1
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Falsaperla R, Sortino V, Schinocca MA, Fusto G, Rizzo R, Barberi C, Ruggieri M, Pappalardo XG. PURA-Related Neurodevelopmental Disorders with Epilepsy Treated with Ketogenic Diet: A Case-Based Review. Genes (Basel) 2024; 15:848. [PMID: 39062627 PMCID: PMC11276249 DOI: 10.3390/genes15070848] [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: 06/10/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
PURA syndrome is a congenital developmental disorder caused by de novo mutations in the PURA gene, which encodes a DNA/RNA-binding protein essential for transcriptional and translational regulation. We present the case of an 11-year-old patient with a de novo frameshift variant in the PURA gene, identified through whole exome sequencing (WES). In addition to the classical PURA deficiency phenotype, our patient exhibited pronounced sialorrhea and seizures, which were effectively treated with the ketogenic diet (KD). Our integrative approach, combining a literature review and bioinformatics data, has led to the first documented clinical case showing improvement in both sialorrhea and seizures with KD treatment, a phenomenon not previously reported. Although a direct relationship between the de novo PURA mutation and the KD was not established, we identified a novel frameshift deletion associated with a new clinical phenotype.
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Affiliation(s)
- Raffaele Falsaperla
- Neonatal Intensive Care Unit and Neonatal Accompaniment Unit, Azienda Ospedaliero-Universitaria Policlinico “Rodolico-San Marco”, San Marco Hospital, University of Catania, 95123 Catania, Italy
- Unit of Pediatrics and Pediatric Emergency, Azienda Ospedaliero-Universitaria Policlinico “Rodolico-San Marco”, San Marco Hospital, 95123 Catania, Italy;
- Department of Medical Science-Pediatrics, University of Ferrara, 44124 Ferrara, Italy
| | - Vincenzo Sortino
- Unit of Pediatrics and Pediatric Emergency, Azienda Ospedaliero-Universitaria Policlinico “Rodolico-San Marco”, San Marco Hospital, 95123 Catania, Italy;
| | - Marina Antonietta Schinocca
- Postgraduate Training Program in Pediatrics, Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy;
| | - Gaia Fusto
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95123 Catania, Italy; (G.F.); (R.R.); (X.G.P.)
| | - Roberta Rizzo
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95123 Catania, Italy; (G.F.); (R.R.); (X.G.P.)
| | - Chiara Barberi
- Postgraduate Training Program in Pediatrics, University of Palermo, 90133 Palermo, Italy;
| | - Martino Ruggieri
- Unit of Clinical Pediatrics and Unit of Rare disease AOU “Policlinico”, PO “G. Rodolico”, University of Catania, 95123 Catania, Italy;
| | - Xena Giada Pappalardo
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95123 Catania, Italy; (G.F.); (R.R.); (X.G.P.)
- National Council of Research, Institute for Research and Biomedical Innovation (IRIB), Unit of Catania, 95123 Catania, Italy
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2
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Alpuche-Lazcano SP, Scarborough RJ, Gatignol A. MicroRNAs and long non-coding RNAs during transcriptional regulation and latency of HIV and HTLV. Retrovirology 2024; 21:5. [PMID: 38424561 PMCID: PMC10905857 DOI: 10.1186/s12977-024-00637-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 02/21/2024] [Indexed: 03/02/2024] Open
Abstract
Human immunodeficiency virus (HIV) and human T cell leukemia virus (HTLV) have replicative and latent stages of infection. The status of the viruses is dependent on the cells that harbour them and on different events that change the transcriptional and post-transcriptional events. Non-coding (nc)RNAs are key factors in the regulation of retrovirus replication cycles. Notably, micro (mi)RNAs and long non-coding (lnc)RNAs are important regulators that can induce switches between active transcription-replication and latency of retroviruses and have important impacts on their pathogenesis. Here, we review the functions of miRNAs and lncRNAs in the context of HIV and HTLV. We describe how specific miRNAs and lncRNAs are involved in the regulation of the viruses' transcription, post-transcriptional regulation and latency. We further discuss treatment strategies using ncRNAs for HIV and HTLV long remission, reactivation or possible cure.
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Affiliation(s)
- Sergio P Alpuche-Lazcano
- Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, 3999, Côte Ste Catherine St., Montréal, QC, H3T 1E2, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H4A 3J1, Canada
- National Research Council Canada, Montréal, QC, H4P 2R2, Canada
| | - Robert J Scarborough
- Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, 3999, Côte Ste Catherine St., Montréal, QC, H3T 1E2, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC, H3A 2B4, Canada
| | - Anne Gatignol
- Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, 3999, Côte Ste Catherine St., Montréal, QC, H3T 1E2, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H4A 3J1, Canada.
- Department of Medicine, Division of Infectious Diseases, McGill University, Montréal, QC, H4A 3J1, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal, QC, H3A 2B4, Canada.
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Liu X, Zhao X, He J, Wang S, Shen X, Liu Q, Wang S. Advances in the Structure of GGGGCC Repeat RNA Sequence and Its Interaction with Small Molecules and Protein Partners. Molecules 2023; 28:5801. [PMID: 37570771 PMCID: PMC10420822 DOI: 10.3390/molecules28155801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
The aberrant expansion of GGGGCC hexanucleotide repeats within the first intron of the C9orf72 gene represent the predominant genetic etiology underlying amyotrophic lateral sclerosis (ALS) and frontal temporal dementia (FTD). The transcribed r(GGGGCC)n RNA repeats form RNA foci, which recruit RNA binding proteins and impede their normal cellular functions, ultimately resulting in fatal neurodegenerative disorders. Furthermore, the non-canonical translation of the r(GGGGCC)n sequence can generate dipeptide repeats, which have been postulated as pathological causes. Comprehensive structural analyses of r(GGGGCC)n have unveiled its polymorphic nature, exhibiting the propensity to adopt dimeric, hairpin, or G-quadruplex conformations, all of which possess the capacity to interact with RNA binding proteins. Small molecules capable of binding to r(GGGGCC)n have been discovered and proposed as potential lead compounds for the treatment of ALS and FTD. Some of these molecules function in preventing RNA-protein interactions or impeding the phase transition of r(GGGGCC)n. In this review, we present a comprehensive summary of the recent advancements in the structural characterization of r(GGGGCC)n, its propensity to form RNA foci, and its interactions with small molecules and proteins. Specifically, we emphasize the structural diversity of r(GGGGCC)n and its influence on partner binding. Given the crucial role of r(GGGGCC)n in the pathogenesis of ALS and FTD, the primary objective of this review is to facilitate the development of therapeutic interventions targeting r(GGGGCC)n RNA.
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Affiliation(s)
- Xiaole Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
| | - Xinyue Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
| | - Jinhan He
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
| | - Sishi Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
| | - Xinfei Shen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
| | - Qingfeng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
| | - Shenlin Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (X.L.); (X.Z.); (J.H.); (S.W.); (X.S.); (Q.L.)
- Beijing NMR Center, Peking University, Beijing 100087, China
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Xu WW, Liao L, Dai W, Zheng CC, Tan XP, He Y, Zhang QH, Huang ZH, Chen WY, Qin YR, Chen KS, He ML, Law S, Lung ML, He QY, Li B. Genome-wide CRISPR/Cas9 screening identifies a targetable MEST-PURA interaction in cancer metastasis. EBioMedicine 2023; 92:104587. [PMID: 37149929 DOI: 10.1016/j.ebiom.2023.104587] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/09/2023] Open
Abstract
BACKGROUND Metastasis is one of the most lethal hallmarks of esophageal squamous cell carcinoma (ESCC), yet the mechanisms remain unclear due to a lack of reliable experimental models and systematic identification of key drivers. There is urgent need to develop useful therapies for this lethal disease. METHODS A genome-wide CRISPR/Cas9 screening, in combination with gene profiling of highly invasive and metastatic ESCC sublines, as well as PDX models, was performed to identify key regulators of cancer metastasis. The Gain- and loss-of-function experiments were taken to examine gene function. Protein interactome, RNA-seq, and whole genome methylation sequencing were used to investigate gene regulation and molecular mechanisms. Clinical significance was analyzed in tumor tissue microarray and TCGA databases. Homology modeling, modified ELISA, surface plasmon resonance and functional assays were performed to identify lead compound which targets MEST to suppress cancer metastasis. FINDINGS High MEST expression was associated with poor patient survival and promoted cancer invasion and metastasis in ESCC. Mechanistically, MEST activates SRCIN1/RASAL1-ERK-snail signaling by interacting with PURA. miR-449a was identified as a direct regulator of MEST, and hypermethylation of its promoter led to MEST upregulation, whereas systemically delivered miR-449a mimic could suppress tumor metastasis without overt toxicity. Furthermore, molecular docking and computational screening in a small-molecule library of 1,500,000 compounds and functional assays showed that G699-0288 targets the MEST-PURA interaction and significantly inhibits cancer metastasis. INTERPRETATION We identified the MEST-PURA-SRCIN1/RASAL1-ERK-snail signaling cascade as an important mechanism underlying cancer metastasis. Blockade of MEST-PURA interaction has therapeutic potential in management of cancer metastasis. FUNDING This work was supported by National Key Research and Development Program of China (2021YFC2501000, 2021YFC2501900, 2017YFA0505100); National Natural Science Foundation of China (31961160727, 82073196, 81973339, 81803551); NSFC/RGC Joint Research Scheme (N_HKU727/19); Natural Science Foundation of Guangdong Province (2021A1515011158, 2021A0505030035); Key Laboratory of Guangdong Higher Education Institutes of China (2021KSYS009).
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Affiliation(s)
- Wen Wen Xu
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes and Key Laboratory of Protein Modification and Degradation, The Fifth Affiliated Hospital of Guangzhou Medical University and School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China; MOE Key Laboratory of Tumor Molecular Biology, National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Long Liao
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes and Key Laboratory of Protein Modification and Degradation, The Fifth Affiliated Hospital of Guangzhou Medical University and School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China; MOE Key Laboratory of Tumor Molecular Biology, National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Wei Dai
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Can-Can Zheng
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes and Key Laboratory of Protein Modification and Degradation, The Fifth Affiliated Hospital of Guangzhou Medical University and School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Xiang-Peng Tan
- Research Center of Cancer Diagnosis and Therapy, and Department of Clinical Oncology, First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Yan He
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes and Key Laboratory of Protein Modification and Degradation, The Fifth Affiliated Hospital of Guangzhou Medical University and School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China; MOE Key Laboratory of Tumor Molecular Biology, National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Qi-Hua Zhang
- MOE Key Laboratory of Tumor Molecular Biology, National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Zhi-Hao Huang
- MOE Key Laboratory of Tumor Molecular Biology, National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Wen-You Chen
- Department of Thoracic Surgery, First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Yan-Ru Qin
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Department of Clinical Oncology, First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Kui-Sheng Chen
- Henan Province Key Laboratory of Tumor Pathology, Department of Pathology, First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Ming-Liang He
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Simon Law
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Maria Li Lung
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
| | - Qing-Yu He
- MOE Key Laboratory of Tumor Molecular Biology, National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, China.
| | - Bin Li
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes and Key Laboratory of Protein Modification and Degradation, The Fifth Affiliated Hospital of Guangzhou Medical University and School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China; MOE Key Laboratory of Tumor Molecular Biology, National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, China.
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5
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Mroczek M, Iyadurai S. Neuromuscular and Neuromuscular Junction Manifestations of the PURA-NDD: A Systematic Review of the Reported Symptoms and Potential Treatment Options. Int J Mol Sci 2023; 24:2260. [PMID: 36768582 PMCID: PMC9917016 DOI: 10.3390/ijms24032260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/14/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
PURA-related neurodevelopmental disorders (PURA-NDDs) are a rare genetic disease caused by pathogenic autosomal dominant variants in the PURA gene or a deletion encompassing the PURA gene. PURA-NDD is clinically characterized by neurodevelopmental delay, learning disability, neonatal hypotonia, feeding difficulties, abnormal movements, and epilepsy. It is generally considered to be central nervous system disorders, with generalized weakness, associated hypotonia, cognitive and development deficits in early development, and seizures in late stages. Although it is classified predominantly as a central nervous syndrome disorder, some phenotypic features, such as myopathic facies, respiratory insufficiency of muscle origin, and myopathic features on muscle biopsy and electrodiagnostic evaluation, point to a peripheral (neuromuscular) source of weakness. Patients with PURA-NDD have been increasingly identified in exome-sequenced cohorts of patients with neuromuscular- and congenital myasthenic syndrome-like phenotypes. Recently, fluctuating weakness noted in a PURA-NDD patient, accompanied by repetitive nerve stimulation abnormalities, suggested the disease to be a channelopathy and, more specifically, a neuromuscular junction disorder. Treatment with pyridostigmine or salbutamol led to clinical improvement of neuromuscular function in two reported cases. The goal of this systematic retrospective review is to highlight the motor symptoms of PURA-NDD, to further describe the neuromuscular phenotype, and to emphasize the role of potential treatment opportunities of the neuromuscular phenotype in the setting of the potential role of PURA protein in the neuromuscular junction and the muscles.
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Affiliation(s)
- Magdalena Mroczek
- Center for Cardiovascular Genetics & Gene Diagnostics, Foundation for People with Rare Diseases, 8952 Schlieren, Switzerland
| | - Stanley Iyadurai
- Division of Neurology, Johns Hopkins All Children’s Hospital, 501 6th Ave S, St. Petersburg, FL 33701, USA
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López-Rivera JJ, Rodríguez-Salazar L, Soto-Ospina A, Estrada-Serrato C, Serrano D, Chaparro-Solano HM, Londoño O, Rueda PA, Ardila G, Villegas-Lanau A, Godoy-Corredor M, Cuartas M, Vélez JI, Vidal OM, Isaza-Ruget MA, Arcos-Burgos M. Structural Protein Effects Underpinning Cognitive Developmental Delay of the PURA p.Phe233del Mutation Modelled by Artificial Intelligence and the Hybrid Quantum Mechanics–Molecular Mechanics Framework. Brain Sci 2022; 12:brainsci12070871. [PMID: 35884678 PMCID: PMC9313109 DOI: 10.3390/brainsci12070871] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/21/2022] [Accepted: 06/24/2022] [Indexed: 02/06/2023] Open
Abstract
A whole-exome capture and next-generation sequencing was applied to an 11 y/o patient with a clinical history of congenital hypotonia, generalized motor and cognitive neurodevelopmental delay, and severe cognitive deficit, and without any identifiable Syndromic pattern, and to her parents, we disclosed a de novo heterozygous pathogenic mutation, c.697_699del p.Phe233del (rs786204835)(ACMG classification PS2, PM1, PM2, PP5), harbored in the PURA gene (MIM*600473) (5q31.3), associated with Autosomal Dominant Mental Retardation 31 (MIM # 616158). We used the significant improvement in the accuracy of protein structure prediction recently implemented in AlphaFold that incorporates novel neural network architectures and training procedures based on the evolutionary, physical, and geometric constraints of protein structures. The wild-type (WT) sequence and the mutated sequence, missing the Phe233, were reconstructed. The predicted local Distance Difference Test (lDDT) for the PURAwt and the PURA–Phe233del showed that the occurrence of the Phe233del affects between 220–320 amino acids. The distortion in the PURA structural conformation in the ~5 Å surrounding area after the p.Phe233del produces a conspicuous disruption of the repeat III, where the DNA and RNA helix unwinding capability occurs. PURA Protein–DNA docking corroborated these results in an in silico analysis that showed a loss of the contact of the PURA–Phe233del III repeat domain model with the DNA. Together, (i) the energetic and stereochemical, (ii) the hydropathic indexes and polarity surfaces, and (iii) the hybrid Quantum Mechanics–Molecular Mechanics (QM–MM) analyses of the PURA molecular models demarcate, at the atomic resolution, the specific surrounding region affected by these mutations and pave the way for future cell-based functional analysis. To the best of our knowledge, this is the first report of a de novo mutation underpinning a PURA syndrome in a Latin American patient and highlights the importance of predicting the molecular effects in protein structure using artificial intelligence algorithms and molecular and atomic resolution stereochemical analyses.
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Affiliation(s)
- Juan Javier López-Rivera
- INPAC Research Group, Fundación Universitaria Sanitas, Bogotá 111321, Colombia;
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Bogotá 111321, Colombia; (C.E.-S.); (D.S.); (H.M.C.-S.); (O.L.)
- Correspondence: (J.J.L.-R.); (M.A.-B.)
| | - Luna Rodríguez-Salazar
- Grupo de Bioinformática, Laboratorio de Clínica Colsanitas, Bogotá 110221, Colombia; (L.R.-S.); (P.A.R.); (G.A.)
| | - Alejandro Soto-Ospina
- Genética Molecular (GenMol), Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín 050012, Colombia; (A.S.-O.); (A.V.-L.)
| | - Carlos Estrada-Serrato
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Bogotá 111321, Colombia; (C.E.-S.); (D.S.); (H.M.C.-S.); (O.L.)
| | - David Serrano
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Bogotá 111321, Colombia; (C.E.-S.); (D.S.); (H.M.C.-S.); (O.L.)
| | - Henry Mauricio Chaparro-Solano
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Bogotá 111321, Colombia; (C.E.-S.); (D.S.); (H.M.C.-S.); (O.L.)
| | - Olga Londoño
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Bogotá 111321, Colombia; (C.E.-S.); (D.S.); (H.M.C.-S.); (O.L.)
| | - Paula A. Rueda
- Grupo de Bioinformática, Laboratorio de Clínica Colsanitas, Bogotá 110221, Colombia; (L.R.-S.); (P.A.R.); (G.A.)
| | - Geraldine Ardila
- Grupo de Bioinformática, Laboratorio de Clínica Colsanitas, Bogotá 110221, Colombia; (L.R.-S.); (P.A.R.); (G.A.)
| | - Andrés Villegas-Lanau
- Genética Molecular (GenMol), Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín 050012, Colombia; (A.S.-O.); (A.V.-L.)
- Grupo de Neurociencias de Antioquia (GNA), Facultad de Medicina, Universidad de Antioquia, Medellín 050012, Colombia
| | | | - Mauricio Cuartas
- Grupo de Investigación Estudios en Psicología, Departamento de Psicología, Escuela de Humanidades, Universidad EAFIT, Medellín 050022, Colombia;
| | - Jorge I. Vélez
- Universidad del Norte, Barranquilla 080001, Colombia; (J.I.V.); (O.M.V.)
| | - Oscar M. Vidal
- Universidad del Norte, Barranquilla 080001, Colombia; (J.I.V.); (O.M.V.)
| | | | - Mauricio Arcos-Burgos
- Grupo de Investigación en Psiquiatría (GIPSI), Departamento de Psiquiatría, Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellín 050012, Colombia
- Correspondence: (J.J.L.-R.); (M.A.-B.)
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Masrori P, Beckers J, Gossye H, Van Damme P. The role of inflammation in neurodegeneration: novel insights into the role of the immune system in C9orf72 HRE-mediated ALS/FTD. Mol Neurodegener 2022; 17:22. [PMID: 35303907 PMCID: PMC8932121 DOI: 10.1186/s13024-022-00525-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/25/2022] [Indexed: 12/13/2022] Open
Abstract
Neuroinflammation is an important hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). An inflammatory reaction to neuronal injury is deemed vital for neuronal health and homeostasis. However, a continued activation of the inflammatory response can be detrimental to remaining neurons and aggravate the disease process. Apart from a disease modifying role, some evidence suggests that neuroinflammation may also contribute to the upstream cause of the disease. In this review, we will first focus on the role of neuroinflammation in the pathogenesis of chromosome 9 open reading frame 72 gene (C9orf72) hexanucleotide repeat expansions (HRE)-mediated ALS/FTD (C9-ALS/FTD). Additionally, we will discuss evidence from ex vivo and in vivo studies and finally, we briefly summarize the trials and progress of anti-inflammatory therapies.
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Affiliation(s)
- Pegah Masrori
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, 3000, Leuven, Belgium.,Laboratory of Neurobiology, Experimental Neurology, Center for Brain and Disease Research, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, 602, 3000, Leuven, PB, Belgium.,Neurology Department, University Hospitals Leuven, Campus Gasthuisberg, Herestraat 49, 3000, Leuven, Belgium.,Department of Neurology, University Hospital Antwerp, 2650, Edegem, Belgium
| | - Jimmy Beckers
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, 3000, Leuven, Belgium.,Laboratory of Neurobiology, Experimental Neurology, Center for Brain and Disease Research, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, 602, 3000, Leuven, PB, Belgium
| | - Helena Gossye
- Department of Neurology, University Hospital Antwerp, 2650, Edegem, Belgium.,VIB Center for Molecular Neurology, Neurodegenerative Brain Diseases, University of Antwerp, 2000, Antwerp, Belgium.,Department of Biomedical Sciences, University of Antwerp, 2000, Antwerp, Belgium
| | - Philip Van Damme
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, 3000, Leuven, Belgium. .,Laboratory of Neurobiology, Experimental Neurology, Center for Brain and Disease Research, VIB, Campus Gasthuisberg, O&N5, Herestraat 49, 602, 3000, Leuven, PB, Belgium. .,Neurology Department, University Hospitals Leuven, Campus Gasthuisberg, Herestraat 49, 3000, Leuven, Belgium.
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8
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Forming cytoplasmic stress granules PURα suppresses mRNA translation initiation of IGFBP3 to promote esophageal squamous cell carcinoma progression. Oncogene 2022; 41:4336-4348. [PMID: 35945453 PMCID: PMC9481463 DOI: 10.1038/s41388-022-02426-3] [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: 04/02/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 01/29/2023]
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most fatal malignancies worldwide. Recently, our group identified purine-rich element binding protein alpha (PURα), a single-stranded DNA/RNA-binding protein, to be significantly associated with the progression of ESCC. Additional immunofluorescence staining demonstrated that PURα forms cytoplasmic stress granules to suppress mRNA translation initiation. The expression level of cytoplasmic PURα in ESCC tumor tissues was significantly higher than that in adjacent epithelia and correlated with a worse patient survival rate by immunohistochemistry. Functionally, PURα strongly preferred to bind to UG-/U-rich motifs and mRNA 3´UTR by CLIP-seq analysis. Moreover, PURα knockout significantly increased the protein level of insulin-like growth factor binding protein 3 (IGFBP3). In addition, it was further demonstrated that PURα-interacting proteins are remarkably associated with translation initiation factors and ribosome-related proteins and that PURα regulates protein expression by interacting with translation initiation factors, such as PABPC1, eIF3B and eIF3F, in an RNA-independent manner, while the interaction with ribosome-related proteins is significantly dependent on RNA. Specifically, PURα was shown to interact with the mRNA 3´UTR of IGFBP3 and inhibit its expression by suppressing mRNA translation initiation. Together, this study identifies cytoplasmic PURα as a modulator of IGFBP3, which could be a promising therapeutic target for ESCC treatment.
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Hypotonic Infant with PURA Syndrome-related Channelopathy Successfully Treated with Pyridostigmine. Neuromuscul Disord 2022; 32:166-169. [DOI: 10.1016/j.nmd.2022.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 10/31/2021] [Accepted: 01/12/2022] [Indexed: 11/21/2022]
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10
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Analysis of the role of Purα in the pathogenesis of Alzheimer's disease based on RNA-seq and ChIP-seq. Sci Rep 2021; 11:12178. [PMID: 34108502 PMCID: PMC8190037 DOI: 10.1038/s41598-021-90982-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 05/19/2021] [Indexed: 11/18/2022] Open
Abstract
Purine rich element binding protein A (Purα), encoded by the Purα gene, is an important transcriptional regulator that binds to DNA and RNA and is involved in processes such as DNA replication and RNA translation. Purα also plays an important role in the nervous system. To identify the function of Pura, we performed RNA sequence (RNA-seq) analysis of Purɑ-KO mouse hippocampal neuron cell line (HT22) to analyze the effect of Purα deletion on neuronal expression profiles. And combined with ChIP-seq analysis to explore the mechanism of Purα on gene regulation. In the end, totaly 656 differentially expressed genes between HT22 and Purα-KO HT22 cells have been found, which include 7 Alzheimer’s disease (AD)-related genes and 5 Aβ clearance related genes. 47 genes were regulated by Purα directly, the evidence based on CHIP-seq, which include Insr, Mapt, Vldlr, Jag1, etc. Our study provides the important informations of Purα in neuro-development. The possible regulative effects of Purα on AD-related genes consist inthe direct and indirect pathways of Purα in the pathogenesis of AD.
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11
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Molitor L, Bacher S, Burczyk S, Niessing D. The Molecular Function of PURA and Its Implications in Neurological Diseases. Front Genet 2021; 12:638217. [PMID: 33777106 PMCID: PMC7990775 DOI: 10.3389/fgene.2021.638217] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/09/2021] [Indexed: 12/19/2022] Open
Abstract
In recent years, genome-wide analyses of patients have resulted in the identification of a number of neurodevelopmental disorders. Several of them are caused by mutations in genes that encode for RNA-binding proteins. One of these genes is PURA, for which in 2014 mutations have been shown to cause the neurodevelopmental disorder PURA syndrome. Besides intellectual disability (ID), patients develop a variety of symptoms, including hypotonia, metabolic abnormalities as well as epileptic seizures. This review aims to provide a comprehensive assessment of research of the last 30 years on PURA and its recently discovered involvement in neuropathological abnormalities. Being a DNA- and RNA-binding protein, PURA has been implicated in transcriptional control as well as in cytoplasmic RNA localization. Molecular interactions are described and rated according to their validation state as physiological targets. This information will be put into perspective with available structural and biophysical insights on PURA’s molecular functions. Two different knock-out mouse models have been reported with partially contradicting observations. They are compared and put into context with cell biological observations and patient-derived information. In addition to PURA syndrome, the PURA protein has been found in pathological, RNA-containing foci of patients with the RNA-repeat expansion diseases such as fragile X-associated tremor ataxia syndrome (FXTAS) and amyotrophic lateral sclerosis (ALS)/fronto-temporal dementia (FTD) spectrum disorder. We discuss the potential role of PURA in these neurodegenerative disorders and existing evidence that PURA might act as a neuroprotective factor. In summary, this review aims at informing researchers as well as clinicians on our current knowledge of PURA’s molecular and cellular functions as well as its implications in very different neuronal disorders.
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Affiliation(s)
- Lena Molitor
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Sabrina Bacher
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Sandra Burczyk
- Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
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12
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Cinquina V, Ciaccio C, Venturini M, Masson R, Ritelli M, Colombi M. Expanding the PURA syndrome phenotype: A child with the recurrent PURA p.(Phe233del) pathogenic variant showing similarities with cutis laxa. Mol Genet Genomic Med 2021; 9:e1562. [PMID: 33275834 PMCID: PMC7963414 DOI: 10.1002/mgg3.1562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/18/2020] [Accepted: 11/09/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND PURA syndrome is rare autosomal dominant condition characterized by moderate to severe neurodevelopmental delay with absence of speech in nearly all patients and lack of independent ambulation in many. Early-onset problems include excessive hiccups, hypotonia, hypersomnolence, hypothermia, feeding difficulties, recurrent apneas, epileptic seizures, and abnormal nonepileptic movements. Other less common manifestations comprise congenital heart defects, urogenital malformations, and various skeletal, ophthalmological, gastrointestinal, and endocrine anomalies. Up to now, 78 individuals with PURA syndrome and 64 different pathogenic variants have been reported, but no clear-cut genotype-phenotype correlations have emerged so far. Herein, we report the clinical and molecular characterization of a 3-year-old girl with severe hypotonia, global developmental delay, and soft, loose skin, who came to our attention with a suspicion of cutis laxa (CL), which denotes another condition with variable neurodevelopmental problems. METHODS Amplicon-based whole exome sequencing was performed, and an in-house pipeline was used to conduct filtering and prioritization of variants. New prediction algorithms for indels were used to validate the pathogenicity of the PURA variant, and results were confirmed with the Sanger method. Finally, we collected clinical and mutational data of all PURA syndrome patients reported yet and compared the clinical features with those of our patient. RESULTS Clinical evaluation and biochemical investigations excluded CL and prompted to perform whole exome sequencing, which confirmed the absence of pathogenic variants in all CL-related genes and revealed the known PURA c.697_699del, p.(Phe233del) variant, identified hitherto in seven additional children with PURA syndrome. CONCLUSIONS Our data expand the phenotypic spectrum of PURA syndrome by showing that it can be regarded as a differential diagnosis for cutis laxa in early infancy. Our patient and literature review emphasize that a wide clinical variability exists not only between individuals with different PURA variants, but also among patients with the same causal mutation.
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Affiliation(s)
- Valeria Cinquina
- Division of Biology and GeneticsDepartment of Molecular and Translational MedicineUniversity of BresciaBresciaItaly
| | - Claudia Ciaccio
- Developmental Neurology UnitFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Marina Venturini
- Division of DermatologyDepartment of Clinical and Experimental SciencesSpedali Civili University Hospital BresciaBresciaItaly
| | - Riccardo Masson
- Developmental Neurology UnitFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Marco Ritelli
- Division of Biology and GeneticsDepartment of Molecular and Translational MedicineUniversity of BresciaBresciaItaly
| | - Marina Colombi
- Division of Biology and GeneticsDepartment of Molecular and Translational MedicineUniversity of BresciaBresciaItaly
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13
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Janowski R, Niessing D. The large family of PC4-like domains - similar folds and functions throughout all kingdoms of life. RNA Biol 2020; 17:1228-1238. [PMID: 32476604 PMCID: PMC7549692 DOI: 10.1080/15476286.2020.1761639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RNA- and DNA-binding domains are essential building blocks for specific regulation of gene expression. While a number of canonical nucleic acid binding domains share sequence and structural conservation, others are less obviously linked by evolutionary traits. In this review, we describe a protein fold of about 150 aa in length, bearing a conserved β-β-β-β-α-linker-β-β-β-β-α topology and similar nucleic acid binding properties but no apparent sequence conservation. The same overall fold can also be achieved by dimerization of two proteins, each bearing a β-β-β-β-α topology. These proteins include but are not limited to the transcription factors PC4 and P24 from humans and plants, respectively, the human RNA-transport factor Pur-α (also termed PURA), as well as the ssDNA-binding SP_0782 protein from Streptococcus pneumonia and the bacteriophage coat proteins PP7 and MS2. Besides their common overall topology, these proteins share common nucleic acids binding surfaces and thus functional similarity. We conclude that these PC4-like domains include proteins from all kingdoms of life and are much more abundant than previously known.
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Affiliation(s)
- Robert Janowski
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health , Neuherberg, Germany
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health , Neuherberg, Germany.,Institute of Pharmaceutical Biotechnology, Ulm University , Ulm, Germany
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14
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Wortman MJ, Dagdanova AV, Clark AM, Godfrey EW, Pascal SM, Johnson EM, Daniel DC. A synthetic Pur-based peptide binds and alters G-quadruplex secondary structure present in the expanded RNA repeat of C9orf72 ALS/FTD. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118674. [PMID: 32035967 DOI: 10.1016/j.bbamcr.2020.118674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/20/2019] [Accepted: 02/02/2020] [Indexed: 12/26/2022]
Abstract
Increased Pur-alpha (Pura) protein levels in animal models alleviate certain cellular symptoms of the disease spectrum amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD). Pura is a member of the Pur family of evolutionarily conserved guanine-rich polynucleotide binding proteins containing a repeated signature PUR domain of 60-80 amino acids. Here we have employed a synthetic peptide, TZIP, similar to a Pur domain, but with sequence alterations based on a consensus of evolutionarily conserved Pur family binding domains and having an added transporter sequence. A major familial form of ALS/FTD, C9orf72 (C9), is due to a hexanucleotide repeat expansion (HRE) of (GGGGCC), a Pur binding element. We show by circular dichroism that RNA oligonucleotides containing this purine-rich sequence consist largely of parallel G-quadruplexes. TZIP peptide binds this repeat sequence in both DNA and RNA. It binds the RNA element, including the G-quadruplexes, with a high degree of specificity versus a random oligonucleotide. In addition, TZIP binds both linear and G-quadruplex repeat RNA to form higher order G-quadruplex secondary structures. This change in conformational form by Pur-based peptide represents a new mechanism for regulating G quadruplex secondary structure within the C9 repeat. TZIP modulation of C9 RNA structural configuration may alter interaction of the complex with other proteins. This Pur-based mechanism provides new targets for therapy, and it may help to explain Pura alleviation of certain cellular pathological aspects of ALS/FTD.
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Affiliation(s)
- Margaret J Wortman
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Ayuna V Dagdanova
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Andrea M Clark
- Old Dominion University, Department of Chemistry and Biochemistry, Norfolk, VA 23529, USA
| | - Earl W Godfrey
- School of Health Professions, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Steven M Pascal
- Old Dominion University, Department of Chemistry and Biochemistry, Norfolk, VA 23529, USA
| | - Edward M Johnson
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Dianne C Daniel
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA.
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15
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Molecular Mechanisms of Neurodegeneration Related to C9orf72 Hexanucleotide Repeat Expansion. Behav Neurol 2019; 2019:2909168. [PMID: 30774737 PMCID: PMC6350563 DOI: 10.1155/2019/2909168] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/28/2018] [Accepted: 09/18/2018] [Indexed: 12/11/2022] Open
Abstract
Two clinically distinct diseases, amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), have recently been classified as two extremes of the FTD/ALS spectrum. The neuropathological correlate of FTD is frontotemporal lobar degeneration (FTLD), characterized by tau-, TDP-43-, and FUS-immunoreactive neuronal inclusions. An earlier discovery that a hexanucleotide repeat expansion mutation in chromosome 9 open reading frame 72 (C9orf72) gene causes ALS and FTD established a special subtype of ALS and FTLD with TDP-43 pathology (C9FTD/ALS). Normal individuals carry 2–10 hexanucleotide GGGGCC repeats in the C9orf72 gene, while more than a few hundred repeats represent a risk for ALS and FTD. The proposed molecular mechanisms by which C9orf72 repeat expansions induce neurodegenerative changes are C9orf72 loss-of-function through haploinsufficiency, RNA toxic gain-of-function, and gain-of-function through the accumulation of toxic dipeptide repeat proteins. However, many more cellular processes are affected by pathological processes in C9FTD/ALS, including nucleocytoplasmic transport, RNA processing, normal function of nucleolus, formation of membraneless organelles, translation, ubiquitin proteasome system, Notch signalling pathway, granule transport, and normal function of TAR DNA-binding protein 43 (TDP-43). Although the exact molecular mechanisms through which C9orf72 repeat expansions account for neurodegeneration have not been elucidated, some potential therapeutics, such as antisense oligonucleotides targeting hexanucleotide GGGGCC repeats in mRNA, were successful in preclinical trials and are awaiting phase 1 clinical trials. In this review, we critically discuss each proposed mechanism and provide insight into the most recent studies aiming to elucidate the molecular underpinnings of C9FTD/ALS.
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16
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Wang Y, Liu Y, Li Y, Liu B, Wu P, Xu S, Shi H. Protective effects of astaxanthin on subarachnoid hemorrhage-induced early brain injury: Reduction of cerebral vasospasm and improvement of neuron survival and mitochondrial function. Acta Histochem 2019; 121:56-63. [PMID: 30392635 DOI: 10.1016/j.acthis.2018.10.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 10/26/2018] [Accepted: 10/26/2018] [Indexed: 11/30/2022]
Abstract
The purpose of this study was to evaluate the neuroprotective effects of astaxanthin on early brain injury (EBI) caused by subarachnoid hemorrhage (SAH) in rats and to explore possible molecular mechanisms. Experimental SAH model was introduced in adult male SD rats by injecting autologous arterial blood into the prechiasmatic cistern. Astaxanthin (75 mg/kg bodyweight) or olive oil was administered by oral gavage at 3 h after SAH. Our results showed that astaxanthin attenuated SAH-induced cerebral vasospasm and reduced neuronal apoptosis. Astaxanthin inhibited mitochondria-associated neuron apoptosis in the prefrontal cortex after SAH: increased mitochondrial membrane potential, decreased Bax/Bcl-2 ratio, inhibited cytochrome C release in cytoplasm, and suppressed caspase-3 enzyme activity. Furthermore, the cerebral expression levels of synaptic proteins (Synapsin-1, postsynaptic density-95 and growth-associated protein-43) and nerve growth and neuronal differentiation factors (brain-derived neurotropic factor and purine-rich binding protein-alpha) were reduced following SAH. Astaxanthin partly restored their expression. In conclusion, our current work demonstrates that astaxanthin attenuates SAH-induced EBI, possibly by improving neuronal survival and mitochondrial function.
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Affiliation(s)
- Yanbin Wang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150081, People's Republic of China
| | - Yao Liu
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150081, People's Republic of China
| | - Yuchen Li
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150081, People's Republic of China
| | - Binbing Liu
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150081, People's Republic of China
| | - Pei Wu
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150081, People's Republic of China
| | - Shancai Xu
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150081, People's Republic of China
| | - Huaizhang Shi
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150081, People's Republic of China.
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17
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Healy MD, Hospenthal MK, Hall RJ, Chandra M, Chilton M, Tillu V, Chen KE, Celligoi DJ, McDonald FJ, Cullen PJ, Lott JS, Collins BM, Ghai R. Structural insights into the architecture and membrane interactions of the conserved COMMD proteins. eLife 2018; 7:e35898. [PMID: 30067224 PMCID: PMC6089597 DOI: 10.7554/elife.35898] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/31/2018] [Indexed: 12/31/2022] Open
Abstract
The COMMD proteins are a conserved family of proteins with central roles in intracellular membrane trafficking and transcription. They form oligomeric complexes with each other and act as components of a larger assembly called the CCC complex, which is localized to endosomal compartments and mediates the transport of several transmembrane cargos. How these complexes are formed however is completely unknown. Here, we have systematically characterised the interactions between human COMMD proteins, and determined structures of COMMD proteins using X-ray crystallography and X-ray scattering to provide insights into the underlying mechanisms of homo- and heteromeric assembly. All COMMD proteins possess an α-helical N-terminal domain, and a highly conserved C-terminal domain that forms a tightly interlocked dimeric structure responsible for COMMD-COMMD interactions. The COMM domains also bind directly to components of CCC and mediate non-specific membrane association. Overall these studies show that COMMD proteins function as obligatory dimers with conserved domain architectures.
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Affiliation(s)
- Michael D Healy
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | | | - Ryan J Hall
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | - Mintu Chandra
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | - Molly Chilton
- School of Biochemistry, Biomedical Sciences BuildingUniversity of BristolBristolUnited Kingdom
| | - Vikas Tillu
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | - Kai-En Chen
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | - Dion J Celligoi
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | | | - Peter J Cullen
- School of Biochemistry, Biomedical Sciences BuildingUniversity of BristolBristolUnited Kingdom
| | - J Shaun Lott
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | - Brett M Collins
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | - Rajesh Ghai
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
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18
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Mayorga L, Gamboni B, Mampel A, Roqué M. A frame-shift deletion in the PURA gene associates with a new clinical finding: Hypoglycorrhachia. Is GLUT1 a new PURA target? Mol Genet Metab 2018; 123:331-336. [PMID: 29307761 DOI: 10.1016/j.ymgme.2017.12.436] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/29/2017] [Accepted: 12/30/2017] [Indexed: 12/24/2022]
Abstract
PURA is a DNA/RNA-binding protein known to have an important role as a transcriptional and translational regulator. Mutations in the PURA gene have been documented to cause mainly a neurologic phenotype including hypotonia, epilepsy, development delay and respiratory alterations. We report here a patient with a frame-shift deletion in the PURA gene that apart from the classical PURA deficiency phenotype had marked hypoglycorrhachia, overlapping the clinical findings with a GLUT1 deficiency syndrome. SLC2A1 (GLUT1) mutations were discarded, so we hypothesized that GLUT1 could be downregulated in this PURA deficient scenario. We confirmed reduced GLUT1 expression in the patient's peripheral blood cells compared to controls predicting that this could also be happening in the blood-brain barrier and in this way explain the hypoglycorrhachia. Based on PURA's known functions as a transcriptional and translational regulator, we propose GLUT1 as a new PURA target. Further in vitro and in vivo studies are needed to confirm this and to uncover the underlying molecular mechanisms.
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Affiliation(s)
- Lía Mayorga
- Instituto de Histología y Embriología de Mendoza (IHEM), Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina.
| | - Beatriz Gamboni
- Instituto de Neurología Infanto Juvenil (Neuroinfan), Mendoza, Argentina
| | - Alejandra Mampel
- Instituto de Genética, Hospital Universitario, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - María Roqué
- Instituto de Histología y Embriología de Mendoza (IHEM), Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina
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19
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Reijnders MRF, Janowski R, Alvi M, Self JE, van Essen TJ, Vreeburg M, Rouhl RPW, Stevens SJC, Stegmann APA, Schieving J, Pfundt R, van Dijk K, Smeets E, Stumpel CTRM, Bok LA, Cobben JM, Engelen M, Mansour S, Whiteford M, Chandler KE, Douzgou S, Cooper NS, Tan EC, Foo R, Lai AHM, Rankin J, Green A, Lönnqvist T, Isohanni P, Williams S, Ruhoy I, Carvalho KS, Dowling JJ, Lev DL, Sterbova K, Lassuthova P, Neupauerová J, Waugh JL, Keros S, Clayton-Smith J, Smithson SF, Brunner HG, van Hoeckel C, Anderson M, Clowes VE, Siu VM, DDD study T, Selber P, Leventer RJ, Nellaker C, Niessing D, Hunt D, Baralle D. PURA syndrome: clinical delineation and genotype-phenotype study in 32 individuals with review of published literature. J Med Genet 2018; 55:104-113. [PMID: 29097605 PMCID: PMC5800346 DOI: 10.1136/jmedgenet-2017-104946] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 08/29/2017] [Accepted: 09/13/2017] [Indexed: 01/09/2023]
Abstract
BACKGROUND De novo mutations in PURA have recently been described to cause PURA syndrome, a neurodevelopmental disorder characterised by severe intellectual disability (ID), epilepsy, feeding difficulties and neonatal hypotonia. OBJECTIVES To delineate the clinical spectrum of PURA syndrome and study genotype-phenotype correlations. METHODS Diagnostic or research-based exome or Sanger sequencing was performed in individuals with ID. We systematically collected clinical and mutation data on newly ascertained PURA syndrome individuals, evaluated data of previously reported individuals and performed a computational analysis of photographs. We classified mutations based on predicted effect using 3D in silico models of crystal structures of Drosophila-derived Pur-alpha homologues. Finally, we explored genotype-phenotype correlations by analysis of both recurrent mutations as well as mutation classes. RESULTS We report mutations in PURA (purine-rich element binding protein A) in 32 individuals, the largest cohort described so far. Evaluation of clinical data, including 22 previously published cases, revealed that all have moderate to severe ID and neonatal-onset symptoms, including hypotonia (96%), respiratory problems (57%), feeding difficulties (77%), exaggerated startle response (44%), hypersomnolence (66%) and hypothermia (35%). Epilepsy (54%) and gastrointestinal (69%), ophthalmological (51%) and endocrine problems (42%) were observed frequently. Computational analysis of facial photographs showed subtle facial dysmorphism. No strong genotype-phenotype correlation was identified by subgrouping mutations into functional classes. CONCLUSION We delineate the clinical spectrum of PURA syndrome with the identification of 32 additional individuals. The identification of one individual through targeted Sanger sequencing points towards the clinical recognisability of the syndrome. Genotype-phenotype analysis showed no significant correlation between mutation classes and disease severity.
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Affiliation(s)
- Margot R F Reijnders
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Robert Janowski
- Institute of Structural Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Mohsan Alvi
- Visual Geometry Group, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Jay E Self
- Department of Ophthalmology, Southampton General Hospital, Southampton, UK
- Department of Clinical and Experimental Sciences, School of Medicine, University of Southampton, Southampton, UK
| | - Ton J van Essen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Maaike Vreeburg
- Department of Clinical Genetics and School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Rob P W Rouhl
- Department of Neurology, Maastricht University Medical Center, Maastricht, The Netherlands
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
- Academic Center for Epileptology, Kempenhaeghe/MUMC, Maastricht, The Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics and School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics and School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jolanda Schieving
- Department of Pediatric Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Katinke van Dijk
- Department of Pediatrics, Rijnstate Hospital, Arnhem, The Netherlands
| | - Eric Smeets
- Department of Clinical Genetics and School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Connie T R M Stumpel
- Department of Clinical Genetics and School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Levinus A Bok
- Department of Pediatrics, Máxima Medisch Centrum, Veldhoven, The Netherlands
| | - Jan Maarten Cobben
- Department of Pediatric Neurology, Academic Medical Center, Amsterdam, The Netherlands
| | - Marc Engelen
- Department of Neurology and Pediatric Neurology, Emma Children’s Hospital/Academic Medical Center, Amsterdam, The Netherlands
| | - Sahar Mansour
- SW Thames Regional Genetics Service, St. George’s University NHS Foundation Trust, London, UK
| | - Margo Whiteford
- Department of Clinical Genetics, Laboratory Medicine Building, Queen Elizabeth University Hospital, Glasgow, UK
| | - Kate E Chandler
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Sofia Douzgou
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Nicola S Cooper
- West Midlands Regional Clinical Genetics Service, Birmingham Women’s NHS Foundation Trust, Birmingham, UK
| | - Ene-Choo Tan
- KK Research Laboratory, KK Women’s and Children’s Hospital, Singapore
| | - Roger Foo
- National University Health Systems, Cardiovascular Research Institute, Singapore, Singapore
- Genome Institute of Singapore, Singapore, Singapore
| | - Angeline H M Lai
- Departmentof Paediatrics, Genetics Service, KK Women’s and Children’s Hospital, Singapore
| | - Julia Rankin
- Department of Clinical Genetics, Royal Devon and Exeter NHS Trust, Exeter, UK
| | - Andrew Green
- Department of Clinical Genetics, School of Medicine and Medical Science, Our Lady’s Hospital, University College Dublin, Dublin, Ireland
| | - Tuula Lönnqvist
- Department of Child Neurology, Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Pirjo Isohanni
- Department of Child Neurology, Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Programs Unit, Molecular Neurology, Biomedicum-Helsinki, University of Helsinki, Helsinki, Finland
| | - Shelley Williams
- Department of Pediatric Neurology, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, USA
| | - Ilene Ruhoy
- Division of Pediatric Neurology, Seattle Children’s Hospital/University of Washington, Seattle, Washington, USA
| | - Karen S Carvalho
- Department of Pediatrics, Section of Neurology, St. Christopher’s Hospital for Children, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - James J Dowling
- Division of Neurology and Program for Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Dorit L Lev
- The Rina Mor Institute of Medical Genetics, Holon, Israel
| | - Katalin Sterbova
- Department of Pediatric Neurology, Second Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Petra Lassuthova
- Department of Pediatric Neurology, Second Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Jana Neupauerová
- Department of Pediatric Neurology, Second Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Jeff L Waugh
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Sotirios Keros
- Sanford Children’s Hospital, University of South Dakota, Sioux Falls, South Dakota, USA
| | - Jill Clayton-Smith
- Faculty of Medical and Human Sciences, Institute of Evolution, Systems and Genomics, University of Manchester, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Sarah F Smithson
- Department of Clinical Genetics, University Hospitals Bristol, Bristol, UK
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Clinical Genetics and School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | | | | | - Virginia E Clowes
- North West Thames Regional Genetics Service, London North West Healthcare NHS Trust, London, UK
| | - Victoria Mok Siu
- Division of Medical Genetics, Department of Pediatrics, Schulich School of Medicine, University of Western Ontario, London, Ontario, Canada
| | - The DDD study
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Paulo Selber
- Department of Orthopaedics, Royal Children’s Hospital, Melbourne, Victoria, Australia
| | - Richard J Leventer
- Department of Neurology, University of Melbourne Department of Paediatrics, The Royal Children’s Hospital, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Christoffer Nellaker
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Nuffield Department of Obstetrics and Gynaecology, John Radcliffe Hospital Women’s Centre, University of Oxford, Oxford, UK
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Oxford, UK
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Department of Cell Biology, Biomedical Center of the Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - David Hunt
- Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Diana Baralle
- Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
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20
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Proteomic alterations of brain subcellular organelles caused by low-dose copper exposure: implication for Alzheimer's disease. Arch Toxicol 2018; 92:1363-1382. [PMID: 29383422 DOI: 10.1007/s00204-018-2163-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 01/17/2018] [Indexed: 12/22/2022]
Abstract
Excessive copper intake can lead to neurotoxicity, but there is a lack of comprehensive understanding on the potential impact of copper exposure especially at a low-dose on brain. We used 3xTg-AD mice to explore the potential neurotoxicity of chronic, low-dose copper treatment (0.13 ppm copper chloride in drinking water) on behavior and the brain hippocampal mitochondrial and nuclear proteome. Low-dose copper increased the spatial memory impairment of these animals, increased accumulation of intracellular amyloid 1-42 (Aβ1-42), decreased ATP content, increased the positive staining of 8-hydroxyguanosine (8-OHdG), a marker of DNA oxidative damage, and caused apoptosis and a decrease in synaptic proteins. Mitochondrial proteomic analysis by two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) revealed modulation of 24 hippocampal mitochondrial proteins (14 increased and 10 decreased) in copper-treated vs. untreated 3xTg-AD mice. Nuclear proteomic analysis revealed 43 modulated hippocampal nuclear proteins (25 increased and 18 decreased) in copper-treated 3xTg-AD vs. untreated mice. Classification of modulated mitochondrial and nuclear proteins included functional categories such as energy metabolism, synaptic-related proteins, DNA damage and apoptosis-related proteins, and oxidative stress-related proteins. Among these differentially expressed mitochondrial and nuclear proteins, nine proteins were abnormally expressed in both hippocampus mitochondria and nuclei, including electron transport chain-related proteins NADH dehydrogenase 1 alpha subcomplex subunit 10 (NDUAA), cytochrome b-c1 complex subunit Rieske (UCRI), cytochrome c oxidase subunit 5B (COX5B), and ATP synthase subunit d (ATP5H), glycolytic-related pyruvate kinase PKM (KPYM) and pyruvate dehydrogenase E1 component subunit alpha (ODPA). Furthermore, we found coenzyme Q10 (CoQ10), an endogenous mitochondrial protective factor/antioxidant, modulated the expression of 12 differentially expressed hippocampal proteins (4 increased and 8 decreased), which could be classified in functional categories such as glycolysis and synaptic-related proteins, oxidative stress-related proteins, implying that CoQ10 improved synaptic function, suppress oxidative stress, and regulate glycolysis. For the proteomics study, we validated the expression of several proteins related to synapses, DNA and apoptosis. The data confirmed that synapsin-2, a synaptic-related protein, was significantly decreased in both mitochondria and nuclei of copper-exposed 3xTg-AD mice. In mitochondria, dynamin-1 (DYN1), an apoptosis-related proteins, was significantly decreased. In the cellular nuclei, paraspeckle protein 1 (PSPC1) and purin-rich element-binding protein alpha (Purα), two DNA damage-related proteins, were significantly decreased and increased, respectively. We conclude that low-dose copper exposure exacerbates the spatial memory impairment of 3xTg-AD mice and perturbs multiple biological/pathogenic processes by dysregulating the mitochondrial and nuclear proteome. Exposure to copper might therefore contribute to the evolution of AD.
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21
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Uversky VN. The roles of intrinsic disorder-based liquid-liquid phase transitions in the "Dr. Jekyll-Mr. Hyde" behavior of proteins involved in amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Autophagy 2017; 13:2115-2162. [PMID: 28980860 DOI: 10.1080/15548627.2017.1384889] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pathological developments leading to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are associated with misbehavior of several key proteins, such as SOD1 (superoxide dismutase 1), TARDBP/TDP-43, FUS, C9orf72, and dipeptide repeat proteins generated as a result of the translation of the intronic hexanucleotide expansions in the C9orf72 gene, PFN1 (profilin 1), GLE1 (GLE1, RNA export mediator), PURA (purine rich element binding protein A), FLCN (folliculin), RBM45 (RNA binding motif protein 45), SS18L1/CREST, HNRNPA1 (heterogeneous nuclear ribonucleoprotein A1), HNRNPA2B1 (heterogeneous nuclear ribonucleoprotein A2/B1), ATXN2 (ataxin 2), MAPT (microtubule associated protein tau), and TIA1 (TIA1 cytotoxic granule associated RNA binding protein). Although these proteins are structurally and functionally different and have rather different pathological functions, they all possess some levels of intrinsic disorder and are either directly engaged in or are at least related to the physiological liquid-liquid phase transitions (LLPTs) leading to the formation of various proteinaceous membrane-less organelles (PMLOs), both normal and pathological. This review describes the normal and pathological functions of these ALS- and FTLD-related proteins, describes their major structural properties, glances at their intrinsic disorder status, and analyzes the involvement of these proteins in the formation of normal and pathological PMLOs, with the ultimate goal of better understanding the roles of LLPTs and intrinsic disorder in the "Dr. Jekyll-Mr. Hyde" behavior of those proteins.
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Affiliation(s)
- Vladimir N Uversky
- a Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute , Morsani College of Medicine , University of South Florida , Tampa , FL , USA.,b Institute for Biological Instrumentation of the Russian Academy of Sciences , Pushchino, Moscow region , Russia
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22
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Daniel DC, Johnson EM. PURA, the gene encoding Pur-alpha, member of an ancient nucleic acid-binding protein family with mammalian neurological functions. Gene 2017; 643:133-143. [PMID: 29221753 DOI: 10.1016/j.gene.2017.12.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 12/04/2017] [Accepted: 12/04/2017] [Indexed: 12/20/2022]
Abstract
The PURA gene encodes Pur-alpha, a 322 amino acid protein with repeated nucleic acid binding domains that are highly conserved from bacteria through humans. PUR genes with a single copy of this domain have been detected so far in spirochetes and bacteroides. Lower eukaryotes possess one copy of the PUR gene, whereas chordates possess 1 to 4 PUR family members. Human PUR genes encode Pur-alpha (Pura), Pur-beta (Purb) and two forms of Pur-gamma (Purg). Pur-alpha is a protein that binds specific DNA and RNA sequence elements. Human PURA, located at chromosome band 5q31, is under complex control of three promoters. The entire protein coding sequence of PURA is contiguous within a single exon. Several studies have found that overexpression or microinjection of Pura inhibits anchorage-independent growth of oncogenically transformed cells and blocks proliferation at either G1-S or G2-M checkpoints. Effects on the cell cycle may be mediated by interaction of Pura with cellular proteins including Cyclin/Cdk complexes and the Rb tumor suppressor protein. PURA knockout mice die shortly after birth with effects on brain and hematopoietic development. In humans environmentally induced heterozygous deletions of PURA have been implicated in forms of myelodysplastic syndrome and progression to acute myelogenous leukemia. Pura plays a role in AIDS through association with the HIV-1 protein, Tat. In the brain Tat and Pura association in glial cells activates transcription and replication of JC polyomavirus, the agent causing the demyelination disease, progressive multifocal leukoencephalopathy. Tat and Pura also act to stimulate replication of the HIV-1 RNA genome. In neurons Pura accompanies mRNA transcripts to sites of translation in dendrites. Microdeletions in the PURA locus have been implicated in several neurological disorders. De novo PURA mutations have been related to a spectrum of phenotypes indicating a potential PURA syndrome. The nucleic acid, G-rich Pura binding element is amplified as expanded polynucleotide repeats in several brain diseases including fragile X syndrome and a familial form of amyotrophic lateral sclerosis/fronto-temporal dementia. Throughout evolution the Pura protein plays a critical role in survival, based on conservation of its nucleic acid binding properties. These Pura properties have been adapted in higher organisms to the as yet unfathomable development of the human brain.
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Affiliation(s)
- Dianne C Daniel
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Edward M Johnson
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA.
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23
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Quantitative Map of Proteome Dynamics during Neuronal Differentiation. Cell Rep 2017; 18:1527-1542. [PMID: 28178528 PMCID: PMC5316641 DOI: 10.1016/j.celrep.2017.01.025] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/08/2017] [Accepted: 01/11/2017] [Indexed: 01/05/2023] Open
Abstract
Neuronal differentiation is a multistep process that shapes and re-shapes neurons by progressing through several typical stages, including axon outgrowth, dendritogenesis, and synapse formation. To systematically profile proteome dynamics throughout neuronal differentiation, we took cultured rat hippocampal neurons at different developmental stages and monitored changes in protein abundance using a combination of stable isotope labeling and high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS). Almost one third of all 4,500 proteins quantified underwent a more than 2-fold expression change during neuronal differentiation, indicating extensive remodeling of the neuron proteome. To highlight the strength of our resource, we studied the neural-cell-adhesion molecule 1 (NCAM1) and found that it stimulates dendritic arbor development by promoting actin filament growth at the dendritic growth cone. We anticipate that our quantitative map of neuronal proteome dynamics is a rich resource for further analyses of the many identified proteins in various neurodevelopmental processes. Systematic profile of proteome dynamics throughout neuronal development in vitro Approximately 1,800 proteins show significant expression changes during differentiation Six expression profile clusters describe stage-specific patterns of protein dynamics This protein database may help to identify neurodevelopment mechanisms
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24
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Banerjee A, Vest KE, Pavlath GK, Corbett AH. Nuclear poly(A) binding protein 1 (PABPN1) and Matrin3 interact in muscle cells and regulate RNA processing. Nucleic Acids Res 2017; 45:10706-10725. [PMID: 28977530 PMCID: PMC5737383 DOI: 10.1093/nar/gkx786] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/27/2017] [Indexed: 01/01/2023] Open
Abstract
The polyadenylate binding protein 1 (PABPN1) is a ubiquitously expressed RNA binding protein vital for multiple steps in RNA metabolism. Although PABPN1 plays a critical role in the regulation of RNA processing, mutation of the gene encoding this ubiquitously expressed RNA binding protein causes a specific form of muscular dystrophy termed oculopharyngeal muscular dystrophy (OPMD). Despite the tissue-specific pathology that occurs in this disease, only recently have studies of PABPN1 begun to explore the role of this protein in skeletal muscle. We have used co-immunoprecipitation and mass spectrometry to identify proteins that interact with PABPN1 in mouse skeletal muscles. Among the interacting proteins we identified Matrin 3 (MATR3) as a novel protein interactor of PABPN1. The MATR3 gene is mutated in a form of distal myopathy and amyotrophic lateral sclerosis (ALS). We demonstrate, that like PABPN1, MATR3 is critical for myogenesis. Furthermore, MATR3 controls critical aspects of RNA processing including alternative polyadenylation and intron retention. We provide evidence that MATR3 also binds and regulates the levels of long non-coding RNA (lncRNA) Neat1 and together with PABPN1 is required for normal paraspeckle function. We demonstrate that PABPN1 and MATR3 are required for paraspeckles, as well as for adenosine to inosine (A to I) RNA editing of Ctn RNA in muscle cells. We provide a functional link between PABPN1 and MATR3 through regulation of a common lncRNA target with downstream impact on paraspeckle morphology and function. We extend our analysis to a mouse model of OPMD and demonstrate altered paraspeckle morphology in the presence of endogenous levels of alanine-expanded PABPN1. In this study, we report protein-binding partners of PABPN1, which could provide insight into novel functions of PABPN1 in skeletal muscle and identify proteins that could be sequestered with alanine-expanded PABPN1 in the nuclear aggregates found in OPMD.
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Affiliation(s)
- Ayan Banerjee
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Katherine E Vest
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Grace K Pavlath
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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25
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Li K, Sun J, Yang J, Roberts SM, Zhang X, Cui X, Wei S, Ma LQ. Molecular Mechanisms of Perfluorooctanoate-Induced Hepatocyte Apoptosis in Mice Using Proteomic Techniques. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:11380-11389. [PMID: 28885018 DOI: 10.1021/acs.est.7b02690] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The stability of perfluorooctanoate (PFOA) coupled with its wide use cause serious concerns regarding its potential risk to human health. The molecular mechanisms of PFOA-induced hepatotoxicity relevant to human health was investigated using both in vivo (mouse model) and in vitro (human hepatocyte cells, HL-7702) techniques. Both male and female Balb/c mice were administered PFOA at 0.05, 0.5, or 2.5 mg/kg-d for 28-d, with serum PFOA concentrations after exposure being found at environmentally relevant levels. Liver samples were examined for histology and proteomic change using iTRAQ and Western Blotting, showing dose-dependent hepatocyte apoptosis and peroxisome proliferation. At high doses, genotoxicity resulting from ROS hypergeneration was due to suppression of Complex I subunits in the electron transport chain and activation of PPARα in both genders. However, at 0.05 mg/kg-d, Complex I suppression occurred only in females, making them more sensitive to PFOA-induced apoptosis. In vitro assays using HL-7702 cells confirmed that apoptosis was also induced through a similar mechanism. The dose/gender-dependent toxicity mechanisms help to explain some epidemiological phenomena, i.e., liver cancer is not often associated with PFOA exposure in professional workers. Our results demonstrated that a proteomic approach is a robust tool to explore molecular mechanisms of toxic chemicals at environmentally relevant levels.
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Affiliation(s)
- Kan Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Jie Sun
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Jingping Yang
- School of the Medicine, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Stephen M Roberts
- Center for Environmental and Human Toxicology, University of Florida , Gainesville, Florida 32611, United States
| | - Xuxiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Xinyi Cui
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Si Wei
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Lena Q Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing, Jiangsu 210046, China
- Soil and Water Science Department, University of Florida , Gainesville, Florida 32611, United States
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26
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Guo S, Zhang B, Yuan C, Li P, Sun T, Cui J. The role of Purα in neuronal development, the relationship between Purα and epilepsy in the current researches. BIO WEB OF CONFERENCES 2017. [DOI: 10.1051/bioconf/20170801056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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27
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Bida O, Gidoni M, Ideses D, Efroni S, Ginsberg D. A novel mitosis-associated lncRNA, MA-linc1, is required for cell cycle progression and sensitizes cancer cells to Paclitaxel. Oncotarget 2016; 6:27880-90. [PMID: 26337085 PMCID: PMC4695032 DOI: 10.18632/oncotarget.4944] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/31/2015] [Indexed: 11/25/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are major regulators of many cellular processes including cell cycle progression and tumorigenesis. In this study, we identify a novel lncRNA, MA-linc1, and reveal its effects on cell cycle progression and cancer growth. Inhibition of MA-linc1 expression alters cell cycle distribution, leading to a decrease in the number of G1 cells and a concomitant increase in all other stages of the cell cycle, and in particular G2/M, suggesting its involvement in the regulation of M phase. Accordingly, knock down of MA-linc1 inhibits M phase exit upon release from a mitotic block. We further demonstrate that MA-linc1 predominantly functions in cis to repress expression of its neighboring gene, Purα, which is often deleted in human cancers and whose ectopic expression inhibits cell cycle progression. Knock down of Purα partially rescues the MA-linc1 dependent inhibition of M phase exit. In agreement with its suggested role in M phase, inhibition of MA-linc1 enhances apoptotic cell death induced by the antimitotic drug, Paclitaxel and this enhancement of apoptosis is rescued by Purα knockdown. Furthermore, high levels of MA-linc1 are associated with reduced survival in human breast and lung cancer patients. Taken together, our data identify MA-linc1 as a novel lncRNA regulator of cell cycle and demonstrate its potential role in cancer progression and treatment.
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Affiliation(s)
- Or Bida
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan 52900, Israel
| | - Moriah Gidoni
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan 52900, Israel
| | - Diana Ideses
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan 52900, Israel
| | - Sol Efroni
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan 52900, Israel
| | - Doron Ginsberg
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan 52900, Israel
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28
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Sariyer IK, Sariyer R, Otte J, Gordon J. Pur-Alpha Induces JCV Gene Expression and Viral Replication by Suppressing SRSF1 in Glial Cells. PLoS One 2016; 11:e0156819. [PMID: 27257867 PMCID: PMC4892494 DOI: 10.1371/journal.pone.0156819] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 05/19/2016] [Indexed: 11/19/2022] Open
Abstract
Objective PML is a rare and fatal demyelinating disease of the CNS caused by the human polyomavirus, JC virus (JCV), which occurs in AIDS patients and those on immunosuppressive monoclonal antibody therapies (mAbs). We sought to identify mechanisms that could stimulate reactivation of JCV in a cell culture model system and targeted pathways which could affect early gene transcription and JCV T-antigen production, which are key steps of the viral life cycle for blocking reactivation of JCV. Two important regulatory partners we have previously identified for T-antigen include Pur-alpha and SRSF1 (SF2/ASF). SRSF1, an alternative splicing factor, is a potential regulator of JCV whose overexpression in glial cells strongly suppresses viral gene expression and replication. Pur-alpha has been most extensively characterized as a sequence-specific DNA- and RNA-binding protein which directs both viral gene transcription and mRNA translation, and is a potent inducer of the JCV early promoter through binding to T-antigen. Methods and Results Pur-alpha and SRSF1 both act directly as transcriptional regulators of the JCV promoter and here we have observed that Pur-alpha is capable of ameliorating SRSF1-mediated suppression of JCV gene expression and viral replication. Interestingly, Pur-alpha exerted its effect by suppressing SRSF1 at both the protein and mRNA levels in glial cells suggesting this effect can occur independent of T-antigen. Pur-alpha and SRSF1 were both localized to oligodendrocyte inclusion bodies by immunohistochemistry in brain sections from patients with HIV-1 associated PML. Interestingly, inclusion bodies were typically positive for either Pur-alpha or SRSF1, though some cells appeared to be positive for both proteins. Conclusions Taken together, these results indicate the presence of an antagonistic interaction between these two proteins in regulating of JCV gene expression and viral replication and suggests that they play an important role during viral reactivation leading to development of PML.
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Affiliation(s)
- Ilker Kudret Sariyer
- Department of Neuroscience, Center for Neurovirology, Temple University Lewis Katz School of Medicine, 3500 North Broad Street, 7th Floor, Philadelphia, PA 19140, United States of America
- * E-mail:
| | - Rahsan Sariyer
- Department of Neuroscience, Center for Neurovirology, Temple University Lewis Katz School of Medicine, 3500 North Broad Street, 7th Floor, Philadelphia, PA 19140, United States of America
| | - Jessica Otte
- Department of Neuroscience, Center for Neurovirology, Temple University Lewis Katz School of Medicine, 3500 North Broad Street, 7th Floor, Philadelphia, PA 19140, United States of America
| | - Jennifer Gordon
- Department of Neuroscience, Center for Neurovirology, Temple University Lewis Katz School of Medicine, 3500 North Broad Street, 7th Floor, Philadelphia, PA 19140, United States of America
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29
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Tanaka AJ, Bai R, Cho MT, Anyane-Yeboa K, Ahimaz P, Wilson AL, Kendall F, Hay B, Moss T, Nardini M, Bauer M, Retterer K, Juusola J, Chung WK. De novo mutations in PURA are associated with hypotonia and developmental delay. Cold Spring Harb Mol Case Stud 2016; 1:a000356. [PMID: 27148565 PMCID: PMC4850890 DOI: 10.1101/mcs.a000356] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
PURA is the leading candidate gene responsible for the developmental phenotype in the 5q31.3 microdeletion syndrome. De novo mutations in PURA were recently reported in 15 individuals with developmental features similar to the 5q31.3 microdeletion syndrome. Here we describe six unrelated children who were identified by clinical whole-exome sequencing (WES) to have novel de novo variants in PURA with a similar phenotype of hypotonia and developmental delay and frequently associated with seizures. The protein Purα (encoded by PURA) is involved in neuronal proliferation, dendrite maturation, and the transport of mRNA to translation sites during neuronal development. Mutations in PURA may alter normal brain development and impair neuronal function, leading to developmental delay and the seizures observed in patients with mutations in PURA.
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Affiliation(s)
- Akemi J Tanaka
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10029, USA
| | - Renkui Bai
- GeneDx, Gaithersburg, Maryland 20877, USA
| | | | - Kwame Anyane-Yeboa
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10029, USA
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10029, USA
| | - Ashley L Wilson
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10029, USA
| | - Fran Kendall
- VMP Genetics, Roswell, Georgia 30076, USA;; Department of Kinesiology, University of Georgia, Athens, Georgia 30605, USA
| | - Beverly Hay
- Division of Genetics, UMass Memorial Medical Center, Worcester, Massachusetts 01655, USA
| | - Timothy Moss
- Center for Personalized Genetic Healthcare, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Monica Nardini
- Center for Personalized Genetic Healthcare, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Mislen Bauer
- Department of Genetics, Miami Children's Hospital, Miami, Florida 33155, USA
| | | | | | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10029, USA;; Department of Medicine, Columbia University Medical Center, New York, New York 10032, USA
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30
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Daigle JG, Krishnamurthy K, Ramesh N, Casci I, Monaghan J, McAvoy K, Godfrey EW, Daniel DC, Johnson EM, Monahan Z, Shewmaker F, Pasinelli P, Pandey UB. Pur-alpha regulates cytoplasmic stress granule dynamics and ameliorates FUS toxicity. Acta Neuropathol 2016; 131:605-20. [PMID: 26728149 DOI: 10.1007/s00401-015-1530-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 12/20/2015] [Accepted: 12/21/2015] [Indexed: 12/13/2022]
Abstract
Amyotrophic lateral sclerosis is characterized by progressive loss of motor neurons in the brain and spinal cord. Mutations in several genes, including FUS, TDP43, Matrin 3, hnRNPA2 and other RNA-binding proteins, have been linked to ALS pathology. Recently, Pur-alpha, a DNA/RNA-binding protein was found to bind to C9orf72 repeat expansions and could possibly play a role in the pathogenesis of ALS. When overexpressed, Pur-alpha mitigates toxicities associated with Fragile X tumor ataxia syndrome (FXTAS) and C9orf72 repeat expansion diseases in Drosophila and mammalian cell culture models. However, the function of Pur-alpha in regulating ALS pathogenesis has not been fully understood. We identified Pur-alpha as a novel component of cytoplasmic stress granules (SGs) in ALS patient cells carrying disease-causing mutations in FUS. When cells were challenged with stress, we observed that Pur-alpha co-localized with mutant FUS in ALS patient cells and became trapped in constitutive SGs. We also found that FUS physically interacted with Pur-alpha in mammalian neuronal cells. Interestingly, shRNA-mediated knock down of endogenous Pur-alpha significantly reduced formation of cytoplasmic stress granules in mammalian cells suggesting that Pur-alpha is essential for the formation of SGs. Furthermore, ectopic expression of Pur-alpha blocked cytoplasmic mislocalization of mutant FUS and strongly suppressed toxicity associated with mutant FUS expression in primary motor neurons. Our data emphasizes the importance of stress granules in ALS pathogenesis and identifies Pur-alpha as a novel regulator of SG dynamics.
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Affiliation(s)
- J Gavin Daigle
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, USA
- Division of Child Neurology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Karthik Krishnamurthy
- Frances and Joseph Weinberg Unit for ALS Research, Department of Neuroscience, Farber Institute for Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - Nandini Ramesh
- Division of Child Neurology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Ian Casci
- Division of Child Neurology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - John Monaghan
- Division of Child Neurology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Kevin McAvoy
- Frances and Joseph Weinberg Unit for ALS Research, Department of Neuroscience, Farber Institute for Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - Earl W Godfrey
- Department of Pathology and Anatomy, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Dianne C Daniel
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Edward M Johnson
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Zachary Monahan
- Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Frank Shewmaker
- Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Piera Pasinelli
- Frances and Joseph Weinberg Unit for ALS Research, Department of Neuroscience, Farber Institute for Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - Udai Bhan Pandey
- Division of Child Neurology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA.
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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The Autographa californica Multiple Nucleopolyhedrovirus ac54 Gene Is Crucial for Localization of the Major Capsid Protein VP39 at the Site of Nucleocapsid Assembly. J Virol 2016; 90:4115-4126. [PMID: 26865720 DOI: 10.1128/jvi.02885-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 02/02/2016] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED Baculovirus DNAs are synthesized and inserted into preformed capsids to form nucleocapsids at a site in the infected cell nucleus, termed the virogenic stroma. Nucleocapsid assembly ofAutographa californicamultiple nucleopolyhedrovirus (AcMNPV) requires the major capsid protein VP39 and nine minor capsid proteins, including VP1054. However, how VP1054 participates in nucleocapsid assembly remains elusive. In this study, the VP1054-encoding gene (ac54) was deleted to generate theac54-knockout AcMNPV (vAc54KO). In vAc54KO-transfected cells, nucleocapsid assembly was disrupted, leading to the formation of abnormally elongated capsid structures. Interestingly, unlike cells transfected with AcMNPV mutants lacking other minor capsid proteins, in which capsid structures were distributed within the virogenic stroma,ac54ablation resulted in a distinctive location of capsid structures and VP39 at the periphery of the nucleus. The altered distribution pattern of capsid structures was also observed in cells transfected with AcMNPV lacking BV/ODV-C42 or in cytochalasind-treated AcMNPV-infected cells. BV/ODV-C42, along with PP78/83, has been shown to promote nuclear filamentous actin (F-actin) formation, which is another requisite for nucleocapsid assembly. Immunofluorescence using phalloidin indicated that the formation and distribution of nuclear F-actin were not affected byac54deletion. However, immunoelectron microscopy revealed that BV/ODV-C42, PP78/83, and 38K failed to integrate into capsid structures in the absence of VP1054, and immunoprecipitation further demonstrated that in transient expression assays, VP1054 interacted with BV/ODV-C42 and VP80 but not VP39. Our findings suggest that VP1054 plays an important role in the transport of capsid proteins to the nucleocapsid assembly site prior to the process of nucleocapsid assembly. IMPORTANCE Baculoviruses are large DNA viruses whose replication occurs within the host nucleus. The localization of capsids into the capsid assembly site requires virus-induced nuclear F-actin; the inhibition of nuclear F-actin formation results in the retention of capsid structures at the periphery of the nucleus. In this paper, we note that the minor capsid protein VP1054 is essential for the localization of capsid structures, the major capsid protein VP39, and the minor capsid protein 38K into the capsid assembly site. Moreover, VP1054 is crucial for correct targeting of the nuclear F-actin factors BV/ODV-C42 and PP78/83 for capsid maturation. However, the formation and distribution of nuclear F-actin are not affected by the lack of VP1054. We further reveal that VP1054 interacts with BV/ODV-C42 and a capsid transport-related protein, VP80. Taken together, our findings suggest that VP1054 plays a unique role in the pathway(s) for transport of capsid proteins.
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Weber J, Bao H, Hartlmüller C, Wang Z, Windhager A, Janowski R, Madl T, Jin P, Niessing D. Structural basis of nucleic-acid recognition and double-strand unwinding by the essential neuronal protein Pur-alpha. eLife 2016; 5:e11297. [PMID: 26744780 PMCID: PMC4764581 DOI: 10.7554/elife.11297] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/07/2016] [Indexed: 01/01/2023] Open
Abstract
The neuronal DNA-/RNA-binding protein Pur-alpha is a transcription regulator and core factor for mRNA localization. Pur-alpha-deficient mice die after birth with pleiotropic neuronal defects. Here, we report the crystal structure of the DNA-/RNA-binding domain of Pur-alpha in complex with ssDNA. It reveals base-specific recognition and offers a molecular explanation for the effect of point mutations in the 5q31.3 microdeletion syndrome. Consistent with the crystal structure, biochemical and NMR data indicate that Pur-alpha binds DNA and RNA in the same way, suggesting binding modes for tri- and hexanucleotide-repeat RNAs in two neurodegenerative RNAopathies. Additionally, structure-based in vitro experiments resolved the molecular mechanism of Pur-alpha's unwindase activity. Complementing in vivo analyses in Drosophila demonstrated the importance of a highly conserved phenylalanine for Pur-alpha's unwinding and neuroprotective function. By uncovering the molecular mechanisms of nucleic-acid binding, this study contributes to understanding the cellular role of Pur-alpha and its implications in neurodegenerative diseases.
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Affiliation(s)
- Janine Weber
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Han Bao
- Department of Human Genetics, Emory University, Atlanta, United States
| | - Christoph Hartlmüller
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Munich, Germany
| | - Zhiqin Wang
- Department of Human Genetics, Emory University, Atlanta, United States
| | - Almut Windhager
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Robert Janowski
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Tobias Madl
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Munich, Germany
- Institute of Molecular Biology & Biochemistry, Center of Molecular Medicine, Medical University of Graz, Graz, Austria
- Omics Center Graz, BioTechMed Graz, Graz, Austria
| | - Peng Jin
- Department of Human Genetics, Emory University, Atlanta, United States
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department Cell Biology, Biomedical Center of the Ludwig-Maximilians-University München, Planegg-Martinsried, Germany
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Pur-alpha functionally interacts with FUS carrying ALS-associated mutations. Cell Death Dis 2015; 6:e1943. [PMID: 26492376 PMCID: PMC4632316 DOI: 10.1038/cddis.2015.295] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 08/24/2015] [Indexed: 02/08/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder due to motor neuron loss. Fused in sarcoma (FUS) protein carrying ALS-associated mutations localizes to stress granules and causes their coalescence into larger aggregates. Here we show that Pur-alpha physically interacts with mutated FUS in an RNA-dependent manner. Pur-alpha colocalizes with FUS carrying mutations in stress granules of motoneuronal cells differentiated from induced pluripotent stem cells and that are derived from ALS patients. We observe that both Pur-alpha and mutated FUS upregulate phosphorylation of the translation initiation factor eukaryotic translation initiation factor 2 alpha and consistently inhibit global protein synthesis. In vivo expression of Pur-alpha in different Drosophila tissues significatively exacerbates the neurodegeneration caused by mutated FUS. Conversely, the downregulation of Pur-alpha in neurons expressing mutated FUS significatively improves fly climbing activity. All these findings suggest that Pur-alpha, through the control of mRNA translation, might be involved in the pathogenesis of ALS associated with the mutation of FUS, and that an alteration of protein synthesis may be directly implicated in the disease. Finally, in vivo RNAi-mediated ablation of Pur-alpha produced locomotion defects in Drosophila, indicating a pivotal role for this protein in the motoneuronal function.
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Hay CW, Hunter I, MacKenzie A, McEwan IJ. An Sp1 Modulated Regulatory Region Unique to Higher Primates Regulates Human Androgen Receptor Promoter Activity in Prostate Cancer Cells. PLoS One 2015; 10:e0139990. [PMID: 26448047 PMCID: PMC4598089 DOI: 10.1371/journal.pone.0139990] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/20/2015] [Indexed: 01/02/2023] Open
Abstract
Androgen receptor (AR) mediated signalling is necessary for normal development of the prostate gland and also drives prostate cancer (PCa) cell growth and survival, with many studies showing a correlation between increased receptor levels and therapy resistance with progression to fatal castrate recurrent PCa (CRPC). Although it has been held for some time that the transcription factor Sp1 is the main stimulator of AR gene transcription, comprehensive knowledge of the regulation of the AR gene remains incomplete. Here we describe and characterise in detail two novel active regulatory elements in the 5’UTR of the human AR gene. Both of these elements contain overlapping binding sites for the positive transcription factor Sp1 and the repressor protein pur-α. Aberrant cell signalling is characteristic of PCa and the transcriptional activity of the AR promoter in PCa cells is dependent upon the relative amounts of the two transcription factors. Together with our corroboration of the dominant role of Sp1, the findings support the rationale of targeting this transcription factor to inhibit tumour progression. This should be of particular therapeutic relevance in CRPC where the levels of the repressor pur-α are reduced.
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Affiliation(s)
- Colin W. Hay
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Irene Hunter
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Alasdair MacKenzie
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Iain J. McEwan
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
- * E-mail:
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35
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Rossi S, Serrano A, Gerbino V, Giorgi A, Di Francesco L, Nencini M, Bozzo F, Schininà ME, Bagni C, Cestra G, Carrì MT, Achsel T, Cozzolino M. Nuclear accumulation of mRNAs underlies G4C2-repeat-induced translational repression in a cellular model of C9orf72 ALS. J Cell Sci 2015; 128:1787-99. [PMID: 25788698 DOI: 10.1242/jcs.165332] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 03/09/2015] [Indexed: 01/13/2023] Open
Abstract
A common feature of non-coding repeat expansion disorders is the accumulation of RNA repeats as RNA foci in the nucleus and/or cytoplasm of affected cells. These RNA foci can be toxic because they sequester RNA-binding proteins, thus affecting various steps of post-transcriptional gene regulation. However, the precise step that is affected by C9orf72 GGGGCC (G4C2) repeat expansion, the major genetic cause of amyotrophic lateral sclerosis (ALS), is still poorly defined. In this work, we set out to characterise these mechanisms by identifying proteins that bind to C9orf72 RNA. Sequestration of some of these factors into RNA foci was observed when a (G4C2)31 repeat was expressed in NSC34 and HeLa cells. Most notably, (G4C2)31 repeats widely affected the distribution of Pur-alpha and its binding partner fragile X mental retardation protein 1 (FMRP, also known as FMR1), which accumulate in intra-cytosolic granules that are positive for stress granules markers. Accordingly, translational repression is induced. Interestingly, this effect is associated with a marked accumulation of poly(A) mRNAs in cell nuclei. Thus, defective trafficking of mRNA, as a consequence of impaired nuclear mRNA export, might affect translation efficiency and contribute to the pathogenesis of C9orf72 ALS.
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Affiliation(s)
- Simona Rossi
- Institute of Translational Pharmacology, CNR, 00133 Rome, Italy Laboratory of Neurochemistry, Fondazione Santa Lucia IRCCS, 00143 Rome, Italy Department of Biology, University of Rome "Tor Vergata", 00133 Rome, Italy
| | - Alessia Serrano
- Institute of Translational Pharmacology, CNR, 00133 Rome, Italy
| | - Valeria Gerbino
- Laboratory of Neurochemistry, Fondazione Santa Lucia IRCCS, 00143 Rome, Italy Department of Biology, University of Rome "Tor Vergata", 00133 Rome, Italy
| | - Alessandra Giorgi
- Department of Biochemical Sciences "A. Rossi Fanelli", University of Rome "Sapienza", Rome 00185, Italy
| | - Laura Di Francesco
- Department of Biochemical Sciences "A. Rossi Fanelli", University of Rome "Sapienza", Rome 00185, Italy
| | - Monica Nencini
- Laboratory of Neurochemistry, Fondazione Santa Lucia IRCCS, 00143 Rome, Italy
| | - Francesca Bozzo
- Laboratory of Neurochemistry, Fondazione Santa Lucia IRCCS, 00143 Rome, Italy Department of Biology, University of Rome "Tor Vergata", 00133 Rome, Italy
| | - Maria Eugenia Schininà
- Department of Biochemical Sciences "A. Rossi Fanelli", University of Rome "Sapienza", Rome 00185, Italy
| | - Claudia Bagni
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata", 00133 Rome, Italy Center for Human Genetics, KU Leuven, 3000 Leuven, Belgium VIB Center for the Biology of Disease, 3000 Leuven, Belgium
| | - Gianluca Cestra
- Institute of Molecular Biology and Pathology, CNR, 00185 Rome, Italy Department of Biology and Biotechnology "Charles Darwin", University of Rome "Sapienza", 00185 Rome, Italy
| | - Maria Teresa Carrì
- Laboratory of Neurochemistry, Fondazione Santa Lucia IRCCS, 00143 Rome, Italy Department of Biology, University of Rome "Tor Vergata", 00133 Rome, Italy
| | - Tilmann Achsel
- Center for Human Genetics, KU Leuven, 3000 Leuven, Belgium VIB Center for the Biology of Disease, 3000 Leuven, Belgium
| | - Mauro Cozzolino
- Institute of Translational Pharmacology, CNR, 00133 Rome, Italy Laboratory of Neurochemistry, Fondazione Santa Lucia IRCCS, 00143 Rome, Italy
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Lalani SR, Zhang J, Schaaf CP, Brown CW, Magoulas P, Tsai ACH, El-Gharbawy A, Wierenga KJ, Bartholomew D, Fong CT, Barbaro-Dieber T, Kukolich MK, Burrage LC, Austin E, Keller K, Pastore M, Fernandez F, Lotze T, Wilfong A, Purcarin G, Zhu W, Craigen WJ, McGuire M, Jain M, Cooney E, Azamian M, Bainbridge MN, Muzny DM, Boerwinkle E, Person RE, Niu Z, Eng CM, Lupski JR, Gibbs RA, Beaudet AL, Yang Y, Wang MC, Xia F. Mutations in PURA cause profound neonatal hypotonia, seizures, and encephalopathy in 5q31.3 microdeletion syndrome. Am J Hum Genet 2014; 95:579-83. [PMID: 25439098 DOI: 10.1016/j.ajhg.2014.09.014] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 09/22/2014] [Indexed: 11/30/2022] Open
Abstract
5q31.3 microdeletion syndrome is characterized by neonatal hypotonia, encephalopathy with or without epilepsy, and severe developmental delay, and the minimal critical deletion interval harbors three genes. We describe 11 individuals with clinical features of 5q31.3 microdeletion syndrome and de novo mutations in PURA, encoding transcriptional activator protein Pur-α, within the critical region. These data implicate causative PURA mutations responsible for the severe neurological phenotypes observed in this syndrome.
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Affiliation(s)
- Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Jing Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Chester W Brown
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pilar Magoulas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anne Chun-Hui Tsai
- Department of Molecular and Medical Genetics, Oregon Health and Sciences University, Portland, OR 97239, USA
| | - Areeg El-Gharbawy
- Department of Pediatrics and Division of Medical Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Klaas J Wierenga
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Dennis Bartholomew
- Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Chin-To Fong
- Clinic of Inherited Metabolic Disease, University of Rochester Medical Center, Rochester, NY 14642, USA
| | | | - Mary K Kukolich
- Clinical Genetics, Cook Children's Hospital, Fort Worth, TX 76102, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elise Austin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kory Keller
- Department of Molecular and Medical Genetics, Oregon Health and Sciences University, Portland, OR 97239, USA
| | - Matthew Pastore
- Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Fabio Fernandez
- Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Timothy Lotze
- Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Angus Wilfong
- Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gabriela Purcarin
- Department of Neurology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Wenmiao Zhu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - William J Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marianne McGuire
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mahim Jain
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Erin Cooney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mahshid Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew N Bainbridge
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Whole Genome Laboratory, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Human Genetics Center, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Richard E Person
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Whole Genome Laboratory, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhiyv Niu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Whole Genome Laboratory, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Whole Genome Laboratory, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Texas Children's Hospital, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Whole Genome Laboratory, Baylor College of Medicine, Houston, TX 77030, USA
| | - Meng C Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Whole Genome Laboratory, Baylor College of Medicine, Houston, TX 77030, USA.
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37
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The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites. Mol Cell 2014; 55:791-802. [PMID: 25155612 DOI: 10.1016/j.molcel.2014.07.012] [Citation(s) in RCA: 493] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 06/09/2014] [Accepted: 07/17/2014] [Indexed: 02/06/2023]
Abstract
Mechanistic roles for many lncRNAs are poorly understood, in part because their direct interactions with genomic loci and proteins are difficult to assess. Using a method to purify endogenous RNAs and their associated factors, we mapped the genomic binding sites for two highly expressed human lncRNAs, NEAT1 and MALAT1. We show that NEAT1 and MALAT1 localize to hundreds of genomic sites in human cells, primarily over active genes. NEAT1 and MALAT1 exhibit colocalization to many of these loci, but display distinct gene body binding patterns at these sites, suggesting independent but complementary functions for these RNAs. We also identified numerous proteins enriched by both lncRNAs, supporting complementary binding and function, in addition to unique associated proteins. Transcriptional inhibition or stimulation alters localization of NEAT1 on active chromatin sites, implying that underlying DNA sequence does not target NEAT1 to chromatin, and that localization responds to cues involved in the transcription process.
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38
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Yokoyama JS, Sirkis DW, Miller BL. C9ORF72 hexanucleotide repeats in behavioral and motor neuron disease: clinical heterogeneity and pathological diversity. AMERICAN JOURNAL OF NEURODEGENERATIVE DISEASE 2014; 3:1-18. [PMID: 24753999 PMCID: PMC3986607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 03/10/2014] [Indexed: 06/03/2023]
Abstract
Hexanucleotide repeat expansion in C9ORF72 is the most common genetic cause of frontotemporal dementia (FTD), a predominantly behavioral disease, and amyotrophic lateral sclerosis (ALS), a disease of motor neurons. The primary objectives of this review are to highlight the clinical heterogeneity associated with C9ORF72 pathogenic expansion and identify potential molecular mechanisms underlying selective vulnerability of distinct neural populations. The proposed mechanisms by which C9ORF72 expansion causes behavioral and motor neuron disease highlight the emerging role of impaired RNA and protein homeostasis in a spectrum of neurodegeneration and strengthen the biological connection between FTD and ALS.
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Affiliation(s)
| | - Daniel W Sirkis
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California at BerkeleyBerkeley, CA, USA
| | - Bruce L Miller
- Department of Neurology, University of CaliforniaSan Francisco, CA, USA
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39
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Gomes C, Merianda TT, Lee SJ, Yoo S, Twiss JL. Molecular determinants of the axonal mRNA transcriptome. Dev Neurobiol 2014; 74:218-32. [PMID: 23959706 PMCID: PMC3933445 DOI: 10.1002/dneu.22123] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 08/05/2013] [Accepted: 08/13/2013] [Indexed: 12/12/2022]
Abstract
Axonal protein synthesis has been shown to play a role in developmental and regenerative growth, as well as in cell body responses to axotomy. Recent studies have begun to identify the protein products that contribute to these autonomous responses of axons. In the peripheral nervous system, intra-axonal protein synthesis has been implicated in the localized in vivo responses to neuropathic stimuli, and there is emerging evidence for protein synthesis in CNS axons in vivo. Despite that hundreds of mRNAs have now been shown to localize into the axonal compartment, knowledge of what RNA binding proteins are responsible for this is quite limited. Here, we review the current state of knowledge of RNA transport mechanisms and highlight recently uncovered mechanisms for dynamically altering the axonal transcriptome. Both changes in the levels or activities of components of the RNA transport apparatus and alterations in transcription of transported mRNAs can effectively shift the axonal mRNA population. Consistent with this, the axonal RNA population shifts with development, with changes in growth state, and in response to extracellular stimulation. Each of these events must impact the transcriptional and transport apparatuses of the neuron, thus directly and indirectly modifying the axonal transcriptome.
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Affiliation(s)
- Cynthia Gomes
- Department of Biology, Drexel University, Philadelphia, Pennsylvania 19104 USA
| | - Tanuja T. Merianda
- Department of Biology, Drexel University, Philadelphia, Pennsylvania 19104 USA
| | - Seung Joon Lee
- Department of Biology, Drexel University, Philadelphia, Pennsylvania 19104 USA
| | - Soonmoon Yoo
- Nemours Biomedical Research, Alfred I. duPont Hospital for Children, Wilmington, Delaware 19803 USA
| | - Jeffery L. Twiss
- Department of Biology, Drexel University, Philadelphia, Pennsylvania 19104 USA
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29201
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40
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Acquisition of an Archaea-like ribonuclease H domain by plant L1 retrotransposons supports modular evolution. Proc Natl Acad Sci U S A 2013; 110:20140-5. [PMID: 24277848 DOI: 10.1073/pnas.1310958110] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although a variety of non-LTR retrotransposons of the L1 superfamily have been found in plant genomes over recent decades, their diversity, distribution, and evolution have yet to be analyzed in depth. Here, we perform comprehensive comparative and evolutionary analyses of L1 retrotransposons from 29 genomes of land plants covering a wide range of taxa. We identify numerous L1 elements in these genomes and detect a striking diversity of their domain composition. We show that all known land plant L1 retrotransposons can be grouped into five major families based on their phylogenetic relationships and domain composition. Moreover, we trace the putative evolution timeline that created the current variants and reveal that evolutionary events included losses and acquisitions of diverse putative RNA-binding domains and the acquisition of an Archaea-like ribonuclease H (RNH) domain. We also show that the latter RNH domain is autonomously active in vitro and speculate that retrotransposons may play a role in the horizontal transfer of RNH between plants, Archaea, and bacteria. The acquisition of an Archaea-like RNH domain by plant L1 retrotransposons negates the hypothesis that RNH domains in non-LTR retrotransposons have a single origin and provides evidence that acquisition happened at least twice. Together, our data indicate that the evolution of the investigated retrotransposons can be mainly characterized by repeated events of domain rearrangements and identify modular evolution as a major trend in the evolution of plant L1 retrotransposons.
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Jutras BL, Jones GS, Verma A, Brown NA, Antonicello AD, Chenail AM, Stevenson B. Posttranscriptional self-regulation by the Lyme disease bacterium's BpuR DNA/RNA-binding protein. J Bacteriol 2013; 195:4915-23. [PMID: 23974034 PMCID: PMC3807498 DOI: 10.1128/jb.00819-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 08/21/2013] [Indexed: 01/21/2023] Open
Abstract
Bacteria require explicit control over their proteomes in order to compete and survive in dynamic environments. The Lyme disease spirochete Borrelia burgdorferi undergoes substantial protein profile changes during its cycling between vector ticks and vertebrate hosts. In an effort to understand regulation of these transitions, we recently isolated and functionally characterized the borrelial nucleic acid-binding protein BpuR, a PUR domain-containing protein. We now report that this regulatory protein governs its own synthesis through direct interactions with bpuR mRNA. In vitro and in vivo techniques indicate that BpuR binds with high affinity and specificity to the 5' region of its message, thereby inhibiting translation. This negative feedback could permit the bacteria to fine-tune cellular BpuR concentrations. These data add to the understanding of this newly described class of prokaryotic DNA- and RNA-binding regulatory proteins.
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Affiliation(s)
| | - Grant S. Jones
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | | | - Nicholas A. Brown
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Alyssa D. Antonicello
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Alicia M. Chenail
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Brian Stevenson
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
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Jutras BL, Chenail AM, Carroll DW, Miller MC, Zhu H, Bowman A, Stevenson B. Bpur, the Lyme disease spirochete's PUR domain protein: identification as a transcriptional modulator and characterization of nucleic acid interactions. J Biol Chem 2013; 288:26220-26234. [PMID: 23846702 PMCID: PMC3764826 DOI: 10.1074/jbc.m113.491357] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The PUR domain is a nucleic acid-binding motif found in critical regulatory proteins of higher eukaryotes and in certain species of bacteria. During investigations into mechanisms by which the Lyme disease spirochete controls synthesis of its Erp surface proteins, it was discovered that the borrelial PUR domain protein, Bpur, binds with high affinity to double-stranded DNA adjacent to the erp transcriptional promoter. Bpur was found to enhance the effects of the erp repressor protein, BpaB. Bpur also bound single-stranded DNA and RNA, with relative affinities RNA > double-stranded DNA > single-stranded DNA. Rational site-directed mutagenesis of Bpur identified amino acid residues and domains critical for interactions with nucleic acids, and it revealed that the PUR domain has a distinct mechanism of interaction with each type of nucleic acid ligand. These data shed light on both gene regulation in the Lyme spirochete and functional mechanisms of the widely distributed PUR domain.
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Affiliation(s)
- Brandon L Jutras
- From the Department of Microbiology, Immunology, and Molecular Genetics and
| | - Alicia M Chenail
- From the Department of Microbiology, Immunology, and Molecular Genetics and
| | - Dustin W Carroll
- the Graduate Center for Toxicology, University of Kentucky College of Medicine, Lexington, Kentucky 40536
| | - M Clarke Miller
- the James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202, and
| | - Haining Zhu
- the Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky 40536
| | - Amy Bowman
- From the Department of Microbiology, Immunology, and Molecular Genetics and
| | - Brian Stevenson
- From the Department of Microbiology, Immunology, and Molecular Genetics and.
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Coulon M, Wellman CL, Marjara IS, Janczak AM, Zanella AJ. Early adverse experience alters dendritic spine density and gene expression in prefrontal cortex and hippocampus in lambs. Psychoneuroendocrinology 2013; 38:1112-21. [PMID: 23265310 DOI: 10.1016/j.psyneuen.2012.10.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 10/22/2012] [Accepted: 10/22/2012] [Indexed: 02/06/2023]
Abstract
In the laboratory, prenatal stress produces alterations in the structure and function of corticolimbic neurons. Here we report changes in gene expression and corticolimbic dendritic spine morphology in the offspring of pregnant ewes subjected to aversive interactions with human handlers during the last five weeks of pregnancy (AVS) compared to control dams that received gentle handling (GEN). AVS lambs had higher spine density on pyramidal neurons in area CA1 of the hippocampus and in medial prefrontal cortex compared to GEN lambs, as well as a lower ratio of mushroom spines to stubby and thin spines in area CA1. Expression of genes involved in brain development and spine morphogenesis was decreased in hippocampus and prefrontal cortex in AVS compared to GEN lambs. This study is the first demonstration that an ecologically relevant aversive experience in a field setting alters neuronal structure similarly to previous reports from laboratory settings and that even for animals domesticated over 12,000 years ago, an apparently mild stressor, resulting from human-animal interactions, can have similarly profound impacts on corticolimbic morphology.
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Affiliation(s)
- Marjorie Coulon
- Department of Production Animal Clinical Sciences, Norwegian School of Veterinary Science, Oslo, Norway.
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Rumora AE, Wang SX, Ferris LA, Everse SJ, Kelm RJ. Structural basis of multisite single-stranded DNA recognition and ACTA2 repression by purine-rich element binding protein B (Purβ). Biochemistry 2013; 52:4439-50. [PMID: 23724822 DOI: 10.1021/bi400283r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A hallmark of dysfunctional fibroblast to myofibroblast differentiation associated with fibrotic disorders is persistent expression of ACTA2, the gene encoding the cyto-contractile protein smooth muscle α-actin. In this study, a PURB-specific gene knockdown approach was used in conjunction with biochemical analyses of protein subdomain structure and function to reveal the mechanism by which purine-rich element binding protein B (Purβ) restricts ACTA2 expression in mouse embryo fibroblasts (MEFs). Consistent with the hypothesized role of Purβ as a suppressor of myofibroblast differentiation, stable short hairpin RNA-mediated knockdown of Purβ in cultured MEFs promoted changes in cell morphology, actin isoform expression, and cell migration indicative of conversion to a myofibroblast-like phenotype. Promoter-reporter assays in transfected Purβ knockdown MEFs confirmed that these changes were attributable, in part, to derepression of ACTA2 transcription. To map the domains in Purβ responsible for ACTA2 repression, several recombinant truncation mutants were generated and analyzed based on hypothetical, computationally derived models of the tertiary and quaternary structure of Purβ. Discrete subdomains mediating sequence- and strand-specific cis-element binding, protein-protein interaction, and inhibition of a composite ACTA2 enhancer were identified using a combination of biochemical, biophysical, and cell-based assays. Our results indicate that the Purβ homodimer possesses three separate but unequal single-stranded DNA-binding modules formed by subdomain-specific inter- and intramolecular interactions. This structural arrangement suggests that the cooperative assembly of the dimeric Purβ repressor on the sense strand of the ACTA2 enhancer is dictated by the association of each subdomain with distinct purine-rich binding sites within the enhancer.
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Affiliation(s)
- Amy E Rumora
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, Vermont 05405, USA
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Baculovirus VP1054 is an acquired cellular PURα, a nucleic acid-binding protein specific for GGN repeats. J Virol 2013; 87:8465-80. [PMID: 23720732 DOI: 10.1128/jvi.00068-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Baculovirus VP1054 protein is a structural component of both of the virion types budded virus (BV) and occlusion-derived virus (ODV), but its exact role in virion morphogenesis is poorly defined. In this paper, we reveal sequence and functional similarity between the baculovirus protein VP1054 and the cellular purine-rich element binding protein PUR-alpha (PURα). The data strongly suggest that gene transfer has occurred from a host to an ancestral baculovirus. Deletion of the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) vp1054 gene completely prevented viral cell-to-cell spread. Electron microscopy data showed that assembly of progeny nucleocapsids is dramatically reduced in the absence of VP1054. More precisely, VP1054 is required for proper viral DNA encapsidation, as deduced from the formation of numerous electron-lucent capsid-like tubules. Complementary searching identified the presence of genetic elements composed of repeated GGN trinucleotide motifs in baculovirus genomes, the target sequence for PURα proteins. Interestingly, these GGN-rich sequences are disproportionally distributed in baculoviral genomes and mostly occurred in proximity to the gene for the major occlusion body protein polyhedrin. We further demonstrate that the VP1054 protein specifically recognizes these GGN-rich islands, which at the same time encode crucial proline-rich domains in p78/83, an essential gene adjacent to the polyhedrin gene in the AcMNPV genome. While some viruses, like human immunodeficiency virus type 1 (HIV-1) and human JC virus (JCV), utilize host PURα protein, baculoviruses encode the PURα-like protein VP1054, which is crucial for viral progeny production.
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Johnson EM, Daniel DC, Gordon J. The pur protein family: genetic and structural features in development and disease. J Cell Physiol 2013; 228:930-7. [PMID: 23018800 PMCID: PMC3747735 DOI: 10.1002/jcp.24237] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 09/21/2012] [Indexed: 12/19/2022]
Abstract
The Pur proteins are an ancient family of sequence-specific single-stranded nucleic acid-binding proteins. They bind a G-rich element in either single- or double-stranded nucleic acids and are capable of displacing the complementary C-rich strand. Recently several reports have described Pur family member knockouts, mutations, and disease aberrations. Together with a recent crystal structure of Purα, these data reveal conserved structural features of these proteins that have been adapted to serve functions unique to higher eukaryotes. In humans Pur proteins are critical for myeloid cell development, muscle development, and brain development, including trafficking of mRNA to neuronal dendrites. Pur family members have been implicated in diseases as diverse as cancer, premature aging, and fragile-X mental retardation syndrome.
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Affiliation(s)
- Edward M Johnson
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507-1696, USA.
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New insights on human polyomavirus JC and pathogenesis of progressive multifocal leukoencephalopathy. Clin Dev Immunol 2013; 2013:839719. [PMID: 23690827 PMCID: PMC3652120 DOI: 10.1155/2013/839719] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/06/2013] [Indexed: 02/06/2023]
Abstract
John Cunningham virus (JCV) is a member of the Polyomaviridae family. It was first isolated from the brain of a patient with Hodgkin disease in 1971, and since then the etiological agent of the progressive multifocal leukoencephalopathy (PML) was considered. Until the human immunodeficiency virus (HIV) pandemic, PML was rare: in fact HIV-induced immunodeficiency is the most common predisposing factor accounting for 85% of all instances of PML. This data led to intense research on JCV infection and resulted in better understanding of epidemiology and clinic-pathologic spectrum. Recently, cases of PML have been observed after the introduction of monoclonal antibodies, such as natalizumab, rituximab, efalizumab, and infliximab, in the treatment of autoimmune disease, underlining the important role of host immunity in PML pathogenesis. In this review current understanding of the JCV infection and the new findings relating to the pathogenesis of PML has been comprehensively revised, focusing our attention on the interaction between the cellular and viral molecular pathways implicated in the JCV infection and the modulating role of host immune surveillance in the viral reactivation from a latent state.
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Polyomavirus JC in the context of immunosuppression: a series of adaptive, DNA replication-driven recombination events in the development of progressive multifocal leukoencephalopathy. Clin Dev Immunol 2013; 2013:197807. [PMID: 23690820 PMCID: PMC3649189 DOI: 10.1155/2013/197807] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Accepted: 03/17/2013] [Indexed: 01/13/2023]
Abstract
Polyomavirus JC (JCV) is the etiological agent of progressive multifocal leukoencephalopathy (PML), a demyelinating infection of oligodendrocytes in the brain. PML, a frequently fatal opportunistic infection in AIDS, has also emerged as a consequence of treatment with several new immunosuppressive therapeutic agents. Although nearly 80% of adults are seropositive, JCV attains an ability to infect glial cells in only a minority of people. Data suggest that JCV undergoes sequence alterations that accompany this ability, and these changes can be derived from an archetype strain by mutation, deletion, and duplication. While the introductory source and primary tissue reservoir of JCV remain unknown, lymphoid cells have been identified as potential intermediaries in progression of JCV to the brain. This review is focused on sequence changes in the noncoding control region (NCCR) of the virus. We propose an adaptive mechanism that involves a sequential series of DNA replication-driven NCCR recombination events involving stalled DNA replication forks at NCCR palindromic secondary structures. We shall describe how the NCCR sequence changes point to a model in which viral DNA replication drives NCCR recombination, allowing JCV adaptation to different cell types in its progression to neurovirulence.
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Expanded GGGGCC repeat RNA associated with amyotrophic lateral sclerosis and frontotemporal dementia causes neurodegeneration. Proc Natl Acad Sci U S A 2013; 110:7778-83. [PMID: 23553836 DOI: 10.1073/pnas.1219643110] [Citation(s) in RCA: 266] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) share phenotypic and pathologic overlap. Recently, an expansion of GGGGCC repeats in the first intron of C9orf72 was found to be a common cause of both illnesses; however, the molecular pathogenesis of this expanded repeat is unknown. Here we developed both Drosophila and mammalian models of this expanded hexanucleotide repeat and showed that expression of the expanded GGGGCC repeat RNA (rGGGGCC) is sufficient to cause neurodegeneration. We further identified Pur α as the RNA-binding protein of rGGGGCC repeats and discovered that Pur α and rGGGGCC repeats interact in vitro and in vivo in a sequence-specific fashion that is conserved between mammals and Drosophila. Furthermore, overexpression of Pur α in mouse neuronal cells and Drosophila mitigates rGGGGCC repeat-mediated neurodegeneration, and Pur α forms inclusions in the fly eye expressing expanded rGGGGCC repeats, as well as in cerebellum of human carriers of expanded GGGGCC repeats. These data suggest that expanded rGGGGCC repeats could sequester specific RNA-binding protein from their normal functions, ultimately leading to cell death. Taken together, these findings suggest that the expanded rGGGGCC repeats could cause neurodegeneration, and that Pur α may play a role in the pathogenesis of amyotrophic lateral sclerosis and frontotemporal dementia.
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Neurobehavioural evidence for the involvement of the FMR1 gene in female carriers of fragile X syndrome. Neurosci Biobehav Rev 2013; 37:522-47. [DOI: 10.1016/j.neubiorev.2013.01.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Revised: 12/11/2012] [Accepted: 01/06/2013] [Indexed: 12/19/2022]
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