1
|
Chang YC, Gnann C, Steimbach RR, Bayer FP, Lechner S, Sakhteman A, Abele M, Zecha J, Trendel J, The M, Lundberg E, Miller AK, Kuster B. Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics. Cell Rep 2024; 43:114272. [PMID: 38795348 DOI: 10.1016/j.celrep.2024.114272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/12/2024] [Accepted: 05/09/2024] [Indexed: 05/27/2024] Open
Abstract
Lysine deacetylase inhibitors (KDACis) are approved drugs for cutaneous T cell lymphoma (CTCL), peripheral T cell lymphoma (PTCL), and multiple myeloma, but many aspects of their cellular mechanism of action (MoA) and substantial toxicity are not well understood. To shed more light on how KDACis elicit cellular responses, we systematically measured dose-dependent changes in acetylation, phosphorylation, and protein expression in response to 21 clinical and pre-clinical KDACis. The resulting 862,000 dose-response curves revealed, for instance, limited cellular specificity of histone deacetylase (HDAC) 1, 2, 3, and 6 inhibitors; strong cross-talk between acetylation and phosphorylation pathways; localization of most drug-responsive acetylation sites to intrinsically disordered regions (IDRs); an underappreciated role of acetylation in protein structure; and a shift in EP300 protein abundance between the cytoplasm and the nucleus. This comprehensive dataset serves as a resource for the investigation of the molecular mechanisms underlying KDACi action in cells and can be interactively explored online in ProteomicsDB.
Collapse
Affiliation(s)
- Yun-Chien Chang
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Bavaria, Germany
| | - Christian Gnann
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Raphael R Steimbach
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, Germany; Biosciences Faculty, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Florian P Bayer
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Bavaria, Germany
| | - Severin Lechner
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Bavaria, Germany
| | - Amirhossein Sakhteman
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Bavaria, Germany
| | - Miriam Abele
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Bavaria, Germany; Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Bavaria, Germany
| | - Jana Zecha
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Bavaria, Germany
| | - Jakob Trendel
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Bavaria, Germany
| | - Matthew The
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Bavaria, Germany
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden; Department of Bioengineering, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University, Stanford, CA, USA
| | - Aubry K Miller
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Baden-Württemberg, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Bavaria, Germany; German Cancer Consortium (DKTK), Partner Site Munich and German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, Germany.
| |
Collapse
|
2
|
Gan X, Zhang Y, Jiang D, Shi J, Zhao H, Xie C, Wang Y, Xu J, Zhang X, Cai G, Wang H, Huang J, Chen X. Proper RPA acetylation promotes accurate DNA replication and repair. Nucleic Acids Res 2023; 51:5565-5583. [PMID: 37140030 PMCID: PMC10287905 DOI: 10.1093/nar/gkad291] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 05/05/2023] Open
Abstract
The single-stranded DNA (ssDNA) binding protein complex RPA plays a critical role in promoting DNA replication and multiple DNA repair pathways. However, how RPA is regulated to achieve its functions precisely in these processes remains elusive. Here, we found that proper acetylation and deacetylation of RPA are required to regulate RPA function in promoting high-fidelity DNA replication and repair. We show that yeast RPA is acetylated on multiple conserved lysines by the acetyltransferase NuA4 upon DNA damage. Mimicking constitutive RPA acetylation or blocking its acetylation causes spontaneous mutations with the signature of micro-homology-mediated large deletions or insertions. In parallel, improper RPA acetylation/deacetylation impairs DNA double-strand break (DSB) repair by the accurate gene conversion or break-induced replication while increasing the error-prone repair by single-strand annealing or alternative end joining. Mechanistically, we show that proper acetylation and deacetylation of RPA ensure its normal nuclear localization and ssDNA binding ability. Importantly, mutation of the equivalent residues in human RPA1 also impairs RPA binding on ssDNA, leading to attenuated RAD51 loading and homologous recombination repair. Thus, timely RPA acetylation and deacetylation likely represent a conserved mechanism promoting high-fidelity replication and repair while discriminating the error-prone repair mechanisms in eukaryotes.
Collapse
Affiliation(s)
- Xiaoli Gan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Yueyue Zhang
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Donghao Jiang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Jingyao Shi
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Han Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Chengyu Xie
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Yanyan Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Jingyan Xu
- Department of Hematology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xinghua Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Gang Cai
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Hailong Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jun Huang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xuefeng Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| |
Collapse
|
3
|
Barreto-Galvez A, Niljikar M, Gagliardi J, Zhang R, Kumar V, Juruwala A, Pradeep A, Shaikh A, Tiwari P, Sharma K, Gerhardt J, Cao J, Kataoka K, Durbin A, Qi J, Ye BH, Madireddy A. Acetyl transferase EP300 deficiency leads to chronic replication stress mediated by defective fork protection at stalled replication forks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.29.538781. [PMID: 37163075 PMCID: PMC10168362 DOI: 10.1101/2023.04.29.538781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Mutations in the epigenetic regulator and global transcriptional activator, E1A binding protein (EP300), is being increasingly reported in aggressive hematological malignancies including adult T-cell leukemia/lymphoma (ATLL). However, the mechanistic contribution of EP300 dysregulation to cancer initiation and progression are currently unknown. Independent inhibition of EP300 in human cells results in the differential expression of genes involved in regulating the cell cycle, DNA replication and DNA damage response. Nevertheless, specific function played by EP300 in DNA replication initiation, progression and replication fork integrity has not been studied. Here, using ATLL cells as a model to study EP300 deficiency and an p300-selective PROTAC degrader, degrader as a pharmacologic tool, we reveal that EP300-mutated cells display prolonged cell cycle kinetics, due to pronounced dysregulations in DNA replication dynamics leading to persistent genomic instability. Aberrant DNA replication in EP300-mutated cells is characterized by elevated replication origin firing due to increased replisome pausing genome-wide. We demonstrate that EP300 deficiency results in nucleolytic degradation of nascently synthesized DNA at stalled forks due to a prominent defect in fork stabilization and protection. This in turn results in the accumulation of single stranded DNA gaps at collapsed replication forks, in EP300-deficient cells. Inhibition of Mre11 nuclease rescues the ssDNA accumulation indicating a dysregulation in downstream mechanisms that restrain nuclease activity at stalled forks. Importantly, we find that the absence of EP300 results in decreased expression of BRCA2 protein expression and a dependency on POLD3-mediated error-prone replication restart mechanisms. The overall S-phase abnormalities observed lead to under-replicated DNA in G2/M that instigates mitotic DNA synthesis. This in turn is associated with mitotic segregation defects characterized by elevated micronuclei formation, accumulation of cytosolic DNA and transmission of unrepaired inherited DNA lesions in the subsequent G1-phase in EP300-deficient cells. We demonstrate that the DNA replication dynamics of EP300-mutated cells ATLL cells recapitulate features of BRCA-deficient cancers. Altogether these results suggest that mutations in EP300 cause chronic DNA replication stress and defective replication fork restart results in persistent genomic instability that underlie aggressive chemo-resistant tumorigenesis in humans.
Collapse
|
4
|
Njeri C, Pepenella S, Battapadi T, Bambara RA, Balakrishnan L. DNA Polymerase Delta Exhibits Altered Catalytic Properties on Lysine Acetylation. Genes (Basel) 2023; 14:genes14040774. [PMID: 37107532 PMCID: PMC10137900 DOI: 10.3390/genes14040774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
DNA polymerase delta is the primary polymerase that is involved in undamaged nuclear lagging strand DNA replication. Our mass-spectroscopic analysis has revealed that the human DNA polymerase δ is acetylated on subunits p125, p68, and p12. Using substrates that simulate Okazaki fragment intermediates, we studied alterations in the catalytic properties of acetylated polymerase and compared it to the unmodified form. The current data show that the acetylated form of human pol δ displays a higher polymerization activity compared to the unmodified form of the enzyme. Additionally, acetylation enhances the ability of the polymerase to resolve complex structures such as G-quadruplexes and other secondary structures that might be present on the template strand. More importantly, the ability of pol δ to displace a downstream DNA fragment is enhanced upon acetylation. Our current results suggest that acetylation has a profound effect on the activity of pol δ and supports the hypothesis that acetylation may promote higher-fidelity DNA replication.
Collapse
Affiliation(s)
- Catherine Njeri
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Sharon Pepenella
- Department of Microbiology and Immunology, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Tripthi Battapadi
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Robert A Bambara
- Department of Microbiology and Immunology, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Lata Balakrishnan
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
- Indiana University Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| |
Collapse
|
5
|
Tang Q, Liu Y, Liu Y, Zhu F, Yu Q, Chen H, Chen L, Ma S, Xu H, Chen K, Li G. Bombyx mori Flap endonuclease 1 correlates with the repair of ultraviolet-induced DNA damage. JOURNAL OF INSECT PHYSIOLOGY 2022; 142:104424. [PMID: 35878701 DOI: 10.1016/j.jinsphys.2022.104424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Solar ultraviolet radiation (UV) can cause DNA damage in microorganisms. Flap endonuclease 1 (FEN1) is a structure-specific nuclease and plays important roles in DNA replication and repair. At present, the properties and functions of FEN1 have not been characterized in detail in invertebrates such as Bombyx mori. In this study, Bombyx mori FEN1 (BmFEN1) was expressed in E. coli, and was shown to have nuclease activity that nonspecifically cleaved DNA in vitro. However, inside the cell, BmFEN1 did not cleave DNA randomly. Truncated BmFEN1 missing the nuclear localization signal (346-380 aa) still had the nuclease activity, but was no longer precisely localized to the sites of UV-induced DNA damage. It was further found that BmFEN1 favored the faster repair of UV-damaged DNA. The present study will provide a reference for further understanding the functions of BmFEN1 and UV-induced DNA damage repair mechanisms in insects.
Collapse
Affiliation(s)
- Qi Tang
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Yue Liu
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Yutong Liu
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Feifei Zhu
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Qian Yu
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Huiqing Chen
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Liang Chen
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Shangshang Ma
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Huixin Xu
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Keping Chen
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China.
| | - Guohui Li
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China.
| |
Collapse
|
6
|
Tarantino ME, Delaney S. Kinetic Analysis of the Effect of N-Terminal Acetylation on Thymine DNA Glycosylase. Biochemistry 2022; 61:895-908. [PMID: 35436101 PMCID: PMC9117521 DOI: 10.1021/acs.biochem.1c00823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Thymine DNA glycosylase (TDG) is tasked with initiating DNA base excision repair by recognizing and removing T, U, the chemotherapeutic 5-fluorouracil (5-FU), and many other oxidized and halogenated pyrimidine bases. TDG contains a long, unstructured N-terminus that contains four known sites of acetylation: lysine (K) residues 59, 83, 84, and 87. Here, K to glutamine (Q) mutants are used as acetyl-lysine (AcK) analogues to probe the effect of N-terminal acetylation on the kinetics of TDG. We find that mimicking acetylation affects neither the maximal single-turnover rate kmax nor the turnover rate kTO, indicating that the steps after initial binding, through chemistry and product release, are not affected. Under subsaturating conditions, however, acetylation changes the processing of U substrates. Subtle differences among AcK analogues are revealed with 5-FU in single-stranded DNA. We propose that the subtleties observed among the AcK analogues may be amplified on the genomic scale, leading to regulation of TDG activity. N-terminal acetylation, though, may also play a structural, rather than kinetic role in vivo.
Collapse
Affiliation(s)
- Mary E. Tarantino
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI 02912, United States
| |
Collapse
|
7
|
Basic V, Zhang B, Domert J, Pellas U, Tot T. Integrative meta-analysis of gene expression profiles identifies FEN1 and ENDOU as potential diagnostic biomarkers for cervical squamous cell carcinoma. Oncol Lett 2021; 22:840. [PMID: 34712364 PMCID: PMC8548783 DOI: 10.3892/ol.2021.13101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/16/2021] [Indexed: 12/23/2022] Open
Abstract
Cervical carcinoma is a global public health burden. Given that it is usually asymptomatic at potentially curative stages, the development of clinically accurate tests is critical for early detection and individual risk stratification. The present study performed an integrative meta-analysis of the transcriptomes from 10 cervical carcinoma cohorts, with the aim of identifying biomarkers that are associated with malignant transformation of cervical epithelium, and establish their clinical applicability. From among the top ranked differentially expressed genes, flap structure-specific endonuclease 1 (FEN1) and poly (U)-specific endoribonuclease (ENDOU) were selected for further validation, and their clinical applicability was assessed using immunohistochemically stained microarrays comprising 110 tissue cores, using p16 and Ki67 staining as the comparator tests. The results demonstrated that FEN1 expression was significantly upregulated in 65% of tumor specimens (P=0.0001), with no detectable expression in the non-tumor tissues. Furthermore, its expression was significantly associated with Ki67 staining in tumor samples (P<0.0001), but no association was observed with p16 expression or the presence of human papilloma virus types 16/18, patient age, tumor grade or stage. FEN1 staining demonstrated lower sensitivity than p16 (69.3 vs. 96.8%) and Ki67 (69.3 vs. 76.3%); however, the specificity was identical to p16 and higher than that of Ki67 (100 vs. 71.4%).ENDOU staining was consistent with the microarray results, demonstrating 1% positivity in tumors and 40% positivity in non-tumor tissues. Gene set enrichment analysis of cervical tumors overexpressing FEN1 revealed its association with enhanced growth factor signaling, immune response inhibition and extracellular matrix remodeling, whereas tumors with low ENDOU expression exhibited inhibition of epithelial development and differentiation processes. Taken together, the results of the present study demonstrate the feasibility of the integrative meta-analysis approach to identify relevant biomarkers associated with cervical carcinogenesis. Thus, FEN1 and ENDOU may be useful diagnostic biomarkers for squamous cervical carcinoma. However, further studies are required to determine their diagnostic performance in larger patient cohorts and validate the results presented here.
Collapse
Affiliation(s)
- Vladimir Basic
- Pathology and Cytology Dalarna, County Hospital Falun, Falun 791 82, Sweden
- Clinical Research Center Dalarna, Uppsala University, Falun 791 82, Sweden
| | - Boxi Zhang
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm 171 65, Sweden
| | - Jakob Domert
- Pathology and Cytology Dalarna, County Hospital Falun, Falun 791 82, Sweden
| | - Ulrika Pellas
- Clinical Research Center Dalarna, Uppsala University, Falun 791 82, Sweden
| | - Tibor Tot
- Pathology and Cytology Dalarna, County Hospital Falun, Falun 791 82, Sweden
| |
Collapse
|
8
|
Tian Y, Zhu Q, Sun Z, Geng D, Lin B, Su X, He J, Guo M, Xu H, Zhao Y, Qin W, Wang PG, Wen L, Yi W. One‐Step Enzymatic Labeling Reveals a Critical Role of O‐GlcNAcylation in Cell‐Cycle Progression and DNA Damage Response. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yinping Tian
- Department of Hepatobiliary and Pancreatic Surgery The First Affiliated Hospital Zhejiang Provincial Key Laboratory of Pancreatic Disease School of Medicine Zhejiang University Hangzhou China
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Qiang Zhu
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Zeyu Sun
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases National Clinical Research Center for Infectious Diseases Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease The First Affiliated Hospital School of Medicine Zhejiang University Hangzhou China
| | - Didi Geng
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Bingyi Lin
- Department of Hepatobiliary and Pancreatic Surgery The First Affiliated Hospital Zhejiang Provincial Key Laboratory of Pancreatic Disease School of Medicine Zhejiang University Hangzhou China
| | - Xiaoling Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases National Clinical Research Center for Infectious Diseases Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease The First Affiliated Hospital School of Medicine Zhejiang University Hangzhou China
| | - Jiahui He
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Miao Guo
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Weijie Qin
- National Center for Protein Sciences Beijing State Key Laboratory of Proteomics, Beijing Proteome Research Center Beijing Institute of Lifeomics Beijing China
| | - Peng George Wang
- School of Medicine Southern University of Science and Technology Shenzhen China
| | - Liuqing Wen
- Carbohydrate-Based Drug Research Center Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai China
| | - Wen Yi
- Department of Hepatobiliary and Pancreatic Surgery The First Affiliated Hospital Zhejiang Provincial Key Laboratory of Pancreatic Disease School of Medicine Zhejiang University Hangzhou China
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| |
Collapse
|
9
|
Tian Y, Zhu Q, Sun Z, Geng D, Lin B, Su X, He J, Guo M, Xu H, Zhao Y, Qin W, Wang PG, Wen L, Yi W. One-Step Enzymatic Labeling Reveals a Critical Role of O-GlcNAcylation in Cell-Cycle Progression and DNA Damage Response. Angew Chem Int Ed Engl 2021; 60:26128-26135. [PMID: 34590401 DOI: 10.1002/anie.202110053] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Indexed: 12/26/2022]
Abstract
O-linked N-acetylglucosamine (O-GlcNAcylation) is a ubiquitous post-translational modification of proteins that is essential for cell function. Perturbation of O-GlcNAcylation leads to altered cell-cycle progression and DNA damage response. However, the underlying mechanisms are poorly understood. Here, we develop a highly sensitive one-step enzymatic strategy for capture and profiling O-GlcNAcylated proteins in cells. Using this strategy, we discover that flap endonuclease 1 (FEN1), an essential enzyme in DNA synthesis, is a novel substrate for O-GlcNAcylation. FEN1 O-GlcNAcylation is dynamically regulated during the cell cycle. O-GlcNAcylation at the serine 352 of FEN1 disrupts its interaction with Proliferating Cell Nuclear Antigen (PCNA) at the replication foci, and leads to altered cell cycle, defects in DNA replication, accumulation of DNA damage, and enhanced sensitivity to DNA damage agents. Thus, our study provides a sensitive method for profiling O-GlcNAcylated proteins, and reveals an unknown mechanism of O-GlcNAcylation in regulating cell cycle progression and DNA damage response.
Collapse
Affiliation(s)
- Yinping Tian
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang Provincial Key Laboratory of Pancreatic Disease, School of Medicine, Zhejiang University, Hangzhou, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qiang Zhu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zeyu Sun
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Didi Geng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Bingyi Lin
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang Provincial Key Laboratory of Pancreatic Disease, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaoling Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiahui He
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Miao Guo
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Weijie Qin
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, China
| | - Peng George Wang
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Liuqing Wen
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Wen Yi
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang Provincial Key Laboratory of Pancreatic Disease, School of Medicine, Zhejiang University, Hangzhou, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| |
Collapse
|
10
|
Lee SY, Kim JJ, Miller KM. Bromodomain proteins: protectors against endogenous DNA damage and facilitators of genome integrity. Exp Mol Med 2021; 53:1268-1277. [PMID: 34548613 PMCID: PMC8492697 DOI: 10.1038/s12276-021-00673-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/13/2021] [Indexed: 12/11/2022] Open
Abstract
Endogenous DNA damage is a major contributor to mutations, which are drivers of cancer development. Bromodomain (BRD) proteins are well-established participants in chromatin-based DNA damage response (DDR) pathways, which maintain genome integrity from cell-intrinsic and extrinsic DNA-damaging sources. BRD proteins are most well-studied as regulators of transcription, but emerging evidence has revealed their importance in other DNA-templated processes, including DNA repair and replication. How BRD proteins mechanistically protect cells from endogenous DNA damage through their participation in these pathways remains an active area of investigation. Here, we review several recent studies establishing BRD proteins as key influencers of endogenous DNA damage, including DNA–RNA hybrid (R-loops) formation during transcription and participation in replication stress responses. As endogenous DNA damage is known to contribute to several human diseases, including neurodegeneration, immunodeficiencies, cancer, and aging, the ability of BRD proteins to suppress DNA damage and mutations is likely to provide new insights into the involvement of BRD proteins in these diseases. Although many studies have focused on BRD proteins in transcription, evidence indicates that BRD proteins have emergent functions in DNA repair and genome stability and are participants in the etiology and treatment of diseases involving endogenous DNA damage. Bromodomain (BRD) proteins, known to regulate gene expression, switching particular genes on and off, also play key roles in repairing DNA damage, and studying them may help identify treatments for various diseases, including cancer. DNA damage can occur during normal cellular metabolism, for example, during copying DNA and gene expression. DNA damage is implicated in tumor formation as well as in neurodegeneration, immunodeficiency, and aging. Seo Yun Lee and colleagues at The University of Texas at Austin, USA, have reviewed new results showing how BRD proteins function in repairing DNA damage. They report that when DNA is damaged during copying in BRD-deficient cells, tumors can result. They also report that defects in BRD proteins are often present in cancers. Studying how BRD proteins function in both healthy and diseased cells could help to identify new therapies.
Collapse
Affiliation(s)
- Seo Yun Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jae Jin Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA. .,Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon, Korea.
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA. .,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA.
| |
Collapse
|
11
|
Wu M, Zhang P, Wang P, Fang Z, Zhu Y. Identification of Flap Endonuclease 1 With Diagnostic and Prognostic Value in Breast Cancer. Front Oncol 2021; 11:603114. [PMID: 34277392 PMCID: PMC8278286 DOI: 10.3389/fonc.2021.603114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 06/10/2021] [Indexed: 12/28/2022] Open
Abstract
Objective This study aims to identify the potential value of flap endonuclease 1 (FEN1) as a diagnostic and prognostic marker for breast cancer (BC). Methods ELISA was used to measure serum FEN1 levels and ECLIA for CA153 and CEA levels. Receiver operating characteristic (ROC) curve analysis was used to evaluate the diagnostic value. Oncomine and UALCAN databases were used to analyze the differences in FEN1 mRNA and protein expressions. Kaplan-Meier Plotter database was then used to assess the prognostic value. Results Bioinformatics analysis showed that the FEN1 mRNA and protein levels were significantly higher in BC tissues than in normal tissues. FEN1 was detected in culture medium of BC cell lines and serum FEN1 concentrations were significantly increased in BC patients than in cancer-free individuals. Besides, FEN1 exhibited higher diagnostic accuracy (AUC values>0.800) than CA153 and CEA for distinguishing BC patients, especially early BC, from the healthy and benign groups, or individually. Additionally, serum FEN1 levels were significantly associated with the stage (P=0.001) and lymph invasion (P=0.016), and serum FEN1 levels were increased with the development of BC. Furthermore, serum FEN1 levels were significantly decreased in post-operative patients than in pre-operative patients (P=0.016). Based on the Kaplan-Meier Plotter database, the survival analysis indicated that FEN1 overexpression was associated with poor prognoses for overall survival (OS), relapse-free survival (RFS), and distant metastasis-free survival (DMFS) in BC patients. Conclusion FEN1 might be a novel diagnostic and prognostic marker for BC.
Collapse
Affiliation(s)
- Min Wu
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Medical College, Yangzhou University, Yangzhou, China
| | - Pan Zhang
- Department of Laboratory Medicine, Northern Jiangsu People's Hospital, Yangzhou, China
| | - Penghui Wang
- Department of Medical Laboratory, The Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Zhen Fang
- Department of Cardiology, Northern Jiangsu People's Hospital, Yangzhou, China
| | - Yaqin Zhu
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Medical College, Yangzhou University, Yangzhou, China
| |
Collapse
|
12
|
Al-Kawaz A, Miligy IM, Toss MS, Mohammed OJ, Green AR, Madhusudan S, Rakha EA. The prognostic significance of Flap Endonuclease 1 (FEN1) in breast ductal carcinoma in situ. Breast Cancer Res Treat 2021; 188:53-63. [PMID: 34117958 PMCID: PMC8233293 DOI: 10.1007/s10549-021-06271-y] [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: 02/12/2021] [Accepted: 05/24/2021] [Indexed: 12/19/2022]
Abstract
Background Impaired DNA repair mechanism is one of the cancer hallmarks. Flap Endonuclease 1 (FEN1) is essential for genomic integrity. FEN1 has key roles during base excision repair (BER) and replication. We hypothesised a role for FEN1 in breast cancer pathogenesis. This study aims to assess the role of FEN1 in breast ductal carcinoma in situ (DCIS). Methods Expression of FEN1 protein was evaluated in a large (n = 1015) well-characterised cohort of DCIS, comprising pure (n = 776) and mixed (DCIS coexists with invasive breast cancer (IBC); n = 239) using immunohistochemistry (IHC). Results FEN1 high expression in DCIS was associated with aggressive and high-risk features including higher nuclear grade, larger tumour size, comedo type necrosis, hormonal receptors negativity, higher proliferation index and triple-negative phenotype. DCIS coexisting with invasive BC showed higher FEN1 nuclear expression compared to normal breast tissue and pure DCIS but revealed significantly lower expression when compared to the invasive component. However, FEN1 protein expression in DCIS was not an independent predictor of local recurrence-free interval. Conclusion High FEN1 expression is linked to features of aggressive tumour behaviour and may play a role in the direct progression of DCIS to invasive disease. Further studies are warranted to evaluate its mechanistic roles in DCIS progression and prognosis. Supplementary Information The online version contains supplementary material available at 10.1007/s10549-021-06271-y.
Collapse
Affiliation(s)
- Abdulbaqi Al-Kawaz
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham, Nottingham, UK.,Department of Pathology, College of Dentistry, Al Mustansiriya University, Baghdad, Iraq
| | - Islam M Miligy
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham, Nottingham, UK.,Department of Pathology, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Michael S Toss
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham, Nottingham, UK
| | - Omar J Mohammed
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham, Nottingham, UK
| | - Andrew R Green
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham, Nottingham, UK
| | - Srinivasan Madhusudan
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham, Nottingham, UK.,Department of Oncology, Nottingham University Hospitals, Nottingham, UK
| | - Emad A Rakha
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham, Nottingham, UK. .,Department of Pathology, Faculty of Medicine, Menoufia University, Menoufia, Egypt.
| |
Collapse
|
13
|
Schilling EM, Scherer M, Rothemund F, Stamminger T. Functional regulation of the structure-specific endonuclease FEN1 by the human cytomegalovirus protein IE1 suggests a role for the re-initiation of stalled viral replication forks. PLoS Pathog 2021; 17:e1009460. [PMID: 33770148 PMCID: PMC8026080 DOI: 10.1371/journal.ppat.1009460] [Citation(s) in RCA: 9] [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: 09/23/2020] [Revised: 04/07/2021] [Accepted: 03/08/2021] [Indexed: 11/19/2022] Open
Abstract
Flap endonuclease 1 (FEN1) is a member of the family of structure-specific endonucleases implicated in regulation of DNA damage response and DNA replication. So far, knowledge on the role of FEN1 during viral infections is limited. Previous publications indicated that poxviruses encode a conserved protein that acts in a manner similar to FEN1 to stimulate homologous recombination, double-strand break (DSB) repair and full-size genome formation. Only recently, cellular FEN1 has been identified as a key component for hepatitis B virus cccDNA formation. Here, we report on a novel functional interaction between Flap endonuclease 1 (FEN1) and the human cytomegalovirus (HCMV) immediate early protein 1 (IE1). Our results provide evidence that IE1 manipulates FEN1 in an unprecedented manner: we observed that direct IE1 binding does not only enhance FEN1 protein stability but also phosphorylation at serine 187. This correlates with nucleolar exclusion of FEN1 stimulating its DSB-generating gap endonuclease activity. Depletion of FEN1 and inhibition of its enzymatic activity during HCMV infection significantly reduced nascent viral DNA synthesis demonstrating a supportive role for efficient HCMV DNA replication. Furthermore, our results indicate that FEN1 is required for the formation of DSBs during HCMV infection suggesting that IE1 acts as viral activator of FEN1 in order to re-initiate stalled replication forks. In summary, we propose a novel mechanism of viral FEN1 activation to overcome replication fork barriers at difficult-to-replicate sites in viral genomes.
Collapse
Affiliation(s)
| | - Myriam Scherer
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
| | | | | |
Collapse
|
14
|
Li S, Shi B, Liu X, An HX. Acetylation and Deacetylation of DNA Repair Proteins in Cancers. Front Oncol 2020; 10:573502. [PMID: 33194676 PMCID: PMC7642810 DOI: 10.3389/fonc.2020.573502] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/17/2020] [Indexed: 12/12/2022] Open
Abstract
Hundreds of DNA repair proteins coordinate together to remove the diverse damages for ensuring the genomic integrity and stability. The repair system is an extensive network mainly encompassing cell cycle arrest, chromatin remodeling, various repair pathways, and new DNA fragment synthesis. Acetylation on DNA repair proteins is a dynamic epigenetic modification orchestrated by lysine acetyltransferases (HATs) and lysine deacetylases (HDACs), which dramatically affects the protein functions through multiple mechanisms, such as regulation of DNA binding ability, protein activity, post-translational modification (PTM) crosstalk, and protein–protein interaction. Accumulating evidence has indicated that the aberrant acetylation of DNA repair proteins contributes to the dysfunction of DNA repair ability, the pathogenesis and progress of cancer, as well as the chemosensitivity of cancer cells. In the present scenario, targeting epigenetic therapy is being considered as a promising method at par with the conventional cancer therapeutic strategies. This present article provides an overview of the recent progress in the functions and mechanisms of acetylation on DNA repair proteins involved in five major repair pathways, which warrants the possibility of regulating acetylation on repair proteins as a therapeutic target in cancers.
Collapse
Affiliation(s)
- Shiqin Li
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Bingbing Shi
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Xinli Liu
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Han-Xiang An
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, Xiamen, China
| |
Collapse
|
15
|
Ononye OE, Sausen CW, Balakrishnan L, Bochman ML. Lysine acetylation regulates the activity of nuclear Pif1. J Biol Chem 2020; 295:15482-15497. [PMID: 32878983 DOI: 10.1074/jbc.ra120.015164] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/28/2020] [Indexed: 12/16/2022] Open
Abstract
In Saccharomyces cerevisiae, the Pif1 helicase functions in both nuclear and mitochondrial DNA replication and repair processes, preferentially unwinding RNA:DNA hybrids and resolving G-quadruplex structures. We sought to determine how the various activities of Pif1 are regulated in vivo Here, we report lysine acetylation of nuclear Pif1 and demonstrate that it influences both Pif1's cellular roles and core biochemical activities. Using Pif1 overexpression toxicity assays, we determined that the acetyltransferase NuA4 and deacetylase Rpd3 are primarily responsible for the dynamic acetylation of nuclear Pif1. MS analysis revealed that Pif1 was modified in several domains throughout the protein's sequence on the N terminus (Lys-118 and Lys-129), helicase domain (Lys-525, Lys-639, and Lys-725), and C terminus (Lys-800). Acetylation of Pif1 exacerbated its overexpression toxicity phenotype, which was alleviated upon deletion of its N terminus. Biochemical assays demonstrated that acetylation of Pif1 stimulated its helicase, ATPase, and DNA-binding activities, whereas maintaining its substrate preferences. Limited proteolysis assays indicate that acetylation of Pif1 induces a conformational change that may account for its altered enzymatic properties. We propose that acetylation is involved in regulating of Pif1 activities, influencing a multitude of DNA transactions vital to the maintenance of genome integrity.
Collapse
Affiliation(s)
- Onyekachi E Ononye
- Department of Biology, School of Science, Indiana University, Purdue University Indianapolis, Indianapolis, Indiana, USA
| | - Christopher W Sausen
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA
| | - Lata Balakrishnan
- Department of Biology, School of Science, Indiana University, Purdue University Indianapolis, Indianapolis, Indiana, USA.
| | - Matthew L Bochman
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA.
| |
Collapse
|
16
|
Lakshmanan MD, Shaheer K. Endocrine disrupting chemicals may deregulate DNA repair through estrogen receptor mediated seizing of CBP/p300 acetylase. J Endocrinol Invest 2020; 43:1189-1196. [PMID: 32253726 DOI: 10.1007/s40618-020-01241-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 03/27/2020] [Indexed: 12/20/2022]
Abstract
PURPOSE Environmental pollutants are known to induce DNA breaks, leading to genomic instability. Here, we propose a novel mechanism for the genotoxic effects exerted by environmentally exposed endocrine-disrupting chemicals (EDCs). METHODS Bibliographic research and presentation of the analysis. DISCUSSION In mammals, nucleotide excision repair, base excision repair, homologous recombination and non-homologous end-joining pathways are some of the major DNA repair pathways. p300 along with CREB-binding protein (CBP) contributes to chromatin remodeling, DNA damage response and repair of both single- and double-stranded DNA breaks. In addition to its role in DNA repair, CBP/p300 also acts as a coactivator to interact with the estrogen receptor and androgen receptor during its estrogen- and androgen-dependent transactivation, respectively. Since activated estrogen receptors (ERs) seize p300 from the repressed genes and redistribute it to the enhancer genes to activate transcription, the cellular functioning may be based on a balance between these pathways and any disturbance in one may alter the other, leading to undesirable physiological effects. CONCLUSION In conclusion, CBP/p300 is important for DNA repair and nuclear hormone receptor transactivation. Activated hormone receptors can sequester p300 to regulate the hormonal effects. Hence, we believe that activation of ERs by EDCs results in sequestration of CBP/p300 for ER transactivation and transcription initiation of its target genes, leading to a competition for CBP/P300, resulting in the deregulation of all other pathways involving p300/CBP.
Collapse
Affiliation(s)
- M D Lakshmanan
- Molecular Biology Division, Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, Karnataka, 575018, India.
| | - K Shaheer
- Molecular Biology Division, Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, Karnataka, 575018, India
| |
Collapse
|
17
|
He L, Hu Z, Sun Y, Zhang M, Zhu H, Jiang L, Zhang Q, Mu D, Zhang J, Gu L, Yang Y, Pan FY, Jia S, Guo Z. PRMT1 is critical to FEN1 expression and drug resistance in lung cancer cells. DNA Repair (Amst) 2020; 95:102953. [PMID: 32861926 DOI: 10.1016/j.dnarep.2020.102953] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/30/2020] [Accepted: 08/12/2020] [Indexed: 12/18/2022]
Abstract
The up-regulation of PRMT1 is critical to the cell growth and cancer progression of lung cancer cells. In our research, we found that PRMT1 is important to the DNA repair ability and drug resistance of lung cancer cells. To demonstrate the functions of PRMT1, we identified Flap endonuclease 1 (FEN1) as a post-translationally modified downstream target protein of PRMT1. As a major component of Base Excision Repair pathway, FEN1 plays an important role in DNA replication and DNA damage repair. However, the detailed mechanism of FEN1 up-regulation in lung cancer cells remains unclear. In our study, we identified PRMT1 as a key factor that maintains the high expression levels of FEN1, which is critical to the DNA repair ability and the chemotherapeutic drug resistance of lung cancer cells.
Collapse
Affiliation(s)
- Lingfeng He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Zhigang Hu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Yuling Sun
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Miaomiao Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Hongqiao Zhu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Longwei Jiang
- Jinlin Hospital of Nanjing University, Nanjing, 210002, China
| | - Qi Zhang
- Department of Infectious Diseases, Nanjing Liuhe District People's Hospital Affiliated to Yangzhou University, Nanjing, 210012, China
| | - Dan Mu
- Affiliated Drum Tower Hospital, Nanjing University School of Medicine, 210008, Nanjing, China
| | - Jing Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Lili Gu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Yang Yang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Fei-Yan Pan
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China.
| | - Shaochang Jia
- Jinlin Hospital of Nanjing University, Nanjing, 210002, China.
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China.
| |
Collapse
|
18
|
Dutto I, Scalera C, Tillhon M, Ticli G, Passaniti G, Cazzalini O, Savio M, Stivala LA, Gervasini C, Larizza L, Prosperi E. Mutations in CREBBP and EP300 genes affect DNA repair of oxidative damage in Rubinstein-Taybi syndrome cells. Carcinogenesis 2020; 41:257-266. [PMID: 31504229 DOI: 10.1093/carcin/bgz149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 07/11/2019] [Accepted: 08/27/2019] [Indexed: 12/27/2022] Open
Abstract
Rubinstein-Taybi syndrome (RSTS) is an autosomal-dominant disorder characterized by intellectual disability, skeletal abnormalities, growth deficiency and an increased risk of tumors. RSTS is predominantly caused by mutations in CREBBP or EP300 genes encoding for CBP and p300 proteins, two lysine acetyl-transferases (KAT) playing a key role in transcription, cell proliferation and DNA repair. However, the efficiency of these processes in RSTS cells is still largely unknown. Here, we have investigated whether pathways involved in the maintenance of genome stability are affected in lymphoblastoid cell lines (LCLs) obtained from RSTS patients with mutations in CREBBP or in EP300 genes. We report that RSTS LCLs with mutations affecting CBP or p300 protein levels or KAT activity, are more sensitive to oxidative DNA damage and exhibit defective base excision repair (BER). We have found reduced OGG1 DNA glycosylase activity in RSTS compared to control cell extracts, and concomitant lower OGG1 acetylation levels, thereby impairing the initiation of the BER process. In addition, we report reduced acetylation of other BER factors, such as DNA polymerase β and Proliferating Cell Nuclear Antigen (PCNA), together with acetylation of histone H3. We also show that complementation of CBP or p300 partially reversed RSTS cell sensitivity to DNA damage. These results disclose a mechanism of defective DNA repair as a source of genome instability in RSTS cells.
Collapse
Affiliation(s)
- Ilaria Dutto
- Istituto di Genetica Molecolare, Unità Stabilità del Genoma CNR, Via Abbiategrasso, Pavia, Italy
| | - Claudia Scalera
- Istituto di Genetica Molecolare, Unità Stabilità del Genoma CNR, Via Abbiategrasso, Pavia, Italy
| | - Micol Tillhon
- Istituto di Genetica Molecolare, Unità Stabilità del Genoma CNR, Via Abbiategrasso, Pavia, Italy
| | - Giulio Ticli
- Istituto di Genetica Molecolare, Unità Stabilità del Genoma CNR, Via Abbiategrasso, Pavia, Italy.,Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata, Pavia, Italy
| | - Gianluca Passaniti
- Istituto di Genetica Molecolare, Unità Stabilità del Genoma CNR, Via Abbiategrasso, Pavia, Italy
| | - Ornella Cazzalini
- Dipartimento di Medicina Molecolare, Unità di Immunologia e Patologia Generale, Università di Pavia, Via Ferrata, Pavia, Italy
| | - Monica Savio
- Dipartimento di Medicina Molecolare, Unità di Immunologia e Patologia Generale, Università di Pavia, Via Ferrata, Pavia, Italy
| | - Lucia A Stivala
- Dipartimento di Medicina Molecolare, Unità di Immunologia e Patologia Generale, Università di Pavia, Via Ferrata, Pavia, Italy
| | - Cristina Gervasini
- Dipartimento di Scienze della Salute, Genetica Medica, Università degli Studi di Milano, Via A. di Rudinì, Milano, Italy
| | - Lidia Larizza
- Laboratorio di Citogenetica Medica e Genetica Molecolare, Centro di Ricerche e Tecnologie Biomediche, Istituto Auxologico Italiano, Via Ariosto, Milano, Italy
| | - Ennio Prosperi
- Istituto di Genetica Molecolare, Unità Stabilità del Genoma CNR, Via Abbiategrasso, Pavia, Italy
| |
Collapse
|
19
|
Abstract
Nε-lysine acetylation was discovered more than half a century ago as a post-translational modification of histones and has been extensively studied in the context of transcription regulation. In the past decade, proteomic analyses have revealed that non-histone proteins are frequently acetylated and constitute a major portion of the acetylome in mammalian cells. Indeed, non-histone protein acetylation is involved in key cellular processes relevant to physiology and disease, such as gene transcription, DNA damage repair, cell division, signal transduction, protein folding, autophagy and metabolism. Acetylation affects protein functions through diverse mechanisms, including by regulating protein stability, enzymatic activity, subcellular localization and crosstalk with other post-translational modifications and by controlling protein-protein and protein-DNA interactions. In this Review, we discuss recent progress in our understanding of the scope, functional diversity and mechanisms of non-histone protein acetylation.
Collapse
|
20
|
Xu X, Shi R, Zheng L, Guo Z, Wang L, Zhou M, Zhao Y, Tian B, Truong K, Chen Y, Shen B, Hua Y, Xu H. SUMO-1 modification of FEN1 facilitates its interaction with Rad9-Rad1-Hus1 to counteract DNA replication stress. J Mol Cell Biol 2019; 10:460-474. [PMID: 30184152 PMCID: PMC6231531 DOI: 10.1093/jmcb/mjy047] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 09/03/2018] [Indexed: 01/25/2023] Open
Abstract
Human flap endonuclease 1 (FEN1) is a structure-specific, multi-functional endonuclease essential for DNA replication and repair. We and others have shown that during DNA replication, FEN1 processes Okazaki fragments via its interaction with the proliferating cell nuclear antigen (PCNA). Alternatively, in response to DNA damage, FEN1 interacts with the PCNA-like Rad9–Rad1–Hus1 complex instead of PCNA to engage in DNA repair activities, such as homology-directed repair of stalled DNA replication forks. However, it is unclear how FEN1 is able to switch between these interactions and its roles in DNA replication and DNA repair. Here, we report that FEN1 undergoes SUMOylation by SUMO-1 in response to DNA replication fork-stalling agents, such as UV irradiation, hydroxyurea, and mitomycin C. This DNA damage-induced SUMO-1 modification promotes the interaction of FEN1 with the Rad9–Rad1–Hus1 complex. Furthermore, we found that FEN1 mutations that prevent its SUMO-1 modification also impair its ability to interact with HUS1 and to rescue stalled replication forks. These impairments lead to the accumulation of DNA damage and heightened sensitivity to fork-stalling agents. Altogether, our findings suggest an important role of the SUMO-1 modification of FEN1 in regulating its roles in DNA replication and repair.
Collapse
Affiliation(s)
- Xiaoli Xu
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Rongyi Shi
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology and College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Liangyan Wang
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Mian Zhou
- Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Ye Zhao
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Bing Tian
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Khue Truong
- Department of Molecular Medicine, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Yuan Chen
- Department of Molecular Medicine, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Yuejin Hua
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Hong Xu
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| |
Collapse
|
21
|
Zaher MS, Rashid F, Song B, Joudeh LI, Sobhy MA, Tehseen M, Hingorani MM, Hamdan SM. Missed cleavage opportunities by FEN1 lead to Okazaki fragment maturation via the long-flap pathway. Nucleic Acids Res 2019; 46:2956-2974. [PMID: 29420814 PMCID: PMC5888579 DOI: 10.1093/nar/gky082] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 01/27/2018] [Indexed: 12/11/2022] Open
Abstract
RNA–DNA hybrid primers synthesized by low fidelity DNA polymerase α to initiate eukaryotic lagging strand synthesis must be removed efficiently during Okazaki fragment (OF) maturation to complete DNA replication. In this process, each OF primer is displaced and the resulting 5′-single-stranded flap is cleaved by structure-specific 5′-nucleases, mainly Flap Endonuclease 1 (FEN1), to generate a ligatable nick. At least two models have been proposed to describe primer removal, namely short- and long-flap pathways that involve FEN1 or FEN1 along with Replication Protein A (RPA) and Dna2 helicase/nuclease, respectively. We addressed the question of pathway choice by studying the kinetic mechanism of FEN1 action on short- and long-flap DNA substrates. Using single molecule FRET and rapid quench-flow bulk cleavage assays, we showed that unlike short-flap substrates, which are bound, bent and cleaved within the first encounter between FEN1 and DNA, long-flap substrates can escape cleavage even after DNA binding and bending. Notably, FEN1 can access both substrates in the presence of RPA, but bending and cleavage of long-flap DNA is specifically inhibited. We propose that FEN1 attempts to process both short and long flaps, but occasional missed cleavage of the latter allows RPA binding and triggers the long-flap OF maturation pathway.
Collapse
Affiliation(s)
- Manal S Zaher
- King Abdullah University of Science and Technology, Division of Biological and Environmental Science and Engineering, Thuwal 23955, Saudi Arabia
| | - Fahad Rashid
- King Abdullah University of Science and Technology, Division of Biological and Environmental Science and Engineering, Thuwal 23955, Saudi Arabia
| | - Bo Song
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Luay I Joudeh
- King Abdullah University of Science and Technology, Division of Biological and Environmental Science and Engineering, Thuwal 23955, Saudi Arabia
| | - Mohamed A Sobhy
- King Abdullah University of Science and Technology, Division of Biological and Environmental Science and Engineering, Thuwal 23955, Saudi Arabia
| | - Muhammad Tehseen
- King Abdullah University of Science and Technology, Division of Biological and Environmental Science and Engineering, Thuwal 23955, Saudi Arabia
| | - Manju M Hingorani
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Samir M Hamdan
- King Abdullah University of Science and Technology, Division of Biological and Environmental Science and Engineering, Thuwal 23955, Saudi Arabia
| |
Collapse
|
22
|
Bao J, Rousseaux S, Shen J, Lin K, Lu Y, Bedford MT. The arginine methyltransferase CARM1 represses p300•ACT•CREMτ activity and is required for spermiogenesis. Nucleic Acids Res 2019; 46:4327-4343. [PMID: 29659998 PMCID: PMC5961101 DOI: 10.1093/nar/gky240] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 03/26/2018] [Indexed: 01/04/2023] Open
Abstract
CARM1 is a protein arginine methyltransferase (PRMT) that has been firmly implicated in transcriptional regulation. However, the molecular mechanisms by which CARM1 orchestrates transcriptional regulation are not fully understood, especially in a tissue-specific context. We found that Carm1 is highly expressed in the mouse testis and localizes to the nucleus in spermatids, suggesting an important role for Carm1 in spermiogenesis. Using a germline-specific conditional Carm1 knockout mouse model, we found that it is essential for the late stages of haploid germ cell development. Loss of Carm1 led to a low sperm count and deformed sperm heads that can be attributed to defective elongation of round spermatids. RNA-seq analysis of Carm1-null spermatids revealed that the deregulated genes fell into similar categories as those impacted by p300-loss, thus providing a link between Carm1 and p300. Importantly, p300 has long been known to be a major Carm1 substrate. We found that CREMτ, a key testis-specific transcription factor, associates with p300 through its activator, ACT, and that this interaction is negatively regulated by the methylation of p300 by Carm1. Thus, high nuclear Carm1 levels negatively impact the p300•ACT•CREMτ axis during late stages of spermiogenesis.
Collapse
Affiliation(s)
- Jianqiang Bao
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Sophie Rousseaux
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, La Tronche, France
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| |
Collapse
|
23
|
Xu H, Shi R, Han W, Cheng J, Xu X, Cheng K, Wang L, Tian B, Zheng L, Shen B, Hua Y, Zhao Y. Structural basis of 5' flap recognition and protein-protein interactions of human flap endonuclease 1. Nucleic Acids Res 2019; 46:11315-11325. [PMID: 30295841 PMCID: PMC6265464 DOI: 10.1093/nar/gky911] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 10/06/2018] [Indexed: 01/30/2023] Open
Abstract
Human flap endonuclease 1 (hFEN1) is a structure-specific nuclease essential for DNA replication and repair processes. hFEN1 has 5′ flap removal activity, as well as gap endonuclease activity that is critical for restarting stalled replication forks. Here, we report the crystal structures of wild-type and mutant hFEN1 proteins in complex with DNA substrates, followed by mutagenesis studies that provide mechanistic insight into the protein–protein interactions of hFEN1. We found that in an α-helix forming the helical gateway of hFEN1 recognizes the 5′ flap prior to its threading into the active site for cleavage. We also found that the β-pin region is rigidified into a short helix in R192F hFEN1–DNA structures, suppressing its gap endonuclease activity and cycle-dependent kinase interactions. Our findings suggest that a single mutation at the primary methylation site can alter the function of hFEN1 and provide insight into the role of the β-pin region in hFEN1 protein interactions that are essential for DNA replication and repair.
Collapse
Affiliation(s)
- Hong Xu
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Rongyi Shi
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Wanchun Han
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Jiahui Cheng
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Xiaoli Xu
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Kaiying Cheng
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Liangyan Wang
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Bing Tian
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA 91010, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA 91010, USA
| | - Yuejin Hua
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Ye Zhao
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, Zhejiang 310029, China
| |
Collapse
|
24
|
Ononye OE, Njeri CW, Balakrishnan L. Analysis of DNA Processing Enzyme FEN1 and Its Regulation by Protein Lysine Acetylation. Methods Mol Biol 2019; 1983:207-224. [PMID: 31087300 DOI: 10.1007/978-1-4939-9434-2_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cellular proteins are modified by lysine acetylation wherein an acetyltransferase transfers an acetyl group from acetyl co enzyme A onto the e-amino group of lysine residues. This modification is extremely dynamic and can be reversed by a deacetylase that removes the acetyl group. Addition of acetyl group to the lysine residue neutralizes its positive charge, thereby functioning as a molecular switch in regulating the enzymatic functions of the protein, its stability, and it cellular localization. Since this modification is extremely dynamic within the cell, biochemical studies characterizing changes in protein function are imperative to understand how this modification alters protein function in a specific cellular pathway. This unit describes in detail expression and purification of a recombinant nuclease and acetyltransferase, in vitro acetylation of the recombinant protein and biochemical assays to study the changes in enzymatic activity of the in vitro acetylated nuclease.
Collapse
Affiliation(s)
- Onyekachi E Ononye
- Department of Biology, School of Science, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA
| | - Catherine W Njeri
- Department of Biology, School of Science, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA
| | - Lata Balakrishnan
- Department of Biology, School of Science, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA.
| |
Collapse
|
25
|
Maneuvers on PCNA Rings during DNA Replication and Repair. Genes (Basel) 2018; 9:genes9080416. [PMID: 30126151 PMCID: PMC6116012 DOI: 10.3390/genes9080416] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/08/2018] [Accepted: 08/09/2018] [Indexed: 12/20/2022] Open
Abstract
DNA replication and repair are essential cellular processes that ensure genome duplication and safeguard the genome from deleterious mutations. Both processes utilize an abundance of enzymatic functions that need to be tightly regulated to ensure dynamic exchange of DNA replication and repair factors. Proliferating cell nuclear antigen (PCNA) is the major coordinator of faithful and processive replication and DNA repair at replication forks. Post-translational modifications of PCNA, ubiquitination and acetylation in particular, regulate the dynamics of PCNA-protein interactions. Proliferating cell nuclear antigen (PCNA) monoubiquitination elicits ‘polymerase switching’, whereby stalled replicative polymerase is replaced with a specialized polymerase, while PCNA acetylation may reduce the processivity of replicative polymerases to promote homologous recombination-dependent repair. While regulatory functions of PCNA ubiquitination and acetylation have been well established, the regulation of PCNA-binding proteins remains underexplored. Considering the vast number of PCNA-binding proteins, many of which have similar PCNA binding affinities, the question arises as to the regulation of the strength and sequence of their binding to PCNA. Here I provide an overview of post-translational modifications on both PCNA and PCNA-interacting proteins and discuss their relevance for the regulation of the dynamic processes of DNA replication and repair.
Collapse
|
26
|
Narasumani M, Harrison PM. Discerning evolutionary trends in post-translational modification and the effect of intrinsic disorder: Analysis of methylation, acetylation and ubiquitination sites in human proteins. PLoS Comput Biol 2018; 14:e1006349. [PMID: 30096183 PMCID: PMC6105011 DOI: 10.1371/journal.pcbi.1006349] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 08/22/2018] [Accepted: 07/07/2018] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered regions (IDRs) of proteins play significant biological functional roles despite lacking a well-defined 3D structure. For example, IDRs provide efficient housing for large numbers of post-translational modification (PTM) sites in eukaryotic proteins. Here, we study the distribution of more than 15,000 experimentally determined human methylation, acetylation and ubiquitination sites (collectively termed 'MAU' sites) in ordered and disordered regions, and analyse their conservation across 380 eukaryotic species. Conservation signals for the maintenance and novel emergence of MAU sites are examined at 11 evolutionary levels from the whole eukaryotic domain down to the ape superfamily, in both ordered and disordered regions. We discover that MAU PTM is a major driver of conservation for arginines and lysines in both ordered and disordered regions, across the 11 levels, most significantly across the mammalian clade. Conservation of human methylatable arginines is very strongly favoured for ordered regions rather than for disordered, whereas methylatable lysines are conserved in either set of regions, and conservation of acetylatable and ubiquitinatable lysines is favoured in disordered over ordered. Notably, we find evidence for the emergence of new lysine MAU sites in disordered regions of proteins in deuterostomes and mammals, and in ordered regions after the dawn of eutherians. For histones specifically, MAU sites demonstrate an idiosyncratic significant conservation pattern that is evident since the last common ancestor of mammals. Similarly, folding-on-binding (FB) regions are highly enriched for MAU sites relative to either ordered or disordered regions, with ubiquitination sites in FBs being highly conserved at all evolutionary levels back as far as mammals. This investigation clearly demonstrates the complex patterns of PTM evolution across the human proteome and that it is necessary to consider conservation of sequence features at multiple evolutionary levels in order not to get an incomplete or misleading picture.
Collapse
|
27
|
Sengupta S, Yang C, Hegde ML, Hegde PM, Mitra J, Pandey A, Dutta A, Datarwala AT, Bhakat KK, Mitra S. Acetylation of oxidized base repair-initiating NEIL1 DNA glycosylase required for chromatin-bound repair complex formation in the human genome increases cellular resistance to oxidative stress. DNA Repair (Amst) 2018; 66-67:1-10. [PMID: 29698889 DOI: 10.1016/j.dnarep.2018.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 04/10/2018] [Indexed: 12/25/2022]
Abstract
Posttranslational modifications of DNA repair proteins have been linked to their function. However, it is not clear if posttranslational acetylation affects subcellular localization of these enzymes. Here, we show that the human DNA glycosylase NEIL1, which is involved in repair of both endo- and exogenously generated oxidized bases via the base excision repair (BER) pathway, is acetylated by histone acetyltransferase p300. Acetylation occurs predominantly at Lys residues 296, 297 and 298 located in NEIL1's disordered C-terminal domain. NEIL1 mutant having the substitution of Lys 296-298 with neutral Ala loses nuclear localization, whereas Lys > Arg substitution (in 3KR mutant) at the same sites does not affect NEIL1's nuclear localization or chromatin binding, presumably due to retention of the positive charge. Although non-acetylated NEIL1 can bind to chromatin, acetylated NEIL1 is exclusively chromatin-bound. NEIL1 acetylation while dispensable for its glycosylase activity enhances it due to increased product release. The acetylation-defective 3KR mutant forms less stable complexes with various chromatin proteins, including histone chaperones and BER/single-strand break repair partners, than the wild-type (WT) NEIL1. We also showed that the repair complex with WT NEIL1 has significantly higher BER activity than the 3KR mutant complex. This is consistent with reduced resistance of non-acetylable mutant NEIL1 expressing cells to oxidative stress relative to cells expressing the acetylable WT enzyme. We thus conclude that the major role of acetylable Lys residues in NEIL1 is to stabilize the formation of chromatin-bound repair complexes which protect cells from oxidative stress.
Collapse
Affiliation(s)
- Shiladitya Sengupta
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA; Weill Cornell Medical College, Cornell University, New York, NY 10065, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Chunying Yang
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Muralidhar L Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA; Weill Cornell Medical College, Cornell University, New York, NY 10065, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Houston Methodist Neurological Institute, Houston, TX 77030, USA
| | - Pavana M Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Joy Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Arvind Pandey
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Arijit Dutta
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Pediatrics, Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Abdul Tayyeb Datarwala
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Biomedical Engineering, University of Houston, Houston, TX 77004, USA
| | - Kishor K Bhakat
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Genetics, Cell Biology and Anatomy, Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Sankar Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA; Weill Cornell Medical College, Cornell University, New York, NY 10065, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| |
Collapse
|
28
|
Deshmukh AL, Chandra S, Singh DK, Siddiqi MI, Banerjee D. Identification of human flap endonuclease 1 (FEN1) inhibitors using a machine learning based consensus virtual screening. MOLECULAR BIOSYSTEMS 2018; 13:1630-1639. [PMID: 28685785 DOI: 10.1039/c7mb00118e] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Human Flap endonuclease1 (FEN1) is an enzyme that is indispensable for DNA replication and repair processes and inhibition of its Flap cleavage activity results in increased cellular sensitivity to DNA damaging agents (cisplatin, temozolomide, MMS, etc.), with the potential to improve cancer prognosis. Reports of the high expression levels of FEN1 in several cancer cells support the idea that FEN1 inhibitors may target cancer cells with minimum side effects to normal cells. In this study, we used large publicly available, high-throughput screening data of small molecule compounds targeted against FEN1. Two machine learning algorithms, Support Vector Machine (SVM) and Random Forest (RF), were utilized to generate four classification models from huge PubChem bioassay data containing probable FEN1 inhibitors and non-inhibitors. We also investigated the influence of randomly selected Zinc-database compounds as negative data on the outcome of classification modelling. The results show that the SVM model with inactive compounds was superior to RF with Matthews's correlation coefficient (MCC) of 0.67 for the test set. A Maybridge database containing approximately 53 000 compounds was screened and top ranking 5 compounds were selected for enzyme and cell-based in vitro screening. The compound JFD00950 was identified as a novel FEN1 inhibitor with in vitro inhibition of flap cleavage activity as well as cytotoxic activity against a colon cancer cell line, DLD-1.
Collapse
Affiliation(s)
- Amit Laxmikant Deshmukh
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Janakipuram Extension, Sitapur Road, Lucknow, 226031, India.
| | - Sharat Chandra
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Janakipuram Extension, Sitapur Road, Lucknow, 226031, India. and AcSIR (Academy of Scientific and Innovative Research), India
| | - Deependra Kumar Singh
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Janakipuram Extension, Sitapur Road, Lucknow, 226031, India.
| | - Mohammad Imran Siddiqi
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Janakipuram Extension, Sitapur Road, Lucknow, 226031, India. and AcSIR (Academy of Scientific and Innovative Research), India
| | - Dibyendu Banerjee
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Janakipuram Extension, Sitapur Road, Lucknow, 226031, India. and AcSIR (Academy of Scientific and Innovative Research), India
| |
Collapse
|
29
|
Dutto I, Scalera C, Prosperi E. CREBBP and p300 lysine acetyl transferases in the DNA damage response. Cell Mol Life Sci 2018; 75:1325-1338. [PMID: 29170789 PMCID: PMC11105205 DOI: 10.1007/s00018-017-2717-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 11/16/2017] [Accepted: 11/20/2017] [Indexed: 12/21/2022]
Abstract
The CREB-binding protein (CREBBP, or in short CBP) and p300 are lysine (K) acetyl transferases (KAT) belonging to the KAT3 family of proteins known to modify histones, as well as non-histone proteins, thereby regulating chromatin accessibility and transcription. Previous studies have indicated a tumor suppressor function for these enzymes. Recently, they have been found to acetylate key factors involved in DNA replication, and in different DNA repair processes, such as base excision repair, nucleotide excision repair, and non-homologous end joining. The growing list of CBP/p300 substrates now includes factors involved in DNA damage signaling, and in other pathways of the DNA damage response (DDR). This review will focus on the role of CBP and p300 in the acetylation of DDR proteins, and will discuss how this post-translational modification influences their functions at different levels, including catalytic activity, DNA binding, nuclear localization, and protein turnover. In addition, we will exemplify how these functions may be necessary to efficiently coordinate the spatio-temporal response to DNA damage. CBP and p300 may contribute to genome stability by fine-tuning the functions of DNA damage signaling and DNA repair factors, thereby expanding their role as tumor suppressors.
Collapse
Affiliation(s)
- Ilaria Dutto
- Istituto di Genetica Molecolare del CNR, Via Abbiategrasso 207, 27100, Pavia, Italy
- IRB, Carrer Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Claudia Scalera
- Istituto di Genetica Molecolare del CNR, Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Ennio Prosperi
- Istituto di Genetica Molecolare del CNR, Via Abbiategrasso 207, 27100, Pavia, Italy.
| |
Collapse
|
30
|
Ding D, Chen LL, Zhai YZ, Hou CJ, Tao LL, Lu SH, Wu J, Liu XP. Trichostatin A inhibits the activation of Hepatic stellate cells by Increasing C/EBP-α Acetylation in vivo and in vitro. Sci Rep 2018. [PMID: 29535398 PMCID: PMC5849734 DOI: 10.1038/s41598-018-22662-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Reversal of activated hepatic stellate cells (HSCs) to a quiescent state and apoptosis of activated HSCs are key elements in the reversion of hepatic fibrosis. CCAAT/enhancer binding protein α (C/EBP-α) has been shown to inhibit HSC activation and promote its apoptosis. This study aims to investigate how C/EBP-α acetylation affects the fate of activated HSCs. Effects of a histone deacetylation inhibitor trichostatin A (TSA) on HSC activation were evaluated in a mouse model of liver fibrosis caused by carbon tetrachloride (CCl4) intoxication. TSA was found to ameliorate CCl4-induced hepatic fibrosis and improve liver function through increasing the protein level and enhancing C/EBP-α acetylation in the mouse liver. C/EBP-α acetylation was determined in HSC lines in the presence or absence of TSA, and the lysine residue K276 was identified as a main acetylation site in C/EBP-α protein. C/EBP-α acetylation increased its stability and protein level, and inhibited HSC activation. The present study demonstrated that C/EBP-α acetylation increases the protein level by inhibiting its ubiquitination-mediated degradation, and may be involved in the fate of activated HSCs. Use of TSA may confer an option in minimizing hepatic fibrosis by suppressing HSC activation, a key process in the initiation and progression of hepatic fibrosis.
Collapse
Affiliation(s)
- Di Ding
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Lin-Lin Chen
- Department of Pathology, The Fifth People's Hospital, Fudan University, Shanghai, 200040, China
| | - Ying-Zhen Zhai
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Chen-Jian Hou
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Li-Li Tao
- Department of Pathology, Peking University, Shenzhen Hospital, Shenzhen, 518036, China
| | - Shu-Han Lu
- Department of Nutrition, University of California at Davis, Davis, California, USA
| | - Jian Wu
- Department of Medical Microbiology, Key Laboratory of Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China. .,Shanghai Institute of Liver Disease, Fudan University, Shanghai, 200032, China.
| | - Xiu-Ping Liu
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China. .,Department of Pathology, The Fifth People's Hospital, Fudan University, Shanghai, 200040, China.
| |
Collapse
|
31
|
Thandapani P, Couturier AM, Yu Z, Li X, Couture JF, Li S, Masson JY, Richard S. Lysine methylation of FEN1 by SET7 is essential for its cellular response to replicative stress. Oncotarget 2017; 8:64918-64931. [PMID: 29029401 PMCID: PMC5630301 DOI: 10.18632/oncotarget.18070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 04/18/2017] [Indexed: 12/17/2022] Open
Abstract
The DNA damage response (DDR) is central to the cell survival and it requires post-translational modifications, in part, to sense the damage, amplify the signaling response and recruit and regulate DNA repair enzymes. Lysine methylation of histones such as H4K20 and non-histone proteins including p53 has been shown to be essential for the mounting of the DDR. It is well-known that the lysine methyltransferase SET7 regulates the DDR, as cells lacking this enzyme are hypersensitive to chemotherapeutic drugs. To define addition substrates of SET7 involved in the DDR, we screened a peptide array encompassing potential lysine methylation sites from >100 key DDR proteins and identified peptides from 58 proteins to be lysine methylated defining a methylation consensus sequence of [S>K-2; S>R-1; K0] consistent with previous findings. We focused on K377 methylation of the Flap endonuclease 1 (FEN1), a structure specific endonuclease with important functions in Okazaki fragment processing during DNA replication as a substrate of SET7. FEN1 was monomethylated by SET7 in vivo in a cell cycle dependent manner with levels increasing as cells progressed through S phase and decreasing as they exited S phase, as detected using K377me1 specific antibodies. Although K377me1 did not affect the enzymatic activity of FEN1, it was required for the cellular response to replicative stress by FEN1. These finding define FEN1 as a new substrate of SET7 required for the DDR.
Collapse
Affiliation(s)
- Palaniraja Thandapani
- Terry Fox Molecular Oncology Group and Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Departments of Oncology and Medicine, McGill University, Montréal, Québec, Canada
| | - Anthony M. Couturier
- Genome Stability Laboratory, Laval University Cancer Research Center, CRCHU de Québec, Québec, Canada
| | - Zhenbao Yu
- Terry Fox Molecular Oncology Group and Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Departments of Oncology and Medicine, McGill University, Montréal, Québec, Canada
| | - Xing Li
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Shawn Li
- Genome Stability Laboratory, Laval University Cancer Research Center, CRCHU de Québec, Québec, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, Laval University Cancer Research Center, CRCHU de Québec, Québec, Canada
| | - Stéphane Richard
- Terry Fox Molecular Oncology Group and Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Departments of Oncology and Medicine, McGill University, Montréal, Québec, Canada
| |
Collapse
|
32
|
Pawłowska E, Szczepanska J, Blasiak J. DNA2-An Important Player in DNA Damage Response or Just Another DNA Maintenance Protein? Int J Mol Sci 2017; 18:ijms18071562. [PMID: 28718810 PMCID: PMC5536050 DOI: 10.3390/ijms18071562] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 07/13/2017] [Accepted: 07/17/2017] [Indexed: 02/01/2023] Open
Abstract
The human DNA2 (DNA replication helicase/nuclease 2) protein is expressed in both the nucleus and mitochondria, where it displays ATPase-dependent nuclease and helicase activities. DNA2 plays an important role in the removing of long flaps in DNA replication and long-patch base excision repair (LP-BER), interacting with the replication protein A (RPA) and the flap endonuclease 1 (FEN1). DNA2 can promote the restart of arrested replication fork along with Werner syndrome ATP-dependent helicase (WRN) and Bloom syndrome protein (BLM). In mitochondria, DNA2 can facilitate primer removal during strand-displacement replication. DNA2 is involved in DNA double strand (DSB) repair, in which it is complexed with BLM, RPA and MRN for DNA strand resection required for homologous recombination repair. DNA2 can be a major protein involved in the repair of complex DNA damage containing a DSB and a 5' adduct resulting from a chemical group bound to DNA 5' ends, created by ionizing radiation and several anticancer drugs, including etoposide, mitoxantrone and some anthracyclines. The role of DNA2 in telomere end maintenance and cell cycle regulation suggests its more general role in keeping genomic stability, which is impaired in cancer. Therefore DNA2 can be an attractive target in cancer therapy. This is supported by enhanced expression of DNA2 in many cancer cell lines with oncogene activation and premalignant cells. Therefore, DNA2 can be considered as a potential marker, useful in cancer therapy. DNA2, along with PARP1 inhibition, may be considered as a potential target for inducing synthetic lethality, a concept of killing tumor cells by targeting two essential genes.
Collapse
Affiliation(s)
- Elzbieta Pawłowska
- Department of Orthodontics, Medical University of Lodz, 92-216 Lodz, Poland.
| | - Joanna Szczepanska
- Department of Pediatric Dentistry, Medical University of Lodz, 92-216 Lodz, Poland.
| | - Janusz Blasiak
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland.
| |
Collapse
|
33
|
Han Z, Chou CW, Yang X, Bartlett MG, Zheng YG. Profiling Cellular Substrates of Lysine Acetyltransferases GCN5 and p300 with Orthogonal Labeling and Click Chemistry. ACS Chem Biol 2017; 12:1547-1555. [PMID: 28426192 DOI: 10.1021/acschembio.7b00114] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
p300 and GCN5 are two representative lysine acetyltransferases (KATs) in mammalian cells. It was recently reported that they possess multiple acyltransferase activities including acetylation, propionylation, and butyrylation of the ε-amino group of lysine residues of histones and non-histone protein substrates. Although thousands of acetylated substrates and acetylation sites have been identified by mass spectrometry-based proteomic screening, our knowledge about the causative connections between individual KAT members and their corresponding sub-acylomes remain very limited. Herein, we applied 3-azidopropionyl CoA (3AZ-CoA) as a bioorthogonal surrogate of acetyl-, propionyl- and butyryl-CoA for KAT substrate identification. We successfully attached the azide as a chemical warhead to cellular substrates of wild-type p300 and engineered GCN5. The substrates were subsequently labeled with biotin tag through the copper-catalyzed azide-alkyne cycloaddition (CuAAC). Following protein enrichment on streptavidin-coated resin, we conducted LC-MS/MS studies from which more than four hundred proteins were identified as GCN5 or p300 substrate candidates. These proteins are either p300- or GCN5-unique or shared by the two KATs and are extensively involved in various biological events including gene expression, cell cycle, and cellular metabolism. We also experimentally validated two novel substrates of GCN5, that is, IQGAP1 and SMC1. These results demonstrate extensive engagement of GCN5 and p300 in cellular pathways and provide new insights into understanding their functions in specific biological processes.
Collapse
Affiliation(s)
- Zhen Han
- Department of Pharmaceutical
and Biomedical Sciences and Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Chau-wen Chou
- Department of Pharmaceutical
and Biomedical Sciences and Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Xiangkun Yang
- Department of Pharmaceutical
and Biomedical Sciences and Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Michael G. Bartlett
- Department of Pharmaceutical
and Biomedical Sciences and Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Y. George Zheng
- Department of Pharmaceutical
and Biomedical Sciences and Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| |
Collapse
|
34
|
Limpose KL, Corbett AH, Doetsch PW. BERing the burden of damage: Pathway crosstalk and posttranslational modification of base excision repair proteins regulate DNA damage management. DNA Repair (Amst) 2017. [PMID: 28629773 DOI: 10.1016/j.dnarep.2017.06.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
DNA base damage and non-coding apurinic/apyrimidinic (AP) sites are ubiquitous types of damage that must be efficiently repaired to prevent mutations. These damages can occur in both the nuclear and mitochondrial genomes. Base excision repair (BER) is the frontline pathway for identifying and excising damaged DNA bases in both of these cellular compartments. Recent advances demonstrate that BER does not operate as an isolated pathway but rather dynamically interacts with components of other DNA repair pathways to modulate and coordinate BER functions. We define the coordination and interaction between DNA repair pathways as pathway crosstalk. Numerous BER proteins are modified and regulated by post-translational modifications (PTMs), and PTMs could influence pathway crosstalk. Here, we present recent advances on BER/DNA repair pathway crosstalk describing specific examples and also highlight regulation of BER components through PTMs. We have organized and reported functional interactions and documented PTMs for BER proteins into a consolidated summary table. We further propose the concept of DNA repair hubs that coordinate DNA repair pathway crosstalk to identify central protein targets that could play a role in designing future drug targets.
Collapse
Affiliation(s)
- Kristin L Limpose
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA, 30322, United States
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA, 30322, United States; Winship Cancer Institute, Emory University, Atlanta, GA 30322, United States.
| | - Paul W Doetsch
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA, 30322, United States; Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, 30322, United States; Winship Cancer Institute, Emory University, Atlanta, GA 30322, United States; Department of Biochemistry, Emory University, Atlanta, GA, 30322, United States.
| |
Collapse
|
35
|
Kathera C, Zhang J, Janardhan A, Sun H, Ali W, Zhou X, He L, Guo Z. Interacting partners of FEN1 and its role in the development of anticancer therapeutics. Oncotarget 2017; 8:27593-27602. [PMID: 28187440 PMCID: PMC5432360 DOI: 10.18632/oncotarget.15176] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/24/2017] [Indexed: 11/25/2022] Open
Abstract
Protein-protein interaction (PPI) plays a key role in cellular communication, Protein-protein interaction connected with each other with hubs and nods involved in signaling pathways. These interactions used to develop network based biomarkers for early diagnosis of cancer. FEN1(Flap endonuclease 1) is a central component in cellular metabolism, over expression and decrease of FEN1 levels may cause cancer, these regulation changes of Flap endonuclease 1reported in many cancer cells, to consider this data may needs to develop a network based biomarker. The current review focused on types of PPI, based on nature, detection methods and its role in cancer. Interacting partners of Flap endonuclease 1 role in DNA replication repair and development of anticancer therapeutics based on Protein-protein interaction data.
Collapse
Affiliation(s)
- Chandrasekhar Kathera
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jing Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Avilala Janardhan
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Hongfang Sun
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wajid Ali
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaolong Zhou
- The Laboratory of Animal Genetics, Breeding, and Reproduction, College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Lingfeng He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| |
Collapse
|
36
|
Dehé PM, Gaillard PHL. Control of structure-specific endonucleases to maintain genome stability. Nat Rev Mol Cell Biol 2017; 18:315-330. [PMID: 28327556 DOI: 10.1038/nrm.2016.177] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Structure-specific endonucleases (SSEs) have key roles in DNA replication, recombination and repair, and emerging roles in transcription. These enzymes have specificity for DNA secondary structure rather than for sequence, and therefore their activity must be precisely controlled to ensure genome stability. In this Review, we discuss how SSEs are controlled as part of genome maintenance pathways in eukaryotes, with an emphasis on the elaborate mechanisms that regulate the members of the major SSE families - including the xeroderma pigmentosum group F-complementing protein (XPF) and MMS and UV-sensitive protein 81 (MUS81)-dependent nucleases, and the flap endonuclease 1 (FEN1), XPG and XPG-like endonuclease 1 (GEN1) enzymes - during processes such as DNA adduct repair, Holliday junction processing and replication stress. We also discuss newly characterized connections between SSEs and other classes of DNA-remodelling enzymes and cell cycle control machineries, which reveal the importance of SSE scaffolds such as the synthetic lethal of unknown function 4 (SLX4) tumour suppressor for the maintenance of genome stability.
Collapse
Affiliation(s)
- Pierre-Marie Dehé
- Centre de Recherche en Cancérologie de Marseille, CRCM, CNRS, Aix Marseille Université, INSERM, Institut Paoli-Calmettes, 27 Boulevard Leï Roure, 13009 Marseille, France
| | - Pierre-Henri L Gaillard
- Centre de Recherche en Cancérologie de Marseille, CRCM, CNRS, Aix Marseille Université, INSERM, Institut Paoli-Calmettes, 27 Boulevard Leï Roure, 13009 Marseille, France
| |
Collapse
|
37
|
Sang Y, Bo L, Gu H, Yang W, Chen Y. Flap endonuclease-1 rs174538 G>A polymorphisms are associated with the risk of esophageal cancer in a Chinese population. Thorac Cancer 2017; 8:192-196. [PMID: 28319330 PMCID: PMC5415465 DOI: 10.1111/1759-7714.12422] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/01/2017] [Accepted: 01/07/2017] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Esophageal cancer has a high mortality rate, particularly in Asia, and there are obvious racial differences in regard to incidence. The purpose of our study was to assess the genetic susceptibility of functional single nucleotide polymorphisms in flap endonuclease-1 (FEN1) in esophageal squamous cell carcinoma ESCC. METHODS Clinical blood samples of 629 ESCC cases and 686 control samples were collected. The ligation detection reaction method was used to determine FEN 1 rs174538 G>A genotypes. RESULTS A significantly decreased risk of ESCC was associated with FEN1 rs174538 GA genotypes among patients under 63 years old. CONCLUSIONS Our results suggest that functional polymorphism FEN1 rs174538 G>A might affect personal susceptibility to ESCC. This result provides a solid theoretical foundation for further clinical study using larger sample sizes.
Collapse
Affiliation(s)
- Yonghua Sang
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Lin Bo
- Department of Rheumatology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Haiyong Gu
- Department of Cardiothoracic Surgery, Shanghai Chest Hospital, Shanghai, China.,Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Wengtao Yang
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yongbing Chen
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| |
Collapse
|
38
|
Attar N, Kurdistani SK. Exploitation of EP300 and CREBBP Lysine Acetyltransferases by Cancer. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026534. [PMID: 27881443 DOI: 10.1101/cshperspect.a026534] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
p300 and CREB-binding protein (CBP), two homologous lysine acetyltransferases in metazoans, have a myriad of cellular functions. They exert their influence mainly through their roles as transcriptional regulators but also via nontranscriptional effects inside and outside of the nucleus on processes such as DNA replication and metabolism. The versatility of p300/CBP as molecular tools has led to their exploitation by viral oncogenes for cellular transformation and by cancer cells to achieve and maintain an oncogenic phenotype. How cancer cells use p300/CBP in their favor varies depending on the cellular context and is evident by the growing list of loss- and gain-of-function genetic alterations in p300 and CBP in solid tumors and hematological malignancies. Here, we discuss the biological functions of p300/CBP and how disruption of these functions by mutations and alterations in expression or subcellular localization contributes to the cancer phenotype.
Collapse
Affiliation(s)
- Narsis Attar
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California 90095.,Molecular Biology Institute, David Geffen School of Medicine, University of California, Los Angeles, California 90095
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California 90095.,Molecular Biology Institute, David Geffen School of Medicine, University of California, Los Angeles, California 90095.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California 90095.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, California 90095
| |
Collapse
|
39
|
Kwon B, Munashingha PR, Shin YK, Lee CH, Li B, Seo YS. Physical and functional interactions between nucleosomes and Rad27, a critical component of DNA processing during DNA metabolism. FEBS J 2016; 283:4247-4262. [DOI: 10.1111/febs.13934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/22/2016] [Accepted: 10/17/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Buki Kwon
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology; Yuseong-gu Daejeon Korea
| | - Palinda Ruvan Munashingha
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology; Yuseong-gu Daejeon Korea
| | - Yong-Keol Shin
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology; Yuseong-gu Daejeon Korea
| | - Chul-Hwan Lee
- Department of Molecular Biology; UT Southwestern Medical Center; Dallas TX USA
| | - Bing Li
- Department of Molecular Biology; UT Southwestern Medical Center; Dallas TX USA
| | - Yeon-Soo Seo
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology; Yuseong-gu Daejeon Korea
| |
Collapse
|
40
|
Zhou L, Dai H, Wu J, Zhou M, Yuan H, Du J, Yang L, Wu X, Xu H, Hua Y, Xu J, Zheng L, Shen B. Role of FEN1 S187 phosphorylation in counteracting oxygen-induced stress and regulating postnatal heart development. FASEB J 2016; 31:132-147. [PMID: 27694478 DOI: 10.1096/fj.201600631r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 09/16/2016] [Indexed: 12/22/2022]
Abstract
Flap endonuclease 1 (FEN1) phosphorylation is proposed to regulate the action of FEN1 in DNA repair as well as Okazaki fragment maturation. However, the biologic significance of FEN1 phosphorylation in response to DNA damage remains unknown. Here, we report an in vivo role for FEN1 phosphorylation, using a mouse line carrying S187A FEN1, which abolishes FEN1 phosphorylation. Although S187A mouse embryonic fibroblast cells showed normal proliferation under low oxygen levels (2%), the mutant cells accumulated oxidative DNA damage, activated DNA damage checkpoints, and showed G1-phase arrest at atmospheric oxygen levels (21%). This suggests an essential role for FEN1 phosphorylation in repairing oxygen-induced DNA damage and maintaining proper cell cycle progression. Consistently, the mutant cardiomyocytes showed G1-phase arrest due to activation of the p53-mediated DNA damage response at the neonatal stage, which reduces the proliferation potential of the cardiomyocytes and impairs heart development. Nearly 50% of newborns with the S187A mutant died in the first week due to failure to undergo the peroxisome proliferator-activated receptor signaling-dependent switch from glycolysis to fatty acid oxidation. The adult mutant mice developed dilated hearts and showed significantly shorter life spans. Altogether, our results reveal an important role of FEN1 phosphorylation to counteract oxygen-induced stress in the heart during the fetal-to-neonatal transition.-Zhou, L., Dai, H., Wu, J., Zhou, M., Yuan, H., Du, J., Yang, L., Wu, X., Xu, H., Hua, Y., Xu, J., Zheng, L., Shen, B. Role of FEN1 S187 phosphorylation in counteracting oxygen-induced stress and regulating postnatal heart development.
Collapse
Affiliation(s)
- Lina Zhou
- College of Life Sciences and Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China.,Department of Cancer Genetics and Epigenetics and Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Huifang Dai
- Department of Cancer Genetics and Epigenetics and Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Jian Wu
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California, USA
| | - Mian Zhou
- Department of Cancer Genetics and Epigenetics and Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Hua Yuan
- Department of Diagnostic Ultrasound, Shaoxing Women and Children's Hospital, Shaoxing, China
| | - Juan Du
- Department of Cancer Genetics and Epigenetics and Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Lu Yang
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California, USA; and
| | - Xiwei Wu
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California, USA; and
| | - Hong Xu
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Yuejin Hua
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Jian Xu
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California, USA
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics and Beckman Research Institute of City of Hope, Duarte, California, USA;
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics and Beckman Research Institute of City of Hope, Duarte, California, USA;
| |
Collapse
|
41
|
Proteome-wide identification of the endogenous ADP-ribosylome of mammalian cells and tissue. Nat Commun 2016; 7:12917. [PMID: 27686526 PMCID: PMC5056437 DOI: 10.1038/ncomms12917] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 08/15/2016] [Indexed: 12/12/2022] Open
Abstract
Although protein ADP-ribosylation is involved in diverse biological processes, it has remained a challenge to identify ADP-ribose acceptor sites. Here, we present an experimental workflow for sensitive and unbiased analysis of endogenous ADP-ribosylation sites, capable of detecting more than 900 modification sites in mammalian cells and mouse liver. In cells, we demonstrate that Lys residues, besides Glu, Asp and Arg residues, are the dominant in vivo targets of ADP-ribosylation during oxidative stress. In normal liver tissue, we find Arg residues to be the predominant modification site. The cellular distribution and biological processes that involve ADP-ribosylated proteins are different in cultured cells and liver tissue, in the latter of which the majority of sites were found to be in cytosolic and mitochondrial protein networks primarily associated with metabolism. Collectively, we describe a robust methodology for the assessment of the role of ADP-ribosylation and ADP-ribosyltransferases in physiological and pathological states. ADP-ribosylation is a reversible post-translational protein modification involved in many cellular processes. Here the authors describe a sensitive approach for the analysis of ADP-ribosylation sites under physiologic conditions and identify lysine residues as in vivo targets of ADP-ribosylation.
Collapse
|
42
|
Xu H, Chen X, Xu X, Shi R, Suo S, Cheng K, Zheng Z, Wang M, Wang L, Zhao Y, Tian B, Hua Y. Lysine Acetylation and Succinylation in HeLa Cells and their Essential Roles in Response to UV-induced Stress. Sci Rep 2016; 6:30212. [PMID: 27452117 PMCID: PMC4959001 DOI: 10.1038/srep30212] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 06/29/2016] [Indexed: 12/16/2022] Open
Abstract
Lysine acetylation and succinylation are major types of protein acylation that are important in many cellular processes including gene transcription, cellular metabolism, DNA damage response. Malfunctions in these post-translational modifications are associated with genome instability and disease in higher organisms. In this study, we used high-resolution nano liquid chromatography-tandem mass spectrometry combined with affinity purification to quantify the dynamic changes of protein acetylation and succinylation in response to ultraviolet (UV)-induced cell stress. A total of 3345 acetylation sites in 1440 proteins and 567 succinylation sites in 246 proteins were identified, many of which have not been reported previously. Bioinformatics analysis revealed that these proteins are involved in many important biological processes, including cell signalling transduction, protein localization and cell metabolism. Crosstalk analysis between these two modifications indicated that modification switches might regulate protein function in response to UV-induced DNA damage. We further illustrated that FEN1 acetylation at different sites could lead to different cellular phenotypes, suggesting the multiple function involvement of FEN1 acetylation under DNA damage stress. These systematic analyses provided valuable resources and new insight into the potential role of lysine acetylation and succinylation under physiological and pathological conditions.
Collapse
Affiliation(s)
- Hong Xu
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
| | - Xuanyi Chen
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
| | - Xiaoli Xu
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
| | - Rongyi Shi
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
| | - Shasha Suo
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
| | - Kaiying Cheng
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
| | - Zhiguo Zheng
- Institute of Zhejiang Cancer Research, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Meixia Wang
- Zhejiang Institute of Microbiology, Hangzhou, 310000, China
| | - Liangyan Wang
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
| | - Ye Zhao
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
| | - Bing Tian
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
| | - Yuejin Hua
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
| |
Collapse
|
43
|
Deshmukh AL, Kumar C, Singh DK, Maurya P, Banerjee D. Dynamics of replication proteins during lagging strand synthesis: A crossroads for genomic instability and cancer. DNA Repair (Amst) 2016; 42:72-81. [DOI: 10.1016/j.dnarep.2016.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/22/2016] [Accepted: 04/22/2016] [Indexed: 01/18/2023]
|
44
|
Abstract
Base excision repair (BER) is an essential DNA repair pathway involved in the maintenance of genome stability and thus in the prevention of human diseases, such as premature aging, neurodegenerative diseases, and cancer. Protein posttranslational modifications (PTMs), including acetylation, methylation, phosphorylation, SUMOylation, and ubiquitylation, have emerged as important contributors in controlling cellular BER protein levels, enzymatic activities, protein-protein interactions, and protein cellular localization. These PTMs therefore play key roles in regulating the BER pathway and are consequently crucial for coordinating an efficient cellular DNA damage response. In this review, we summarize the presently available data on characterized PTMs of key BER proteins, the functional consequences of these modifications at the protein level, and also the impact on BER in vitro and in vivo.
Collapse
|
45
|
Piekna-Przybylska D, Bambara RA, Balakrishnan L. Acetylation regulates DNA repair mechanisms in human cells. Cell Cycle 2016; 15:1506-17. [PMID: 27104361 DOI: 10.1080/15384101.2016.1176815] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The p300-mediated acetylation of enzymes involved in DNA repair and replication has been previously shown to stimulate or inhibit their activities in reconstituted systems. To explore the role of acetylation on DNA repair in cells we constructed plasmid substrates carrying inactivating damages in the EGFP reporter gene, which should be repaired in cells through DNA mismatch repair (MMR) or base excision repair (BER) mechanisms. We analyzed efficiency of repair within these plasmid substrates in cells exposed to deacetylase and acetyltransferase inhibitors, and also in cells deficient in p300 acetyltransferase. Our results indicate that protein acetylation improves DNA mismatch repair in MMR-proficient HeLa cells and also in MMR-deficient HCT116 cells. Moreover, results suggest that stimulated repair of mismatches in MMR-deficient HCT116 cells is done though a strand-displacement synthesis mechanism described previously for Okazaki fragments maturation and also for the EXOI-independent pathway of MMR. Loss of p300 reduced repair of mismatches in MMR-deficient cells, but did not have evident effects on BER mechanisms, including the long patch BER pathway. Hypoacetylation of the cells in the presence of acetyltransferase inhibitor, garcinol generally reduced efficiency of BER of 8-oxoG damage, indicating that some steps in the pathway are stimulated by acetylation.
Collapse
Affiliation(s)
- Dorota Piekna-Przybylska
- a Department of Microbiology and Immunology , School of Medicine and Dentistry, University of Rochester , Rochester , NY , USA
| | - Robert A Bambara
- a Department of Microbiology and Immunology , School of Medicine and Dentistry, University of Rochester , Rochester , NY , USA
| | - Lata Balakrishnan
- b Department of Biology , Indiana University-Purdue University Indianapolis , Indianapolis , IN , USA
| |
Collapse
|
46
|
Cheng IC, Chen BC, Shuai HH, Chien FC, Chen P, Hsieh TS. Wuho Is a New Member in Maintaining Genome Stability through its Interaction with Flap Endonuclease 1. PLoS Biol 2016; 14:e1002349. [PMID: 26751069 PMCID: PMC4709127 DOI: 10.1371/journal.pbio.1002349] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 12/04/2015] [Indexed: 11/18/2022] Open
Abstract
Replication forks are vulnerable to wayward nuclease activities. We report here our discovery of a new member in guarding genome stability at replication forks. We previously isolated a Drosophila mutation, wuho (wh, no progeny), characterized by a severe fertility defect and affecting expression of a protein (WH) in a family of conserved proteins with multiple WD40 repeats. Knockdown of WH by siRNA in Drosophila, mouse, and human cultured cells results in DNA damage with strand breaks and apoptosis through ATM/Chk2/p53 signaling pathway. Mice with mWh knockout are early embryonic lethal and display DNA damage. We identify that the flap endonuclease 1 (FEN1) is one of the interacting proteins. Fluorescence microscopy showed the localization of WH at the site of nascent DNA synthesis along with other replication proteins, including FEN1 and PCNA. We show that WH is able to modulate FEN1's endonucleolytic activities depending on the substrate DNA structure. The stimulatory or inhibitory effects of WH on FEN1's flap versus gap endonuclease activities are consistent with the proposed WH's functions in protecting the integrity of replication fork. These results suggest that wh is a new member of the guardians of genome stability because it regulates FEN1's potential DNA cleavage threat near the site of replication.
Collapse
Affiliation(s)
- I-Cheng Cheng
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Betty Chamay Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Hung-Hsun Shuai
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Fan-Ching Chien
- Department of Optics and Photonics, National Central University, Chung-Li, Taiwan
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Tao-shih Hsieh
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.,Department of Biochemistry, Duke University, Durham, North Carolina, United States of America
| |
Collapse
|
47
|
Kang L, Zhao W, Zhang G, Wu J, Guan H. Acetylated 8-oxoguanine DNA glycosylase 1 and its relationship with p300 and SIRT1 in lens epithelium cells from age-related cataract. Exp Eye Res 2015; 135:102-8. [PMID: 25660075 DOI: 10.1016/j.exer.2015.02.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/03/2015] [Accepted: 02/04/2015] [Indexed: 12/20/2022]
Abstract
The human 8-oxoguanine-DNA glycosylase 1 (OGG1) is the major DNA glycosylase responsible for repair of 7,8-dihydro-8-oxoguanine (8-oxoG) and ring-opened fapyguanine, critical mutagenic DNA lesions that are induced by reactive oxygen species. OGG1 acetylation has been demonstrated playing an important role in response to DNA damage. Here, we investigated the relationship between acetylated OGG1 (Ac-OGG1) and ARC, and clarified the effect of p300 and SIRT1 on the 8-oxoG excision ability of OGG1 in ARC development. Our results showed that anterior lens capsules from ARC group had higher proportion of 8-oxoG positive LECs than those from control group. OGG1 mRNA and protein levels significantly increased in ARC group compared with control group, while the protein levels of Ac-OGG1 were lower in ARC group. We investigated the factors involved in OGG1 acetylation and found that p300 and SIRT1 are the major acetyltransferases for OGG1 acetylation. We also identified acetylation of K338/K341 lysine residues in OGG1 has an important role on the repair activity of OGG1 to oxidative damage after H2O2 exposure in human lens epithelial cells (HLE-B3). Taken together, these data demonstrate that OGG1 acetylation regulates its function in response to DNA damage and could be one of the mechanisms of ARC.
Collapse
Affiliation(s)
- Lihua Kang
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Weijie Zhao
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China; Department of Ophthalmology, First People's Hospital of Changshu City, Affiliated Hospital of Soochow University, Changshu, Jiangsu Province, China
| | - Guowei Zhang
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Jian Wu
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Huaijin Guan
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China.
| |
Collapse
|
48
|
Cîrneci D, Silaghi-Dumitrescu R. Learning tasks as a possible treatment for DNA lesions induced by oxidative stress in hippocampal neurons. Neural Regen Res 2014; 8:3063-70. [PMID: 25206627 PMCID: PMC4146205 DOI: 10.3969/j.issn.1673-5374.2013.32.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 09/26/2013] [Indexed: 11/18/2022] Open
Abstract
Reactive oxygen species have been implicated in conditions ranging from cardiovascular dysfunc-tion, arthritis, cancer, to aging and age-related disorders. The organism developed several path-ways to counteract these effects, with base excision repair being responsible for repairing one of the major base lesions (8-oxoG) in all organisms. Epidemiological evidence suggests that cognitive stimulation makes the brain more resilient to damage or degeneration. Recent studies have linked enriched environment to reduction of oxidative stressin neurons of mice with Alzheimer's dis-ease-like disease, but given its complexity it is not clear what specific aspect of enriched environ-ment has therapeutic effects. Studies from molecular biology have shown that the protein p300, which is a transcription co-activator required for consolidation of memories during specific learning tasks, is at the same time involved in DNA replication and repair, playing a central role in the long-patch pathway of base excision repair. Based on the evidence, we propose that learning tasks such as novel object recognition could be tested as possible methods of base excision repair faci-litation, hence inducing DNA repair in the hippocampal neurons. If this method proves to be effective, it could be the start for designing similar tasks for humans, as a behavioral therapeutic complement to the classical drug-based therapy in treating neurodegenerative disorders. This review presents the current status of therapeutic methods used in treating neurodegenerative diseases induced by reactive oxygen species and proposes a new approach based on existing data.
Collapse
Affiliation(s)
- Dragoş Cîrneci
- Brain Research Institute, Synergon Consulting, Bucharest 010094, Romania
| | - Radu Silaghi-Dumitrescu
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj Napoca, 400165, Romania
| |
Collapse
|
49
|
Henry RA, Kuo YM, Andrews AJ. Differences in specificity and selectivity between CBP and p300 acetylation of histone H3 and H3/H4. Biochemistry 2013; 52:5746-59. [PMID: 23862699 PMCID: PMC3756530 DOI: 10.1021/bi400684q] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
![]()
Although
p300 and CBP lysine acetyltransferases are often treated
interchangeably, the inability of one enzyme to compensate for the
loss of the other suggests unique roles for each. As these deficiencies
coincide with aberrant levels of histone acetylation, we hypothesized
that the key difference between p300 and CBP activity is differences
in their specificity/selectivity for lysines within the histones.
Utilizing a label-free, quantitative mass spectrometry based technique,
we determined the kinetic parameters of both CBP and p300 at each
lysine of H3 and H4, under conditions we would expect to encounter
in the cell (either limiting acetyl-CoA or histone). Our results show
that while p300 and CBP acetylate many common residues on H3 and H4,
they do in fact possess very different specificities, and these specificities
are dependent on whether histone or acetyl-CoA is limiting. Steady-state
experiments with limiting H3 demonstrate that both CBP and p300 acetylate
H3K14, H3K18, H3K23, with p300 having specificities up to 1010-fold higher than CBP. Utilizing tetramer as a substrate, both enzymes
also acetylate H4K5, H4K8, H4K12, and H4K16. With limiting tetramer,
CBP displays higher specificities, especially at H3K18, where CBP
specificity is 1032-fold higher than p300. With limiting
acetyl-CoA, p300 has the highest specificity at H4K16, where specificity
is 1018-fold higher than CBP. This discovery of unique
specificity for targets of CBP- vs p300-mediated acetylation of histone
lysine residues presents a new model for understanding their respective
biological roles and possibly an opportunity for selective therapeutic
intervention.
Collapse
Affiliation(s)
- Ryan A Henry
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States
| | | | | |
Collapse
|
50
|
The role of arginine methylation in the DNA damage response. DNA Repair (Amst) 2013; 12:459-65. [DOI: 10.1016/j.dnarep.2013.04.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 04/13/2013] [Indexed: 12/20/2022]
|