCA3 pathophysiology, and that administration of this protein through viral vector-mediated delivery may constitute a putative approach to therapy for these diseases, and possibly other polyglutamine disorders.
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Affiliation(s)
- Rebekah Koppenol
- ABC-RI, Algarve Biomedical Center Research Institute, 8005-139 Faro, Portugal
- PhD Program in Biomedial Sciences, Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139 Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139 Faro, Portugal
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
| | - André Conceição
- ABC-RI, Algarve Biomedical Center Research Institute, 8005-139 Faro, Portugal
- PhD Program in Biomedial Sciences, Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139 Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139 Faro, Portugal
| | - Inês T Afonso
- ABC-RI, Algarve Biomedical Center Research Institute, 8005-139 Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139 Faro, Portugal
| | - Ricardo Afonso-Reis
- ABC-RI, Algarve Biomedical Center Research Institute, 8005-139 Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139 Faro, Portugal
| | - Rafael G Costa
- ABC-RI, Algarve Biomedical Center Research Institute, 8005-139 Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139 Faro, Portugal
| | - Sandra Tomé
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Diogo Teixeira
- ABC-RI, Algarve Biomedical Center Research Institute, 8005-139 Faro, Portugal
| | | | - José Miguel Côdesso
- ABC-RI, Algarve Biomedical Center Research Institute, 8005-139 Faro, Portugal
- PhD Program in Biomedial Sciences, Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139 Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139 Faro, Portugal
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
| | - David V C Brito
- ABC-RI, Algarve Biomedical Center Research Institute, 8005-139 Faro, Portugal
| | - Liliana Mendonça
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Adriana Marcelo
- ABC-RI, Algarve Biomedical Center Research Institute, 8005-139 Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139 Faro, Portugal
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Luís Pereira de Almeida
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Carlos A Matos
- ABC-RI, Algarve Biomedical Center Research Institute, 8005-139 Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139 Faro, Portugal
| | - Clévio Nóbrega
- ABC-RI, Algarve Biomedical Center Research Institute, 8005-139 Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139 Faro, Portugal
- Champalimaud Research Program, Champalimaud Center for the Unknown, 1400-038 Lisbon, Portugal
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Sousa A, Rocha S, Vieira J, Reboiro-Jato M, López-Fernández H, Vieira CP. On the identification of potential novel therapeutic targets for spinocerebellar ataxia type 1 (SCA1) neurodegenerative disease using EvoPPI3. J Integr Bioinform 2023; 20:jib-2022-0056. [PMID: 36848492 PMCID: PMC10561075 DOI: 10.1515/jib-2022-0056] [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: 11/06/2022] [Accepted: 11/26/2022] [Indexed: 03/01/2023] Open
Abstract
EvoPPI (http://evoppi.i3s.up.pt), a meta-database for protein-protein interactions (PPI), has been upgraded (EvoPPI3) to accept new types of data, namely, PPI from patients, cell lines, and animal models, as well as data from gene modifier experiments, for nine neurodegenerative polyglutamine (polyQ) diseases caused by an abnormal expansion of the polyQ tract. The integration of the different types of data allows users to easily compare them, as here shown for Ataxin-1, the polyQ protein involved in spinocerebellar ataxia type 1 (SCA1) disease. Using all available datasets and the data here obtained for Drosophila melanogaster wt and exp Ataxin-1 mutants (also available at EvoPPI3), we show that, in humans, the Ataxin-1 network is much larger than previously thought (380 interactors), with at least 909 interactors. The functional profiling of the newly identified interactors is similar to the ones already reported in the main PPI databases. 16 out of 909 interactors are putative novel SCA1 therapeutic targets, and all but one are already being studied in the context of this disease. The 16 proteins are mainly involved in binding and catalytic activity (mainly kinase activity), functional features already thought to be important in the SCA1 disease.
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Affiliation(s)
- André Sousa
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135Porto, Portugal
| | - Sara Rocha
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135Porto, Portugal
| | - Jorge Vieira
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135Porto, Portugal
| | - Miguel Reboiro-Jato
- Department of Computer Science, CINBIO, Universidade de Vigo, ESEI – Escuela Superior de Ingeniería Informática, 32004Ourense, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain
| | - Hugo López-Fernández
- Department of Computer Science, CINBIO, Universidade de Vigo, ESEI – Escuela Superior de Ingeniería Informática, 32004Ourense, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain
| | - Cristina P. Vieira
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135Porto, Portugal
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8
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Tan D, Wei C, Chen Z, Huang Y, Deng J, Li J, Liu Y, Bao X, Xu J, Hu Z, Wang S, Fan Y, Jiang Y, Wu Y, Wu Y, Wang S, Liu P, Zhang Y, Yang Z, Jiang Y, Zhang H, Hong D, Zhong N, Jiang H, Xiong H. CAG Repeat Expansion in THAP11 Is Associated with a Novel Spinocerebellar Ataxia. Mov Disord 2023. [PMID: 37148549 DOI: 10.1002/mds.29412] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/22/2023] [Accepted: 04/05/2023] [Indexed: 05/08/2023] Open
Abstract
BACKGROUND More than 50 loci are associated with spinocerebellar ataxia (SCA), and the most frequent subtypes share nucleotide repeats expansion, especially CAG expansion. OBJECTIVE The objective of this study was to confirm a novel SCA subtype caused by CAG expansion. METHODS We performed long-read whole-genome sequencing combined with linkage analysis in a five-generation Chinese family, and the finding was validated in another pedigree. The three-dimensional structure and function of THAP11 mutant protein were predicted. Polyglutamine (polyQ) toxicity of THAP11 gene with CAG expansion was assessed in skin fibroblasts of patients, human embryonic kidney 293 and Neuro-2a cells. RESULTS We identified THAP11 as the novel causative SCA gene with CAG repeats ranging from 45 to 100 in patients with ataxia and from 20 to 38 in healthy control subjects. Among the patients, the number of CAA interruptions within CAG repeats was decreased to 3 (up to 5-6 in controls), whereas the number of 3' pure CAG repeats was up to 32 to 87 (4-16 in controls), suggesting that the toxicity of polyQ protein was length dependent on the pure CAG repeats. Intracellular aggregates were observed in cultured skin fibroblasts from patients. THAP11 polyQ protein was more intensely distributed in the cytoplasm of cultured skin fibroblasts from patients, which was replicated with in vitro cultured neuro-2a transfected with 54 or 100 CAG repeats. CONCLUSIONS This study identified a novel SCA subtype caused by intragenic CAG repeat expansion in THAP11 with intracellular aggregation of THAP11 polyQ protein. Our findings extended the spectrum of polyQ diseases and offered a new perspective in understanding polyQ-mediated toxic aggregation. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Dandan Tan
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
| | - Cuijie Wei
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
| | - Zhao Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Yu Huang
- Department of Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, P.R. China
| | - Jianwen Deng
- Department of Neurology, Peking University First Hospital, Beijing, P.R. China
| | | | - Yidan Liu
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
| | - Xinhua Bao
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, P.R. China
| | - Jin Xu
- Center of Ultrastructural Pathology, Lab of Electron Microscopy, Peking University First Hospital, Beijing, P.R. China
| | - Zhengmao Hu
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, P.R. China
| | - Suxia Wang
- Center of Ultrastructural Pathology, Lab of Electron Microscopy, Peking University First Hospital, Beijing, P.R. China
| | - Yanbin Fan
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
| | - Yizheng Jiang
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, P.R. China
| | - Ye Wu
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, P.R. China
| | - Yuan Wu
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
| | - Shuang Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
| | - Panyan Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Yuehua Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, P.R. China
| | - Zhixian Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, P.R. China
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, P.R. China
| | - Hong Zhang
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Peking University Health Science Center, Beijing, P.R. China
| | - Daojun Hong
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, P.R. China
| | - Nanbert Zhong
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, USA
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, P.R. China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, P.R. China
- National Clinical Research Center for Geriatric Diseases, Central South University, Changsha, P.R. China
- National International Collaborative Research Center for Medical Metabolomics, Central South University, Changsha, P.R. China
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Hui Xiong
- Department of Pediatrics, Peking University First Hospital, Beijing, P.R. China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, P.R. China
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Sousa e Silva R, Sousa AD, Vieira J, Vieira CP. The Josephin domain (JD) containing proteins are predicted to bind to the same interactors: Implications for spinocerebellar ataxia type 3 (SCA3) studies using Drosophila melanogaster mutants. Front Mol Neurosci 2023; 16:1140719. [PMID: 37008788 PMCID: PMC10050893 DOI: 10.3389/fnmol.2023.1140719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/21/2023] [Indexed: 03/17/2023] Open
Abstract
Spinocerebellar ataxia type 3, also known as Machado-Joseph disease (SCA3/ MJD), is the most frequent polyglutamine (polyQ) neurodegenerative disorder. It is caused by a pathogenic expansion of the polyQ tract, located at the C-terminal region of the protein encoded by the ATXN3 gene. This gene codes for a deubiquitinating enzyme (DUB) that belongs to a gene family, that in humans is composed by three more genes (ATXN3L, JOSD1, and JOSD2), that define two gene lineages (the ATXN3 and the Josephins). These proteins have in common the N-terminal catalytic domain (Josephin domain, JD), that in Josephins is the only domain present. In ATXN3 knock-out mouse and nematode models, the SCA3 neurodegeneration phenotype is not, however, reproduced, suggesting that in the genome of these species there are other genes that are able to compensate for the lack of ATXN3. Moreover, in mutant Drosophila melanogaster, where the only JD protein is coded by a Josephin-like gene, expression of the expanded human ATXN3 gene reproduces multiple aspects of the SCA3 phenotype, in contrast with the results of the expression of the wild type human form. In order to explain these findings, phylogenetic, as well as, protein–protein docking inferences are here performed. Here we show multiple losses of JD containing genes across the animal kingdom, suggesting partial functional redundancy of these genes. Accordingly, we predict that the JD is essential for binding with ataxin-3 and proteins of the Josephin lineages, and that D. melanogaster mutants are a good model of SCA3 despite the absence of a gene from the ATXN3 lineage. The molecular recognition regions of the ataxin-3 binding and those predicted for the Josephins are, however, different. We also report different binding regions between the two ataxin-3 forms (wild-type (wt) and expanded (exp)). The interactors that show an increase in the interaction strength with exp ataxin-3, are enriched in extrinsic components of mitochondrial outer membrane and endoplasmatic reticulum membrane. On the other hand, the group of interactors that show a decrease in the interaction strength with exp ataxin-3 is significantly enriched in extrinsic component of cytoplasm.
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Shukla S, Lazarchuk P, Pavlova MN, Sidorova JM. Genome-wide survey of D/E repeats in human proteins uncovers their instability and aids in identifying their role in the chromatin regulator ATAD2. iScience 2022; 25:105464. [PMCID: PMC9672403 DOI: 10.1016/j.isci.2022.105464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/03/2022] [Accepted: 10/26/2022] [Indexed: 11/15/2022] Open
Abstract
D/E repeats are stretches of aspartic and/or glutamic acid residues found in over 150 human proteins. We examined genomic stability of D/E repeats and functional characteristics of D/E repeat-containing proteins vis-à-vis the proteins with poly-Q or poly-A repeats, which are known to undergo pathologic expansions. Mining of tumor sequencing data revealed that D/E repeat-coding regions are similar to those coding poly-Qs and poly-As in increased incidence of trinucleotide insertions/deletions but differ in types and incidence of substitutions. D/E repeat-containing proteins preferentially function in chromatin metabolism and are the more likely to be nuclear and interact with core histones, the longer their repeats are. One of the longest D/E repeats of unknown function is in ATAD2, a bromodomain family ATPase frequently overexpressed in tumors. We demonstrate that D/E repeat deletion in ATAD2 suppresses its binding to nascent and mature chromatin and to the constitutive pericentromeric heterochromatin, where ATAD2 represses satellite transcription. Many human proteins contain runs of aspartic/glutamic acid residues (D/E repeats) D/E repeats show increased incidence of in-frame insertions/deletions in tumors Nuclear and histone-interacting proteins often have long D/E repeats D/E repeat of the oncogene ATAD2 controls its binding to pericentric chromatin
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Affiliation(s)
- Shalabh Shukla
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific St., Box 357705, Seattle, WA 98195, USA
| | - Pavlo Lazarchuk
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific St., Box 357705, Seattle, WA 98195, USA
| | - Maria N. Pavlova
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific St., Box 357705, Seattle, WA 98195, USA
| | - Julia M. Sidorova
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific St., Box 357705, Seattle, WA 98195, USA
- Corresponding author
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Mier P, Andrade-Navarro MA. Regions with two amino acids in protein sequences: a step forward from homorepeats into the low complexity landscape. Comput Struct Biotechnol J 2022; 20:5516-5523. [PMID: 36249567 PMCID: PMC9550522 DOI: 10.1016/j.csbj.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
Low complexity regions (LCRs) differ in amino acid composition from the background provided by the corresponding proteomes. The simplest LCRs are homorepeats (or polyX), regions composed of mostly-one amino acid type. Extensive research has been done to characterize homorepeats, and their taxonomic, functional and structural features depend on the amino acid type and sequence context. From them, the next step towards the study of LCRs are the regions composed of two types of amino acids, which we call polyXY. We classify polyXY in three categories based on the arrangement of the two amino acid types ‘X’ and ‘Y’: direpeats (e.g. ‘XYXYXY’), joined (e.g. ‘XXXYYY’) and shuffled (e.g. ‘XYYXXY’). We developed a script to search for polyXY, and located them in a comprehensive set of 20,340 reference proteomes. These results are available in a dedicated web server called XYs, in which the user can also submit their own protein datasets to detect polyXY. We studied the distribution of polyXY types by amino acid pair XY and category, and show that polyXY in Eukaryota are mainly located within intrinsically disordered regions. Our study provides a first step towards the characterization of polyXY as protein motifs.
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Affiliation(s)
- Pablo Mier
- Corresponding author at: Hanns-Dieter-Hüsch-Weg 15 55118 Mainz (Germany).
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