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Guilleminault L, Mazzone SB, Chazelas P, Frachet S, Lia AS, Magy L. Cerebellar ataxia, neuropathy and vestibular areflexia syndrome: a neurogenic cough prototype. ERJ Open Res 2024; 10:00024-2024. [PMID: 39076534 PMCID: PMC11284589 DOI: 10.1183/23120541.00024-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/08/2024] [Indexed: 07/31/2024] Open
Abstract
Chronic cough is a frequent disorder that is defined by cough of more than 8 weeks duration. Despite extensive investigation, some patients exhibit no aetiology and others do not respond to specific treatments directed against apparent causes of cough. Such patients are identified as having unexplained or refractory chronic cough. Recently, a high proportion of patients with chronic cough in the context of cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS) was highlighted. CANVAS is a rare neurological disorder with a biallelic variation in the replication factor C subunit 1 (RFC1) gene corresponding mostly to an intronic AAGGG repeat expansion. Chronic cough in patients with CANVAS shares similar characteristics with cough hypersensitivity syndrome. The high prevalence of chronic cough in CANVAS gives the opportunity to better understand the neurogenic mechanism of chronic cough. In this review, we will describe the characteristics and mechanisms of CANVAS. We will also address the potential mechanisms responsible for chronic cough in CANVAS. Finally, we will address chronic cough management in the context of CANVAS.
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Affiliation(s)
- Laurent Guilleminault
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse III, Toulouse, France
- Department of Respiratory Medicine, Faculty of Medicine, Toulouse University Hospital, Toulouse, France
- These authors contributed equally to this work
| | - Stuart B. Mazzone
- Department of Anatomy and Physiology, University of Melbourne, Victoria, Australia
- These authors contributed equally to this work
| | - Pauline Chazelas
- Service de Biochimie et Génétique Moléculaire, CHU Limoges, Limoges, France
- NeurIT-UR20218, Université de Limoges, Limoges, France
| | - Simon Frachet
- NeurIT-UR20218, Université de Limoges, Limoges, France
- Service et Laboratoire de Neurologie, Centre de Référence “Neuropathies Périphériques Rares (NNerf)”, CHU Limoges, Limoges, France
| | - Anne-Sophie Lia
- Service de Biochimie et Génétique Moléculaire, CHU Limoges, Limoges, France
- NeurIT-UR20218, Université de Limoges, Limoges, France
- Service de Bioinformatique, CHU Limoges, Limoges, France
| | - Laurent Magy
- NeurIT-UR20218, Université de Limoges, Limoges, France
- Service et Laboratoire de Neurologie, Centre de Référence “Neuropathies Périphériques Rares (NNerf)”, CHU Limoges, Limoges, France
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Turner RD, Hirons B, Cortese A, Birring SS. Chronic Cough as a Genetic Neurological Disorder? Insights from Cerebellar Ataxia with Neuropathy and Vestibular Areflexia Syndrome (CANVAS). Lung 2023; 201:511-519. [PMID: 37979058 PMCID: PMC10673766 DOI: 10.1007/s00408-023-00660-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Chronic cough is common, and in many cases unexplained or refractory to otherwise effective treatment of associated medical conditions. Cough hypersensitivity has developed as a paradigm that helps to explain clinical and research observations that frequently point towards chronic cough as a neuropathic disorder. Cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS) is a recently described neurological condition whose clinical features include gait ataxia, unsteadiness, peripheral neuropathy, and autonomic dysfunction. Chronic cough is also a common feature of the syndrome, with features of hypersensitivity, often preceding core neurological symptoms by up to 30 years or more. The genetic basis in a majority of cases of CANVAS appears to be biallelic variable repeat intron expansion sequences within RFC1, a gene normally involved in the regulation of DNA replication and repair. The same polymorphism has now been identified at an increased frequency in patients with unexplained or refractory chronic cough in the absence of defining clinical features of CANVAS. This review expands on these points, aiming to increase the awareness of CANVAS amongst clinicians and researchers working with chronic cough. We discuss the implications of a link between RFC1 disease and cough. Improved understanding of CANVAS may lead to an enhanced grasp of the pathophysiology of chronic cough, and new approaches to antitussive treatments.
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Affiliation(s)
- Richard D Turner
- Department of Respiratory Medicine, Gold Coast University Hospital, Southport, QLD, Australia.
- School of Medicine and Dentistry, Griffith University, Southport, QLD, Australia.
| | - Barnaby Hirons
- Department of Respiratory Medicine, King's College Hospital, London, UK
- Centre for Human and Applied Physiological Sciences, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Andrea Cortese
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, UK
- Department of Brain and Behaviour Sciences, University of Pavia, Pavia, Italy
| | - Surinder S Birring
- Department of Respiratory Medicine, King's College Hospital, London, UK
- Centre for Human and Applied Physiological Sciences, School of Basic and Medical Biosciences, King's College London, London, UK
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Magrino J, Munford V, Martins DJ, Homma TK, Page B, Gaubitz C, Freire BL, Lerario AM, Vilar JB, Amorin A, Leão EKE, Kok F, Menck CF, Jorge AA, Kelch BA. A thermosensitive PCNA allele underlies an ataxia-telangiectasia-like disorder. J Biol Chem 2023; 299:104656. [PMID: 36990216 PMCID: PMC10165274 DOI: 10.1016/j.jbc.2023.104656] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/25/2023] [Accepted: 03/10/2023] [Indexed: 03/29/2023] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a sliding clamp protein that coordinates DNA replication with various DNA maintenance events that are critical for human health. Recently, a hypomorphic homozygous serine to isoleucine (S228I) substitution in PCNA was described to underlie a rare DNA repair disorder known as PCNA-associated DNA repair disorder (PARD). PARD symptoms range from UV sensitivity, neurodegeneration, telangiectasia, and premature aging. We, and others, previously showed that the S228I variant changes the protein-binding pocket of PCNA to a conformation that impairs interactions with specific partners. Here, we report a second PCNA substitution (C148S) that also causes PARD. Unlike PCNA-S228I, PCNA-C148S has WT-like structure and affinity toward partners. In contrast, both disease-associated variants possess a thermostability defect. Furthermore, patient-derived cells homozygous for the C148S allele exhibit low levels of chromatin-bound PCNA and display temperature-dependent phenotypes. The stability defect of both PARD variants indicates that PCNA levels are likely an important driver of PARD disease. These results significantly advance our understanding of PARD and will likely stimulate additional work focused on clinical, diagnostic, and therapeutic aspects of this severe disease.
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Affiliation(s)
- Joseph Magrino
- Department of Biochemistry and Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Veridiana Munford
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Davi Jardim Martins
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Thais K Homma
- Genetic Endocrinology Unit, Cellular and Molecular Endocrinology Laboratory LIM25, Endocrinology Discipline of the Faculty of Medicine of the University of São Paulo, São Paulo, Brazil; Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics LIM42, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil
| | - Brendan Page
- Department of Biochemistry and Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Christl Gaubitz
- Department of Biochemistry and Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Bruna L Freire
- Genetic Endocrinology Unit, Cellular and Molecular Endocrinology Laboratory LIM25, Endocrinology Discipline of the Faculty of Medicine of the University of São Paulo, São Paulo, Brazil; Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics LIM42, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil
| | - Antonio M Lerario
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics LIM42, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil; Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, Michigan, USA
| | - Juliana Brandstetter Vilar
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Antonio Amorin
- Neurogenetics, Neurology Department, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil
| | - Emília K E Leão
- Medical Genetics Service of the Professor Edgard Santos University Hospital - Federal University of Bahia, Salvador, Brazil
| | - Fernando Kok
- Neurogenetics, Neurology Department, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil; Mendelics Genomic Analysis, São Paulo, São Paulo, Brazil
| | - Carlos Fm Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alexander Al Jorge
- Genetic Endocrinology Unit, Cellular and Molecular Endocrinology Laboratory LIM25, Endocrinology Discipline of the Faculty of Medicine of the University of São Paulo, São Paulo, Brazil
| | - Brian A Kelch
- Department of Biochemistry and Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA.
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Kim S, Kim Y, Kim Y, Yoon S, Lee KY, Lee Y, Kang S, Myung K, Oh CK. PCNA Ser46-Leu47 residues are crucial in preserving genomic integrity. PLoS One 2023; 18:e0285337. [PMID: 37205694 DOI: 10.1371/journal.pone.0285337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/19/2023] [Indexed: 05/21/2023] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a maestro of DNA replication. PCNA forms a homotrimer and interacts with various proteins, such as DNA polymerases, DNA ligase I (LIG1), and flap endonuclease 1 (FEN1) for faithful DNA replication. Here, we identify the crucial role of Ser46-Leu47 residues of PCNA in maintaining genomic integrity using in vitro, and cell-based assays and structural prediction. The predicted PCNAΔSL47 structure shows the potential distortion of the central loop and reduced hydrophobicity. PCNAΔSL47 shows a defective interaction with PCNAWT leading to defects in homo-trimerization in vitro. PCNAΔSL47 is defective in the FEN1 and LIG1 interaction. PCNA ubiquitination and DNA-RNA hybrid processing are defective in PCNAΔSL47-expressing cells. Accordingly, PCNAΔSL47-expressing cells exhibit an increased number of single-stranded DNA gaps and higher levels of γH2AX, and sensitivity to DNA-damaging agents, highlighting the importance of PCNA Ser46-Leu47 residues in maintaining genomic integrity.
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Affiliation(s)
- Sangin Kim
- Institute for Basic Science, Center for Genomic Integrity, Ulsan, Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, College of Information-Bio Convergence Engineering, Ulsan, Korea
| | - Yeongjae Kim
- Institute for Basic Science, Center for Genomic Integrity, Ulsan, Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, College of Information-Bio Convergence Engineering, Ulsan, Korea
| | - Youyoung Kim
- Institute for Basic Science, Center for Genomic Integrity, Ulsan, Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, College of Information-Bio Convergence Engineering, Ulsan, Korea
| | - Suhyeon Yoon
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Integrated Data Sciences Section, Research Technologies Branch, Bethesda, MD, United States of America
| | - Kyoo-Young Lee
- Institute for Basic Science, Center for Genomic Integrity, Ulsan, Korea
- Department of Biochemistry, College of Medicine, Hallym University, Chuncheon, Gangwon-do, Korea
| | - Yoonsung Lee
- Clinical Research Institute, Kyung Hee University Hospital at Gangdong, College of Medicine, Kyung Hee University, Seoul, Korea
| | - Sukhyun Kang
- Institute for Basic Science, Center for Genomic Integrity, Ulsan, Korea
| | - Kyungjae Myung
- Institute for Basic Science, Center for Genomic Integrity, Ulsan, Korea
- Ulsan National Institute of Science and Technology, Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan, Korea
| | - Chang-Kyu Oh
- Department of Biochemistry, Pusan National University, School of Medicine, Yangsan, Korea
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Davies K, Szmulewicz DJ, Corben LA, Delatycki M, Lockhart PJ. RFC1-Related Disease. Neurol Genet 2022; 8:e200016. [PMID: 36046423 PMCID: PMC9425222 DOI: 10.1212/nxg.0000000000200016] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/22/2022] [Indexed: 01/03/2023]
Abstract
In 2019, a biallelic pentanucleotide repeat expansion in the gene encoding replication factor C subunit 1 (RFC1) was reported as a cause of cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS). In addition, biallelic expansions were shown to account for up to 22% of cases with late-onset ataxia. Since this discovery, the phenotypic spectrum reported to be associated with RFC1 expansions has extended beyond the initial conditions to include pure cerebellar ataxia, isolated somatosensory impairment, combinations of the 2, and parkinsonism, leading to a potentially broad differential diagnosis. Genetic studies suggest RFC1 expansions may be the most common genetic cause of ataxia and are likely underdiagnosed. This review summarizes the current molecular and clinical knowledge of RFC1-related disease, with a focus on the evaluation of recent phenotype associations and highlighting the current challenges in clinical pathways to diagnosis and molecular testing.
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Bhardwaj VK, Purohit R. A lesson for the maestro of the replication fork: Targeting the protein-binding interface of proliferating cell nuclear antigen for anticancer therapy. J Cell Biochem 2022; 123:1091-1102. [PMID: 35486518 DOI: 10.1002/jcb.30265] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/31/2022] [Accepted: 04/18/2022] [Indexed: 12/14/2022]
Abstract
The proliferating cell nuclear antigen (PCNA) has emerged as a promising candidate for the development of novel cancer therapeutics. PCNA is a nononcogenic mediator of DNA replication that regulates a diverse range of cellular functions and pathways through a comprehensive list of protein-protein interactions. The hydrophobic binding pocket on PCNA offers an opportunity for the development of inhibitors to target various types of cancers and modulate protein-protein interactions. In the present study, we explored the binding modes and affinity of molecule I1 (standard molecule) with the previously suggested dimer interface pocket and the hydrophobic pocket present on the frontal side of the PCNA monomer. We also identified potential lead molecules from the library of in-house synthesized 3-methylenisoindolin-1-one based molecules to inhibit the protein-protein interactions of PCNA. Our results were based on robust computational methods, including molecular docking, conventional, steered, and umbrella sampling molecular dynamics simulations. Our results suggested that the standard inhibitor I1 interacts with the hydrophobic pocket of PCNA with a higher affinity than the previously suggested binding site. Also, the proposed molecules showed better or comparable binding free energies as calculated by the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach and further validated by enhanced umbrella sampling simulations. In vitro and in vivo methods could test the computationally suggested molecules for advancement in the drug discovery pipeline.
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Affiliation(s)
- Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India.,Division of Biotechnology, CSIR-IHBT, Palampur, Himachal Pradesh, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India.,Division of Biotechnology, CSIR-IHBT, Palampur, Himachal Pradesh, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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Kumar Bhardwaj V, Purohit R. Taming the ringmaster of the genome (PCNA): Phytomolecules for anticancer therapy against a potential non-oncogenic target. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116437] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Costales M, Casanueva R, Suárez V, Asensi JM, Cifuentes GA, Diñeiro M, Cadiñanos J, López F, Álvarez-Marcos C, Otero A, Gómez J, Llorente JL, Cabanillas R. CANVAS: A New Genetic Entity in the Otorhinolaryngologist's Differential Diagnosis. Otolaryngol Head Neck Surg 2021; 166:74-79. [PMID: 33940977 DOI: 10.1177/01945998211008398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVE The biallelic inheritance of an expanded intronic pentamer (AAGGG)exp in the gene encoding replication factor C subunit 1 (RFC1) has been found to be a cause of cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS). This study describes clinical and genetic features of our patients with clinical suspicion of the syndrome. STUDY DESIGN A retrospective descriptive study from an ataxia database comprising 500 patients. SETTING The study was performed at the Otorhinolaryngology Department of a hospital in the north of Spain. METHODS Specific genetic testing for CANVAS was performed in 13 patients with clinical suspicion of complete or incomplete syndrome. The clinical diagnosis was supported by quantitative vestibular hypofunction, cerebellar atrophy, and abnormal sensory nerve conduction testing. RESULTS Nine of 13 (69%) patients met clinical diagnostic criteria for definite CANVAS disease. The first manifestation of the syndrome was lower limb dysesthesia in 8 of 13 patients and gait imbalance in 5 of 13. Eleven of 13 (85%) patients were carriers of the biallelic (AAGGG)exp in RFC1. CONCLUSION A genetic cause of CANVAS has recently been discovered. We propose genetic screening for biallelic expansions of the AAGGG pentamer of RFC1 in all patients with clinical suspicion of CANVAS, since accurate early diagnosis could improve the quality of life of these patients.
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Affiliation(s)
- María Costales
- Otorhinolaryngoly Department, Hospital Central de Asturias, Oviedo, Asturias, Spain
| | - Rodrigo Casanueva
- Otorhinolaryngoly Department, Hospital Central de Asturias, Oviedo, Asturias, Spain
| | - Vanessa Suárez
- Otorhinolaryngoly Department, Hospital Central de Asturias, Oviedo, Asturias, Spain
| | | | - Guadalupe A Cifuentes
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), Gijón, Asturias, Spain
| | - Marta Diñeiro
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), Gijón, Asturias, Spain
| | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), Gijón, Asturias, Spain
| | - Fernando López
- Otorhinolaryngoly Department, Hospital Central de Asturias, Oviedo, Asturias, Spain
| | - César Álvarez-Marcos
- Otorhinolaryngoly Department, Hospital Central de Asturias, Oviedo, Asturias, Spain
| | - Andrea Otero
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), Gijón, Asturias, Spain
| | - Justo Gómez
- Otorhinolaryngoly Department, Hospital Central de Asturias, Oviedo, Asturias, Spain
| | - José Luis Llorente
- Otorhinolaryngoly Department, Hospital Central de Asturias, Oviedo, Asturias, Spain
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Update on Cerebellar Ataxia with Neuropathy and Bilateral Vestibular Areflexia Syndrome (CANVAS). THE CEREBELLUM 2020; 20:687-700. [PMID: 33011895 PMCID: PMC8629873 DOI: 10.1007/s12311-020-01192-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 09/13/2020] [Indexed: 02/06/2023]
Abstract
The syndrome of cerebellar ataxia with neuropathy and bilateral vestibular areflexia (CANVAS) has emerged progressively during the last 30 years. It was first outlined by the neurootology/neurophysiology community in the vestibular areflexic patients, through the description of patients slowly developing late-onset cerebellar ataxia and bilateral vestibulopathy. The characteristic deficit of visuo-vestibulo-ocular reflex (VVOR) due to the impaired slow stabilizing eye movements was put forward and a specific disease subtending this syndrome was suggested. The association to a peripheral sensory axonal neuropathy was described later on, with neuropathological studies demonstrating that both sensory neuropathy and vestibular areflexia were diffuse ganglionopathy. Clinical and electrophysiological criteria of CANVAS were then proposed in 2016. Besides the classical triad, frequent chronic cough, signs of dysautonomia and neurogenic pains were frequently observed. From the beginning of published cohorts, sporadic as well as familial cases were reported, the last suggestive of an autosomal recessive mode of transmission. The genetic disorder was discovered in 2019, under the form of abnormal biallelic expansion in the replication factor C subunit 1 (RFC1) in a population of late-onset ataxia. This pathological expansion was found in 100% of the familial form and 92% of sporadic ones when the triad was complete. But using the genetic criteria, the phenotype of CANVAS seems to expand, for exemple including patients with isolated neuronopathy. We propose here to review the clinical, electrophysiological, anatomical, genetic aspect of CANVAS in light of the recent discovery of the genetic aetiology, and discuss differential diagnosis, neuropathology and physiopathology.
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A new insight into protein-protein interactions and the effect of conformational alterations in PCNA. Int J Biol Macromol 2020; 148:999-1009. [DOI: 10.1016/j.ijbiomac.2020.01.212] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/21/2020] [Accepted: 01/21/2020] [Indexed: 12/14/2022]
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Lee CC, Wang JW, Leu WM, Huang YT, Huang YW, Hsu YH, Meng M. Proliferating Cell Nuclear Antigen Suppresses RNA Replication of Bamboo Mosaic Virus through an Interaction with the Viral Genome. J Virol 2019; 93:e00961-19. [PMID: 31511381 PMCID: PMC6819918 DOI: 10.1128/jvi.00961-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/30/2019] [Indexed: 11/20/2022] Open
Abstract
Bamboo mosaic virus (BaMV), a member of the Potexvirus genus, has a monopartite positive-strand RNA genome on which five open reading frames (ORFs) are organized. ORF1 encodes a 155-kDa nonstructural protein (REPBaMV) that plays a core function in replication/transcription of the viral genome. To find out cellular factors modulating the replication efficiency of BaMV, a putative REPBaMV-associated protein complex from Nicotiana benthamiana leaf was isolated on an SDS-PAGE gel, and a few proteins preferentially associated with REPBaMV were identified by tandem mass spectrometry. Among them, proliferating cell nuclear antigen (PCNA) was particularly noted. Overexpression of PCNA strongly suppressed the accumulation of BaMV coat protein and RNAs in leaf protoplasts. In addition, PCNA exhibited an inhibitory effect on BaMV polymerase activity. A pulldown assay confirmed a binding capability of PCNA toward BaMV genomic RNA. Mutations at D41 or F114 residues, which are critical for PCNA to function in nuclear DNA replication and repair, disabled PCNA from binding BaMV genomic RNA as well as suppressing BaMV replication. This suggests that PCNA bound to the viral RNA may interfere with the formation of a potent replication complex or block the replication process. Interestingly, BaMV is almost invisible in the newly emerging leaves where PCNA is actively expressed. Accordingly, PCNA is probably one of the factors restricting the proliferation of BaMV in young leaves. Foxtail mosaic virus and Potato virus X were also suppressed by PCNA in the protoplast experiment, suggesting a general inhibitory effect of PCNA on the replication of potexviruses.IMPORTANCE Knowing the dynamic interplay between plant RNA viruses and their host is a basic step toward first understanding how the viruses survive the plant defense mechanisms and second gaining knowledge of pathogenic control in the field. This study found that plant proliferating cell nuclear antigen (PCNA) imposes a strong inhibition on the replication of several potexviruses, including Bamboo mosaic virus, Foxtail mosaic virus, and Potato virus X Based on the tests on Bamboo mosaic virus, PCNA is able to bind the viral genomic RNA, and this binding is a prerequisite for the protein to suppress the virus replication. This study also suggests that PCNA plays an important role in restricting the proliferation of potexviruses in the rapidly dividing tissues of plants.
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Affiliation(s)
- Cheng-Cheng Lee
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Jhih-Wei Wang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Wei-Ming Leu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Ting Huang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Ying-Wen Huang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Menghsiao Meng
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
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Rafehi H, Szmulewicz DJ, Bennett MF, Sobreira NLM, Pope K, Smith KR, Gillies G, Diakumis P, Dolzhenko E, Eberle MA, Barcina MG, Breen DP, Chancellor AM, Cremer PD, Delatycki MB, Fogel BL, Hackett A, Halmagyi GM, Kapetanovic S, Lang A, Mossman S, Mu W, Patrikios P, Perlman SL, Rosemergy I, Storey E, Watson SRD, Wilson MA, Zee DS, Valle D, Amor DJ, Bahlo M, Lockhart PJ. Bioinformatics-Based Identification of Expanded Repeats: A Non-reference Intronic Pentamer Expansion in RFC1 Causes CANVAS. Am J Hum Genet 2019; 105:151-165. [PMID: 31230722 PMCID: PMC6612533 DOI: 10.1016/j.ajhg.2019.05.016] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/21/2019] [Indexed: 01/28/2023] Open
Abstract
Genomic technologies such as next-generation sequencing (NGS) are revolutionizing molecular diagnostics and clinical medicine. However, these approaches have proven inefficient at identifying pathogenic repeat expansions. Here, we apply a collection of bioinformatics tools that can be utilized to identify either known or novel expanded repeat sequences in NGS data. We performed genetic studies of a cohort of 35 individuals from 22 families with a clinical diagnosis of cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome (CANVAS). Analysis of whole-genome sequence (WGS) data with five independent algorithms identified a recessively inherited intronic repeat expansion [(AAGGG)exp] in the gene encoding Replication Factor C1 (RFC1). This motif, not reported in the reference sequence, localized to an Alu element and replaced the reference (AAAAG)11 short tandem repeat. Genetic analyses confirmed the pathogenic expansion in 18 of 22 CANVAS-affected families and identified a core ancestral haplotype, estimated to have arisen in Europe more than twenty-five thousand years ago. WGS of the four RFC1-negative CANVAS-affected families identified plausible variants in three, with genomic re-diagnosis of SCA3, spastic ataxia of the Charlevoix-Saguenay type, and SCA45. This study identified the genetic basis of CANVAS and demonstrated that these improved bioinformatics tools increase the diagnostic utility of WGS to determine the genetic basis of a heterogeneous group of clinically overlapping neurogenetic disorders.
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Affiliation(s)
- Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - David J Szmulewicz
- Cerebellar Ataxia Clinic, Neuroscience Department, Alfred Health, Melbourne, VIC 3004, Australia; Balance Disorders and Ataxia Service, Royal Victorian Eye & Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Mark F Bennett
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC 3052, Australia; Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, 245 Burgundy Street, Heidelberg, VIC 3084, Australia
| | - Nara L M Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kate Pope
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia
| | - Katherine R Smith
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Greta Gillies
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia
| | - Peter Diakumis
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia
| | - Egor Dolzhenko
- Illumina Inc, 5200 Illumina Way, San Diego, CA 92122, USA
| | | | - María García Barcina
- Genetic Unit, Basurto University Hospital, OSI Bilbao-Basurto, avenida Montevideo 18, 48013 Bilbao, Spain
| | - David P Breen
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, Scotland; Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh EH16 4SB, Scotland; Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh EH16 4UX, Scotland
| | - Andrew M Chancellor
- Department of Neurology, Tauranga Hospital, Private Bag, Cameron Road, Tauranga 3171, New Zealand
| | - Phillip D Cremer
- University of Sydney, Camperdown, NSW 2006, Australia; Royal North Shore Hospital, Pacific Hwy, St Leonards, NSW 2065, Australia
| | - Martin B Delatycki
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Rd, Parkville, VIC 3052, Australia
| | - Brent L Fogel
- Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Anna Hackett
- Hunter Genetics, Hunter New England Health Service, Waratah, Newcastle, NSW 2300, Australia; University of Newcastle, Newcastle, NSW 2300, Australia
| | - G Michael Halmagyi
- Neurology Department, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; Central Clinical School, University of Sydney, Camperdown, NSW 2050, Australia
| | - Solange Kapetanovic
- Servicio de Neurología, Hospital de Basurto, Avenida de Montevideo 18, 48013 Bilbao, Bizkaia, Spain
| | - Anthony Lang
- Edmond J. Safra Program in Parkinson disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, Toronto, ON M5T 2S8, Canada; Department of Medicine, Division of Neurology, University Health Network and the University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Stuart Mossman
- Department of Neurology, Wellington Hospital, Wellington 6021, New Zealand
| | - Weiyi Mu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Susan L Perlman
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Ian Rosemergy
- Department of Neurology, Wellington Hospital, Newtown, Wellington 6021, New Zealand
| | - Elsdon Storey
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Hospital Campus, Commercial Road, Melbourne, VIC 3004, Australia
| | - Shaun R D Watson
- Institute of Neurological Sciences, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - Michael A Wilson
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia
| | - David S Zee
- Department of Neurology, Johns Hopkins Hospital, Baltimore, MD 21287, USA
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David J Amor
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Rd, Parkville, VIC 3052, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Rd, Parkville, VIC 3052, Australia.
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13
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Identification of RFC5 as a novel potential prognostic biomarker in lung cancer through bioinformatics analysis. Oncol Lett 2018; 16:4201-4210. [PMID: 30214556 PMCID: PMC6126192 DOI: 10.3892/ol.2018.9221] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 04/18/2018] [Indexed: 01/04/2023] Open
Abstract
Lung cancer is the leading cause of mortalities among all types of cancer. Therefore, the screening of biomarkers that are related with the progression of lung cancer is crucial for early diagnosis and efficient therapy of lung cancer. In the present study, bioinformatic analysis identified replication factor C 5 (RFC5) as a potential novel oncogene in lung cancer. RFC5 functions as a clamp loader and is involved in DNA replication and repair. Analysis of public databases and reverse transcription-quantitative polymerase chain reaction indicated that RFC5 was significantly increased in tumor tissues compared with adjacent normal tissues. A high RFC5 expression was observed to be associated with more aggressive malignant clinicopathological features, including higher T stage, more advanced regional lymph node metastasis and a higher probability of relapse. Notably, there were notable differences in overall survival (OS), first progression and post-progression survival between the high RFC5 expression group and low RFC5 expression group. Univariate and multivariate Cox regression analyses indicated that RFC5 was an independent risk factor that was associated with poorer OS and disease-free survival. According to GSEA, several gene sets that are associated with cell cycle and DNA damage were enriched in the RFC5 overexpression group, which indicated that RFC5 might promote the proliferation of lung cancer cells. Our finding indicated that RFC5 might be a novel prognostic biomarker of lung cancer, and it might be serve as a potential diagnosis and therapy target for lung cancer in the future.
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14
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Hedglin M, Aitha M, Benkovic SJ. Monitoring the Retention of Human Proliferating Cell Nuclear Antigen at Primer/Template Junctions by Proteins That Bind Single-Stranded DNA. Biochemistry 2017; 56:3415-3421. [PMID: 28590137 DOI: 10.1021/acs.biochem.7b00386] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In humans, proliferating cell nuclear antigen (PCNA) sliding clamps encircling DNA coordinate various aspects of DNA metabolism throughout the cell cycle. A critical aspect of this is restricting PCNA to the vicinity of its DNA target site. For example, PCNA must be maintained at or near primer/template (P/T) junctions during DNA synthesis. With a diverse array of cellular factors implicated, many of which interact with PCNA, DNA, or both, it is unknown how this critical feat is achieved. Furthermore, current biochemical assays that examine the retention of PCNA near P/T junctions are inefficient, discontinuous, and qualitative and significantly deviate from physiologically relevant conditions. To overcome these challenges and limitations, we recently developed a novel and convenient Förster resonance energy transfer (FRET) assay that directly and continuously monitors the retention of human PCNA at a P/T junction. Here we describe in detail the design, methodology, interpretation, and limitations of this quantitative FRET assay using the single-stranded DNA-binding protein, SSB, from Escherichia coli as an example. This powerful tool is broadly applicable to any single-stranded DNA-binding protein and may be utilized and/or expanded upon to dissect DNA metabolic pathways that are dependent upon PCNA.
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Affiliation(s)
- Mark Hedglin
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Mahesh Aitha
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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15
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Hedglin M, Benkovic SJ. Replication Protein A Prohibits Diffusion of the PCNA Sliding Clamp along Single-Stranded DNA. Biochemistry 2017; 56:1824-1835. [PMID: 28177605 PMCID: PMC5382571 DOI: 10.1021/acs.biochem.6b01213] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The replicative polymerases cannot accommodate distortions to the native DNA sequence such as modifications (lesions) to the native template bases from exposure to reactive metabolites and environmental mutagens. Consequently, DNA synthesis on an afflicted template abruptly stops upon encountering these lesions, but the replication fork progresses onward, exposing long stretches of the damaged template before eventually stalling. Such arrests may be overcome by translesion DNA synthesis (TLS) in which specialized TLS polymerases bind to the resident proliferating cell nuclear antigen (PCNA) and replicate the damaged DNA. Hence, a critical aspect of TLS is maintaining PCNA at or near a blocked primer/template (P/T) junction upon uncoupling of fork progression from DNA synthesis by the replicative polymerases. The single-stranded DNA (ssDNA) binding protein, replication protein A (RPA), coats the exposed template and might prohibit diffusion of PCNA along the single-stranded DNA adjacent to a blocked P/T junction. However, this idea had yet to be directly tested. We recently developed a unique Cy3-Cy5 Forster resonance energy transfer (FRET) pair that directly reports on the occupancy of DNA by PCNA. In this study, we utilized this FRET pair to directly and continuously monitor the retention of human PCNA at a blocked P/T junction. Results from extensive steady state and pre-steady state FRET assays indicate that RPA binds tightly to the ssDNA adjacent to a blocked P/T junction and restricts PCNA to the upstream duplex region by physically blocking diffusion of PCNA along ssDNA.
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Affiliation(s)
- Mark Hedglin
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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16
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Novel Implications in Molecular Diagnosis of Lynch Syndrome. Gastroenterol Res Pract 2017; 2017:2595098. [PMID: 28250766 PMCID: PMC5303590 DOI: 10.1155/2017/2595098] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/05/2017] [Indexed: 02/07/2023] Open
Abstract
About 10% of total colorectal cancers are associated with known Mendelian inheritance, as Familial Adenomatous Polyposis (FAP) and Lynch syndrome (LS). In these cancer types the clinical manifestations of disease are due to mutations in high-risk alleles, with a penetrance at least of 70%. The LS is associated with germline mutations in the DNA mismatch repair (MMR) genes. However, the mutation detection analysis of these genes does not always provide informative results for genetic counseling of LS patients. Very often, the molecular analysis reveals the presence of variants of unknown significance (VUSs) whose interpretation is not easy and requires the combination of different analytical strategies to get a proper assessment of their pathogenicity. In some cases, these VUSs may make a more substantial overall contribution to cancer risk than the well-assessed severe Mendelian variants. Moreover, it could also be possible that the simultaneous presence of these genetic variants in several MMR genes that behave as low risk alleles might contribute in a cooperative manner to increase the risk of hereditary cancer. In this paper, through a review of the recent literature, we have speculated a novel inheritance model in the Lynch syndrome; this could pave the way toward new diagnostic perspectives.
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17
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Deshmukh AL, Kumar C, Singh DK, Maurya P, Banerjee D. Dynamics of replication proteins during lagging strand synthesis: A crossroads for genomic instability and cancer. DNA Repair (Amst) 2016; 42:72-81. [DOI: 10.1016/j.dnarep.2016.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/22/2016] [Accepted: 04/22/2016] [Indexed: 01/18/2023]
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18
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Campos EI, Smits AH, Kang YH, Landry S, Escobar TM, Nayak S, Ueberheide BM, Durocher D, Vermeulen M, Hurwitz J, Reinberg D. Analysis of the Histone H3.1 Interactome: A Suitable Chaperone for the Right Event. Mol Cell 2015; 60:697-709. [PMID: 26527279 DOI: 10.1016/j.molcel.2015.08.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 06/17/2015] [Accepted: 08/07/2015] [Indexed: 11/17/2022]
Abstract
Despite minimal disparity at the sequence level, mammalian H3 variants bind to distinct sets of polypeptides. Although histone H3.1 predominates in cycling cells, our knowledge of the soluble complexes that it forms en route to deposition or following eviction from chromatin remains limited. Here, we provide a comprehensive analysis of the H3.1-binding proteome, with emphasis on its interactions with histone chaperones and components of the replication fork. Quantitative mass spectrometry revealed 170 protein interactions, whereas a large-scale biochemical fractionation of H3.1 and associated enzymatic activities uncovered over twenty stable protein complexes in dividing human cells. The sNASP and ASF1 chaperones play pivotal roles in the processing of soluble histones but do not associate with the active CDC45/MCM2-7/GINS (CMG) replicative helicase. We also find TONSL-MMS22L to function as a H3-H4 histone chaperone. It associates with the regulatory MCM5 subunit of the replicative helicase.
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Affiliation(s)
- Eric I Campos
- Howard Hughes Medical Institute, New York University School of Medicine, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, NY 10016, USA
| | - Arne H Smits
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands 6525 GA
| | - Young-Hoon Kang
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, NY 10021, USA
| | - Sébastien Landry
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, and Department of Molecular Genetics, University of Toronto, Toronto M5G 1X5, Canada
| | - Thelma M Escobar
- Howard Hughes Medical Institute, New York University School of Medicine, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, NY 10016, USA
| | - Shruti Nayak
- Office of Collaborative Science, New York University School of Medicine, NY 10016, USA
| | - Beatrix M Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, NY 10016, USA
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, and Department of Molecular Genetics, University of Toronto, Toronto M5G 1X5, Canada
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands 6525 GA
| | - Jerard Hurwitz
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, NY 10021, USA
| | - Danny Reinberg
- Howard Hughes Medical Institute, New York University School of Medicine, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, NY 10016, USA.
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Chen G, Fang X, Yu M. Regulation of gene expression in rats with spinal cord injury based on microarray data. Mol Med Rep 2015; 12:2465-72. [PMID: 25936407 PMCID: PMC4464272 DOI: 10.3892/mmr.2015.3670] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 03/09/2015] [Indexed: 02/06/2023] Open
Abstract
The present study aimed to investigate the molecular mechanisms of spinal cord injury (SCI) in rats. First, the differentially expressed genes (DGEs) were screened based on GSE45006 microarray data downloaded from Gene Expression Omnibus using the significant analysis of microarray (SAM) method. Screening was performed for DEGs which were negatively or possibly correlated with time and subsequently subjected to gene ontology (GO) functional annotation. Furthermore, pathway enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes was also performed. In addition, a protein-protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins database. Finally, GeneCodis was used to seek transcription factors and microRNAs that are involved in the regulation of DEGs. A total of 806 DEGs were upregulated and 549 DEGs were downregulated in the rats with SCI. Cholesterol metabolism-associated genes (e.g. HMGCS1, FDFT1 and IDI1) were negatively correlated with time, while injury genes (e.g. SERPING1, C1S and RAB27A) were positively correlated with time after SCI. PCNA, MCM2, JUN and SNAP25 were the hub proteins of the PPI network. The transcription factors LEF1 and SP1 were observed to be associated with the regulation of two DEGs that were involved in the cholesterol-associated metabolism as well as injury responses. A number of microRNAs (e.g. miR210, miR-487b and miR-16) were observed to target cholesterol metabolism-associated DGEs. The hub genes PCNA, MCM2, JUN and SNAP25 presumably have critical roles in rats with SCI, and the transcription factors LEF1 and SP1 may be important for the regulation of cholesterol metabolism and injury responses following SCI.
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Affiliation(s)
- Guoqiang Chen
- Department of Orthopedics, Beijing Shijitan Hospital Affiliated to Capital Medical University, Beijing 100038, P.R. China
| | - Xiutong Fang
- Department of Orthopedics, Beijing Shijitan Hospital Affiliated to Capital Medical University, Beijing 100038, P.R. China
| | - Meng Yu
- Department of Orthopedics, Beijing Shijitan Hospital Affiliated to Capital Medical University, Beijing 100038, P.R. China
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20
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Phosphorylation of PCNA by EGFR inhibits mismatch repair and promotes misincorporation during DNA synthesis. Proc Natl Acad Sci U S A 2015; 112:5667-72. [PMID: 25825764 DOI: 10.1073/pnas.1417711112] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) plays essential roles in eukaryotic cells during DNA replication, DNA mismatch repair (MMR), and other events at the replication fork. Earlier studies show that PCNA is regulated by posttranslational modifications, including phosphorylation of tyrosine 211 (Y211) by the epidermal growth factor receptor (EGFR). However, the functional significance of Y211-phosphorylated PCNA remains unknown. Here, we show that PCNA phosphorylation by EGFR alters its interaction with mismatch-recognition proteins MutSα and MutSβ and interferes with PCNA-dependent activation of MutLα endonuclease, thereby inhibiting MMR at the initiation step. Evidence is also provided that Y211-phosphorylated PCNA induces nucleotide misincorporation during DNA synthesis. These findings reveal a novel mechanism by which Y211-phosphorylated PCNA promotes cancer development and progression via facilitating error-prone DNA replication and suppressing the MMR function.
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21
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Evison BJ, Actis ML, Wu SZ, Shao Y, Heath RJ, Yang L, Fujii N. A site-selective, irreversible inhibitor of the DNA replication auxiliary factor proliferating cell nuclear antigen (PCNA). Bioorg Med Chem 2014; 22:6333-43. [PMID: 25438756 DOI: 10.1016/j.bmc.2014.09.058] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/18/2014] [Accepted: 09/29/2014] [Indexed: 01/09/2023]
Abstract
Proliferating cell nuclear antigen (PCNA) assumes an indispensable role in supporting cellular DNA replication and repair by organizing numerous protein components of these pathways via a common PCNA-interacting sequence motif called a PIP-box. Given the multifunctional nature of PCNA, the selective inhibition of PIP-box-mediated interactions may represent a new strategy for the chemosensitization of cancer cells to existing DNA-directed therapies; however, promiscuous blockage of these interactions may also be universally deleterious. To address these possibilities, we utilized a chemical strategy to irreversibly block PIP-box-mediated interactions. Initially, we identified and validated PCNA methionine 40 (M40) and histidine 44 (H44) as essential residues for PCNA/PIP-box interactions in general and, more specifically, for efficient PCNA loading onto chromatin within cells. Next, we created a novel small molecule incorporating an electrophilic di-chloro platinum moiety that preferentially alkylated M40 and H44 residues. The compound, designated T2Pt, covalently cross-linked wild-type but not M40A/H44A PCNA, irreversibly inhibited PCNA/PIP-box interactions, and mildly alkylated plasmid DNA in vitro. In cells, T2Pt persistently induced cell cycle arrest, activated ATR-Chk1 signaling and modestly induced DNA strand breaks, features typical of cellular replication stress. Despite sustained activation of the replication stress response by the compound and its modestly genotoxic nature, T2Pt demonstrated little activity in clonogenic survival assays as a single agent, yet sensitized cells to cisplatin. The discovery of T2Pt represents an original effort directed at the development of irreversible PCNA inhibitors and sets the stage for the discovery of analogues more selective for PCNA over other cellular nucleophiles.
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Affiliation(s)
- Benjamin J Evison
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Marcelo L Actis
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Sean Z Wu
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Youming Shao
- Protein Production Facility, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Richard J Heath
- Protein Production Facility, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Naoaki Fujii
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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22
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Leman AR, Noguchi E. The replication fork: understanding the eukaryotic replication machinery and the challenges to genome duplication. Genes (Basel) 2014; 4:1-32. [PMID: 23599899 PMCID: PMC3627427 DOI: 10.3390/genes4010001] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Eukaryotic cells must accurately and efficiently duplicate their genomes during each round of the cell cycle. Multiple linear chromosomes, an abundance of regulatory elements, and chromosome packaging are all challenges that the eukaryotic DNA replication machinery must successfully overcome. The replication machinery, the “replisome” complex, is composed of many specialized proteins with functions in supporting replication by DNA polymerases. Efficient replisome progression relies on tight coordination between the various factors of the replisome. Further, replisome progression must occur on less than ideal templates at various genomic loci. Here, we describe the functions of the major replisome components, as well as some of the obstacles to efficient DNA replication that the replisome confronts. Together, this review summarizes current understanding of the vastly complicated task of replicating eukaryotic DNA.
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Affiliation(s)
- Adam R. Leman
- Authors to whom correspondence should be addressed; E-Mails: (A.R.L.); (E.N.); Tel.: +1-215-762-4825 (E.N.); Fax: +1-215-762-4452 (E.N.)
| | - Eishi Noguchi
- Authors to whom correspondence should be addressed; E-Mails: (A.R.L.); (E.N.); Tel.: +1-215-762-4825 (E.N.); Fax: +1-215-762-4452 (E.N.)
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23
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Cell cycle: mechanisms of control and dysregulation in cancer. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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24
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Marchionni L, Afsari B, Geman D, Leek JT. A simple and reproducible breast cancer prognostic test. BMC Genomics 2013; 14:336. [PMID: 23682826 PMCID: PMC3662649 DOI: 10.1186/1471-2164-14-336] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 05/04/2013] [Indexed: 11/10/2022] Open
Abstract
Background A small number of prognostic and predictive tests based on gene expression are currently offered as reference laboratory tests. In contrast to such success stories, a number of flaws and errors have recently been identified in other genomic-based predictors and the success rate for developing clinically useful genomic signatures is low. These errors have led to widespread concerns about the protocols for conducting and reporting of computational research. As a result, a need has emerged for a template for reproducible development of genomic signatures that incorporates full transparency, data sharing and statistical robustness. Results Here we present the first fully reproducible analysis of the data used to train and test MammaPrint, an FDA-cleared prognostic test for breast cancer based on a 70-gene expression signature. We provide all the software and documentation necessary for researchers to build and evaluate genomic classifiers based on these data. As an example of the utility of this reproducible research resource, we develop a simple prognostic classifier that uses only 16 genes from the MammaPrint signature and is equally accurate in predicting 5-year disease free survival. Conclusions Our study provides a prototypic example for reproducible development of computational algorithms for learning prognostic biomarkers in the era of personalized medicine.
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Affiliation(s)
- Luigi Marchionni
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21231, USA
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25
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Hedglin M, Perumal SK, Hu Z, Benkovic S. Stepwise assembly of the human replicative polymerase holoenzyme. eLife 2013; 2:e00278. [PMID: 23577232 PMCID: PMC3614016 DOI: 10.7554/elife.00278] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 02/19/2013] [Indexed: 02/06/2023] Open
Abstract
In most organisms, clamp loaders catalyze both the loading of sliding clamps onto DNA and their removal. How these opposing activities are regulated during assembly of the DNA polymerase holoenzyme remains unknown. By utilizing FRET to monitor protein-DNA interactions, we examined assembly of the human holoenzyme. The results indicate that assembly proceeds in a stepwise manner. The clamp loader (RFC) loads a sliding clamp (PCNA) onto a primer/template junction but remains transiently bound to the DNA. Unable to slide away, PCNA re-engages with RFC and is unloaded. In the presence of polymerase (polδ), loaded PCNA is captured from DNA-bound RFC which subsequently dissociates, leaving behind the holoenzyme. These studies suggest that the unloading activity of RFC maximizes the utilization of PCNA by inhibiting the build-up of free PCNA on DNA in the absence of polymerase and recycling limited PCNA to keep up with ongoing replication. DOI:http://dx.doi.org/10.7554/eLife.00278.001.
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Affiliation(s)
- Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, United States
| | - Senthil K Perumal
- Department of Chemistry, The Pennsylvania State University, University Park, United States
| | - Zhenxin Hu
- Department of Chemistry, The Pennsylvania State University, University Park, United States
| | - Stephen Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, United States
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26
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Abstract
To achieve the high degree of processivity required for DNA replication, DNA polymerases associate with ring-shaped sliding clamps that encircle the template DNA and slide freely along it. The closed circular structure of sliding clamps necessitates an enzyme-catalyzed mechanism, which not only opens them for assembly and closes them around DNA, but specifically targets them to sites where DNA synthesis is initiated and orients them correctly for replication. Such a feat is performed by multisubunit complexes known as clamp loaders, which use ATP to open sliding clamp rings and place them around the 3' end of primer-template (PT) junctions. Here we discuss the structure and composition of sliding clamps and clamp loaders from the three domains of life as well as T4 bacteriophage, and provide our current understanding of the clamp-loading process.
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Affiliation(s)
- Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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Abstract
Activation of a host DNA damage response (DDR) is essential for DNA replication of minute virus of canines (MVC), a member of the genus Bocavirus of the Parvoviridae family; however, the mechanism by which DDR contributes to viral DNA replication is unknown. In the current study, we demonstrate that MVC infection triggers the intra-S-phase arrest to slow down host cellular DNA replication and to recruit cellular DNA replication factors for viral DNA replication. The intra-S-phase arrest is regulated by ATM (ataxia telangiectasia-mutated kinase) signaling in a p53-independent manner. Moreover, we demonstrate that SMC1 (structural maintenance of chromosomes 1) is the key regulator of the intra-S-phase arrest induced during infection. Either knockdown of SMC1 or complementation with a dominant negative SMC1 mutant blocks both the intra-S-phase arrest and viral DNA replication. Finally, we show that the intra-S-phase arrest induced during MVC infection was caused neither by damaged host cellular DNA nor by viral proteins but by replicating viral genomes physically associated with the DNA damage sensor, the Mre11-Rad50-Nbs1 (MRN) complex. In conclusion, the feedback loop between MVC DNA replication and the intra-S-phase arrest is mediated by ATM-SMC1 signaling and plays a critical role in MVC DNA replication. Thus, our findings unravel the mechanism underlying DDR signaling-facilitated MVC DNA replication and demonstrate a novel strategy of DNA virus-host interaction.
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Wang X, Li J, Schowalter RM, Jiao J, Buck CB, You J. Bromodomain protein Brd4 plays a key role in Merkel cell polyomavirus DNA replication. PLoS Pathog 2012; 8:e1003021. [PMID: 23144621 PMCID: PMC3493480 DOI: 10.1371/journal.ppat.1003021] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 09/24/2012] [Indexed: 12/15/2022] Open
Abstract
Merkel cell polyomavirus (MCV or MCPyV) is the first human polyomavirus to be definitively linked to cancer. The mechanisms of MCV-induced oncogenesis and much of MCV biology are largely unexplored. In this study, we demonstrate that bromodomain protein 4 (Brd4) interacts with MCV large T antigen (LT) and plays a critical role in viral DNA replication. Brd4 knockdown inhibits MCV replication, which can be rescued by recombinant Brd4. Brd4 colocalizes with the MCV LT/replication origin complex in the nucleus and recruits replication factor C (RFC) to the viral replication sites. A dominant negative inhibitor of the Brd4-MCV LT interaction can dissociate Brd4 and RFC from the viral replication complex and abrogate MCV replication. Furthermore, obstructing the physiologic interaction between Brd4 and host chromatin with the chemical compound JQ1(+) leads to enhanced MCV DNA replication, demonstrating that the role of Brd4 in MCV replication is distinct from its role in chromatin-associated transcriptional regulation. Our findings demonstrate mechanistic details of the MCV replication machinery; providing novel insight to elucidate the life cycle of this newly discovered oncogenic DNA virus. MCV is a novel human polyomavirus that has recently been discovered in Merkel cell carcinoma (MCC), a rare but highly aggressive skin cancer. Several independent studies have confirmed that MCV is present in ∼80% of MCC tumors. However, very little is known about how the interaction between MCV and its human hosts contributes to the virus-induced cancers. Many aspects of the infectious life cycle of MCV are largely unexplored. In this study, we demonstrate that the MCV-encoded large T antigen can bind to host protein Brd4, which in turn serves as a scaffold that functionally recruits cellular DNA replication factors for replication of MCV viral DNA in host cells. This study is the first report to demonstrate mechanistic details of MCV's recruitment of the host cell DNA replication machinery; providing novel insight to elucidate the life cycle of this newly discovered oncogenic DNA virus. Importantly, our work demonstrates that blocking the Brd4 and MCV LT interaction can prevent MCV from replicating in host cells. This study identifies the Brd4-MCV LT interaction as an important target for potential development of effective therapeutic strategies to treat MCV infection.
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Affiliation(s)
- Xin Wang
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jing Li
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Rachel M. Schowalter
- Tumor Virus Molecular Biology Section, Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Jing Jiao
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Christopher B. Buck
- Tumor Virus Molecular Biology Section, Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Jianxin You
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Maeng S, Kim GJ, Choi EJ, Yang HO, Lee DS, Sohn YC. 9-Cis-retinoic acid induces growth inhibition in retinoid-sensitive breast cancer and sea urchin embryonic cells via retinoid X receptor α and replication factor C3. Mol Endocrinol 2012; 26:1821-35. [PMID: 22949521 DOI: 10.1210/me.2012-1104] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
There is widespread interest in defining factors and mechanisms that suppress the proliferation of cancer cells. Retinoic acid (RA) is a potent suppressor of mammary cancer and developmental embryonic cell proliferation. However, the molecular mechanisms by which 9-cis-RA signaling induces growth inhibition in RA-sensitive breast cancer and embryonic cells are not apparent. Here, we provide evidence that the inhibitory effect of 9-cis-RA on cell proliferation depends on 9-cis-RA-dependent interaction of retinoid X receptor α (RXRα) with replication factor C3 (RFC3), which is a subunit of the RFC heteropentamer that opens and closes the circular proliferating cell nuclear antigen (PCNA) clamp on DNA. An RFC3 ortholog in a sea urchin cDNA library was isolated by using the ligand-binding domain of RXRα as bait in a yeast two-hybrid screening. The interaction of RFC3 with RXRα depends on 9-cis-RA and bexarotene, but not on all-trans-RA or an RA receptor (RAR)-selective ligand. Truncation and mutagenesis experiments demonstrated that the C-terminal LXXLL motifs in both human and sea urchin RFC3 are critical for the interaction with RXRα. The transient interaction between 9-cis-RA-activated RXRα and RFC3 resulted in reconfiguration of the PCNA-RFC complex. Furthermore, we found that knockdown of RXRα or overexpression of RFC3 impairs the ability of 9-cis-RA to inhibit proliferation of MCF-7 breast cancer cells and sea urchin embryogenesis. Our results indicate that 9-cis-RA-activated RXRα suppresses the growth of RA-sensitive breast cancer and embryonic cells through RFC3.
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Affiliation(s)
- Sejung Maeng
- Department of Marine Molecular Biotechnology, College of Life Sciences, Gangneung-Wonju National University, Gangneung 210-702, Republic of Korea
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Zhang CD, Li FF, Chen XY, Huang MH, Zhang J, Cui H, Pan MH, Lu C. DNA replication events during larval silk gland development in the silkworm, Bombyx mori. JOURNAL OF INSECT PHYSIOLOGY 2012; 58:974-978. [PMID: 22609363 DOI: 10.1016/j.jinsphys.2012.04.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 04/28/2012] [Accepted: 04/30/2012] [Indexed: 06/01/2023]
Abstract
The silk gland is an important organ in silkworm as it synthesizes silk proteins and is critical to spinning. The genomic DNA content of silk gland cells dramatically increases 200-400 thousand times for the larval life span through the process of endomitosis. Using in vitro culture, DNA synthesis was measured using BrdU labeling during the larval molt and intermolt periods. We found that the cell cycle of endomitosis was activated during the intermolt and was inhibited during the molt phase. The anterior silk gland, middle silk gland, and posterior silk gland cells asynchronously exit the endomitotic cycle after day 6 in 5th instar larvae, which correlated with the reduced expression of the cell cycle-related cdt1, pcna, cyclin E, cdk2 and cdk1 mRNAs in the wandering phase. Additional starvation had no effect on the initiation of silk gland DNA synthesis of the freshly ecdysed larvae.
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Affiliation(s)
- Chun-Dong Zhang
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, PR China
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Sacco E, Hasan MM, Alberghina L, Vanoni M. Comparative analysis of the molecular mechanisms controlling the initiation of chromosomal DNA replication in yeast and in mammalian cells. Biotechnol Adv 2012; 30:73-98. [DOI: 10.1016/j.biotechadv.2011.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 09/14/2011] [Indexed: 11/26/2022]
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ATP binding and hydrolysis-driven rate-determining events in the RFC-catalyzed PCNA clamp loading reaction. J Mol Biol 2011; 416:176-91. [PMID: 22197378 DOI: 10.1016/j.jmb.2011.12.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 11/30/2011] [Accepted: 12/07/2011] [Indexed: 11/20/2022]
Abstract
The multi-subunit replication factor C (RFC) complex loads circular proliferating cell nuclear antigen (PCNA) clamps onto DNA where they serve as mobile tethers for polymerases and coordinate the functions of many other DNA metabolic proteins. The clamp loading reaction is complex, involving multiple components (RFC, PCNA, DNA, and ATP) and events (minimally: PCNA opening/closing, DNA binding/release, and ATP binding/hydrolysis) that yield a topologically linked clamp·DNA product in less than a second. Here, we report pre-steady-state measurements of several steps in the reaction catalyzed by Saccharomyces cerevisiae RFC and present a comprehensive kinetic model based on global analysis of the data. Highlights of the reaction mechanism are that ATP binding to RFC initiates slow activation of the clamp loader, enabling it to open PCNA (at ~2 s(-1)) and bind primer-template DNA (ptDNA). Rapid binding of ptDNA leads to formation of the RFC·ATP·PCNA(open)·ptDNA complex, which catalyzes a burst of ATP hydrolysis. Another slow step in the reaction follows ATP hydrolysis and is associated with PCNA closure around ptDNA (8 s(-1)). Dissociation of PCNA·ptDNA from RFC leads to catalytic turnover. We propose that these early and late rate-determining events are intramolecular conformational changes in RFC and PCNA that control clamp opening and closure, and that ATP binding and hydrolysis switch RFC between conformations with high and low affinities, respectively, for open PCNA and ptDNA, and thus bookend the clamp loading reaction.
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Jayasena CS, Trinh LA, Bronner M. Live imaging of endogenous periodic tryptophan protein 2 gene homologue during zebrafish development. Dev Dyn 2011; 240:2578-83. [PMID: 21954116 DOI: 10.1002/dvdy.22744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2011] [Indexed: 11/10/2022] Open
Abstract
Yeast Periodic tryptophan protein 2 gene (Pwp2) is involved in ribosome biogenesis and has been implicated in regulation of the cell cycle in yeast. Here, we report a zebrafish protein-trap line that produces fluorescently tagged Periodic tryptophan protein 2 gene homologue (Pwp2h) protein, which can be dynamically tracked in living fish at subcellular resolution. We identified both full-length zebrafish Pwp2h and a short variant. The expression results show that Pwp2h is present in numerous sites in the early developing embryo, but later is restricted to highly proliferative regions, including the forebrain ventricular zone and endoderm-derived organs in the early larval stage. At the subcellular level, Pwp2h protein appears to be localized to the region of the nucleolus consistent with its presumed function in ribosomal RNA synthesis. This Pwp2h protein trap line offers a powerful tool to study the link between ribosome biogenesis and cell cycle progression during vertebrate development.
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Affiliation(s)
- Chathurani S Jayasena
- Division of Biology 139-74, California Institute of Technology, Pasadena, California 91125, USA
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Sinicrope FA, Broaddus R, Joshi N, Gerner E, Half E, Kirsch I, Lewin J, Morlan B, Hong WK. Evaluation of difluoromethylornithine for the chemoprevention of Barrett's esophagus and mucosal dysplasia. Cancer Prev Res (Phila) 2011; 4:829-39. [PMID: 21636549 DOI: 10.1158/1940-6207.capr-10-0243] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Patients with Barrett's esophagus (BE) and dysplasia are candidates for chemopreventive strategies to reduce cancer risk. We determined the effects of difluoromethylornithine (DMFO) on mucosal polyamines, gene expression, and histopathology in BE. Ten patients with BE and low-grade dysplasia participated in a single-arm study of DFMO (0.5 g/m(2)/d) given continuously for 6 months. Esophagoscopy with biopsies was conducted at baseline, 3, 6, and 12 months. Dysplasia was graded by a gastrointestinal pathologist. Audiology was assessed (at baseline and at 6 months). Mucosal polyamines were measured by high-performance liquid chromatography. Microarray-based gene expression was analyzed using a cDNA two-color chip. DFMO suppressed levels of the polyamines putrescine (P = 0.02) and spermidine (P = 0.02) and the spermidine/spermine ratio (P < 0.01) in dysplastic BE (6 months vs. baseline) that persisted at 6 months following drug cessation. Among the top 25 modulated genes, we found those regulating p53-mediated cell signaling (RPL11), cell-cycle regulation (cyclin E2), and cell adhesion and invasion (Plexin1). DFMO downregulated Krüppel-like factor 5 (KLF5), a transcription factor promoting cell proliferation, and suppressed RFC5 whose protein interacts with proliferating cell nuclear antigen. Histopathology showed regression of dysplasia (n = 1), stable disease (n = 8), and progression to high-grade dysplasia (n = 1). Polyamines were suppressed in the responder to a greater extent than in stable cases. DFMO was well tolerated, and one patient had subclinical, unilateral ototoxicity. DFMO suppressed mucosal polyamines and modulated genes that may be mechanistically related to its chemopreventive effect. Further study of DFMO for the chemoprevention of esophageal cancer in BE patients is warranted.
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Identification, mRNA expression and characterization of proliferating cell nuclear antigen gene from Chinese mitten crab Eriocheir japonica sinensis. Comp Biochem Physiol A Mol Integr Physiol 2010; 157:170-6. [PMID: 20542131 DOI: 10.1016/j.cbpa.2010.06.163] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Revised: 06/05/2010] [Accepted: 06/07/2010] [Indexed: 11/22/2022]
Abstract
The sliding clamp proliferating cell nuclear antigen (PCNA) plays important roles in nucleic acid metabolism. In this work, we isolated a PCNA gene (designated as EjsPCNA, accession: FJ483830) by rapid amplification of cDNA ends approach from the Chinese mitten crab Eriocheir japonica sinensis. The full-length cDNA of EjsPCNA consists of 1123 nucleotides with an open-reading frame of 780bp encoding 259 amino acids (28.62kDa) and containing an interdomain connecting loop, C-terminal tail, and center loop. Sequence alignment, phylogenetic analyses, and structure comparison revealed that EjsPCNA is a member of the PCNA family. Real-time RT-PCR results indicate that EjsPCNA is expressed throughout three developmental stages. EjsPCNA mRNA expression levels at the first crab stage are significantly higher than that of the other two stages. Present data showed that the expression levels of EjsPCNA in E. j. sinensis are likely related to proliferation activity of tissues, and suggested that EjsPCNA gene is probably involved in the crabs' early developmental regulation.
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36
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Zhuang Z, Ai Y. Processivity factor of DNA polymerase and its expanding role in normal and translesion DNA synthesis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:1081-93. [PMID: 19576301 DOI: 10.1016/j.bbapap.2009.06.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 06/16/2009] [Accepted: 06/22/2009] [Indexed: 11/30/2022]
Abstract
Clamp protein or clamp, initially identified as the processivity factor of the replicative DNA polymerase, is indispensable for the timely and faithful replication of DNA genome. Clamp encircles duplex DNA and physically interacts with DNA polymerase. Clamps from different organisms share remarkable similarities in both structure and function. Loading of clamp onto DNA requires the activity of clamp loader. Although all clamp loaders act by converting the chemical energy derived from ATP hydrolysis to mechanical force, intriguing differences exist in the mechanistic details of clamp loading. The structure and function of clamp in normal and translesion DNA synthesis has been subjected to extensive investigations. This review summarizes the current understanding of clamps from three kingdoms of life and the mechanism of loading by their cognate clamp loaders. We also discuss the recent findings on the interactions between clamp and DNA, as well as between clamp and DNA polymerase (both the replicative and specialized DNA polymerases). Lastly the role of clamp in modulating polymerase exchange is discussed in the context of translesion DNA synthesis.
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Affiliation(s)
- Zhihao Zhuang
- Department of Chemistry and Biochemistry, 214A Drake Hall, University of Delaware, Newark, DE, 19716, USA.
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Mechanism of ATP-driven PCNA clamp loading by S. cerevisiae RFC. J Mol Biol 2009; 388:431-42. [PMID: 19285992 DOI: 10.1016/j.jmb.2009.03.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Revised: 03/05/2009] [Accepted: 03/09/2009] [Indexed: 11/20/2022]
Abstract
Circular clamps tether polymerases to DNA, serving as essential processivity factors in genome replication, and function in other critical cellular processes as well. Clamp loaders catalyze clamp assembly onto DNA, and the question of how these proteins construct a topological link between a clamp and DNA, especially the mechanism by which ATP is utilized for the task, remains open. Here we describe pre-steady-state analysis of ATP hydrolysis, proliferating cell nuclear antigen (PCNA) clamp opening, and DNA binding by Saccharomyces cerevisiae replication factor C (RFC), and present the first kinetic model of a eukaryotic clamp-loading reaction validated by global data analysis. ATP binding to multiple RFC subunits initiates a slow conformational change in the clamp loader, enabling it to bind and open PCNA and to bind DNA as well. PCNA opening locks RFC into an active state, and the resulting RFC.ATP.PCNA((open)) intermediate is ready for the entry of DNA into the clamp. DNA binding commits RFC to ATP hydrolysis, which is followed by PCNA closure and PCNA.DNA release. This model enables quantitative understanding of the multistep mechanism of a eukaryotic clamp loader and furthermore facilitates comparative analysis of loaders from diverse organisms.
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Erdogan E, Klee EW, Thompson EA, Fields AP. Meta-analysis of oncogenic protein kinase Ciota signaling in lung adenocarcinoma. Clin Cancer Res 2009; 15:1527-33. [PMID: 19223491 DOI: 10.1158/1078-0432.ccr-08-2459] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
PURPOSE Atypical protein kinase Ciota (PKCiota) is an oncogene in non-small cell lung cancer (NSCLC). Here, we identify four functional gene targets of PKCiota in lung adenocarcinoma (LAC), the most prominent form of NSCLC. EXPERIMENTAL DESIGN Three independent public domain gene expression data sets were interrogated to identify genes coordinately expressed with PKCiota in primary LAC tumors. Results were validated by QPCR in an independent set of primary LAC tumors. RNAi-mediated knockdown of PKCiota and the target genes was used to determine whether expression of the identified genes was regulated by PKCiota, and whether these target genes play a role in anchorage-independent growth and invasion of LAC cells. RESULTS Meta-analysis identified seven genes whose expression correlated with PKCiota in primary LAC. Subsequent QPCR analysis confirmed coordinate overexpression of four genes (COPB2, ELF3, RFC4, and PLS1) in an independent set of LAC samples. RNAi-mediated knockdown showed that PKCiota regulates expression of all four genes in LAC cells, and that the four PKCiota target genes play an important role in the anchorage-independent growth and invasion of LAC cells. Meta-analysis of gene expression data sets from lung squamous cell, breast, colon, prostate, and pancreas carcinomas, as well as glioblastoma, revealed that a subset of PKCiota target genes, particularly COPB2 and RFC4, correlate with PKCiota expression in many tumor types. CONCLUSION Meta-analysis of public gene expression data are useful in identifying novel gene targets of oncogenic PKCiota signaling. Our data indicate that both common and cell type-specific signaling mechanisms contribute to PKCiota-dependent transformation.
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Affiliation(s)
- Eda Erdogan
- Department of Cancer Biology, Mayo Clinic College of Medicine, Jacksonville, Florida 32224, USA
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Hong Z, Jiang J, Hashiguchi K, Hoshi M, Lan L, Yasui A. Recruitment of mismatch repair proteins to the site of DNA damage in human cells. J Cell Sci 2008; 121:3146-54. [DOI: 10.1242/jcs.026393] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mismatch repair (MMR) proteins contribute to genome stability by excising DNA mismatches introduced by DNA polymerase. Although MMR proteins are also known to influence cellular responses to DNA damage, how MMR proteins respond to DNA damage within the cell remains unknown. Here, we show that MMR proteins are recruited immediately to the sites of various types of DNA damage in human cells. MMR proteins are recruited to single-strand breaks in a poly(ADP-ribose)-dependent manner as well as to double-strand breaks. Using mutant cells, RNA interference and expression of fluorescence-tagged proteins, we show that accumulation of MutSβ at the DNA damage site is solely dependent on the PCNA-binding domain of MSH3, and that of MutSα depends on a region near the PCNA-binding domain of MSH6. MSH2 is recruited to the DNA damage site through interactions with either MSH3 or MSH6, and is required for recruitment of MLH1 to the damage site. We found, furthermore, that MutSβ is also recruited to UV-irradiated sites in nucleotide-excision-repair- and PCNA-dependent manners. Thus, MMR and its proteins function not only in replication but also in DNA repair.
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Affiliation(s)
- Zehui Hong
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Seiryomachi 4-1, Aobaku, Sendai 980-8575, Japan
| | - Jie Jiang
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Seiryomachi 4-1, Aobaku, Sendai 980-8575, Japan
| | - Kazunari Hashiguchi
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Seiryomachi 4-1, Aobaku, Sendai 980-8575, Japan
| | - Mikiko Hoshi
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Seiryomachi 4-1, Aobaku, Sendai 980-8575, Japan
| | - Li Lan
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Seiryomachi 4-1, Aobaku, Sendai 980-8575, Japan
| | - Akira Yasui
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Seiryomachi 4-1, Aobaku, Sendai 980-8575, Japan
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uvsF RFC1, the large subunit of replication factor C in Aspergillus nidulans, is essential for DNA replication, functions in UV repair and is upregulated in response to MMS-induced DNA damage. Fungal Genet Biol 2008; 45:1227-34. [PMID: 18655840 DOI: 10.1016/j.fgb.2008.06.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Revised: 06/26/2008] [Accepted: 06/26/2008] [Indexed: 11/22/2022]
Abstract
uvsF201 was the first highly UV-sensitive repair-defective mutation isolated in Aspergillus nidulans. It showed epistasis only with postreplication repair mutations, but caused lethal interactions with many other repair-defective strains. Unexpectedly, closest homology of uvsF was found to the large subunit of human DNA replication factor RFC that is essential for DNA replication. Sequencing of the uvsF201 region identified changes at two close base pairs and the corresponding amino acids in the 5'-region of uvsF(RFC1). This viable mutant represents a novel and possibly important type. Additional sequencing of the uvsF region confirmed a mitochondrial ribosomal protein gene, mrpA(L16), closely adjacent, head-to-head with a 0.2kb joint promoter region. MMS-induced transcription of both the genes, but especially uvsF(RFC1), providing evidence for a function in DNA damage response.
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Uhlmann F. What is your assay for sister-chromatid cohesion? EMBO J 2007; 26:4609-18. [PMID: 17962808 PMCID: PMC2080813 DOI: 10.1038/sj.emboj.7601898] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Accepted: 10/01/2007] [Indexed: 12/25/2022] Open
Affiliation(s)
- Frank Uhlmann
- Chromosome Segregation Laboratory, Cancer Research UK London Research Institute, London, UK.
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Imazawa T, Nishikawa A, Miyauchi M, Okazaki K, Takahashi S, Umemura T, Hirose M. DNA Adduct Formation, Nucleolar Segregation and Cell Proliferation in Rats Treated with 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine. J Toxicol Pathol 2007. [DOI: 10.1293/tox.20.39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Takayoshi Imazawa
- Division of Pathology, National Institute of Health Sciences
- Toxicogenomics Project, National Institute of Biomedical Innovation
| | | | - Makoto Miyauchi
- Division of Pathology, National Institute of Health Sciences
| | - Kazushi Okazaki
- Division of Pathology, National Institute of Health Sciences
| | - Satoru Takahashi
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences
| | - Takashi Umemura
- Division of Pathology, National Institute of Health Sciences
| | - Masao Hirose
- Division of Pathology, National Institute of Health Sciences
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Ward NE, Pellis NR, Risin SA, Risin D. Gene expression alterations in activated human T-cells induced by modeled microgravity. J Cell Biochem 2006; 99:1187-202. [PMID: 16795038 DOI: 10.1002/jcb.20988] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Studies conducted in real Space and in ground-based microgravity analog systems (MAS) have demonstrated changes in numerous lymphocyte functions. In this investigation we explored whether the observed functional changes in lymphocytes in MAS are associated with changes in gene expression. NASA-developed Rotating Wall Vessel (RWV) bioreactor was utilized as a MAS. Activated T lymphocytes were obtained by adding 100 ng/ml of anti-CD3 and 100 U/ml of IL-2 in RPMI medium to blood donor mononuclear cells for 4 days. After that the cells were washed and additionally cultured for up to 2 weeks with media (RPMI, 10% FBS and 100 U/ml IL-2) replacement every 3-4 days. Flow cytometry analysis had proven that activated T lymphocytes were the only cells remaining in culture by that time. They were split into two portions, cultured for additional 24 h in either static or simulated microgravity conditions, and used for RNA extraction. The gene expression was assessed by Affymetrix GeneChip Human U133A array allowing screening for expression of 18,400 genes. About 4-8% of tested genes responded to MG by more than a 1.5-fold change in expression; however, reproducible changes were observed only in 89 genes. Ten of these genes were upregulated and 79 were downregulated. These genes were categorized by associated pathways and viewed graphically through histogram analysis. Separate histograms of each pathway were then constructed representing individual gene expression fold changes. Possible functional consequences of the identified reproducible gene expression changes are discussed.
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Daikoku T, Kudoh A, Sugaya Y, Iwahori S, Shirata N, Isomura H, Tsurumi T. Postreplicative Mismatch Repair Factors Are Recruited to Epstein-Barr Virus Replication Compartments. J Biol Chem 2006; 281:11422-30. [PMID: 16510450 DOI: 10.1074/jbc.m510314200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The mismatch repair (MMR) system, highly conserved throughout evolution, corrects nucleotide mispairing that arise during cellular DNA replication. We report here that proliferating cell nuclear antigen (PCNA), the clamp loader complex (RF-C), and a series of MMR proteins like MSH-2, MSH-6, MLH1, and hPSM2 can be assembled to Epstein-Barr virus replication compartments, the sites of viral DNA synthesis. Levels of the DNA-bound form of PCNA increased with progression of viral productive replication. Bromodeoxyuridine-labeled chromatin immunodepletion analyses confirmed that PCNA is loaded onto newly synthesized viral DNA as well as BALF2 and BMRF1 viral proteins during lytic replication. Furthermore, the anti-PCNA, -MSH2, -MSH3, or -MSH6 antibodies could immunoprecipitate BMRF1 replication protein probably via the viral DNA genome. PCNA loading might trigger transfer of a series of host MMR proteins to the sites of viral DNA synthesis. The MMR factors might function for the repair of mismatches that arise during viral replication or act to inhibit recombination between moderately divergent (homologous) sequences.
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Affiliation(s)
- Tohru Daikoku
- Division of Virology, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya 464-8681, Japan
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Xia L, Zheng L, Lee HW, Bates SE, Federico L, Shen B, O'Connor TR. Human 3-methyladenine-DNA glycosylase: effect of sequence context on excision, association with PCNA, and stimulation by AP endonuclease. J Mol Biol 2005; 346:1259-74. [PMID: 15713479 DOI: 10.1016/j.jmb.2005.01.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2004] [Revised: 12/29/2004] [Accepted: 01/05/2005] [Indexed: 01/26/2023]
Abstract
Human 3-methyladenine-DNA glycosylase (MPG protein) is involved in the base excision repair (BER) pathway responsible mainly for the repair of small DNA base modifications. It initiates BER by recognizing DNA adducts and cleaving the glycosylic bond leaving an abasic site. Here, we explore several of the factors that could influence excision of adducts recognized by MPG, including sequence context, effect of APE1, and interaction with other proteins. To investigate sequence context, we used 13 different 25 bp oligodeoxyribonucleotides containing a unique hypoxanthine residue (Hx) and show that the steady-state specificity of Hx excision by MPG varied by 17-fold. If APE1 protein is used in the reaction for Hx removal by MPG, the steady-state kinetic parameters increase by between fivefold and 27-fold, depending on the oligodeoxyribonucleotide. Since MPG has a role in removing adducts such as 3-methyladenine that block DNA synthesis and there is a potential sequence for proliferating cell nuclear antigen (PCNA) interaction, we hypothesized that MPG protein could interact with PCNA, a protein involved in repair and replication. We demonstrate that PCNA associates with MPG using immunoprecipitation with either purified proteins or whole cell extracts. Moreover, PCNA binds to both APE1 and MPG at different sites, and loading PCNA onto a nicked, closed circular substrate with a unique Hx residue enhances MPG catalyzed excision. These data are consistent with an interaction that facilitates repair by MPG or APE1 by association with PCNA. Thus, PCNA could have a role in short-patch BER as well as in long-patch BER. Overall, the data reported here show how multiple factors contribute to the activity of MPG in cells.
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Affiliation(s)
- Liqun Xia
- Biology Division, Beckman Research Institute, City of Hope National Medical Center, 1450 East Duarte Road, Duarte, CA 91010, USA
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Levin DS, Vijayakumar S, Liu X, Bermudez VP, Hurwitz J, Tomkinson AE. A Conserved Interaction between the Replicative Clamp Loader and DNA Ligase in Eukaryotes. J Biol Chem 2004; 279:55196-201. [PMID: 15502161 DOI: 10.1074/jbc.m409250200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The recruitment of DNA ligase I to replication foci and the efficient joining of Okazaki fragments is dependent on the interaction between DNA ligase I and proliferating cell nuclear antigen (PCNA). Although the PCNA sliding clamp tethers DNA ligase I to nicked duplex DNA circles, the interaction does not enhance DNA joining. This suggests that other factors may be involved in the joining of Okazaki fragments. In this study, we describe an association between replication factor C (RFC), the clamp loader, and DNA ligase I in human cell extracts. Subsequently, we demonstrate that there is a direct physical interaction between these proteins that involves both the N- and C-terminal domains of DNA ligase I, the N terminus of the large RFC subunit p140, and the p36 and p38 subunits of RFC. Although RFC inhibited DNA joining by DNA ligase I, the addition of PCNA alleviated inhibition by RFC. Notably, the effect of PCNA on ligation was dependent on the PCNA-binding site of DNA ligase I. Together, these results provide a molecular explanation for the key in vivo role of the DNA ligase I/PCNA interaction and suggest that the joining of Okazaki fragments is coordinated by pairwise interactions among RFC, PCNA, and DNA ligase I.
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Affiliation(s)
- David S Levin
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center, San Antonio, TX 78245, USA
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Asthana S, King OD, Gibbons FD, Roth FP. Predicting protein complex membership using probabilistic network reliability. Genome Res 2004; 14:1170-5. [PMID: 15140827 PMCID: PMC419795 DOI: 10.1101/gr.2203804] [Citation(s) in RCA: 147] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Evidence for specific protein-protein interactions is increasingly available from both small- and large-scale studies, and can be viewed as a network. It has previously been noted that errors are frequent among large-scale studies, and that error frequency depends on the large-scale method used. Despite knowledge of the error-prone nature of interaction evidence, edges (connections) in this network are typically viewed as either present or absent. However, use of a probabilistic network that considers quantity and quality of supporting evidence should improve inference derived from protein networks. Here we demonstrate inference of membership in a partially known protein complex by using a probabilistic network model and an algorithm previously used to evaluate reliability in communication networks.
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Affiliation(s)
- Saurabh Asthana
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Guo S, Presnell SR, Yuan F, Zhang Y, Gu L, Li GM. Differential Requirement for Proliferating Cell Nuclear Antigen in 5′ and 3′ Nick-directed Excision in Human Mismatch Repair. J Biol Chem 2004; 279:16912-7. [PMID: 14871894 DOI: 10.1074/jbc.m313213200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is involved in mammalian mismatch repair at a step prior to or at mismatch excision, but the molecular mechanism of this process is not fully understood. To examine the role of PCNA in mismatch-provoked and nick-directed excision, orientation-specific mismatch removal of heteroduplexes with a pre-existing nick was monitored in human nuclear extracts supplemented with the PCNA inhibitor protein p21. We show here that, whereas 3' nick-directed mismatch excision was completely inhibited by low concentrations of p21 or a p21 C-terminal fusion protein, 5' nick-directed excision was only partially blocked under the same conditions. No further reduction of the 5' excision was detected when a much higher concentration of p21 C-terminal protein was used. These results suggest the following. (i) There is a differential requirement for PCNA in 3' and 5' nick-directed excision; and (ii) 5' nick-directed excision is conducted by a manner either dependent on or independent of PCNA. Our in vitro reconstitution experiments indeed identified a 5' nick-directed excision pathway that is dependent on PCNA, hMutSalpha, and a partially purified fraction from a HeLa nuclear extract.
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Affiliation(s)
- Shuangli Guo
- Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky Medical Center, Lexington, Kentucky 40536, USA
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Riva F, Savio M, Cazzalini O, Stivala LA, Scovassi IA, Cox LS, Ducommun B, Prosperi E. Distinct pools of proliferating cell nuclear antigen associated to DNA replication sites interact with the p125 subunit of DNA polymerase δ or DNA ligase I. Exp Cell Res 2004; 293:357-67. [PMID: 14729473 DOI: 10.1016/j.yexcr.2003.10.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Proliferating cell nuclear antigen (PCNA) plays an essential role in DNA replication, repair, and cell cycle control. PCNA is a homotrimeric ring that, when encircling DNA, is not easily extractable. Consequently, the dynamics of protein-protein interactions established by PCNA at DNA replication sites is not well understood. We have used DNase I to release DNA-bound PCNA together with replication proteins including the p125-catalytic subunit of DNA polymerase delta (p125-pol delta), DNA ligase I, cyclin A, and cyclin-dependent kinase 2 (CDK2). Interaction with these proteins was investigated by immunoprecipitation with antibodies binding near the interdomain connector loop or to the C-terminal domain of PCNA, respectively, or with antibodies to p125-pol delta or DNA ligase I. PCNA interaction with p125-pol delta or DNA ligase I was detected only by the latter antibodies, and found to be mutually exclusive. In contrast, antibodies to PCNA co-immunoprecipitated only CDK2. A GST-p21(waf1/cip1) C-terminal peptide displaced p125-pol delta and DNA ligase I, but not CDK2, from PCNA. These results suggest that PCNA trimers bound to DNA during the S phase are organized as distinct pools able to bind selectively different partners. Among them, p125-pol delta and DNA ligase I interact with PCNA in a mutually exclusive manner.
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Affiliation(s)
- Federica Riva
- Istituto di Genetica Molecolare del CNR, Dipartimento di Biologia Animale, sezione Istochimica e Citometria, Università di Pavia, Piazza Botta 10, 27100 Pavia, Italy
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Zou L, Liu D, Elledge SJ. Replication protein A-mediated recruitment and activation of Rad17 complexes. Proc Natl Acad Sci U S A 2003; 100:13827-32. [PMID: 14605214 PMCID: PMC283506 DOI: 10.1073/pnas.2336100100] [Citation(s) in RCA: 319] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human Rad17-Rfc2-5 and Rad9-Rad1-Hus1 complexes play crucial roles in the activation of the ATR-mediated DNA damage and DNA replication stress response pathways. In response to DNA damage, Rad9 is recruited to chromatin in a Rad17-dependent manner in human cells. However, the DNA structures recognized by the Rad17-Rfc2-5 complex during the damage response have not been defined. Here, we show that replication protein A (RPA) stimulates the binding of the Rad17-Rfc2-5 complex to single-stranded DNA (ssDNA), primed ssDNA, and a gapped DNA structure. Furthermore, RPA facilitates the recruitment of the Rad9-Rad1-Hus1 complex by the Rad17-Rfc2-5 complex to primed and gapped DNA structures in vitro. These findings suggest that RPA-coated ssDNA is an important part of the structures recognized by the Rad17-Rfc2-5 complex. Unlike replication factor C (RFC), which uses the 3' primer/template junction to recruit proliferating cell nuclear antigen (PCNA), the Rad17-Rfc2-5 complex can use both the 5' and the 3' primer/template junctions to recruit the Rad9-Rad1-Hus1 complex, and it shows a preference for gapped DNA structures. These results explain how the Rad17-Rfc2-5 complex senses DNA damage and DNA replication stress to initiate checkpoint signaling.
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Affiliation(s)
- Lee Zou
- Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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