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Demir D. Insights into the New Molecular Updates in Acute Myeloid Leukemia Pathogenesis. Genes (Basel) 2023; 14:1424. [PMID: 37510328 PMCID: PMC10378849 DOI: 10.3390/genes14071424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/28/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
As our understanding of the biologic basis of acute myeloid leukemia evolves, so do the classification systems used to describe this group of cancers. Early classification systems focused on the morphologic features of blasts and other cell populations; however, the explosion in genomic technologies has led to rapid growth in our understanding of these diseases and thus the refinement of classification systems. Recently, two new systems, the International Consensus Classification system and the 5th edition of the World Health Organization classification of tumors of hematopoietic and lymphoid tissues, were published to incorporate the latest genomic advances in blood cancer. This article reviews the major updates in acute myeloid leukemia in both systems and highlights the biologic insights that have driven these changes.
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Affiliation(s)
- Derya Demir
- Department of Pathology, Ege University Faculty of Medicine, Izmir 35100, Turkey
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2
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Vijay Kumar MJ, Morales R, Tsvetkov AS. G-quadruplexes and associated proteins in aging and Alzheimer's disease. FRONTIERS IN AGING 2023; 4:1164057. [PMID: 37323535 PMCID: PMC10267416 DOI: 10.3389/fragi.2023.1164057] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Abstract
Aging is a prominent risk factor for many neurodegenerative disorders, such as Alzheimer's disease (AD). Alzheimer's disease is characterized by progressive cognitive decline, memory loss, and neuropsychiatric and behavioral symptoms, accounting for most of the reported dementia cases. This disease is now becoming a major challenge and burden on modern society, especially with the aging population. Over the last few decades, a significant understanding of the pathophysiology of AD has been gained by studying amyloid deposition, hyperphosphorylated tau, synaptic dysfunction, oxidative stress, calcium dysregulation, and neuroinflammation. This review focuses on the role of non-canonical secondary structures of DNA/RNA G-quadruplexes (G4s, G4-DNA, and G4-RNA), G4-binding proteins (G4BPs), and helicases, and their roles in aging and AD. Being critically important for cellular function, G4s are involved in the regulation of DNA and RNA processes, such as replication, transcription, translation, RNA localization, and degradation. Recent studies have also highlighted G4-DNA's roles in inducing DNA double-strand breaks that cause genomic instability and G4-RNA's participation in regulating stress granule formation. This review emphasizes the significance of G4s in aging processes and how their homeostatic imbalance may contribute to the pathophysiology of AD.
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Affiliation(s)
- M. J. Vijay Kumar
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
| | - Rodrigo Morales
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- Centro Integrativo de Biologia y Quimica Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago, Chile
| | - Andrey S. Tsvetkov
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
- UTHealth Consortium on Aging, The University of Texas McGovern Medical School, Houston, TX, United States
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3
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Liu Y, Zhu X, Wang K, Zhang B, Qiu S. The Cellular Functions and Molecular Mechanisms of G-Quadruplex Unwinding Helicases in Humans. Front Mol Biosci 2021; 8:783889. [PMID: 34912850 PMCID: PMC8667583 DOI: 10.3389/fmolb.2021.783889] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/02/2021] [Indexed: 01/19/2023] Open
Abstract
G-quadruplexes (G4s) are stable non-canonical secondary structures formed by G-rich DNA or RNA sequences. They play various regulatory roles in many biological processes. It is commonly agreed that G4 unwinding helicases play key roles in G4 metabolism and function, and these processes are closely related to physiological and pathological processes. In recent years, more and more functional and mechanistic details of G4 helicases have been discovered; therefore, it is necessary to carefully sort out the current research efforts. Here, we provide a systematic summary of G4 unwinding helicases from the perspective of functions and molecular mechanisms. First, we provide a general introduction about helicases and G4s. Next, we comprehensively summarize G4 unfolding helicases in humans and their proposed cellular functions. Then, we review their study methods and molecular mechanisms. Finally, we share our perspective on further prospects. We believe this review will provide opportunities for researchers to reach the frontiers in the functions and molecular mechanisms of human G4 unwinding helicases.
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Affiliation(s)
- Yang Liu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Xinting Zhu
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Kejia Wang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Bo Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Shuyi Qiu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
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Linke R, Limmer M, Juranek SA, Heine A, Paeschke K. The Relevance of G-Quadruplexes for DNA Repair. Int J Mol Sci 2021; 22:12599. [PMID: 34830478 PMCID: PMC8620898 DOI: 10.3390/ijms222212599] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 01/28/2023] Open
Abstract
DNA molecules can adopt a variety of alternative structures. Among these structures are G-quadruplex DNA structures (G4s), which support cellular function by affecting transcription, translation, and telomere maintenance. These structures can also induce genome instability by stalling replication, increasing DNA damage, and recombination events. G-quadruplex-driven genome instability is connected to tumorigenesis and other genetic disorders. In recent years, the connection between genome stability, DNA repair and G4 formation was further underlined by the identification of multiple DNA repair proteins and ligands which bind and stabilize said G4 structures to block specific DNA repair pathways. The relevance of G4s for different DNA repair pathways is complex and depends on the repair pathway itself. G4 structures can induce DNA damage and block efficient DNA repair, but they can also support the activity and function of certain repair pathways. In this review, we highlight the roles and consequences of G4 DNA structures for DNA repair initiation, processing, and the efficiency of various DNA repair pathways.
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Affiliation(s)
- Rebecca Linke
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michaela Limmer
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
| | - Stefan A. Juranek
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
| | - Annkristin Heine
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
| | - Katrin Paeschke
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
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5
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Du X, Zhang C, Yin C, Wang W, Yan X, Xie D, Zheng X, Zheng Q, Li M, Song Z. High BLM Expression Predicts Poor Clinical Outcome and Contributes to Malignant Progression in Human Cholangiocarcinoma. Front Oncol 2021; 11:633899. [PMID: 33828983 PMCID: PMC8019910 DOI: 10.3389/fonc.2021.633899] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/09/2021] [Indexed: 12/24/2022] Open
Abstract
Molecular mechanisms underlying the tumorigenesis of a highly malignant cancer, cholangiocarcinoma (CCA), are still obscure. In our study, the CCA expression profile data were acquired from The Cancer Genome Atlas (TCGA) database, and differentially expressed genes (DEGs) in the TCGA-Cholangiocarcinoma (TCGA-CHOL) data set were utilized to construct a co-expression network via weighted gene co-expression network analysis (WGCNA). The blue gene module associated with the histopathologic grade of CCA was screened. Then, five candidate hub genes were screened by combining the co-expression network with protein–protein interaction (PPI) network. After progression and survival analyses, bloom syndrome helicase (BLM) was ultimately identified as a real hub gene. Moreover, the receiver operating characteristic (ROC) curve analysis suggested that BLM had a favorable diagnostic and predictive recurrence value for CCA. The gene set enrichment analysis (GSEA) results for a single hub gene revealed the importance of cell cycle-related pathways in the CCA progression and prognosis. Furthermore, we detected the BLM expression in vitro, and the results demonstrated that the expression level of BLM was much higher in the CCA tissues and cells relative to adjacent non-tumor samples and normal bile duct epithelial cells. Additionally, after further silencing the BLM expression by small interfering RNA (siRNA), the proliferation and migration ability of CCA cells were all inhibited, and the cell cycle was arrested. Altogether, a real hub gene (BLM) and cell cycle-related pathways were identified in the present study, and the gene BLM may be involved in the CCA progression and could act as a reliable biomarker for potential diagnosis and prognostic evaluation.
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Affiliation(s)
- Xiaolong Du
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chen Zhang
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chuanzheng Yin
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenjie Wang
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xueke Yan
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dawei Xie
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xichuan Zheng
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qichang Zheng
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Li
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zifang Song
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Chen TJ, Wang HJ, Liu JS, Cheng HH, Hsu SC, Wu MC, Lu CH, Wu YF, Wu JW, Liu YY, Kung HJ, Wang WC. Mutations in the PKM2 exon-10 region are associated with reduced allostery and increased nuclear translocation. Commun Biol 2019; 2:105. [PMID: 30911680 PMCID: PMC6420622 DOI: 10.1038/s42003-019-0343-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 02/08/2019] [Indexed: 12/27/2022] Open
Abstract
PKM2 is a key metabolic enzyme central to glucose metabolism and energy expenditure. Multiple stimuli regulate PKM2's activity through allosteric modulation and post-translational modifications. Furthermore, PKM2 can partner with KDM8, an oncogenic demethylase and enter the nucleus to serve as a HIF1α co-activator. Yet, the mechanistic basis of the exon-10 region in allosteric regulation and nuclear translocation remains unclear. Here, we determined the crystal structures and kinetic coupling constants of exon-10 tumor-related mutants (H391Y and R399E), showing altered structural plasticity and reduced allostery. Immunoprecipitation analysis revealed increased interaction with KDM8 for H391Y, R399E, and G415R. We also found a higher degree of HIF1α-mediated transactivation activity, particularly in the presence of KDM8. Furthermore, overexpression of PKM2 mutants significantly elevated cell growth and migration. Together, PKM2 exon-10 mutations lead to structure-allostery alterations and increased nuclear functions mediated by KDM8 in breast cancer cells. Targeting the PKM2-KDM8 complex may provide a potential therapeutic intervention.
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Affiliation(s)
- Tsan-Jan Chen
- Institute of Molecular and Cellular Biology and Department of Life Science, National Tsing-Hua University, Hsinchu, 30013 Taiwan
| | - Hung-Jung Wang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, 35053 Taiwan
| | - Jai-Shin Liu
- Institute of Molecular and Cellular Biology and Department of Life Science, National Tsing-Hua University, Hsinchu, 30013 Taiwan
| | - Hsin-Hung Cheng
- Institute of Molecular and Cellular Biology and Department of Life Science, National Tsing-Hua University, Hsinchu, 30013 Taiwan
| | - Sheng-Chieh Hsu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, 35053 Taiwan
- Institute of Biotechnology, National Tsing-Hua University, Hsinchu, 30013 Taiwan
| | - Meng-Chen Wu
- Institute of Molecular and Cellular Biology and Department of Life Science, National Tsing-Hua University, Hsinchu, 30013 Taiwan
| | - Chien-Hung Lu
- Institute of Molecular and Cellular Biology and Department of Life Science, National Tsing-Hua University, Hsinchu, 30013 Taiwan
| | - Yu-Fang Wu
- Institute of Molecular and Cellular Biology and Department of Life Science, National Tsing-Hua University, Hsinchu, 30013 Taiwan
| | - Jing-Wen Wu
- Institute of Molecular and Cellular Biology and Department of Life Science, National Tsing-Hua University, Hsinchu, 30013 Taiwan
| | - Ying-Yuan Liu
- Institute of Molecular and Cellular Biology and Department of Life Science, National Tsing-Hua University, Hsinchu, 30013 Taiwan
| | - Hsing-Jien Kung
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, 35053 Taiwan
- Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, University of California Davis Cancer Centre, Sacramento, CA 95817 USA
| | - Wen-Ching Wang
- Institute of Molecular and Cellular Biology and Department of Life Science, National Tsing-Hua University, Hsinchu, 30013 Taiwan
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7
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Abstract
Timely recruitment of DNA damage response proteins to sites of genomic structural lesions is very important for signaling mechanisms to activate appropriate cell cycle checkpoints but also repair the altered DNA sequence to suppress mutagenesis. The eukaryotic cell is characterized by a complex cadre of players and pathways to ensure genomic stability in the face of replication stress or outright genomic insult by endogenous metabolites or environmental agents. Among the key performers are molecular motor DNA unwinding enzymes known as helicases that sense genomic perturbations and separate structured DNA strands so that replacement of a damaged base or sugar-phosphate backbone lesion can occur efficiently. Mutations in the BLM gene encoding the DNA helicase BLM leads to a rare chromosomal instability disorder known as Bloom's syndrome. In a recent paper by the Sengupta lab, BLM's role in the correction of double-strand breaks (DSB), a particularly dangerous form of DNA damage, was investigated. Adding to the complexity, BLM appears to be a key ringmaster of DSB repair as it acts both positively and negatively to regulate correction pathways of high or low fidelity. The FANCJ DNA helicase, mutated in another chromosomal instability disorder known as Fanconi Anemia, is an important player that likely coordinates with BLM in the balancing act. Further studies to dissect the roles of DNA helicases like FANCJ and BLM in DSB repair are warranted.
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Affiliation(s)
- Srijita Dhar
- a Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health , NIH Biomedical Research Center , Baltimore , MD , USA
| | - Robert M Brosh
- a Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health , NIH Biomedical Research Center , Baltimore , MD , USA
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8
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Allen CP, Hirakawa H, Nakajima NI, Moore S, Nie J, Sharma N, Sugiura M, Hoki Y, Araki R, Abe M, Okayasu R, Fujimori A, Nickoloff JA. Low- and High-LET Ionizing Radiation Induces Delayed Homologous Recombination that Persists for Two Weeks before Resolving. Radiat Res 2017; 188:82-93. [PMID: 28535128 DOI: 10.1667/rr14748.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Genome instability is a hallmark of cancer cells and dysregulation or defects in DNA repair pathways cause genome instability and are linked to inherited cancer predisposition syndromes. Ionizing radiation can cause immediate effects such as mutation or cell death, observed within hours or a few days after irradiation. Ionizing radiation also induces delayed effects many cell generations after irradiation. Delayed effects include hypermutation, hyper-homologous recombination, chromosome instability and reduced clonogenic survival (delayed death). Delayed hyperrecombination (DHR) is mechanistically distinct from delayed chromosomal instability and delayed death. Using a green fluorescent protein (GFP) direct repeat homologous recombination system, time-lapse microscopy and colony-based assays, we demonstrate that DHR increases several-fold in response to low-LET X rays and high-LET carbon-ion radiation. Time-lapse analyses of DHR revealed two classes of recombinants not detected in colony-based assays, including cells that recombined and then senesced or died. With both low- and high-LET radiation, DHR was evident during the first two weeks postirradiation, but resolved to background levels during the third week. The results indicate that the risk of radiation-induced genome destabilization via DHR is time limited, and suggest that there is little or no additional risk of radiation-induced genome instability mediated by DHR with high-LET radiation compared to low-LET radiation.
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Affiliation(s)
- Christopher P Allen
- a Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, Colorado
| | - Hirokazu Hirakawa
- b Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, Chiba, Japan
| | - Nakako Izumi Nakajima
- b Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, Chiba, Japan
| | - Sophia Moore
- a Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, Colorado
| | - Jingyi Nie
- a Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, Colorado
| | - Neelam Sharma
- a Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, Colorado
| | - Mayumi Sugiura
- c Division of Natural Sciences, Research Group of Biological Sciences, Nara Women's University, Nara, Japan
| | - Yuko Hoki
- b Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, Chiba, Japan
| | - Ryoko Araki
- b Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, Chiba, Japan
| | - Masumi Abe
- b Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, Chiba, Japan
| | - Ryuichi Okayasu
- b Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, Chiba, Japan
| | - Akira Fujimori
- b Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, Chiba, Japan
| | - Jac A Nickoloff
- a Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, Colorado
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Paudyal SC, You Z. Sharpening the ends for repair: mechanisms and regulation of DNA resection. Acta Biochim Biophys Sin (Shanghai) 2016; 48:647-57. [PMID: 27174871 DOI: 10.1093/abbs/gmw043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 04/12/2016] [Indexed: 12/23/2022] Open
Abstract
DNA end resection is a key process in the cellular response to DNA double-strand break damage that is essential for genome maintenance and cell survival. Resection involves selective processing of 5' ends of broken DNA to generate ssDNA overhangs, which in turn control both DNA repair and checkpoint signaling. DNA resection is the first step in homologous recombination-mediated repair and a prerequisite for the activation of the ataxia telangiectasia mutated and Rad3-related (ATR)-dependent checkpoint that coordinates repair with cell cycle progression and other cellular processes. Resection occurs in a cell cycle-dependent manner and is regulated by multiple factors to ensure an optimal amount of ssDNA required for proper repair and genome stability. Here, we review the latest findings on the molecular mechanisms and regulation of the DNA end resection process and their implications for cancer formation and treatment.
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Affiliation(s)
- Sharad C Paudyal
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Zhongsheng You
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, MO 63110, USA
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10
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Abstract
As defined initially, chromosome instability syndromes (CIS) are a group of inherited conditions transmitted in autosomal recessive pattern characterised with both mental and physical development delay generally. They are also with other medical complications in individuals with CIS commonly including different degree of dysmorphics, organs/systems dys-function and high risk of cancer predisposition. Chromosomal breakage from CIS can be seen either in spontaneous breakage around 10-15% observed in Fanconi anemia or induced by clastogenic agents such as mitomycin (MMC), diepoxybutane (DEB). The spontaneous chromosome breakage is less common but it correlates with patient clinical severity. Relative high rates of some types of CIS can occur in certain ethnic groups. Individuals with CIS are commonly in childhood and these disorders are often lethal. Diagnosis is complicated usually because the symptoms presented from individuals with CIS may be varied and complex. Advances in molecular level have identified genes responsible for such group diseases/disorders demonstrated that CIS are characterized by the genome instability, defect in DNA repair mechanisms. Latest advances in high-throughput technologies have been increasing sequencing capabilities to facilitate more accurate data for such syndrome researches. CIS are the typical rare diseases and becoming more challenges in pediatrics clinic. In the last two decades, there were no many articles to review and analysis CIS together to comparing their phenotypes and genotypes. In this article, the similarity and differences of the phenotypes and genotypes of CIS were reviewed to understanding the whole profiles of CIS to assist laboratory genetic diagnostic services in CIS and for the confirmation from the clinical referrals.
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Affiliation(s)
- Zhan-He Wu
- Western Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, NSW, Australia
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11
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Hong Y, Sonneville R, Agostinho A, Meier B, Wang B, Blow JJ, Gartner A. The SMC-5/6 Complex and the HIM-6 (BLM) Helicase Synergistically Promote Meiotic Recombination Intermediate Processing and Chromosome Maturation during Caenorhabditis elegans Meiosis. PLoS Genet 2016; 12:e1005872. [PMID: 27010650 PMCID: PMC4807058 DOI: 10.1371/journal.pgen.1005872] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/25/2016] [Indexed: 11/19/2022] Open
Abstract
Meiotic recombination is essential for the repair of programmed double strand breaks (DSBs) to generate crossovers (COs) during meiosis. The efficient processing of meiotic recombination intermediates not only needs various resolvases but also requires proper meiotic chromosome structure. The Smc5/6 complex belongs to the structural maintenance of chromosome (SMC) family and is closely related to cohesin and condensin. Although the Smc5/6 complex has been implicated in the processing of recombination intermediates during meiosis, it is not known how Smc5/6 controls meiotic DSB repair. Here, using Caenorhabditis elegans we show that the SMC-5/6 complex acts synergistically with HIM-6, an ortholog of the human Bloom syndrome helicase (BLM) during meiotic recombination. The concerted action of the SMC-5/6 complex and HIM-6 is important for processing recombination intermediates, CO regulation and bivalent maturation. Careful examination of meiotic chromosomal morphology reveals an accumulation of inter-chromosomal bridges in smc-5; him-6 double mutants, leading to compromised chromosome segregation during meiotic cell divisions. Interestingly, we found that the lethality of smc-5; him-6 can be rescued by loss of the conserved BRCA1 ortholog BRC-1. Furthermore, the combined deletion of smc-5 and him-6 leads to an irregular distribution of condensin and to chromosome decondensation defects reminiscent of condensin depletion. Lethality conferred by condensin depletion can also be rescued by BRC-1 depletion. Our results suggest that SMC-5/6 and HIM-6 can synergistically regulate recombination intermediate metabolism and suppress ectopic recombination by controlling chromosome architecture during meiosis.
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Affiliation(s)
- Ye Hong
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Remi Sonneville
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Ana Agostinho
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Bettina Meier
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Bin Wang
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - J. Julian Blow
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Anton Gartner
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
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12
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Abstract
Members of the conserved FANCM family of DNA motor proteins play key roles in genome maintenance processes. In this review, Xue et al. provide an integrated view of the functions and regulation of these enzymes in humans and model organisms and how they advance our understanding of genome maintenance processes. Members of the conserved FANCM family of DNA motor proteins play key roles in genome maintenance processes. FANCM supports genome duplication and repair under different circumstances and also functions in the ATR-mediated DNA damage checkpoint. Some of these roles are shared among lower eukaryotic family members. Human FANCM has been linked to Fanconi anemia, a syndrome characterized by cancer predisposition, developmental disorder, and bone marrow failure. Recent studies on human FANCM and its orthologs from other organisms have provided insights into their biological functions, regulation, and collaboration with other genome maintenance factors. This review summarizes the progress made, with the goal of providing an integrated view of the functions and regulation of these enzymes in humans and model organisms and how they advance our understanding of genome maintenance processes.
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Affiliation(s)
- Xiaoyu Xue
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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13
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Abstract
Fanconi anemia (FA) is a rare recessive genetic disease characterized by congenital abnormalities, bone marrow failure and heightened cancer susceptibility in early adulthood. FA is caused by biallelic germ-line mutation of any one of 16 genes. While several functions for the FA proteins have been ascribed, the prevailing hypothesis is that the FA proteins function cooperatively in the FA-BRCA pathway to repair damaged DNA. A pivotal step in the activation of the FA-BRCA pathway is the monoubiquitination of the FANCD2 and FANCI proteins. Despite their importance for DNA repair, the domain structure, regulation, and function of FANCD2 and FANCI remain poorly understood. In this review, we provide an overview of our current understanding of FANCD2 and FANCI, with an emphasis on their posttranslational modification and common and unique functions.
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Key Words
- AML , acute myeloid leukemia
- APC/C, anaphase-promoting complex/cyclosome
- APH, aphidicolin
- ARM, armadillo repeat domain
- AT, ataxia-telangiectasia
- ATM, ataxia-telangiectasia mutated
- ATR, ATM and Rad3-related
- BAC, bacterial-artificial-chromosome
- BS, Bloom syndrome
- CUE, coupling of ubiquitin conjugation to endoplasmic reticulum degradation
- ChIP-seq, CHIP sequencing
- CtBP, C-terminal binding protein
- CtIP, CtBP-interacting protein
- DNA interstrand crosslink repair
- DNA repair
- EPS15, epidermal growth factor receptor pathway substrate 15
- FA, Fanconi anemia
- FAN1, FANCD2-associated nuclease1
- FANCD2
- FANCI
- FISH, fluorescence in situ hybridization
- Fanconi anemia
- HECT, homologous to E6-AP Carboxy Terminus
- HJ, Holliday junction
- HR, homologous recombination
- MCM2-MCM7, minichromosome maintenance 2–7
- MEFs, mouse embryonic fibroblasts
- MMC, mitomycin C
- MRN, MRE11/RAD50/NBS1
- NLS, nuclear localization signal
- PCNA, proliferating cell nuclear antigen
- PIKK, phosphatidylinositol-3-OH-kinase-like family of protein kinases
- PIP-box, PCNA-interacting protein motif
- POL κ, DNA polymerase κ
- RACE, rapid amplification of cDNA ends
- RING, really interesting new gene
- RTK, receptor tyrosine kinase
- SCF, Skp1/Cullin/F-box protein complex
- SCKL1, seckel syndrome
- SILAC, stable isotope labeling with amino acids in cell culture
- SLD1/SLD2, SUMO-like domains
- SLIM, SUMO-like domain interacting motif
- TIP60, 60 kDa Tat-interactive protein
- TLS, Translesion DNA synthesis
- UAF1, USP1-associated factor 1
- UBD, ubiquitin-binding domain
- UBZ, ubiquitin-binding zinc finger
- UFB, ultra-fine DNA bridges
- UIM, ubiquitin-interacting motif
- ULD, ubiquitin-like domain
- USP1, ubiquitin-specific protease 1
- VRR-nuc, virus-type replication repair nuclease
- iPOND, isolation of proteins on nascent DNA
- ubiquitin
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Affiliation(s)
- Rebecca A Boisvert
- a Department of Cell and Molecular Biology ; University of Rhode Island ; Kingston , RI USA
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Wu WQ, Hou XM, Li M, Dou SX, Xi XG. BLM unfolds G-quadruplexes in different structural environments through different mechanisms. Nucleic Acids Res 2015; 43:4614-26. [PMID: 25897130 PMCID: PMC4482088 DOI: 10.1093/nar/gkv361] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/06/2015] [Accepted: 04/07/2015] [Indexed: 11/30/2022] Open
Abstract
Mutations in the RecQ DNA helicase gene BLM give rise to Bloom's syndrome, which is a rare autosomal recessive disorder characterized by genetic instability and cancer predisposition. BLM helicase is highly active in binding and unwinding G-quadruplexes (G4s), which are physiological targets for BLM, as revealed by genome-wide characterizations of gene expression of cells from BS patients. With smFRET assays, we studied the molecular mechanism of BLM-catalyzed G4 unfolding and showed that ATP is required for G4 unfolding. Surprisingly, depending on the molecular environments of G4, BLM unfolds G4 through different mechanisms: unfolding G4 harboring a 3'-ssDNA tail in three discrete steps with unidirectional translocation, and unfolding G4 connected to dsDNA by ssDNA in a repetitive manner in which BLM remains anchored at the ss/dsDNA junction, and G4 was unfolded by reeling in ssDNA. This indicates that one BLM molecule may unfold G4s in different molecular environments through different mechanisms.
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Affiliation(s)
- Wen-Qiang Wu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, Centre National de la Recherche Scientifique, 61 Avenue du Président Wilson, 94235 Cachan, France
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15
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Gaillard C, Strauss F. Construction of DNA hemicatenanes from two small circular DNA molecules. PLoS One 2015; 10:e0119368. [PMID: 25799010 PMCID: PMC4370885 DOI: 10.1371/journal.pone.0119368] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 01/13/2015] [Indexed: 11/18/2022] Open
Abstract
DNA hemicatenanes, one of the simplest possible junctions between two double stranded DNA molecules, have frequently been mentioned in the literature for their possible function in DNA replication, recombination, repair, and organization in chromosomes. They have been little studied experimentally, however, due to the lack of an appropriate method for their preparation. Here we have designed a method to build hemicatenanes from two small circular DNA molecules. The method involves, first, the assembly of two linear single strands and their circularization to form a catenane of two single stranded circles, and, second, the addition and base-pairing of the two single stranded circles complementary to the first ones, followed by their annealing using DNA topoisomerase I. The product was purified by gel electrophoresis and characterized. The arrangement of strands was as expected for a hemicatenane and clearly distinct from a full catenane. In addition, each circle was unwound by an average of half a double helical turn, also in excellent agreement with the structure of a hemicatenane. It was also observed that hemicatenanes are quickly destabilized by a single cut on either of the two strands passing inside the junction, strongly suggesting that DNA strands are able to slide easily inside the hemicatenane. This method should make it possible to study the biochemical properties of hemicatenanes and to test some of the hypotheses that have been proposed about their function, including a possible role for this structure in the organization of complex genomes in loops and chromosomal domains.
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16
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DNA and RNA quadruplex-binding proteins. Int J Mol Sci 2014; 15:17493-517. [PMID: 25268620 PMCID: PMC4227175 DOI: 10.3390/ijms151017493] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 09/15/2014] [Accepted: 09/22/2014] [Indexed: 02/01/2023] Open
Abstract
Four-stranded DNA structures were structurally characterized in vitro by NMR, X-ray and Circular Dichroism spectroscopy in detail. Among the different types of quadruplexes (i-Motifs, minor groove quadruplexes, G-quadruplexes, etc.), the best described are G-quadruplexes which are featured by Hoogsteen base-paring. Sequences with the potential to form quadruplexes are widely present in genome of all organisms. They are found often in repetitive sequences such as telomeric ones, and also in promoter regions and 5' non-coding sequences. Recently, many proteins with binding affinity to G-quadruplexes have been identified. One of the initially portrayed G-rich regions, the human telomeric sequence (TTAGGG)n, is recognized by many proteins which can modulate telomerase activity. Sequences with the potential to form G-quadruplexes are often located in promoter regions of various oncogenes. The NHE III1 region of the c-MYC promoter has been shown to interact with nucleolin protein as well as other G-quadruplex-binding proteins. A number of G-rich sequences are also present in promoter region of estrogen receptor alpha. In addition to DNA quadruplexes, RNA quadruplexes, which are critical in translational regulation, have also been predicted and observed. For example, the RNA quadruplex formation in telomere-repeat-containing RNA is involved in interaction with TRF2 (telomere repeat binding factor 2) and plays key role in telomere regulation. All these fundamental examples suggest the importance of quadruplex structures in cell processes and their understanding may provide better insight into aging and disease development.
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17
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Lee T, Di Paola D, Malina A, Mills JR, Kreps A, Grosse F, Tang H, Zannis-Hadjopoulos M, Larsson O, Pelletier J. Suppression of the DHX9 helicase induces premature senescence in human diploid fibroblasts in a p53-dependent manner. J Biol Chem 2014; 289:22798-22814. [PMID: 24990949 PMCID: PMC4132785 DOI: 10.1074/jbc.m114.568535] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 07/02/2014] [Indexed: 12/28/2022] Open
Abstract
DHX9 is an ATP-dependent DEXH box helicase with a multitude of cellular functions. Its ability to unwind both DNA and RNA, as well as aberrant, noncanonical polynucleotide structures, has implicated it in transcriptional and translational regulation, DNA replication and repair, and maintenance of genome stability. We report that loss of DHX9 in primary human fibroblasts results in premature senescence, a state of irreversible growth arrest. This is accompanied by morphological defects, elevation of senescence-associated β-galactosidase levels, and changes in gene expression closely resembling those encountered during replicative (telomere-dependent) senescence. Activation of the p53 signaling pathway was found to be essential to this process. ChIP analysis and investigation of nascent DNA levels revealed that DHX9 is associated with origins of replication and that its suppression leads to a reduction of DNA replication. Our results demonstrate an essential role of DHX9 in DNA replication and normal cell cycle progression.
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Affiliation(s)
- Teresa Lee
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Domenic Di Paola
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Abba Malina
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - John R Mills
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Amina Kreps
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Frank Grosse
- Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena D-07745, Germany
| | - Hengli Tang
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306
| | - Maria Zannis-Hadjopoulos
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada,; Department of Oncology, McGill University, Montreal, Quebec H3A 1A3, Canada; The Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec H3A 1A3, Canada, and
| | - Ola Larsson
- Department of Oncology-Pathology, Karolinska Institute, Stockholm 171 77, Sweden
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada,; Department of Oncology, McGill University, Montreal, Quebec H3A 1A3, Canada; The Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec H3A 1A3, Canada, and.
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18
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Chen SH, Plank JL, Willcox S, Griffith JD, Hsieh TS. Top3α is required during the convergent migration step of double Holliday junction dissolution. PLoS One 2014; 9:e83582. [PMID: 24392087 PMCID: PMC3879244 DOI: 10.1371/journal.pone.0083582] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 11/06/2013] [Indexed: 11/19/2022] Open
Abstract
Although Blm and Top3α are known to form a minimal dissolvasome that can uniquely undo a double Holliday junction structure, the details of the mechanism remain unknown. It was originally suggested that Blm acts first to create a hemicatenane structure from branch migration of the junctions, followed by Top3α performing strand passage to decatenate the interlocking single strands. Recent evidence suggests that Top3α may also be important for assisting in the migration of the junctions. Using a mismatch-dHJ substrate (MM-DHJS) and eukaryotic Top1 (in place of Top3α), we show that the presence of a topoisomerase is required for Blm to substantially migrate a topologically constrained Holliday junction. When investigated by electron microscopy, these migrated structures did not resemble a hemicatenane. However, when Blm is together with Top3α, the dissolution reaction is processive with no pausing at a partially migrated structure. Potential mechanisms are discussed.
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Affiliation(s)
- Stefanie Hartman Chen
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Jody L. Plank
- Department of Microbiology, University of California Davis, Davis, California, United States of America
| | - Smaranda Willcox
- Lineberger Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jack D. Griffith
- Lineberger Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Tao-shih Hsieh
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- * E-mail:
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Abstract
While the majority of leukemia cases occur in the absence of any known predisposing factor, there are germline mutations that significantly increase the risk of developing hematopoietic malignancies in childhood. In this review article, we describe a number of these mutations and their clinical features. These predispositions can be broadly classified as those leading to bone marrow failure, those involving tumor suppressor genes, DNA repair defects, immunodeficiencies or other congenital syndromes associated with transient myeloid disorders. While leukemia can develop as a secondary event in the aforementioned syndromes, there are also several syndromes that specifically lead to the development of leukemia as their primary phenotype. Many of the genes discussed in this review can also be somatically mutated in other cancers, highlighting the importance of understanding shared alterations and mechanisms underpinning syndromic and sporadic leukemia.
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Affiliation(s)
- Elliot Stieglitz
- Department of Pediatrics, Benioff Children's Hospital, University of California San Francisco, USA
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20
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Xue X, Raynard S, Busygina V, Singh AK, Sung P. Role of replication protein A in double holliday junction dissolution mediated by the BLM-Topo IIIα-RMI1-RMI2 protein complex. J Biol Chem 2013; 288:14221-14227. [PMID: 23543748 DOI: 10.1074/jbc.m113.465609] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The conserved BTR complex, composed of the Bloom's syndrome helicase (BLM), topoisomerase IIIα, RMI1, and RMI2, regulates homologous recombination in favor of non-crossover formation via the dissolution of the double Holliday Junction (dHJ). Here we show enhancement of the BTR-mediated dHJ dissolution reaction by the heterotrimeric single-stranded DNA binding protein replication protein A (RPA). Our results suggest that RPA acts by sequestering a single-stranded DNA intermediate during dHJ dissolution. We provide evidence that RPA physically interacts with RMI1. The RPA interaction domain in RMI1 has been mapped, and RMI1 mutants impaired for RPA interaction have been generated. Examination of these mutants ascertains the significance of the RMI1-RPA interaction in dHJ dissolution. Our results thus implicate RPA as a cofactor of the BTR complex in dHJ dissolution.
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Affiliation(s)
- Xiaoyu Xue
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Steven Raynard
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Valeria Busygina
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Akhilesh K Singh
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520.
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21
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Role of E1B55K in E4orf6/E1B55K E3 ligase complexes formed by different human adenovirus serotypes. J Virol 2013; 87:6232-45. [PMID: 23536656 DOI: 10.1128/jvi.00384-13] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The E4orf6 protein of serotypes representing all human adenovirus species forms Cullin-based E3 ubiquitin ligase complexes that facilitate virus infection by inducing degradation of cellular proteins that impede efficient viral replication. This complex also includes the viral E1B55K product believed to bind and introduce substrates for ubiquitination. Heterogeneity in the composition of these ligases exists, as some serotypes form Cul5-based complexes whereas others utilize Cul2. Significant variations in substrate specificities also exist among serotypes, as some degrade certain substrates very efficiently whereas others induce more modest or little degradation. As E1B55K is believed to function as the substrate acquisition component of the ligase, we undertook studies to compare the ability of representative E1B55K proteins to bind substrates with the efficacy of degradation by their respective E4orf6-based ligases. Interestingly, although efficient degradation in some cases corresponded to the ability of E1B55K to bind to or relocalize substrates, there were several examples of substrates that bound efficiently to E1B55K but were not degraded and others in which substrates were degraded even though binding to E1B55K was low or undetectable. These results suggest that transient interactions with E1B55K may be sufficient for efficient substrate degradation and that binding alone is not sufficient, implying that the orientation of the substrate in the ligase complex is probably crucial. Nevertheless, we found that the substrate specificity of certain E4orf6-based ligases could be altered through the formation of hybrid complexes containing E1B55K from another serotype, thus confirming identification of E1B55K as the substrate acquisition component of the complex.
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22
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Moskalev AA, Shaposhnikov MV, Plyusnina EN, Zhavoronkov A, Budovsky A, Yanai H, Fraifeld VE. The role of DNA damage and repair in aging through the prism of Koch-like criteria. Ageing Res Rev 2013; 12:661-84. [PMID: 22353384 DOI: 10.1016/j.arr.2012.02.001] [Citation(s) in RCA: 222] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 01/27/2012] [Accepted: 02/06/2012] [Indexed: 12/21/2022]
Abstract
Since the first publication on Somatic Mutation Theory of Aging (Szilárd, 1959), a great volume of knowledge in the field has been accumulated. Here we attempted to organize the evidence "for" and "against" the hypothesized causal role of DNA damage and mutation accumulation in aging in light of four Koch-like criteria. They are based on the assumption that some quantitative relationship between the levels of DNA damage/mutations and aging rate should exist, so that (i) the longer-lived individuals or species would have a lower rate of damage than the shorter-lived, and (ii) the interventions that modulate the level of DNA damage and repair capacity should also modulate the rate of aging and longevity and vice versa. The analysis of how the existing data meets the proposed criteria showed that many gaps should still be filled in order to reach a clear-cut conclusion. As a perspective, it seems that the main emphasis in future studies should be put on the role of DNA damage in stem cell aging.
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23
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Early steps of double-strand break repair in Bacillus subtilis. DNA Repair (Amst) 2013; 12:162-76. [PMID: 23380520 DOI: 10.1016/j.dnarep.2012.12.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 12/04/2012] [Accepted: 12/14/2012] [Indexed: 11/22/2022]
Abstract
All organisms rely on integrated networks to repair DNA double-strand breaks (DSBs) in order to preserve the integrity of the genetic information, to re-establish replication, and to ensure proper chromosomal segregation. Genetic, cytological, biochemical and structural approaches have been used to analyze how Bacillus subtilis senses DNA damage and responds to DSBs. RecN, which is among the first responders to DNA DSBs, promotes the ordered recruitment of repair proteins to the site of a lesion. Cells have evolved different mechanisms for efficient end processing to create a 3'-tailed duplex DNA, the substrate for RecA binding, in the repair of one- and two-ended DSBs. Strand continuity is re-established via homologous recombination (HR), utilizing an intact homologous DNA molecule as a template. In the absence of transient diploidy or of HR, however, two-ended DSBs can be directly re-ligated via error-prone non-homologous end-joining. Here we review recent findings that shed light on the early stages of DSB repair in Firmicutes.
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24
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Shcherbakov VP, Plugina L, Shcherbakova T, Kudryashova E, Sizova S. Double-strand break repair and recombination-dependent replication of DNA in bacteriophage T4 in the absence of UvsX recombinase: replicative resolution pathway. DNA Repair (Amst) 2012; 11:470-9. [PMID: 22365497 DOI: 10.1016/j.dnarep.2012.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 01/23/2012] [Accepted: 01/30/2012] [Indexed: 11/19/2022]
Abstract
The effects of mutations in bacteriophage T4 genes uvsX and 49 on the double-strand break (DSB)-promoted recombination were studied in crosses, in which DSBs were induced site-specifically within the rIIB gene by SegC endonuclease in the DNA of only one of the parents. Frequency of rII+ recombinants was measured in two-factor crosses of the type i×ets1 and in three-factor crosses of the type i×ets1 a6, where ets1 is an insertion in the rIIB gene carrying the cleavage site for SegC; i's are rIIB or rIIA point mutations located at various distances (12-2040 bp) from the ets1 site, and a6 is rIIA point mutation located at 2040 bp from ets1. The frequency/distance relationships were obtained in crosses of the wild-type phage and of the amber mutant S17 (gene uvsX) and the double mutant S17 E727 (genes uvsX and 49). These data provide information about the frequency and distance distribution of the single-exchange (splices) and double-exchange (patches) events. The extended variant of the splice/patch coupling (SPC) model of recombination, which includes transition to the replication resolution (RR) alternative is substantiated and used for interpretation of the frequency/distance relationships. We conclude that the uvsX mutant executes recombination-dependent replication but does it by a qualitatively different way. In the absence of UvsX function, the DSB repair runs largely through the RR subpathway because of inability of the mutant to form a Holliday junction. In the two-factor crosses, the double uvsX 49- is recombinationally more proficient than the single uvsX mutant (partial suppression of the uvsX deficiency), while the patch-related double exchanges are virtually eliminated in this background.
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Affiliation(s)
- Victor P Shcherbakov
- Institute of Problems of Chemical Physics RAS, Chernogolovka, Moscow Region 142432, Russia.
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25
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Common fragile sites: mechanisms of instability revisited. Trends Genet 2011; 28:22-32. [PMID: 22094264 DOI: 10.1016/j.tig.2011.10.003] [Citation(s) in RCA: 207] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 10/05/2011] [Accepted: 10/05/2011] [Indexed: 12/22/2022]
Abstract
Common fragile sites (CFSs) are large chromosomal regions prone to breakage upon replication stress that are considered a driving force of oncogenesis. CFSs were long believed to contain sequences blocking fork progression, thus impeding replication completion and leading to DNA breaks upon chromosome condensation. However, recent studies show that delayed completion of DNA replication instead depends on a regional paucity in initiation events. Because the distribution and the timing of these events are cell type dependent, different chromosomal regions can be committed to fragility in different cell types. These new data reveal the epigenetic nature of CFSs and open the way to a reevaluation of the role played by these sites in the formation of chromosome rearrangements found in tumors from different tissues.
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26
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Andersen SL, Kuo HK, Savukoski D, Brodsky MH, Sekelsky J. Three structure-selective endonucleases are essential in the absence of BLM helicase in Drosophila. PLoS Genet 2011; 7:e1002315. [PMID: 22022278 PMCID: PMC3192830 DOI: 10.1371/journal.pgen.1002315] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 08/03/2011] [Indexed: 02/03/2023] Open
Abstract
DNA repair mechanisms in mitotically proliferating cells avoid generating crossovers, which can contribute to genome instability. Most models for the production of crossovers involve an intermediate with one or more four-stranded Holliday junctions (HJs), which are resolved into duplex molecules through cleavage by specialized endonucleases. In vitro studies have implicated three nuclear enzymes in HJ resolution: MUS81–EME1/Mms4, GEN1/Yen1, and SLX4–SLX1. The Bloom syndrome helicase, BLM, plays key roles in preventing mitotic crossover, either by blocking the formation of HJ intermediates or by removing HJs without cleavage. Saccharomyces cerevisiae mutants that lack Sgs1 (the BLM ortholog) and either Mus81–Mms4 or Slx4–Slx1 are inviable, but mutants that lack Sgs1 and Yen1 are viable. The current view is that Yen1 serves primarily as a backup to Mus81–Mms4. Previous studies with Drosophila melanogaster showed that, as in yeast, loss of both DmBLM and MUS81 or MUS312 (the ortholog of SLX4) is lethal. We have now recovered and analyzed mutations in Drosophila Gen. As in yeast, there is some redundancy between Gen and mus81; however, in contrast to the case in yeast, GEN plays a more predominant role in responding to DNA damage than MUS81–MMS4. Furthermore, loss of DmBLM and GEN leads to lethality early in development. We present a comparison of phenotypes occurring in double mutants that lack DmBLM and either MUS81, GEN, or MUS312, including chromosome instability and deficiencies in cell proliferation. Our studies of synthetic lethality provide insights into the multiple functions of DmBLM and how various endonucleases may function when DmBLM is absent. The maintenance of a stable genome is crucial to organismal survival. Genome stability is perpetually threatened by spontaneous DNA damage, and DNA repair proteins are required to accurately and efficiently repair DNA damage in ways that minimize genome alterations. Some repair pathways are linked to increased risk of genome changes. One example is repair associated with the production of crossovers between homologous chromosomes. The DNA helicase BLM suppresses genome changes by promoting non-crossover forms of repair; without BLM, spontaneous crossovers, deletions, and genome rearrangements increase. Using Drosophila as a model organism, our studies reveal the complex interactions between BLM and three structure-selective endonucleases with overlapping substrate specificities and partial functional redundancy. Loss of BLM and any one of the nucleases results in severe genome instability, reduced cell proliferation, and, ultimately, death of the animal. Our work suggests that these nucleases differentially rescue the loss of functions of BLM associated with problems that arise during DNA replication, illuminating the complexity of repair mechanisms required to maintain genome stability during replication. Further, our work advances models of replication-associated repair by suggesting specific roles for BLM and structure-selective endonucleases.
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Affiliation(s)
- Sabrina L Andersen
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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27
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Wang Y, Smith K, Waldman BC, Waldman AS. Depletion of the bloom syndrome helicase stimulates homology-dependent repair at double-strand breaks in human chromosomes. DNA Repair (Amst) 2011; 10:416-26. [PMID: 21300576 DOI: 10.1016/j.dnarep.2011.01.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 12/10/2010] [Accepted: 01/14/2011] [Indexed: 12/29/2022]
Abstract
Mutation of BLM helicase causes Blooms syndrome, a disorder associated with genome instability, high levels of sister chromatid exchanges, and cancer predisposition. To study the influence of BLM on double-strand break (DSB) repair in human chromosomes, we stably transfected a normal human cell line with a DNA substrate that contained a thymidine kinase (tk)-neo fusion gene disrupted by the recognition site for endonuclease I-SceI. The substrate also contained a closely linked functional tk gene to serve as a recombination partner for the tk-neo fusion gene. We derived two cell lines each containing a single integrated copy of the DNA substrate. In these cell lines, a DSB was introduced within the tk-neo fusion gene by expression of I-SceI. DSB repair events that occurred via homologous recombination (HR) or nonhomologous end-joining (NHEJ) were recovered by selection for G418-resistant clones. DSB repair was examined under conditions of either normal BLM expression or reduced BLM expression brought about by RNA interference. We report that BLM knockdown in both cell lines specifically increased the frequency of HR events that produced deletions by crossovers or single-strand annealing while leaving the frequency of gene conversions unchanged or reduced. We observed no change in the accuracy of individual HR events and no substantial alteration of the nature of individual NHEJ events when BLM expression was reduced. Our work provides the first direct evidence that BLM influences DSB repair pathway choice in human chromosomes and suggests that BLM deficiency can engender genomic instability by provoking an increased frequency of HR events of a potentially deleterious nature.
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Affiliation(s)
- Yibin Wang
- Department of Biological Science, University of South Carolina, 700 Sumter Street, Columbia, SC 29208, USA.
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Abstract
Faithful replication of chromosomes is essential for maintaining genome stability. Telomeres, the chromosomal termini, pose quite a challenge to replication machinery due to the complexity in their structures and sequences. Efficient and complete replication of chromosomes is critical to prevent aberrant telomeres as well as to avoid unnecessary loss of telomere DNA. Compelling evidence supports the emerging picture of synergistic actions between DNA replication proteins and telomere protective components in telomere synthesis. This review discusses the actions of various replication and telomere-specific binding proteins that ensure accurate telomere replication and their roles in telomere maintenance and protection.
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Affiliation(s)
- Shilpa Sampathi
- WWAMI Medical Education Program, Washington State University, Spokane, WA 99210-1495, USA
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Deckbar D, Jeggo PA, Löbrich M. Understanding the limitations of radiation-induced cell cycle checkpoints. Crit Rev Biochem Mol Biol 2011; 46:271-83. [PMID: 21524151 PMCID: PMC3171706 DOI: 10.3109/10409238.2011.575764] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The DNA damage response pathways involve processes of double-strand break (DSB) repair and cell cycle checkpoint control to prevent or limit entry into S phase or mitosis in the presence of unrepaired damage. Checkpoints can function to permanently remove damaged cells from the actively proliferating population but can also halt the cell cycle temporarily to provide time for the repair of DSBs. Although efficient in their ability to limit genomic instability, checkpoints are not foolproof but carry inherent limitations. Recent work has demonstrated that the G1/S checkpoint is slowly activated and allows cells to enter S phase in the presence of unrepaired DSBs for about 4–6 h post irradiation. During this time, only a slowing but not abolition of S-phase entry is observed. The G2/M checkpoint, in contrast, is quickly activated but only responds to a level of 10–20 DSBs such that cells with a low number of DSBs do not initiate the checkpoint or terminate arrest before repair is complete. Here, we discuss the limitations of these checkpoints in the context of the current knowledge of the factors involved. We suggest that the time needed to fully activate G1/S arrest reflects the existence of a restriction point in G1-phase progression. This point has previously been defined as the point when mitogen starvation fails to prevent cells from entering S phase. However, cells that passed the restriction point can respond to DSBs, albeit with reduced efficiency.
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Affiliation(s)
- Dorothee Deckbar
- Darmstadt University of Technology, Radiation Biology and DNA Repair, Darmstadt, Germany
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30
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Abstract
The American Cancer Society's 2009 statistics estimate that 1 out of every 4 deaths is cancer related. Genomic instability is a common feature of cancerous states, and an increase in genomic instability is the diagnostic feature of Bloom Syndrome. Bloom Syndrome, a rare disorder characterized by a predisposition to cancer, is caused by mutations of the BLM gene. This study focuses on the partnerships of BLM protein to RAD51, a Homologous Recombination repair protein essential for survival. A systematic set of BLM deletion fragments were generated to refine the protein binding domains of BLM to RAD51 and determine interacting regions of BLM and ssDNA. Results show that RAD51 and ssDNA interact in overlapping regions; BLM₁₀₀₋₂₁₄ and BLM₁₃₁₇₋₁₃₆₇. The overlapping nature of these regions suggests a preferential binding for one partner that could function to regulate homologous recombination and therefore helps to clarify the role of BLM in maintaining genomic stability.
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31
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Abstract
Bloom Syndrome (BS) is an autosomal recessive disorder due to mutation in Bloom helicase (referred in literature either as BLM helicase or BLM). Patients with BS are predisposed to almost all forms of cancer. BS patients are even today diagnosed in the clinics by hyper-recombination phenotype that is manifested by high rates of Sister Chromatid Exchange. The function of BLM as a helicase and its role during the regulation of homologous recombination (HR) is well characterized. However in the last few years the role of BLM as a DNA damage sensor has been revealed. For example, it has been demonstrated that BLM can stimulate the ATPase and chromatin remodeling activities of RAD54 in vitro. This indicates that BLM may increase the accessibility of the sensor proteins that recognize the lesion. Over the years evidence has accumulated that BLM is one of the earliest proteins that accumulates at the site of the lesion. Finally BLM also acts like a "molecular node" by integrating the upstream signals and acting as a bridge between the transducer and effector proteins (which again includes BLM itself), which in turn repair the DNA damage. Hence BLM seems to be a protein involved in multiple functions - all of which may together contribute to its reported role as a "caretaker tumor suppressor". In this review the recent literature documenting the upstream BLM functions has been elucidated and future directions indicated.
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Affiliation(s)
- Shweta Tikoo
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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32
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Takaku M, Takahashi D, Machida S, Ueno H, Hosoya N, Ikawa S, Miyagawa K, Shibata T, Kurumizaka H. Single-stranded DNA catenation mediated by human EVL and a type I topoisomerase. Nucleic Acids Res 2010; 38:7579-86. [PMID: 20639531 PMCID: PMC2995056 DOI: 10.1093/nar/gkq630] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The human Ena/Vasp-like (EVL) protein is considered to be a bifunctional protein, involved in both actin remodeling and homologous recombination. In the present study, we found that human EVL forms heat-stable multimers of circular single-stranded DNA (ssDNA) molecules in the presence of a type I topoisomerase in vitro. An electron microscopic analysis revealed that the heat-stable ssDNA multimers formed by EVL and topoisomerase were ssDNA catemers. The ssDNA catenation did not occur when either EVL or topoisomerase was omitted from the reaction mixture. A deletion analysis revealed that the ssDNA catenation completely depended on the annealing activity of EVL. Human EVL was captured from a human cell extract by TOPO IIIα-conjugated beads, and the interaction between EVL and TOPO IIIα was confirmed by a surface plasmon resonance analysis. Purified TOPO IIIα catalyzed the ssDNA catenation with EVL as efficiently as the Escherichia coli topoisomerase I. Since the ssDNA cutting and rejoining reactions, which are the sub-steps of ssDNA catenation, may be an essential process in homologous recombination, EVL and TOPO IIIα may function in the processing of DNA intermediates formed during homologous recombination.
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Affiliation(s)
- Motoki Takaku
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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Yang J, Bachrati CZ, Ou J, Hickson ID, Brown GW. Human topoisomerase IIIalpha is a single-stranded DNA decatenase that is stimulated by BLM and RMI1. J Biol Chem 2010; 285:21426-36. [PMID: 20445207 DOI: 10.1074/jbc.m110.123216] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human topoisomerase IIIalpha is a type IA DNA topoisomerase that functions with BLM and RMI1 to resolve DNA replication and recombination intermediates. BLM, human topoisomerase IIIalpha, and RMI1 catalyze the dissolution of double Holliday junctions into noncrossover products via a strand-passage mechanism. We generated single-stranded catenanes that resemble the proposed dissolution intermediate recognized by human topoisomerase IIIalpha. We demonstrate that human topoisomerase IIIalpha is a single-stranded DNA decatenase that is specifically stimulated by the BLM-RMI1 pair. In addition, RMI1 interacts with human topoisomerase IIIalpha, and the interaction is required for the stimulatory effect of RMI1 on decatenase activity. Our data provide direct evidence that human topoisomerase IIIalpha functions as a decatenase with the assistance of BLM and RMI1 to facilitate the processing of homologous recombination intermediates without crossing over as a mechanism to preserve genome integrity.
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Affiliation(s)
- Jay Yang
- Department of Biochemistry and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada and
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34
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Mutational analysis of Bloom helicase. Methods Mol Biol 2010. [PMID: 20225149 DOI: 10.1007/978-1-60327-355-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
DNA helicases are biomolecular motors that convert the chemical energy derived from the hydrolysis of nucleotide triphosphate (usually ATP) into mechanical energy to unwind double-stranded DNA. The unwinding of double-stranded DNA is an essential process for DNA replication, repair, recombination, and transcription. Mutations in human RecQ helicases result in inherent human disease including Bloom's syndrome, Werner's syndrome, and Rothmund-Thomson syndrome. Bloom's syndrome (BS) is a rare human autosomal recessive disorder characterized by a strong predisposition to a wide range of cancers commonly affecting the general population. In order to understand the molecular basis of BS pathology and the mechanism underlying the function of Bloom helicase, we have analyzed BS-causing missense mutations by a combination of structural modeling, site-directed mutagenesis, and biochemical and biophysical approaches. Here, we describe the methods and protocols for measuring ATPase, ATP and DNA binding, DNA strand annealing, and DNA unwinding activities of Bloom protein and its mutant variants. These approaches should be applicable and useful for studying other helicases.
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Abstract
DNA double-strand breaks are repaired by different mechanisms, including homologous recombination and nonhomologous end-joining. DNA-end resection, the first step in recombination, is a key step that contributes to the choice of DSB repair. Resection, an evolutionarily conserved process that generates single-stranded DNA, is linked to checkpoint activation and is critical for survival. Failure to regulate and execute this process results in defective recombination and can contribute to human disease. Here I review recent findings on the mechanisms of resection in eukaryotes, from yeast to vertebrates, provide insights into the regulatory strategies that control it, and highlight the consequences of both its impairment and its deregulation.
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36
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Tahmaseb K, Matson SW. Rapid purification of helicase proteins and in vitro analysis of helicase activity. Methods 2010; 51:322-8. [PMID: 20153831 DOI: 10.1016/j.ymeth.2010.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 02/08/2010] [Accepted: 02/09/2010] [Indexed: 11/29/2022] Open
Abstract
Most processes involving an organism's genetic material, including replication, repair and recombination, require access to single-stranded DNA as a template or reaction intermediate. To disrupt the hydrogen bonds between the two strands in double-stranded DNA, organisms utilize proteins called DNA helicases. DNA helicases use duplex DNA as a substrate to create single-stranded DNA in a reaction that requires ATP hydrolysis. Due to their critical role in cellular function, understanding the reaction catalyzed by helicases is essential to understanding DNA metabolism. Helicases are also important in many disease processes due to their role in DNA maintenance and replication. Here we discuss ways to rapidly purify helicases in sufficient quantity for biochemical analysis. We also briefly discuss potential substrates to use with helicases to establish some of their critical biochemical parameters. Through the use of methods that simplify the study of helicases, our understanding of these essential proteins can be accelerated.
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Affiliation(s)
- Kambiz Tahmaseb
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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37
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Orozco-Mosqueda MDC, Altamirano-Hernandez J, Farias-Rodriguez R, Valencia-Cantero E, Santoyo G. Homologous recombination and dynamics of rhizobial genomes. Res Microbiol 2009; 160:733-41. [DOI: 10.1016/j.resmic.2009.09.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 09/17/2009] [Accepted: 09/21/2009] [Indexed: 10/20/2022]
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38
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Plank J, Hsieh TS. Helicase-appended topoisomerases: new insight into the mechanism of directional strand transfer. J Biol Chem 2009; 284:30737-41. [PMID: 19726668 DOI: 10.1074/jbc.r109.051268] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA strand passage through an enzyme-mediated gate is a key step in the catalytic cycle of topoisomerases to produce topological transformations in DNA. In most of the reactions catalyzed by topoisomerases, strand passage is not directional; thus, the enzyme simply provides a transient DNA gate through which DNA transport is allowed and thereby resolves the topological entanglement. When studied in isolation, the type IA topoisomerase family appears to conform to this rule. Interestingly, type IA enzymes can carry out directional strand transport as well. We examined here the biochemical mechanism for directional strand passage of two type IA topoisomerases: reverse gyrase and a protein complex of topoisomerase III alpha and Bloom helicase. These enzymes are able to generate vectorial strand transport independent of the supercoiling energy stored in the DNA molecule. Reverse gyrase is able to anneal single strands, thereby increasing linkage number of a DNA molecule. However, topoisomerase III alpha and Bloom helicase can dissolve DNA conjoined with a double Holliday junction, thus reducing DNA linkage. We propose here that the helicase or helicase-like component plays a determinant role in the directionality of strand transport. There is thus a common biochemical ground for the directional strand passage for the type IA topoisomerases.
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Affiliation(s)
- Jody Plank
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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39
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Xu Y, Lei Z, Huang H, Dui W, Liang X, Ma J, Jiao R. dRecQ4 is required for DNA synthesis and essential for cell proliferation in Drosophila. PLoS One 2009; 4:e6107. [PMID: 19572017 PMCID: PMC2700968 DOI: 10.1371/journal.pone.0006107] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Accepted: 06/02/2009] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The family of RecQ DNA helicases plays an important role in the maintenance of genomic integrity. Mutations in three of the five known RecQ family members in humans, BLM, WRN and RecQ4, lead to disorders that are characterized by predisposition to cancer and premature aging. METHODOLOGY/PRINCIPAL FINDINGS To address the in vivo functions of Drosophila RecQ4 (dRecQ4), we generated mutant alleles of dRecQ4 using the targeted gene knock-out technique. Our data show that dRecQ4 mutants are homozygous lethal with defects in DNA replication, cell cycle progression and cell proliferation. Two sets of experiments suggest that dRecQ4 also plays a role in DNA double strand break repair. First, mutant animals exhibit sensitivity to gamma irradiation. Second, the efficiency of DsRed reconstitution via single strand annealing repair is significantly reduced in the dRecQ4 mutant animals. Rescue experiments further show that both the N-terminal domain and the helicase domain are essential to dRecQ4 function in vivo. The N-terminal domain is sufficient for the DNA repair function of dRecQ4. CONCLUSIONS/SIGNIFICANCE Together, our results show that dRecQ4 is an essential gene that plays an important role in not only DNA replication but also DNA repair and cell cycle progression in vivo.
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Affiliation(s)
- Yanjuan Xu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, the Chinese Academy of Sciences, Beijing, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Zhiyong Lei
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, the Chinese Academy of Sciences, Beijing, China
| | - Hai Huang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, the Chinese Academy of Sciences, Beijing, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Wen Dui
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, the Chinese Academy of Sciences, Beijing, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Xuehong Liang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, the Chinese Academy of Sciences, Beijing, China
| | - Jun Ma
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, the Chinese Academy of Sciences, Beijing, China
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, Ohio, United States of America
| | - Renjie Jiao
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, the Chinese Academy of Sciences, Beijing, China
- * E-mail:
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40
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Abstract
Post-translational modification of the cell's proteome by ubiquitin and ubiquitin-like proteins provides dynamic functional regulation. Ubiquitin and SUMO are well-studied post-translational modifiers that typically impart distinct effects on their targets. The recent discovery that modification by SUMO can target proteins for ubiquitination and proteasomal degradation sets a new paradigm in the field, and offers insights into the roles of SUMO and ubiquitin in genome stability.
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41
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Rego MA, Kolling FW, Howlett NG. The Fanconi anemia protein interaction network: casting a wide net. Mutat Res 2008; 668:27-41. [PMID: 19101576 DOI: 10.1016/j.mrfmmm.2008.11.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Revised: 11/16/2008] [Accepted: 11/25/2008] [Indexed: 11/26/2022]
Abstract
It has long been hypothesized that a defect in the repair of damaged DNA is central to the etiology of Fanconi anemia (FA). Indeed, an increased sensitivity of FA patient-derived cells to the lethal effects of various forms of DNA damaging agents was described over three decades ago [A.J. Fornace, Jr., J.B. Little, R.R. Weichselbaum, DNA repair in a Fanconi's anemia fibroblast cell strain, Biochim. Biophys. Acta 561 (1979) 99-109; Y. Fujiwara, M. Tatsumi, Repair of mitomycin C damage to DNA in mammalian cells and its impairment in Fanconi's anemia cells, Biochem. Biophys. Res. Commun. 66 (1975) 592-598; A.J. Rainbow, M. Howes, Defective repair of ultraviolet- and gamma-ray-damaged DNA in Fanconi's anaemia, Int. J. Radiat. Biol. Relat. Stud. Phys. Chem. Med. 31 (1977) 191-195]. Furthermore, the cytological hallmark of FA, the DNA crosslink-induced radial chromosome formation, exemplifies an innate impairment in the repair of these particularly cytotoxic DNA lesions [A.D. Auerbach, Fanconi anemia diagnosis and the diepoxybutane (DEB) test, Exp. Hematol. 21 (1993) 731-733]. Precisely defining the collective role of the FA proteins in DNA repair, however, continues to be one of the most enigmatic and challenging questions in the FA field. The first six identified FA proteins (A, C, E, F, G, and D2) harbored no recognizable enzymatic features, precluding association with a specific metabolic process. Consequently, our knowledge of the role of the FA proteins in the DNA damage response has been gleaned primarily through biochemical association studies with non-FA proteins. Here, we provide a chronological discourse of the major FA protein interaction network discoveries, with particular emphasis on the DNA damage response, that have defined our current understanding of the molecular basis of FA.
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Affiliation(s)
- Meghan A Rego
- Department of Cell and Molecular Biology, University of Rhode Island, 115 Morrill Hall, 45 Lower College Road, Kingston, RI 02881, USA
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42
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Siehler SY, Schrauder M, Gerischer U, Cantor S, Marra G, Wiesmüller L. Human MutL-complexes monitor homologous recombination independently of mismatch repair. DNA Repair (Amst) 2008; 8:242-52. [PMID: 19022408 DOI: 10.1016/j.dnarep.2008.10.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Revised: 09/10/2008] [Accepted: 10/21/2008] [Indexed: 12/19/2022]
Abstract
The role of mismatch repair proteins has been well studied in the context of DNA repair following DNA polymerase errors. Particularly in yeast, MSH2 and MSH6 have also been implicated in the regulation of genetic recombination, whereas MutL homologs appeared to be less important. So far, little is known about the role of the human MutL homolog hMLH1 in recombination, but recently described molecular interactions suggest an involvement. To identify activities of hMLH1 in this process, we applied an EGFP-based assay for the analysis of different mechanisms of DNA repair, initiated by a targeted double-stranded DNA break. We analysed 12 human cellular systems, differing in the hMLH1 and concomitantly in the hPMS1 and hPMS2 status via inducible protein expression, genetic reconstitution, or RNA interference. We demonstrate that hMLH1 and its complex partners hPMS1 and hPMS2 downregulate conservative homologous recombination (HR), particularly when involving DNA sequences with only short stretches of uninterrupted homology. Unexpectedly, hMSH2 is dispensable for this effect. Moreover, the damage-signaling kinase ATM and its substrates BLM and BACH1 are not strictly required, but the combined effect of ATM/ATR-signaling components may mediate the anti-recombinogenic effect. Our data indicate a protective role of hMutL-complexes in a process which may lead to detrimental genome rearrangements, in a manner which does not depend on mismatch repair.
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43
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Hu Y, Lu X, Zhou G, Barnes EL, Luo G. Recql5 plays an important role in DNA replication and cell survival after camptothecin treatment. Mol Biol Cell 2008; 20:114-23. [PMID: 18987339 DOI: 10.1091/mbc.e08-06-0565] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Disruption of replication can lead to loss of genome integrity and increase of cancer susceptibility in mammals. Thus, a replication impediment constitutes a formidable challenge to these organisms. Recent studies indicate that homologous recombination (HR) plays an important role in suppressing genome instability and promoting cell survival after exposure to various replication inhibitors, including a topoisomerase I inhibitor, camptothecin (CPT). Here, we report that the deletion of RecQ helicase Recql5 in mouse ES cells and embryonic fibroblast (MEF) cells resulted in a significant increase in CPT sensitivity and a profound reduction in DNA replication after the treatment with CPT, but not other DNA-damaging agents. This CPT-induced cell death is replication dependent and occurs primarily after the cells had exited the first cell cycle after CPT treatment. Furthermore, we show that Recql5 functions nonredundantly with Rad51, a key factor for HR to protect mouse ES cells from CPT-induced cytotoxicity. These new findings strongly suggest that Recql5 plays an important role in maintaining active DNA replication to prevent the collapse of replication forks and the accumulation of DSBs in order to preserve genome integrity and to prevent cell death after replication stress as a result of topoisomerase I poisoning.
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Affiliation(s)
- Yiduo Hu
- Department of Genetics, Case Comprehensive Cancer Center, University Hospitals of Cleveland and Case Western Reserve University, Cleveland, OH 44106, USA
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44
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Zhu J, Zhu S, Guzzo CM, Ellis NA, Sung KS, Choi CY, Matunis MJ. Small ubiquitin-related modifier (SUMO) binding determines substrate recognition and paralog-selective SUMO modification. J Biol Chem 2008; 283:29405-15. [PMID: 18708356 DOI: 10.1074/jbc.m803632200] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Small ubiquitin-related modifiers (SUMOs) regulate diverse cellular processes through their covalent attachment to target proteins. Vertebrates express three SUMO paralogs: SUMO-1, SUMO-2, and SUMO-3 (SUMO-2 and SUMO-3 are approximately 96% identical and referred to as SUMO-2/3). SUMO-1 and SUMO-2/3 are conjugated, at least in part, to unique subsets of proteins and thus regulate distinct cellular pathways. However, how different proteins are selectively modified by SUMO-1 and SUMO-2/3 is unknown. We demonstrate that BLM, the RecQ DNA helicase mutated in Bloom syndrome, is preferentially modified by SUMO-2/3 both in vitro and in vivo. Our findings indicate that non-covalent interactions between SUMO and BLM are required for modification at non-consensus sites and that preferential SUMO-2/3 modification is determined by preferential SUMO-2/3 binding. We also present evidence that sumoylation of a C-terminal fragment of HIPK2 is dependent on SUMO binding, indicating that non-covalent interactions between SUMO and target proteins provide a general mechanism for SUMO substrate selection and possible paralog-selective modification.
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Affiliation(s)
- Jianmei Zhu
- Bloomberg School of Public Health, Department of Biochemistry and Molecular Biology, The Johns Hopkins University, Baltimore, Maryland 21205, USA
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45
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Banerjee S, Smith S, Oum JH, Liaw HJ, Hwang JY, Sikdar N, Motegi A, Lee SE, Myung K. Mph1p promotes gross chromosomal rearrangement through partial inhibition of homologous recombination. ACTA ACUST UNITED AC 2008; 181:1083-93. [PMID: 18591428 PMCID: PMC2442200 DOI: 10.1083/jcb.200711146] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Gross chromosomal rearrangement (GCR) is a type of genomic instability associated with many cancers. In yeast, multiple pathways cooperate to suppress GCR. In a screen for genes that promote GCR, we identified MPH1, which encodes a 3′–5′ DNA helicase. Overexpression of Mph1p in yeast results in decreased efficiency of homologous recombination (HR) as well as delayed Rad51p recruitment to double-strand breaks (DSBs), which suggests that Mph1p promotes GCR by partially suppressing HR. A function for Mph1p in suppression of HR is further supported by the observation that deletion of both mph1 and srs2 synergistically sensitize cells to methyl methanesulfonate-induced DNA damage. The GCR-promoting activity of Mph1p appears to depend on its interaction with replication protein A (RPA). Consistent with this observation, excess Mph1p stabilizes RPA at DSBs. Furthermore, spontaneous RPA foci at DSBs are destabilized by the mph1Δ mutation. Therefore, Mph1p promotes GCR formation by partially suppressing HR, likely through its interaction with RPA.
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Affiliation(s)
- Soma Banerjee
- Genome Instability Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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46
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Hyun M, Bohr VA, Ahn B. Biochemical characterization of the WRN-1 RecQ helicase of Caenorhabditis elegans. Biochemistry 2008; 47:7583-93. [PMID: 18558712 DOI: 10.1021/bi800197m] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The highly conserved RecQ helicases are essential for the maintenance of genomic stability. Werner syndrome protein, WRN, is one of five human RecQ helicase homologues, and a deficiency of the protein causes a hereditary premature aging disorder that is characterized by genomic instability. A WRN orthologue, wrn-1 lacking the exonuclease domain, has been identified in the nematode Caenorhabditis elegans. wrn-1(RNAi) in C. elegans has a shortened life span, increased sensitivity to DNA damage, and accelerated aging phenotypes. However, little is known about its enzymatic activity. We purified the recombinant C. elegans WRN-1 protein (CeWRN-1) and then investigated its substrate specificity in vitro to improve our understanding of its function in vivo. We found that CeWRN-1 is an ATP-dependent 3'-5' helicase capable of unwinding a variety of DNA structures such as forked duplexes, Holliday junctions, bubble substrates, D-loops, and flap duplexes, and 3'-tailed duplex substrates. Distinctly, CeWRN-1 is able to unwind a long forked duplex compared to human WRN. Furthermore, CeWRN-1 helicase activity on a long DNA duplex is stimulated by C. elegans replication protein A (CeRPA) that is shown to interact with CeWRN-1 by a dot blot. The ability of CeWRN-1 to unwind these DNA structures may improve the access for DNA repair and replication proteins that are important for preventing the accumulation of abnormal structures, contributing to genomic stability.
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Affiliation(s)
- Moonjung Hyun
- Department of Life Sciences, University of Ulsan, Ulsan 680749, Korea
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47
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Raynard S, Zhao W, Bussen W, Lu L, Ding YY, Busygina V, Meetei AR, Sung P. Functional role of BLAP75 in BLM-topoisomerase IIIalpha-dependent holliday junction processing. J Biol Chem 2008; 283:15701-8. [PMID: 18390547 DOI: 10.1074/jbc.m802127200] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The BLAP75 protein combines with the BLM helicase and topoisomerase (Topo) IIIalpha to form an evolutionarily conserved complex, termed the BTB complex, that functions to regulate homologous recombination. BLAP75 binds DNA, associates with both BLM and Topo IIIalpha, and enhances the ability of the BLM-Topo IIIalpha pair to branch migrate the Holliday junction (HJ) or dissolve the double Holliday junction (dHJ) structure to yield non-crossover recombinants. Here we seek to understand the relevance of the biochemical attributes of BLAP75 in HJ processing. With the use of a series of BLAP75 protein fragments, we show that the evolutionarily conserved N-terminal third of BLAP75 mediates complex formation with BLM and Topo IIIalpha and that the DNA binding activity resides in the C-terminal third of this novel protein. Interestingly, the N-terminal third of BLAP75 is just as adept as the full-length protein in the promotion of dHJ dissolution and HJ unwinding by BLM-Topo IIIalpha. Thus, the BLAP75 DNA binding activity is dispensable for the ability of the BTB complex to process the HJ in vitro. Lastly, we show that a BLAP75 point mutant (K166A), defective in Topo IIIalpha interaction, is unable to promote dHJ dissolution and HJ unwinding by BLM-Topo IIIalpha. This result provides proof that the functional integrity of the BTB complex is contingent upon the interaction of BLAP75 with Topo IIIalpha.
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Affiliation(s)
- Steven Raynard
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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48
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Weinstein J, Rothstein R. The genetic consequences of ablating helicase activity and the Top3 interaction domain of Sgs1. DNA Repair (Amst) 2008; 7:558-71. [PMID: 18272435 PMCID: PMC2359228 DOI: 10.1016/j.dnarep.2007.12.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Revised: 12/08/2007] [Accepted: 12/11/2007] [Indexed: 10/22/2022]
Abstract
Sgs1, the RecQ helicase homolog, and Top3, the type-IA topoisomerase, physically interact and are required for genomic stability in budding yeast. Similarly, topoisomerase III genes physically pair with homologs of SGS1 in humans that are involved in the cancer predisposition and premature aging diseases Bloom, Werner, and Rothmund-Thompson syndromes. In the absence of Top1 activity, sgs1 mutants are severely growth impaired. Here, we investigate the role of Sgs1 helicase activity and its N-terminal Top3 interaction domain by using an allele-replacement technique to integrate mutant alleles at the native SGS1 genomic locus. We compare the phenotype of helicase-defective (sgs1-hd) and N-terminal deletion (sgs1-NDelta) strains to wild-type and sgs1 null strains. Like the sgs1 null, sgs1-hd mutations suppress top3 slow growth, cause a growth defect in the absence of Srs2 helicase, and impair meiosis. However, for recombination and the synthetic interaction with top1Delta mutations, loss of helicase activity exhibits a less severe phenotype than the null. Interestingly, deletion of the Top3 interaction domain of Sgs1 causes a top3-like phenotype, and furthermore, this effect is dependent on helicase activity. These results suggest that the protein-protein interaction between these two DNA-metabolism enzymes, even in the absence of helicase activity, is important for their function in catalyzing specific changes in DNA topology.
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Affiliation(s)
- Justin Weinstein
- Department of Genetics & Development, Columbia University Medical Center, 701 West 168th Street, New York, NY 10032-2704, USA
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49
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Kanaar R, Wyman C, Rothstein R. Quality control of DNA break metabolism: in the 'end', it's a good thing. EMBO J 2008; 27:581-8. [PMID: 18285819 DOI: 10.1038/emboj.2008.11] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Accepted: 01/14/2008] [Indexed: 12/27/2022] Open
Abstract
DNA ends pose specific problems in the control of genetic information quality. Ends of broken DNA need to be rejoined to avoid genome rearrangements, whereas natural DNA ends of linear chromosomes, telomeres, need to be stable and hidden from the DNA damage response. Efficient DNA end metabolism, either at induced DNA breaks or telomeres, does not result from the machine-like precision of molecular reactions, but rather from messier, more stochastic processes. The necessary molecular interactions are dynamically unstable, with constructive and destructive processes occurring in competition. In the end, quality control comes from the constant building up and tearing down of inappropriate, but also appropriate reaction steps in combination with factors that only slightly shift the equilibrium to eventually favour appropriate events. Thus, paradoxically, enzymes antagonizing DNA end metabolism help to ensure that genome maintenance becomes a robust process.
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Affiliation(s)
- Roland Kanaar
- Department of Cell Biology and Genetics, Erasmus Medical Center, Rotterdam, The Netherlands.
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50
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Abstract
Rmi1 is a conserved oligonucleotide and oligosaccharide binding-fold protein that is associated with RecQ DNA helicase complexes from humans (BLM-TOP3 alpha) and yeast (Sgs1-Top3). Although human RMI1 stimulates the dissolution activity of BLM-TOP3 alpha, its biochemical function is unknown. Here we examined the role of Rmi1 in the yeast complex. Consistent with the similarity of top3Delta and rmi1Delta phenotypes, we find that a stable Top3.Rmi1 complex can be isolated from yeast cells overexpressing these two subunits. Compared with Top3 alone, this complex displays increased superhelical relaxation activity. The isolated Rmi1 subunit also stimulates Top3 activity in reconstitution experiments. In both cases elevated temperatures are required for optimal relaxation unless the substrate contains a single-strand DNA (ssDNA) bubble. Interestingly, Rmi1 binds only weakly to ssDNA on its own, but it stimulates the ssDNA binding activity of Top3 5-fold. Top3 and Rmi1 also cooperate to bind the Sgs1 N terminus and promote its interaction with ssDNA. These results demonstrate that Top3-Rmi1 functions as a complex and suggest that Rmi1 stimulates Top3 by promoting its interaction with ssDNA.
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Affiliation(s)
- Chi-Fu Chen
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| | - Steven J Brill
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854.
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