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Mangiapane G, Notarangelo M, Canarutto G, Fabbiano F, Dalla E, Degrassi M, Antoniali G, Gualandi N, De Sanctis V, Piazza S, D'Agostino VG, Tell G. The DNA-repair protein APE1 participates with hnRNPA2B1 to motif-enriched and prognostic miRNA secretion. Oncogene 2024; 43:1861-1876. [PMID: 38664500 DOI: 10.1038/s41388-024-03039-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 06/12/2024]
Abstract
The base excision repair (BER) Apurinic/apyrimidinic endonuclease 1 (APE1) enzyme is endowed with several non-repair activities including miRNAs processing. APE1 is overexpressed in many cancers but its causal role in the tumorigenic processes is largely unknown. We recently described that APE1 can be actively secreted by mammalian cells through exosomes. However, APE1 role in EVs or exosomes is still unknown, especially regarding a putative regulatory function on vesicular small non-coding RNAs. Through dedicated transcriptomic analysis on cellular and vesicular small RNAs of different APE1-depleted cancer cell lines, we found that miRNAs loading into EVs is a regulated process, dependent on APE1, distinctly conveying RNA subsets into vesicles. We identified APE1-dependent secreted miRNAs characterized by enriched sequence motifs and possible binding sites for APE1. In 33 out of 34 APE1-dependent-miRNA precursors, we surprisingly found EXO-motifs and proved that APE1 cooperates with hnRNPA2B1 for the EV-sorting of a subset of miRNAs, including miR-1246, through direct binding to GGAG stretches. Using TCGA-datasets, we showed that these miRNAs identify a signature with high prognostic significance in cancer. In summary, we provided evidence that the ubiquitous DNA-repair enzyme APE1 is part of the EV protein cargo with a novel post-transcriptional role for this ubiquitous DNA-repair enzyme that could explain its role in cancer progression. These findings could open new translational perspectives in cancer biology.
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Affiliation(s)
- Giovanna Mangiapane
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DMED), University of Udine, Udine, Italy
| | - Michela Notarangelo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Yale University School of Medicine, New Haven, CT, USA
| | - Giulia Canarutto
- Computational Biology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Fabrizio Fabbiano
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Emiliano Dalla
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DMED), University of Udine, Udine, Italy
| | - Monica Degrassi
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DMED), University of Udine, Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DMED), University of Udine, Udine, Italy
| | - Nicolò Gualandi
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DMED), University of Udine, Udine, Italy
| | - Veronica De Sanctis
- Next Generation Sequencing Facility, Department CIBIO, University of Trento, Trento, Italy
| | - Silvano Piazza
- Computational Biology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy.
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy.
| | - Vito Giuseppe D'Agostino
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DMED), University of Udine, Udine, Italy.
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Wang T, Zou Y, Meng H, Zheng P, Teng J, Huang N, Chen J. Securin acetylation prevents precocious separase activation and premature sister chromatid separation. Curr Biol 2024; 34:1295-1308.e5. [PMID: 38452759 DOI: 10.1016/j.cub.2024.02.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 01/08/2024] [Accepted: 02/15/2024] [Indexed: 03/09/2024]
Abstract
Lysine acetylation of non-histone proteins plays crucial roles in many cellular processes. In this study, we examine the role of lysine acetylation during sister chromatid separation in mitosis. We investigate the acetylation of securin at K21 by cell-cycle-dependent acetylome analysis and uncover its role in separase-triggered chromosome segregation during mitosis. Prior to the onset of anaphase, the acetylated securin via TIP60 prevents its degradation by the APC/CCDC20-mediated ubiquitin-proteasome system. This, in turn, restrains precocious activation of separase and premature separation of sister chromatids. Additionally, the acetylation-dependent stability of securin is also enhanced by its dephosphorylation. As anaphase approaches, HDAC1-mediated deacetylation of securin promotes its degradation, allowing released separase to cleave centromeric cohesin. Blocking securin deacetylation leads to longer anaphase duration and errors in chromosome segregation. Thus, this study illustrates the emerging role of securin acetylation dynamics in mitotic progression and genetic stability.
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Affiliation(s)
- Tianning Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China; Breast Disease Diagnosis and Treatment Center/Department of Thyroid Surgery, Central Hospital Affiliated to Shandong First Medical University, Jinan 250013, China; Research Center of Translational Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan 250013, China
| | - Yuhong Zou
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China
| | - Hui Meng
- Institute of Neuroscience, Translational Medicine Institute, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Pengli Zheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Junlin Teng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China.
| | - Ning Huang
- Institute of Neuroscience, Translational Medicine Institute, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Jianguo Chen
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China; Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
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3
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Parolini I, Degrassi M, Spadaro F, Caponnetto F, Fecchi K, Mastantuono S, Zhouyiyuan X, Demple B, Cesselli D, Tell G. Intraluminal vesicle trafficking is involved in the secretion of base excision repair protein APE1. FEBS J 2024. [PMID: 38401056 DOI: 10.1111/febs.17088] [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: 07/18/2023] [Revised: 11/24/2023] [Accepted: 01/31/2024] [Indexed: 02/26/2024]
Abstract
The apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) is an essential enzyme of the base excision repair pathway of non-distorting DNA lesions. In response to genotoxic treatments, APE1 is highly secreted (sAPE1) in association with small-extracellular vesicles (EVs). Interestingly, its presence in the serum of patients with hepatocellular or non-small-cell-lung cancers may represent a prognostic biomarker. The mechanism driving APE1 to associate with EVs is unknown, but is of paramount importance in better understanding the biological roles of sAPE1. Because APE1 lacks an endoplasmic reticulum-targeting signal peptide, it can be secreted through an unconventional protein secretion endoplasmic reticulum-Golgi-independent pathway, which includes an endosome-based secretion of intraluminal vesicles, mediated by multivesicular bodies (MVBs). Using HeLa and A549 cell lines, we investigated the role of endosomal sorting complex required for transport protein pathways (either-dependent or -independent) in the constitutive or trichostatin A-induced secretion of sAPE1, by means of manumycin A and GW 4869 treatments. Through an in-depth biochemical analysis of late-endosomes (LEs) and early-endosomes (EEs), we observed that the distribution of APE1 on density gradient corresponded to that of LE-CD63, LE-Rab7, EE-EEA1 and EE-Rab 5. Interestingly, the secretion of sAPE1, induced by cisplatin genotoxic stress, involved an autophagy-based unconventional secretion requiring MVBs. The present study enlightens the central role played by MVBs in the secretion of sAPE1 under various stimuli, and offers new perspectives in understanding the biological relevance of sAPE1 in cancer cells.
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Affiliation(s)
- Isabella Parolini
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Italy
| | - Monica Degrassi
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Italy
| | - Francesca Spadaro
- Core Facilities - Confocal Microscopy Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Federica Caponnetto
- Department of Medicine, University of Udine, Italy
- Institute of Pathology, Academic Hospital Santa Maria della Misericordia, Udine, Italy
| | - Katia Fecchi
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Serena Mastantuono
- Department of Medicine, University of Udine, Italy
- Institute of Pathology, Academic Hospital Santa Maria della Misericordia, Udine, Italy
| | - Xue Zhouyiyuan
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Bruce Demple
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Daniela Cesselli
- Department of Medicine, University of Udine, Italy
- Institute of Pathology, Academic Hospital Santa Maria della Misericordia, Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Italy
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Florio D, Marasco D. Could Targeting NPM1c+ Misfolding Be a Promising Strategy for Combating Acute Myeloid Leukemia? Int J Mol Sci 2024; 25:811. [PMID: 38255885 PMCID: PMC10815591 DOI: 10.3390/ijms25020811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/30/2023] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous group of diseases classified into various types on the basis of distinct features concerning the morphology, cytochemistry and cytogenesis of leukemic cells. Among the different subtypes, the group "AML with gene mutations" includes the variations of the gene of the multifunctional protein nucleophosmin 1 (NPM1). These mutations are the most frequent (~30-35% of AML adult patients and less in pediatric ones) and occur predominantly in the C-terminal domain (CTD) of NPM1. The most important mutation is the insertion at W288, which determines the frame shift W288Cfs12/Ffs12/Lfs*12 and leads to the addition of 2-12 amino acids, which hamper the correct folding of NPM1. This mutation leads to the loss of the nuclear localization signal (NoLS) and to aberrant cytoplasmic localization, denoted as NPM1c+. Many investigations demonstrated that interfering with the cellular location and oligomerization status of NPM1 can influence its biological functions, including the proper buildup of the nucleolus, and therapeutic strategies have been proposed to target NPM1c+, particularly the use of drugs able to re-direct NPM1 localization. Our studies unveiled a direct link between AML mutations and the neat amyloidogenic character of the CTDs of NPM1c+. Herein, with the aim of exploiting these conformational features, novel therapeutic strategies are proposed that rely on the induction of the selective self-cytotoxicity of leukemic blasts by focusing on agents such as peptides, peptoids or small molecules able to enhance amyloid aggregation and targeting selectively AML-NPM1c+ mutations.
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Affiliation(s)
| | - Daniela Marasco
- Department of Pharmacy, University of Naples “Federico II”, 80131 Naples, Italy;
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Ma Y, Huang L, Zhang Z, Yang P, Chen Q, Zeng X, Tan F, Wang C, Ruan X, Liao X. CD36 promotes tubular ferroptosis by regulating the ubiquitination of FSP1 in acute kidney injury. Genes Dis 2024; 11:449-463. [PMID: 37588197 PMCID: PMC10425750 DOI: 10.1016/j.gendis.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/20/2022] [Accepted: 12/01/2022] [Indexed: 01/05/2023] Open
Abstract
Reactive oxidative species (ROS) production-driven ferroptosis plays a role in acute kidney injury (AKI). However, its exact molecular mechanism is poorly understood. Scavenger receptor CD36 has important roles in oxidizing lipids, lipid accumulation, metabolic syndrome, and insulin resistance in chronic kidney disease, but its roles remain unexplored in AKI. The present study investigated the role and mechanism of CD36 in regulating proximal tubular cell ferroptosis and AKI. The expression of CD36 was found to be significantly up-regulated in AKI renal tissues and correlated with renal function, which might serve as an independent biomarker for AKI patients. Moreover, in adult mice subjected to AKI, deletion of CD36 (CD36-/-) induced tubular cell ROS accumulation, ferroptosis activation, and renal injury. Mechanistically, combining LC-MS/MS, co-IP, and ubiquitination analyses revealed that CD36 could specifically bind to ferroptosis suppressor protein 1 (FSP1) and regulate its ubiquitination at sites K16 and K24, leading to FSP1 degradation and progression of ferroptosis in AKI. The present results emphasize a novel mechanism of CD36 in cisplatin-induced AKI. The discovery of the special CD36 roles in promoting ferroptosis and AKI development by regulating the ubiquitination of FSP1 in proximal tubular cells may be potential therapeutic targets for AKI. Moreover, CD36 may play a key role in the progression of AKI. Therefore, targeting CD36 may provide a promising treatment option for AKI.
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Affiliation(s)
- Yixin Ma
- Department of Nephrology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, China
| | - Lili Huang
- Department of Nephrology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, China
| | - Zheng Zhang
- Department of Nephrology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, China
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, China
| | - Pengfei Yang
- Department of Nephrology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, China
| | - Qingsong Chen
- Department of Nephrology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, China
| | - Xujia Zeng
- Department of Nephrology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, China
| | - Fangyan Tan
- Department of Nephrology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, China
| | - Chunxia Wang
- Department of Nephrology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, China
| | - Xiongzhong Ruan
- Centre for Nephrology, Royal Free and University College Medical School, University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
- Centre for Lipid Research, Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, China
- Kuanren Laboratory of Translational Lipidology, Centre for Lipid Research, Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Xiaohui Liao
- Department of Nephrology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, China
- Kuanren Laboratory of Translational Lipidology, Centre for Lipid Research, Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
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Lin Y, Li J, Zhao H, McMahon A, McGhee K, Yan S. APE1 recruits ATRIP to ssDNA in an RPA-dependent and -independent manner to promote the ATR DNA damage response. eLife 2023; 12:82324. [PMID: 37216274 DOI: 10.7554/elife.82324] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 05/08/2023] [Indexed: 05/24/2023] Open
Abstract
Cells have evolved the DNA damage response (DDR) pathways in response to DNA replication stress or DNA damage. In the ATR-Chk1 DDR pathway, it has been proposed that ATR is recruited to RPA-coated single-stranded DNA (ssDNA) by direct ATRIP-RPA interaction. However, it remains elusive how ATRIP is recruited to ssDNA in an RPA-independent manner. Here, we provide evidence that APE1 directly associates ssDNA to recruit ATRIP onto ssDNA in an RPA-independent fashion. The N-terminal motif within APE1 is required and sufficient for the APE1-ATRIP interaction in vitro and the distinct APE1-ATRIP interaction is required for ATRIP recruitment to ssDNA and the ATR-Chk1 DDR pathway activation in Xenopus egg extracts. In addition, APE1 directly associates with RPA70 and RPA32 via two distinct motifs. Taken together, our evidence suggests that APE1 recruits ATRIP onto ssDNA in an RPA-dependent and -independent manner in the ATR DDR pathway.
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Affiliation(s)
- Yunfeng Lin
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, United States
| | - Jia Li
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, United States
| | - Haichao Zhao
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, United States
| | - Anne McMahon
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, United States
| | - Kelly McGhee
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, United States
| | - Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, United States
- School of Data Science, University of North Carolina at Charlotte, Charlotte, United States
- Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, United States
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Bakman AS, Kuznetsova AA, Yanshole LV, Ishchenko AA, Saparbaev M, Fedorova OS, Kuznetsov NA. Fluorescently labeled human apurinic/apyrimidinic endonuclease APE1 reveals effects of DNA polymerase β on the APE1-DNA interaction. DNA Repair (Amst) 2023; 123:103450. [PMID: 36689867 DOI: 10.1016/j.dnarep.2023.103450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/26/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
The base excision repair (BER) pathway involves sequential action of DNA glycosylases and apurinic/apyrimidinic (AP) endonucleases to incise damaged DNA and prepare DNA termini for incorporation of a correct nucleotide by DNA polymerases. It has been suggested that the enzymatic steps in BER include recognition of a product-enzyme complex by the next enzyme in the pathway, resulting in the "passing-the-baton" model of transfer of DNA intermediates between enzymes. To verify this model, in this work, we aimed to create a suitable experimental system. We prepared APE1 site-specifically labeled with a fluorescent reporter that is sensitive to stages of APE1-DNA binding, of formation of the catalytic complex, and of subsequent dissociation of the enzyme-product complex. Interactions of the labeled APE1 with various model DNA substrates (containing an abasic site) of varied lengths revealed that the enzyme remains mostly in complex with the DNA product. By means of the fluorescently labeled APE1 in combination with a stopped-flow fluorescence assay, it was found that Polβ stimulates both i) APE1 binding to an abasic-site-containing DNA duplex with the formation of a catalytically competent complex and ii) the dissociation of APE1 from its product. These findings confirm DNA-mediated coordination of APE1 and Polβ activities and suggest that Polβ is the key trigger of the DNA transfer between the enzymes participating in initial steps of BER.
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Affiliation(s)
- Artemiy S Bakman
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia
| | - Aleksandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia
| | - Lyudmila V Yanshole
- International Tomography Center SB RAS, 3a Institutskaya Str., Novosibirsk 630090, Russia
| | - Alexander A Ishchenko
- Group "Mechanisms of DNA Repair and Carcinogenesis", Gustave Roussy Cancer Campus, CNRS UMR9019, Université Paris-Saclay, 94805 Villejuif, France
| | - Murat Saparbaev
- Group "Mechanisms of DNA Repair and Carcinogenesis", Gustave Roussy Cancer Campus, CNRS UMR9019, Université Paris-Saclay, 94805 Villejuif, France; NCJSC "Al-Farabi Kazakh National University" Almaty, Kazakhstan
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia; Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia.
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8
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Li J, Zhao H, McMahon A, Yan S. APE1 assembles biomolecular condensates to promote the ATR-Chk1 DNA damage response in nucleolus. Nucleic Acids Res 2022; 50:10503-10525. [PMID: 36200829 PMCID: PMC9561277 DOI: 10.1093/nar/gkac853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/14/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Multifunctional protein APE1/APEX1/HAP1/Ref-1 (designated as APE1) plays important roles in nuclease-mediated DNA repair and redox regulation in transcription. However, it is unclear how APE1 regulates the DNA damage response (DDR) pathways. Here we show that siRNA-mediated APE1-knockdown or APE1 inhibitor treatment attenuates the ATR–Chk1 DDR under stress conditions in multiple immortalized cell lines. Congruently, APE1 overexpression (APE1-OE) activates the ATR DDR under unperturbed conditions, which is independent of APE1 nuclease and redox functions. Structural and functional analysis reveals a direct requirement of the extreme N-terminal motif within APE1 in the assembly of distinct biomolecular condensates in vitro and DNA/RNA-independent activation of the ATR DDR. Overexpressed APE1 co-localizes with nucleolar NPM1 and assembles biomolecular condensates in nucleoli in cancer but not non-malignant cells, which recruits ATR and activator molecules TopBP1 and ETAA1. APE1 protein can directly activate ATR to phosphorylate its substrate Chk1 in in vitro kinase assays. W119R mutant of APE1 is deficient in nucleolar condensation, and is incapable of activating nucleolar ATR DDR in cells and ATR kinase in vitro. APE1-OE-induced nucleolar ATR DDR activation leads to compromised ribosomal RNA transcription and reduced cell viability. Taken together, we propose distinct mechanisms by which APE1 regulates ATR DDR pathways.
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Affiliation(s)
- Jia Li
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Haichao Zhao
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Anne McMahon
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.,School of Data Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.,Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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Xue Z, Demple B. Knockout and Inhibition of Ape1: Roles of Ape1 in Base Excision DNA Repair and Modulation of Gene Expression. Antioxidants (Basel) 2022; 11:antiox11091817. [PMID: 36139891 PMCID: PMC9495735 DOI: 10.3390/antiox11091817] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/31/2022] [Accepted: 09/07/2022] [Indexed: 11/21/2022] Open
Abstract
Apurinic/apyrimidinic endonuclease 1/redox effector-1 (Ape1/Ref-1) is the major apurinic/apyrimidinic (AP) endonuclease in mammalian cells. It functions mainly in the base excision repair pathway to create a suitable substrate for DNA polymerases. Human Ape1 protein can activate some transcription factors to varying degrees, dependent on its N-terminal, unstructured domain, and some of the cysteines within it, apparently via a redox mechanism in some cases. Many cancer studies also suggest that Ape1 has potential for prognosis in terms of the protein level or intracellular localization. While homozygous disruption of the Ape1 structural gene APEX1 in mice causes embryonic lethality, and most studies in cell culture indicate that the expression of Ape1 is essential, some recent studies reported the isolation of viable APEX1 knockout cells with only mild phenotypes. It has not been established by what mechanism the Ape1-null cell lines cope with the endogenous DNA damage that the enzyme normally handles. We review the enzymatic and other activities of Ape1 and the recent studies of the properties of the APEX1 knockout lines. The APEX1 deletions in CH12F3 and HEK293 FT provide an opportunity to test for possible off-target effects of Ape1 inhibition. For this work, we tested the Ape1 endonuclease inhibitor Compound 3 and the redox inhibitor APX2009. Our results confirmed that both APEX1 knockout cell lines are modestly more sensitive to killing by an alkylating agent than their Ape1-proficient cells. Surprisingly, the knockout lines showed equal sensitivity to direct killing by either inhibitor, despite the lack of the target protein. Moreover, the CH12F3 APEX1 knockout was even more sensitive to Compound 3 than its APEX1+ counterpart. Thus, it appears that both Compound 3 and APX2009 have off-target effects. In cases where this issue may be important, it is advisable that more specific endpoints than cell survival be tested for establishing mechanism.
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Affiliation(s)
- Zhouyiyuan Xue
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794-8651, USA
- Molecular and Cellular Biochemistry Program, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Bruce Demple
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794-8651, USA
- Correspondence: ; Tel.: +1-(631)-444-3978
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10
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Comparative Analysis of Exo- and Endonuclease Activities of APE1-like Enzymes. Int J Mol Sci 2022; 23:ijms23052869. [PMID: 35270011 PMCID: PMC8911113 DOI: 10.3390/ijms23052869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/05/2022] Open
Abstract
Apurinic/apyrimidinic (AP)-endonucleases are multifunctional enzymes that are required for cell viability. AP-endonucleases incise DNA 5′ to an AP-site; can recognize and process some damaged nucleosides; and possess 3′-phosphodiesterase, 3′-phosphatase, and endoribonuclease activities. To elucidate the mechanism of substrate cleavage in detail, we analyzed the effect of mono- and divalent metal ions on the exo- and endonuclease activities of four homologous APE1-like endonucleases (from an insect (Rrp1), amphibian (xAPE1), fish (zAPE1), and from humans (hAPE1)). It was found that the enzymes had similar patterns of dependence on metal ions’ concentrations in terms of AP-endonuclease activity, suggesting that the main biological function (AP-site cleavage) was highly conserved among evolutionarily distant species. The efficiency of the 3′-5′ exonuclease activity was the highest in hAPE1 among these enzymes. In contrast, the endoribonuclease activity of the enzymes could be ranked as hAPE1 ≈ zAPE1 ≤ xAPE1 ≤ Rrp1. Taken together, the results revealed that the tested enzymes differed significantly in their capacity for substrate cleavage, even though the most important catalytic and substrate-binding amino acid residues were conserved. It can be concluded that substrate specificity and cleavage efficiency were controlled by factors external to the catalytic site, e.g., the N-terminal domain of these enzymes.
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11
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Fleming AM, Manage SAH, Burrows CJ. Binding of AP endonuclease-1 to G-quadruplex DNA depends on the N-terminal domain, Mg 2+ and ionic strength. ACS BIO & MED CHEM AU 2021; 1:44-56. [PMID: 35005714 DOI: 10.1021/acsbiomedchemau.1c00031] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The base excision repair enzyme apurinic/apyrimidinic endonuclease-1 (APE1) is also engaged in transcriptional regulation. APE1 can function in both pathways when the protein binds to a promoter G-quadruplex (G4) bearing an abasic site (modeled with tetrahydrofuran, F) that leads to enzymatic stalling on the non-canonical fold to recruit activating transcription factors. Biochemical and biophysical studies to address APE1's binding and catalytic activity with the vascular endothelial growth factor (VEGF) promoter G4 are lacking, and the present work provides insight on this topic. Herein, the native APE1 was used for cleavage assays, and the catalytically inactive mutant D210A was used for binding assays with double-stranded DNA (dsDNA) versus the native G4 or the G4 with F at various positions, revealing dependencies of the interaction on the cation concentrations K+ and Mg2+ and the N-terminal domain of the protein. Assays in 0, 1, or 10 mM Mg2+ found that dsDNA and G4 substrates required the cation for both binding and catalysis, in which G4 binding increased with [Mg2+]. Studies with 50 versus physiological 140 mM K+ ions showed that F-containing dsDNA was bound and cleaved by APE1; whereas, the G4s with F were poorly cleaved in low salt and not cleaved at all at higher salt while the binding remained robust. Using Δ33 or Δ61 N-terminal truncated APE1 proteins, the binding and cleavage of dsDNA with F was minimally impacted; in contrast, the G4s required the N-terminus for binding and catalysis is nearly abolished without the N-terminus. With this knowledge, we found APE1 could remodel the F-containing VEGF promoter dsDNA→G4 folds in solution. Lastly, the addition of the G4 ligand pyridostatin inhibited APE1 binding and cleavage of F-containing G4s but not dsDNA. The biological and medicinal chemistry implications of the results are discussed.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
| | - Shereen A Howpay Manage
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
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12
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Fleming AM, Burrows CJ. Oxidative stress-mediated epigenetic regulation by G-quadruplexes. NAR Cancer 2021; 3:zcab038. [PMID: 34541539 PMCID: PMC8445369 DOI: 10.1093/narcan/zcab038] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/20/2021] [Accepted: 09/06/2021] [Indexed: 02/06/2023] Open
Abstract
Many cancer-associated genes are regulated by guanine (G)-rich sequences that are capable of refolding from the canonical duplex structure to an intrastrand G-quadruplex. These same sequences are sensitive to oxidative damage that is repaired by the base excision repair glycosylases OGG1 and NEIL1–3. We describe studies indicating that oxidation of a guanosine base in a gene promoter G-quadruplex can lead to up- and downregulation of gene expression that is location dependent and involves the base excision repair pathway in which the first intermediate, an apurinic (AP) site, plays a key role mediated by AP endonuclease 1 (APE1/REF1). The nuclease activity of APE1 is paused at a G-quadruplex, while the REF1 capacity of this protein engages activating transcription factors such as HIF-1α, AP-1 and p53. The mechanism has been probed by in vitro biophysical studies, whole-genome approaches and reporter plasmids in cellulo. Replacement of promoter elements by a G-quadruplex sequence usually led to upregulation, but depending on the strand and precise location, examples of downregulation were also found. The impact of oxidative stress-mediated lesions in the G-rich sequence enhanced the effect, whether it was positive or negative.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850, USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850, USA
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Kuznetsova AA, Senchurova SI, Ishchenko AA, Saparbaev M, Fedorova OS, Kuznetsov NA. Common Kinetic Mechanism of Abasic Site Recognition by Structurally Different Apurinic/Apyrimidinic Endonucleases. Int J Mol Sci 2021; 22:ijms22168874. [PMID: 34445579 PMCID: PMC8396254 DOI: 10.3390/ijms22168874] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 02/03/2023] Open
Abstract
Apurinic/apyrimidinic (AP) endonucleases Nfo (Escherichia coli) and APE1 (human) represent two conserved structural families of enzymes that cleave AP-site–containing DNA in base excision repair. Nfo and APE1 have completely different structures of the DNA-binding site, catalytically active amino acid residues and catalytic metal ions. Nonetheless, both enzymes induce DNA bending, AP-site backbone eversion into the active-site pocket and extrusion of the nucleotide located opposite the damage. All these stages may depend on local stability of the DNA duplex near the lesion. Here, we analysed effects of natural nucleotides located opposite a lesion on catalytic-complex formation stages and DNA cleavage efficacy. Several model DNA substrates that contain an AP-site analogue [F-site, i.e., (2R,3S)-2-(hydroxymethyl)-3-hydroxytetrahydrofuran] opposite G, A, T or C were used to monitor real-time conformational changes of the tested enzymes during interaction with DNA using changes in the enzymes’ intrinsic fluorescence intensity mainly caused by Trp fluorescence. The extrusion of the nucleotide located opposite F-site was recorded via fluorescence intensity changes of two base analogues. The catalytic rate constant slightly depended on the opposite-nucleotide nature. Thus, structurally different AP endonucleases Nfo and APE1 utilise a common strategy of damage recognition controlled by enzyme conformational transitions after initial DNA binding.
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Affiliation(s)
- Alexandra A. Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.A.K.); (S.I.S.)
| | - Svetlana I. Senchurova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.A.K.); (S.I.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexander A. Ishchenko
- Group Mechanisms of DNA Repair and Carcinogenesis, Equipe Labellisée LIGUE 2016, CNRS UMR9019, Gustave Roussy Cancer Campus, Université Paris-Saclay, F-94805 Villejuif, France; (A.A.I.); (M.S.)
| | - Murat Saparbaev
- Group Mechanisms of DNA Repair and Carcinogenesis, Equipe Labellisée LIGUE 2016, CNRS UMR9019, Gustave Roussy Cancer Campus, Université Paris-Saclay, F-94805 Villejuif, France; (A.A.I.); (M.S.)
| | - Olga S. Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.A.K.); (S.I.S.)
- Correspondence: (O.S.F.); (N.A.K.)
| | - Nikita A. Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.A.K.); (S.I.S.)
- Correspondence: (O.S.F.); (N.A.K.)
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La Manna S, Florio D, Di Natale C, Scognamiglio PL, Sibillano T, Netti PA, Giannini C, Marasco D. Type F mutation of nucleophosmin 1 Acute Myeloid Leukemia: A tale of disorder and aggregation. Int J Biol Macromol 2021; 188:207-214. [PMID: 34364939 DOI: 10.1016/j.ijbiomac.2021.08.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 07/19/2021] [Accepted: 08/03/2021] [Indexed: 01/15/2023]
Abstract
Protein aggregation is suggested as a reversible, wide-spread physiological process used by cells to regulate their growth and adapt to different stress conditions. Nucleophosmin 1(NPM1) protein is an abundant multifunctional nucleolar chaperone and its gene is the most frequently mutated in Acute Myeloid Leukemia (AML) patients. So far, the role of NPM1 mutations in leukemogenesis has remained largely elusive considering that they have the double effect of unfolding the C-terminal domain (CTD) and delocalizing the protein in the cytosol (NPM1c+). This mislocalization heavily impacts on cell cycle regulation. Our recent investigations unequivocally demonstrated an amyloid aggregation propensity introduced by AML mutations. Herein, employing complementary biophysical assays, we have characterized a N-terminal extended version of type F AML mutation of CTD and proved that it is able to form assemblies with amyloid character and fibrillar morphology. The present study represents an additional phase of knowledge to deepen the roles exerted by different types of cytoplasmatic NPM1c+ forms to develop in the future potential therapeutics for their selective targeting.
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Affiliation(s)
- Sara La Manna
- Department of Pharmacy, University of Naples "Federico II", 80134 Naples, Italy
| | - Daniele Florio
- Department of Pharmacy, University of Naples "Federico II", 80134 Naples, Italy
| | - Concetta Di Natale
- Interdisciplinary Research Centre on Biomaterials (CRIB), Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples "Federico II", Italy
| | - Pasqualina Liana Scognamiglio
- Interdisciplinary Research Centre on Biomaterials (CRIB), Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples "Federico II", Italy
| | - Teresa Sibillano
- Institute of Crystallography (IC), National Research Council, 70125 Bari, Italy
| | - Paolo A Netti
- Interdisciplinary Research Centre on Biomaterials (CRIB), Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples "Federico II", Italy
| | - Cinzia Giannini
- Institute of Crystallography (IC), National Research Council, 70125 Bari, Italy
| | - Daniela Marasco
- Department of Pharmacy, University of Naples "Federico II", 80134 Naples, Italy.
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15
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Hatakeyama D, Shoji M, Ogata S, Masuda T, Nakano M, Komatsu T, Saitoh A, Makiyama K, Tsuneishi H, Miyatake A, Takahira M, Nishikawa E, Ohkubo A, Noda T, Kawaoka Y, Ohtsuki S, Kuzuhara T. Acetylation of the influenza A virus polymerase subunit PA in the N-terminal domain positively regulates its endonuclease activity. FEBS J 2021; 289:231-245. [PMID: 34270849 DOI: 10.1111/febs.16123] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/07/2021] [Accepted: 07/15/2021] [Indexed: 01/06/2023]
Abstract
The post-translational acetylation of lysine residues is found in many nonhistone proteins and is involved in a wide range of biological processes. Recently, we showed that the nucleoprotein of the influenza A virus is acetylated by histone acetyltransferases (HATs), a phenomenon that affects viral transcription. Here, we report that the PA subunit of influenza A virus RNA-dependent RNA polymerase is acetylated by the HATs, P300/CREB-binding protein-associated factor (PCAF), and general control nonderepressible 5 (GCN5), resulting in accelerated endonuclease activity. Specifically, the full-length PA subunit expressed in cultured 293T cells was found to be strongly acetylated. Moreover, the partial recombinant protein of the PA N-terminal region containing the endonuclease domain was also acetylated by PCAF and GCN5 in vitro, which facilitated its endonuclease activity. Mass spectrometry analyses identified K19 as a candidate acetylation target in the PA N-terminal region. Notably, the substitution of the lysine residue at position 19 with glutamine, a mimic of the acetyl-lysine residue, enhanced its endonuclease activity in vitro; this point mutation also accelerated influenza A virus RNA-dependent RNA polymerase activity in the cell. Our findings suggest that PA acetylation is important for the regulation of the endonuclease and RNA polymerase activities of the influenza A virus.
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Affiliation(s)
- Dai Hatakeyama
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Japan
| | - Masaki Shoji
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Japan
| | - Seiryo Ogata
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, Japan
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, Japan
| | - Masahiro Nakano
- Institute for Frontier Life and Medical Sciences, Kyoto University, Japan
| | - Tsugunori Komatsu
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Japan
| | - Ayaka Saitoh
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Japan
| | - Kyoko Makiyama
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Japan
| | - Hazuki Tsuneishi
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Japan
| | - Asuka Miyatake
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Japan
| | - Mizuki Takahira
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Japan
| | - Erina Nishikawa
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Japan
| | - Ayana Ohkubo
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Japan
| | - Takeshi Noda
- Institute for Frontier Life and Medical Sciences, Kyoto University, Japan
| | - Yoshihiro Kawaoka
- Institute of Medical Science, University of Tokyo, Japan.,School of Veterinary Medicine, University of Wisconsin-Madison, WI, USA
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, Japan
| | - Takashi Kuzuhara
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Japan
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Molecular Mechanisms Regulating the DNA Repair Protein APE1: A Focus on Its Flexible N-Terminal Tail Domain. Int J Mol Sci 2021; 22:ijms22126308. [PMID: 34208390 PMCID: PMC8231204 DOI: 10.3390/ijms22126308] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023] Open
Abstract
APE1 (DNA (apurinic/apyrimidinic site) endonuclease 1) is a key enzyme of one of the major DNA repair routes, the BER (base excision repair) pathway. APE1 fulfils additional functions, acting as a redox regulator of transcription factors and taking part in RNA metabolism. The mechanisms regulating APE1 are still being deciphered. Structurally, human APE1 consists of a well-characterized globular catalytic domain responsible for its endonuclease activity, preceded by a conformationally flexible N-terminal extension, acquired along evolution. This N-terminal tail appears to play a prominent role in the modulation of APE1 and probably in BER coordination. Thus, it is primarily involved in mediating APE1 localization, post-translational modifications, and protein–protein interactions, with all three factors jointly contributing to regulate the enzyme. In this review, recent insights on the regulatory role of the N-terminal region in several aspects of APE1 function are covered. In particular, interaction of this region with nucleophosmin (NPM1) might modulate certain APE1 activities, representing a paradigmatic example of the interconnection between various regulatory factors.
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17
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Malfatti MC, Antoniali G, Codrich M, Tell G. Coping with RNA damage with a focus on APE1, a BER enzyme at the crossroad between DNA damage repair and RNA processing/decay. DNA Repair (Amst) 2021; 104:103133. [PMID: 34049077 DOI: 10.1016/j.dnarep.2021.103133] [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: 03/18/2021] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 12/17/2022]
Abstract
Interest in RNA damage as a novel threat associated with several human pathologies is rapidly increasing. Knowledge on damaged RNA recognition, repair, processing and decay is still scanty. Interestingly, in the last few years, more and more evidence put a bridge between DNA damage repair enzymes and the RNA world. The Apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) was firstly identified as a crucial enzyme of the base excision repair (BER) pathway preserving genome stability toward non-distorting DNA lesion-induced damages. Later, an unsuspected role of APE1 in controlling gene expression was discovered and its pivotal involvement in several human pathologies, ranging from tumor progression to neurodegenerative diseases, has emerged. Recent novel findings indicate a role of APE1 in RNA metabolism, particularly in processing activities of damaged (abasic and oxidized) RNA and in the regulation of oncogenic microRNAs (miRNAs). Even though the role of miRNAs in human pathologies is well-known, the mechanisms underlying their quality control are still totally unexplored. A detailed knowledge of damaged RNA decay processes in human cells is crucial in order to understand the molecular processes involved in multiple pathologies. This cutting-edge perspective article will highlight these emerging aspects of damaged RNA processing and decay, focusing the attention on the involvement of APE1 in RNA world.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Piazzale M. Kolbe 4, 33100 Udine, Italy.
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Piazzale M. Kolbe 4, 33100 Udine, Italy.
| | - Marta Codrich
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Piazzale M. Kolbe 4, 33100 Udine, Italy.
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Piazzale M. Kolbe 4, 33100 Udine, Italy.
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18
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Durojaye OA, Okoro NO, Odiba AS. Characterization of the SARS-CoV-2 coronavirus X4-like accessory protein. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021; 22:48. [PMID: 38624802 PMCID: PMC8105150 DOI: 10.1186/s43042-021-00160-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/24/2021] [Indexed: 11/10/2022] Open
Abstract
Background The novel coronavirus SARS-CoV-2 is currently a global threat to health and economies. Therapeutics and vaccines are in rapid development; however, none of these therapeutics are considered as absolute cure, and the potential to mutate makes it necessary to find therapeutics that target a highly conserved regions of the viral structure. Results In this study, we characterized an essential but poorly understood coronavirus accessory X4 protein, a core and stable component of the SARS-CoV family. Sequence analysis shows a conserved ~ 90% identity between the SARS-CoV-2 and previously characterized X4 protein in the database. QMEAN Z score of the model protein shows a value of around 0.5, within the acceptable range 0-1. A MolProbity score of 2.96 was obtained for the model protein and indicates a good quality model. The model has Ramachandran values of φ = - 57o and ψ = - 47o for α-helices and values of φ = - 130o and ψ = + 140o for twisted sheets. Conclusions The protein data obtained from this study provides robust information for further in vitro and in vivo experiment, targeted at devising therapeutics against the virus. Phylogenetic analysis further supports previous evidence that the SARS-CoV-2 is positioned with the SL-CoVZC45, BtRs-BetaCoV/YN2018B and the RS4231 Bat SARS-like corona viruses.
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Affiliation(s)
- Olanrewaju Ayodeji Durojaye
- Department of Molecular and Cell Biology, University of Science and Technology of China, Hefei, People’s Republic of China
| | - Nkwachukwu Oziamara Okoro
- Guangxi Bioscience and Technology Research Centre, Guangxi Academy of Sciences, Nanning, 530007 People’s Republic of China
- Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, 410001 Nigeria
| | - Arome Solomon Odiba
- Guangxi Bioscience and Technology Research Centre, Guangxi Academy of Sciences, Nanning, 530007 People’s Republic of China
- Department of Molecular Genetics and Biotechnology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State 410001 Nigeria
- Department of Biochemistry, College of Life Science and Technology, Guangxi University, Nanning, 530007 People’s Republic of China
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19
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Davletgildeeva AT, Ishchenko AA, Saparbaev M, Fedorova OS, Kuznetsov NA. The Enigma of Substrate Recognition and Catalytic Efficiency of APE1-Like Enzymes. Front Cell Dev Biol 2021; 9:617161. [PMID: 33842455 PMCID: PMC8033172 DOI: 10.3389/fcell.2021.617161] [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: 10/14/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Despite significant achievements in the elucidation of the nature of protein-DNA contacts that control the specificity of nucleotide incision repair (NIR) by apurinic/apyrimidinic (AP) endonucleases, the question on how a given nucleotide is accommodated by the active site of the enzyme remains unanswered. Therefore, the main purpose of our study was to compare kinetics of conformational changes of three homologous APE1-like endonucleases (insect Drosophila melanogaster Rrp1, amphibian Xenopus laevis xAPE1, and fish Danio rerio zAPE1) during their interaction with various damaged DNA substrates, i.e., DNA containing an F-site (an uncleavable by DNA-glycosylases analog of an AP-site), 1,N6-ethenoadenosine (εA), 5,6-dihydrouridine (DHU), uridine (U), or the α-anomer of adenosine (αA). Pre-steady-state analysis of fluorescence time courses obtained for the interaction of the APE1-like enzymes with DNA substrates containing various lesions allowed us to outline a model of substrate recognition by this class of enzymes. It was found that the differences in rates of DNA substrates’ binding do not lead to significant differences in the cleavage efficiency of DNA containing a damaged base. The results suggest that the formation of enzyme–substrate complexes is not the key factor that limits enzyme turnover; the mechanisms of damage recognition and cleavage efficacy are related to fine conformational tuning inside the active site.
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Affiliation(s)
- Anastasiia T Davletgildeeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Alexander A Ishchenko
- Group "Mechanisms of DNA Repair and Carcinogenesis", Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Saclay, Villejuif, France
| | - Murat Saparbaev
- Group "Mechanisms of DNA Repair and Carcinogenesis", Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Saclay, Villejuif, France
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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20
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Mangiapane G, Parolini I, Conte K, Malfatti MC, Corsi J, Sanchez M, Pietrantoni A, D'Agostino VG, Tell G. Enzymatically active apurinic/apyrimidinic endodeoxyribonuclease 1 is released by mammalian cells through exosomes. J Biol Chem 2021; 296:100569. [PMID: 33753167 PMCID: PMC8080531 DOI: 10.1016/j.jbc.2021.100569] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 03/11/2021] [Accepted: 03/18/2021] [Indexed: 12/11/2022] Open
Abstract
The apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1), the main AP-endonuclease of the DNA base excision repair pathway, is a key molecule of interest to researchers due to its unsuspected roles in different nonrepair activities, such as: i) adaptive cell response to genotoxic stress, ii) regulation of gene expression, and iii) processing of microRNAs, which make it an excellent drug target for cancer treatment. We and others recently demonstrated that APE1 can be secreted in the extracellular environment and that serum APE1 may represent a novel prognostic biomarker in hepatocellular and non-small-cell lung cancers. However, the mechanism by which APE1 is released extracellularly was not described before. Here, using three different approaches for exosomes isolation: commercial kit, nickel-based isolation, and ultracentrifugation methods and various mammalian cell lines, we elucidated the mechanisms responsible for APE1 secretion. We demonstrated that APE1 p37 and p33 forms are actively secreted through extracellular vesicles (EVs), including exosomes from different mammalian cell lines. We then observed that APE1 p33 form is generated by proteasomal-mediated degradation and is enzymatically active in EVs. Finally, we revealed that the p33 form of APE1 accumulates in EVs upon genotoxic treatment by cisplatin and doxorubicin, compounds commonly found in chemotherapy pharmacological treatments. Taken together, these findings provide for the first time evidence that a functional Base Excision Repair protein is delivered through exosomes in response to genotoxic stresses, shedding new light into the complex noncanonical biological functions of APE1 and opening new intriguing perspectives on its role in cancer biology.
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Affiliation(s)
- Giovanna Mangiapane
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Isabella Parolini
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Kristel Conte
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Jessica Corsi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | | | - Vito G D'Agostino
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy.
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21
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Malfatti MC, Antoniali G, Codrich M, Burra S, Mangiapane G, Dalla E, Tell G. New perspectives in cancer biology from a study of canonical and non-canonical functions of base excision repair proteins with a focus on early steps. Mutagenesis 2021; 35:129-149. [PMID: 31858150 DOI: 10.1093/mutage/gez051] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022] Open
Abstract
Alterations of DNA repair enzymes and consequential triggering of aberrant DNA damage response (DDR) pathways are thought to play a pivotal role in genomic instabilities associated with cancer development, and are further thought to be important predictive biomarkers for therapy using the synthetic lethality paradigm. However, novel unpredicted perspectives are emerging from the identification of several non-canonical roles of DNA repair enzymes, particularly in gene expression regulation, by different molecular mechanisms, such as (i) non-coding RNA regulation of tumour suppressors, (ii) epigenetic and transcriptional regulation of genes involved in genotoxic responses and (iii) paracrine effects of secreted DNA repair enzymes triggering the cell senescence phenotype. The base excision repair (BER) pathway, canonically involved in the repair of non-distorting DNA lesions generated by oxidative stress, ionising radiation, alkylation damage and spontaneous or enzymatic deamination of nucleotide bases, represents a paradigm for the multifaceted roles of complex DDR in human cells. This review will focus on what is known about the canonical and non-canonical functions of BER enzymes related to cancer development, highlighting novel opportunities to understand the biology of cancer and representing future perspectives for designing new anticancer strategies. We will specifically focus on APE1 as an example of a pleiotropic and multifunctional BER protein.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Marta Codrich
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Silvia Burra
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giovanna Mangiapane
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Emiliano Dalla
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
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22
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Davletgildeeva AT, Kuznetsova AA, Fedorova OS, Kuznetsov NA. Activity of Human Apurinic/Apyrimidinic Endonuclease APE1 Toward Damaged DNA and Native RNA With Non-canonical Structures. Front Cell Dev Biol 2020; 8:590848. [PMID: 33195255 PMCID: PMC7662432 DOI: 10.3389/fcell.2020.590848] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/30/2020] [Indexed: 01/02/2023] Open
Abstract
The primary role of apurinic/apyrimidinic (AP) endonuclease APE1 in human cells is the cleavage of the sugar phosphate backbone 5' to an AP site in DNA to produce a single-strand break with a 5'-deoxyribose phosphate and 3'-hydroxyl end groups. APE1 can also recognize and incise some damaged or modified nucleotides and possesses some minor activities: 3'-5' exonuclease, 3'-phosphodiesterase, 3'-phosphatase, and RNase H. A molecular explanation for the discrimination of structurally different substrates by the single active site of the enzyme remains elusive. Here, we report a mechanism of target nucleotide recognition by APE1 as revealed by the results of an analysis of the APE1 process involving damaged DNA and native RNA substrates with non-canonical structures. The mechanism responsible for substrate specificity proved to be directly related to the ability of a target nucleotide to get into the active site of APE1 in response to an enzyme-induced DNA distortion.
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Affiliation(s)
- Anastasia T Davletgildeeva
- Institute of Chemical Biology and Fundamental Medicine of the SB RAS, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Alexandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine of the SB RAS, Novosibirsk, Russia
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine of the SB RAS, Novosibirsk, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine of the SB RAS, Novosibirsk, Russia
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23
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Zhang Y, Zhang Q, Li L, Mu D, Hua K, Ci S, Shen L, Zheng L, Shen B, Guo Z. Arginine methylation of APE1 promotes its mitochondrial translocation to protect cells from oxidative damage. Free Radic Biol Med 2020; 158:60-73. [PMID: 32679368 PMCID: PMC8195256 DOI: 10.1016/j.freeradbiomed.2020.06.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 06/09/2020] [Accepted: 06/17/2020] [Indexed: 02/07/2023]
Abstract
Apurinic/apyrimidinic endonuclease 1 (APE1) is an essential multifunctional protein in mammals that plays critical roles in DNA repair and redox signaling within the cell. Impaired APE1 function or dysregulation is associated with disease susceptibility and poor cancer prognosis. Orchestrated regulatory mechanisms are crucial to ensure its function in a specific subcellular location at specific time. Here, we report arginine methylation as a post-translational modification (PTM) that regulates APE1 translocation to mitochondria in HeLa and HEK-293 cells. Protein arginine methyl-transferase 1 (PRMT1) was shown to methylate APE1 in vitro. Site-directed mutagenesis identified R301 as the major methylation site. We confirmed that APE1 is methylated in cells and that the R301K mutation significantly reduces its methylation. Baseline mitochondrial APE1 levels were low under standard culture conditions, but they could be induced by oxidative agents. Methylation-deficient APE1 showed reduced mitochondrial translocation. Methylation affected the interaction of APE1 with Tom20, translocase of the outer mitochondrial membrane. Methylation-deficient APE1 resulted in increased mitochondrial DNA damage and increased cytochrome c release after stimuli. These data suggest that methylation of APE1 promotes its mitochondrial translocation and protects cells from oxidative damage. This work describes a novel PTM regulation model of APE1 subcellular distribution through arginine methylation.
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Affiliation(s)
- Yilan Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Qi Zhang
- Department of Infectious Disease, Nanjing Liuhe District People's Hospital, Yangzhou University, Nanjing, 211500, China
| | - LuLu Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Dan Mu
- Department of Radiology, Affiliated Drum Tower Hospital, Nanjing University School of Medicine, Nanjing, 210008, China
| | - Ke Hua
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Shusheng Ci
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Lei Shen
- Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, 91010, USA
| | - 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.
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China.
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24
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López DJ, Rodríguez JA, Bañuelos S. Nucleophosmin, a multifunctional nucleolar organizer with a role in DNA repair. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140532. [PMID: 32853771 DOI: 10.1016/j.bbapap.2020.140532] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022]
Abstract
Nucleophosmin (NPM1) is a mostly nucleolar protein with crucial functions in cell growth and homeostasis, including regulation of ribosome biogenesis and stress response. Such multiple activities rely on its ability to interact with nucleic acids and with hundreds of proteins, as well as on a dynamic subcellular distribution. NPM1 is thus regulated by a complex interplay between localization and interactions, further modulated by post-translational modifications. NPM1 is a homopentamer, with globular domains connected by long, intrinsically disordered linkers. This configuration allows NPM1 to engage in liquid-liquid phase separation phenomena, which could underlie a key role in nucleolar organization. Here, we will discuss NPM1 conformational and functional versatility, emphasizing its emerging, and still largely unexplored, role in DNA damage repair. Since NPM1 is altered in a subtype of acute myeloid leukaemia (AML), we will also present ongoing research on the molecular mechanisms underlying its pathogenic role and potential NPM1-targeting therapeutic strategies.
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Affiliation(s)
- David J López
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - José A Rodríguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Sonia Bañuelos
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain.
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25
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Moor N, Vasil’eva I, Lavrik O. Functional Role of N-Terminal Extension of Human AP Endonuclease 1 In Coordination of Base Excision DNA Repair via Protein-Protein Interactions. Int J Mol Sci 2020; 21:ijms21093122. [PMID: 32354179 PMCID: PMC7247576 DOI: 10.3390/ijms21093122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
Human apurinic/apyrimidinic endonuclease 1 (APE1) has multiple functions in base excision DNA repair (BER) and other cellular processes. Its eukaryote-specific N-terminal extension plays diverse regulatory roles in interaction with different partners. Here, we explored its involvement in interaction with canonical BER proteins. Using fluorescence based-techniques, we compared binding affinities of the full-length and N-terminally truncated forms of APE1 (APE1NΔ35 and APE1NΔ61) for functionally and structurally different DNA polymerase β (Polβ), X-ray repair cross-complementing protein 1 (XRCC1), and poly(adenosine diphosphate (ADP)-ribose) polymerase 1 (PARP1), in the absence and presence of model DNA intermediates. Influence of the N-terminal truncation on binding the AP site-containing DNA was additionally explored. These data suggest that the interaction domain for proteins is basically formed by the conserved catalytic core of APE1. The N-terminal extension being capable of dynamically interacting with the protein and DNA partners is mostly responsible for DNA-dependent modulation of protein–protein interactions. Polβ, XRCC1, and PARP1 were shown to more efficiently regulate the endonuclease activity of the full-length protein than that of APE1NΔ61, further suggesting contribution of the N-terminal extension to BER coordination. Our results advance the understanding of functional roles of eukaryote-specific protein extensions in highly coordinated BER processes.
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Affiliation(s)
- Nina Moor
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (N.M.); (I.V.)
| | - Inna Vasil’eva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (N.M.); (I.V.)
| | - Olga Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (N.M.); (I.V.)
- Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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26
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Cleavage of the APE1 N-Terminal Domain in Acute Myeloid Leukemia Cells Is Associated with Proteasomal Activity. Biomolecules 2020; 10:biom10040531. [PMID: 32244430 PMCID: PMC7226146 DOI: 10.3390/biom10040531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 02/02/2023] Open
Abstract
Apurinic/apyrimidinic endonuclease 1 (APE1), the main mammalian AP-endonuclease for the resolution of DNA damages through the base excision repair (BER) pathway, acts as a multifunctional protein in different key cellular processes. The signals to ensure temporo-spatial regulation of APE1 towards a specific function are still a matter of debate. Several studies have suggested that post-translational modifications (PTMs) act as dynamic molecular mechanisms for controlling APE1 functionality. Interestingly, the N-terminal region of APE1 is a disordered portion functioning as an interface for protein binding, as an acceptor site for PTMs and as a target of proteolytic cleavage. We previously demonstrated a cytoplasmic accumulation of truncated APE1 in acute myeloid leukemia (AML) cells in association with a mutated form of nucleophosmin having aberrant cytoplasmic localization (NPM1c+). Here, we mapped the proteolytic sites of APE1 in AML cells at Lys31 and Lys32 and showed that substitution of Lys27, 31, 32 and 35 with alanine impairs proteolysis. We found that the loss of the APE1 N-terminal domain in AML cells is dependent on the proteasome, but not on granzyme A/K as described previously. The present work identified the proteasome as a contributing machinery involved in APE1 cleavage in AML cells, suggesting that acetylation can modulate this process.
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27
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Reading Targeted DNA Damage in the Active Demethylation Pathway: Role of Accessory Domains of Eukaryotic AP Endonucleases and Thymine-DNA Glycosylases. J Mol Biol 2020:S0022-2836(19)30720-X. [DOI: 10.1016/j.jmb.2019.12.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/24/2019] [Accepted: 12/05/2019] [Indexed: 01/07/2023]
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28
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López DJ, de Blas A, Hurtado M, García-Alija M, Mentxaka J, de la Arada I, Urbaneja MA, Alonso-Mariño M, Bañuelos S. Nucleophosmin interaction with APE1: Insights into DNA repair regulation. DNA Repair (Amst) 2020; 88:102809. [PMID: 32092641 DOI: 10.1016/j.dnarep.2020.102809] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 11/17/2022]
Abstract
Nucleophosmin (NPM1), an abundant, nucleolar protein with multiple functions affecting cell homeostasis, has also been recently involved in DNA damage repair. The roles of NPM1 in different repair pathways remain however to be elucidated. NPM1 has been described to interact with APE1 (apurinic apyrimidinic endonuclease 1), a key enzyme of the base excision repair (BER) pathway, which could reflect a direct participation of NPM1 in this route. To gain insight into the possible role(s) of NPM1 in BER, we have explored the interplay between the subnuclear localization of both APE1 and NPM1, the in vitro interaction they establish, the effect of binding to abasic DNA on APE1 conformation, and the modulation by NPM1 of APE1 binding and catalysis on DNA. We have found that, upon oxidative damage, NPM1 is released from nucleoli and locates on patches throughout the chromatin, perhaps co-localizing with APE1, and that this traffic could be mediated by phosphorylation of NPM1 on T199. NPM1 and APE1 form a complex in vitro, involving, apart from the core domain, at least part of the linker region of NPM1, whereas the C-terminal domain is dispensable for binding, which explains that an AML leukemia-related NPM1 mutant with an unfolded C-terminal domain can bind APE1. APE1 interaction with abasic DNA stabilizes APE1 structure, as based on thermal unfolding. Moreover, our data suggest that NPM1, maybe by keeping APE1 in an "open" conformation, favours specific recognition of abasic sites on DNA, competing with off-target associations. Therefore, NPM1 might participate in BER favouring APE1 target selection as well as turnover from incised abasic DNA.
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Affiliation(s)
- David J López
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Ander de Blas
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Mikel Hurtado
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Mikel García-Alija
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Jon Mentxaka
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Igor de la Arada
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - María A Urbaneja
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Marián Alonso-Mariño
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Sonia Bañuelos
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain.
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Architecture of The Human Ape1 Interactome Defines Novel Cancers Signatures. Sci Rep 2020; 10:28. [PMID: 31913336 PMCID: PMC6949240 DOI: 10.1038/s41598-019-56981-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 12/16/2019] [Indexed: 12/19/2022] Open
Abstract
APE1 is essential in cancer cells due to its central role in the Base Excision Repair pathway of DNA lesions and in the transcriptional regulation of genes involved in tumor progression/chemoresistance. Indeed, APE1 overexpression correlates with chemoresistance in more aggressive cancers, and APE1 protein-protein interactions (PPIs) specifically modulate different protein functions in cancer cells. Although important, a detailed investigation on the nature and function of protein interactors regulating APE1 role in tumor progression and chemoresistance is still lacking. The present work was aimed at analyzing the APE1-PPI network with the goal of defining bad prognosis signatures through systematic bioinformatics analysis. By using a well-characterized HeLa cell model stably expressing a flagged APE1 form, which was subjected to extensive proteomics analyses for immunocaptured complexes from different subcellular compartments, we here demonstrate that APE1 is a central hub connecting different subnetworks largely composed of proteins belonging to cancer-associated communities and/or involved in RNA- and DNA-metabolism. When we performed survival analysis in real cancer datasets, we observed that more than 80% of these APE1-PPI network elements is associated with bad prognosis. Our findings, which are hypothesis generating, strongly support the possibility to infer APE1-interactomic signatures associated with bad prognosis of different cancers; they will be of general interest for the future definition of novel predictive disease biomarkers. Future studies will be needed to assess the function of APE1 in the protein complexes we discovered. Data are available via ProteomeXchange with identifier PXD013368.
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30
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Shining light on the response to repair intermediates in DNA of living cells. DNA Repair (Amst) 2019; 85:102749. [PMID: 31790865 DOI: 10.1016/j.dnarep.2019.102749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/03/2019] [Accepted: 11/08/2019] [Indexed: 11/22/2022]
Abstract
Fluorescently-tagged repair proteins have been widely used to probe recruitment to micro-irradiation-induced nuclear DNA damage in living cells. Here, we quantify APE1 dynamics after micro-irradiation. Markers of DNA damage are characterized and UV-A laser micro-irradiation energy conditions are selected for formation of oxidatively-induced DNA base damage and single strand breaks, but without detectable double strand breaks. Increased energy of laser micro-irradiation, compared with that used previously in our work, enables study of APE1 dynamics at the lesion site. APE1 shows rapid transient kinetics, with recruitment half-time of less than 1 s and dissociation half-time of less than 15 s. In cells co-transfected with APE1 and PARP1, the recruitment half-time of PARP1 was slower than that of APE1, indicating APE1 is a rapid responder to the damage site. While recruitment of APE1 is unchanged in the presence of co-transfected PARP1, APE1 dissociation is 3-fold slower, revealing PARP1 involvement in APE1 dynamics. Further, we find that APE1 dissociation kinetics are strongly modified in the absence of DNA polymerase β (pol β). After unchanged recruitment to the damage site, dissociation of APE1 became undetectable. This indicates a necessary role for pol β in APE1 release after its recruitment to the damage site. These observations represent an advance in our understanding of in vivo dynamics of base excision repair factors APE1, PARP1 and pol β.
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31
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Bazlekowa-Karaban M, Prorok P, Baconnais S, Taipakova S, Akishev Z, Zembrzuska D, Popov AV, Endutkin AV, Groisman R, Ishchenko AA, Matkarimov BT, Bissenbaev A, Le Cam E, Zharkov DO, Tudek B, Saparbaev M. Mechanism of stimulation of DNA binding of the transcription factors by human apurinic/apyrimidinic endonuclease 1, APE1. DNA Repair (Amst) 2019; 82:102698. [PMID: 31518879 DOI: 10.1016/j.dnarep.2019.102698] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 08/11/2019] [Accepted: 08/31/2019] [Indexed: 12/22/2022]
Abstract
Aerobic respiration generates reactive oxygen species (ROS), which can damage nucleic acids, proteins and lipids. A number of transcription factors (TFs) contain redox-sensitive cysteine residues at their DNA-binding sites, hence ROS-induced thiol oxidation strongly inhibits their recognition of the cognate DNA sequences. Major human apurinic/apyrimidinic (AP) endonuclease 1 (APE1/APEX1/HAP-1), referred also as a redox factor 1 (Ref-1), stimulates the DNA binding activities of the oxidized TFs such as AP-1 and NF-κB. Also, APE1 participates in the base excision repair (BER) and nucleotide incision repair (NIR) pathways to remove oxidative DNA base damage. At present, the molecular mechanism underlying the TF-stimulating/redox function of APE1 and its biological role remains disputed. Here, we provide evidence that, instead of direct cysteine reduction in TFs by APE1, APE1-catalyzed NIR and TF-stimulating activities may be based on transient cooperative binding of APE1 to DNA and induction of conformational changes in the helix. The structure of DNA duplex strongly influences NIR and TF-stimulating activities. Homologous plant AP endonucleases lacking conserved cysteine residues stimulate DNA binding of the p50 subunit of NF-κB. APE1 acts synergistically with low-molecular-weight reducing agents on TFs. Finally, APE1 stimulates DNA binding of the redox-insensitive p50-C62S mutant protein. Electron microscopy imaging of APE1 complexes with DNA revealed preferential polymerization of APE1 on the gapped and intrinsically curved DNA duplexes. Molecular modeling offers a structural explanation how full-length APE1 can oligomerize on DNA. In conclusion, we propose that DNA-directed APE1 oligomerization can be regarded as a substitute for diffusion of APE1 along the DNA contour to probe for anisotropic flexibility. APE1 oligomers exacerbate pre-existing distortions in DNA and enable both NIR activity and DNA binding by TFs regardless of their oxidation state.
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Affiliation(s)
- Milena Bazlekowa-Karaban
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale Contre le Cancer, CNRS UMR8200, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Paulina Prorok
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale Contre le Cancer, CNRS UMR8200, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Institute of Human Genetics, UMR 9002, CNRS - University of Montpellier, Replication and Genome Dynamics, 141 rue de la Cardonille, 34396, Montpellier, France
| | - Sonia Baconnais
- CNRS UMR8126, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Sabira Taipakova
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan
| | - Zhiger Akishev
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan
| | - Dominika Zembrzuska
- Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Alexander V Popov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anton V Endutkin
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Regina Groisman
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale Contre le Cancer, CNRS UMR8200, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Alexander A Ishchenko
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale Contre le Cancer, CNRS UMR8200, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Bakhyt T Matkarimov
- National laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Amangeldy Bissenbaev
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan
| | - Eric Le Cam
- CNRS UMR8126, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Barbara Tudek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Murat Saparbaev
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale Contre le Cancer, CNRS UMR8200, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France.
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Malfatti MC, Gerratana L, Dalla E, Isola M, Damante G, Di Loreto C, Puglisi F, Tell G. APE1 and NPM1 protect cancer cells from platinum compounds cytotoxicity and their expression pattern has a prognostic value in TNBC. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:309. [PMID: 31307523 PMCID: PMC6631760 DOI: 10.1186/s13046-019-1294-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 06/25/2019] [Indexed: 02/07/2023]
Abstract
Background Triple negative breast cancer (TNBC) is a breast cancer subgroup characterized by a lack of hormone receptors’ expression and no HER2 overexpression. These molecular features both drastically reduce treatment options and confer poor prognosis. Platinum (Pt)-salts are being investigated as a new therapeutic strategy. The base excision repair (BER) pathway is important for resistance to Pt-based therapies. Overexpression of APE1, a pivotal enzyme of the BER pathway, as well as the expression of NPM1, a functional regulator of APE1, are associated with poor outcome and resistance to Pt-based therapies. Methods We evaluated the role of NPM1, APE1 and altered NPM1/APE1 interaction in the response to Pt-salts treatment in different cell lines: APE1 knockout (KO) cells, NPM1 KO cells, cell line models having an altered APE1/NPM1 interaction and HCC70 and HCC1937 TNBC cell lines, having different levels of APE1/NPM1. We evaluated the TNBC cells response to new chemotherapeutic small molecules targeting the endonuclease activity of APE1 or the APE1/NPM1 interaction, in combination with Pt-salts treatments. Expression levels’ correlation between APE1 and NPM1 and their impact on prognosis was analyzed in a cohort of TNBC patients through immunohistochemistry. Bioinformatics analysis, using TCGA datasets, was performed to predict a molecular signature of cancers based on APE1 and NPM1 expression. Results APE1 and NPM1, and their interaction as well, protect from the cytotoxicity induced by Pt-salts treatment. HCC1937 cells, having higher levels of APE1/NPM1 proteins, are more resistant to Pt-salts treatment compared to the HCC70 cells. A sensitization effect by APE1 inhibitors to Pt-compounds was observed. The association of NPM1/APE1 with cancer gene signatures highlighted alterations concerning cell-cycle dependent proteins. Conclusions APE1 and NPM1 protect cancer cells from Pt-compounds cytotoxicity, suggesting a possible improvement of the activity of Pt-based therapy for TNBC, using the NPM1 and APE1 proteins as secondary therapeutic targets. Based on positive or negative correlation with APE1 and NPM1 gene expression levels, we finally propose several TNBC gene signatures that should deserve further attention for their potential impact on TNBC precision medicine approaches. Electronic supplementary material The online version of this article (10.1186/s13046-019-1294-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Lorenzo Gerratana
- Department of Medicine (DAME), University of Udine, Piazzale M. Kolbe 4, 33100, Udine, Italy.,Department of Oncology, ASUI Udine SMM University Hospital Udine, Udine, Italy
| | - Emiliano Dalla
- Department of Medicine (DAME), University of Udine, Piazzale M. Kolbe 4, 33100, Udine, Italy
| | - Miriam Isola
- Department of Medicine (DAME), University of Udine, Piazzale M. Kolbe 4, 33100, Udine, Italy
| | - Giuseppe Damante
- Department of Medicine (DAME), University of Udine, Piazzale M. Kolbe 4, 33100, Udine, Italy
| | - Carla Di Loreto
- Department of Medicine (DAME), University of Udine, Piazzale M. Kolbe 4, 33100, Udine, Italy.,Department of Pathology, ASUI Udine SMM University Hospital Udine, Udine, Italy
| | - Fabio Puglisi
- Department of Medicine (DAME), University of Udine, Piazzale M. Kolbe 4, 33100, Udine, Italy.,Department of Medical Oncology, Centro di Riferimento Oncologico (CRO), IRCCS, Aviano, Italy
| | - Gianluca Tell
- Department of Medicine (DAME), University of Udine, Piazzale M. Kolbe 4, 33100, Udine, Italy.
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Sun Y, Feng Y, Zhang G, Xu Y. The endonuclease APE1 processes miR-92b formation, thereby regulating expression of the tumor suppressor LDLR in cervical cancer cells. Ther Adv Med Oncol 2019; 11:1758835919855859. [PMID: 31320936 PMCID: PMC6624912 DOI: 10.1177/1758835919855859] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 05/01/2019] [Indexed: 12/25/2022] Open
Abstract
Background The molecular mechanisms underlying cervical cancer require elucidation to identify novel therapeutic targets. Apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) is a multifunctional apurinic/apyrimidinic (AP) endonuclease that influences the transcription of many cancer-related genes via microRNome regulation. Herein, we examine the role of miR-92b-3p (hereinafter miR-92b), whose processing may be regulated by APE1, in cervical cancer progression. Methods APE1's processing of miR-92b from its pri-miR form was measured by a quantitative reverse transcription polymerase chain reaction (qRT-PCR)-based ratio. APE1's endonuclease activity was measured with AP-site incision assays. APE1-DROSHA interaction was studied with immunofluorescence, confocal and proximity ligation analyses. The miR-92b's targeting of low-density lipoprotein receptor (LDLR) was investigated with luciferase reporter assays. The miR-92b mimics and shRNA-based miR-92b silencing, as well as LDLR overexpression and short interfering RNA (siRNA)-based LDLR silencing, were employed in CaSki and SiHa cervical cancer cells. Cell proliferation and chemosensitivity to paclitaxel and cisplatin were assayed. Cell-cycle progression and apoptosis were assessed by flow cytometry. Tumor growth was studied in a murine xenograft model. Results APE1's endonuclease activity, via association with the DROSHA-processing complex, is necessary for processing mature miR-92b, thereby regulating expression of miR-92b's direct target LDLR. The miR-92b promotes cell proliferation in vitro and in vivo, promotes cell-cycle progression, and reduces apoptosis and chemosensitivity. LDLR silencing recapitulated miR-92b's transformative effects, while LDLR overexpression rescued these effects. Conclusions APE1 enhances miR-92b processing, thereby suppressing LDLR expression and enhancing cervical carcinoma progression. Our identification of the novel APE1-miR-92b-LDLR axis improves our understanding of the complex pathogenesis of cervical carcinoma and reveals a novel therapeutic strategy for combating this disease.
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Affiliation(s)
- Yi Sun
- Department of Clinical Laboratory Medicine, the First People's Hospital of Yunnan Province, No. 157, Jinbi Road, Kunming, Yunnan Province, China
| | - Yun Feng
- Department of Reproductive Gynecology, The First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Guiqian Zhang
- Department of Clinical Laboratory Medicine, The First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Ya Xu
- Department of Clinical Laboratory Medicine, The First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
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Somatostatin as Inflow Modulator in Liver-transplant Recipients With Severe Portal Hypertension. Ann Surg 2019; 269:1025-1033. [DOI: 10.1097/sla.0000000000003062] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Di Natale C, La Manna S, Malfitano AM, Di Somma S, Florio D, Scognamiglio PL, Novellino E, Netti PA, Marasco D. Structural insights into amyloid structures of the C-terminal region of nucleophosmin 1 in type A mutation of acute myeloid leukemia. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:637-644. [PMID: 30710643 DOI: 10.1016/j.bbapap.2019.01.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/11/2019] [Accepted: 01/26/2019] [Indexed: 12/22/2022]
Abstract
Acute myeloid leukemia (AML) is a clinically and a molecularly heterogeneous disease characterized by the accumulation of undifferentiated and uncontrolled proliferation of hematopoietic progenitor cells. The sub-group named "AML with gene mutations" includes mutations in nucleophosmin (NPM1) assumed as a distinct leukemic entity. NPM1 is an abundant multifunctional protein belonging to the nucleoplasmin family of nuclear chaperones. AML mutated protein is translocated into the cytoplasm (NPM1c+) retaining all functional domains except the loss of a unique NoLs (nucleolar localization signal) at the C-term domain (CTD) and the subsequent disruption of a three helix bundle as tertiary structure. The oligomeric state of NPM1 is of outmost importance for its biological roles and our previous studies linked an aggregation propensity of distinct regions of CTD to leukomogenic potentials of AML mutations. Here we investigated a polypeptide spanning the third and second helices of the bundle of type A mutated CTD. By a combination of several techniques, we ascertained the amyloid character of the aggregates and of fibrils resulting from a self-recognition mechanism. Further amyloid assemblies resulted cytoxic in MTT assay strengthening a new idea of a therapeutic strategy in AML consisting in the self-degradation of mutated NPM1.
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Affiliation(s)
- Concetta Di Natale
- Department of Pharmacy, University of Naples "Federico II", Italy; Center for Advanced Biomaterial for Health Care (CABHC), Istituto Italiano di Tecnologia, Naples, Italy
| | - Sara La Manna
- Department of Pharmacy, University of Naples "Federico II", Italy
| | | | - Sarah Di Somma
- Department of Translational Medicine, University of Naples "Federico II", Italy
| | - Daniele Florio
- Department of Pharmacy, University of Naples "Federico II", Italy
| | | | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II", Italy
| | - Paolo Antonio Netti
- Center for Advanced Biomaterial for Health Care (CABHC), Istituto Italiano di Tecnologia, Naples, Italy
| | - Daniela Marasco
- Department of Pharmacy, University of Naples "Federico II", Italy.
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Serum AP-endonuclease 1 (sAPE1) as novel biomarker for hepatocellular carcinoma. Oncotarget 2019; 10:383-394. [PMID: 30719231 PMCID: PMC6349448 DOI: 10.18632/oncotarget.26555] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 12/27/2018] [Indexed: 12/24/2022] Open
Abstract
Late diagnosis for Hepatocellular Carcinoma (HCC) remains one of the leading causes for the high mortality rate. The apurinic/apyrimidinic endonuclease 1 (APE1), an essential member of the base excision DNA repair (BER) pathway, contributes to cell response to oxidative stress and has other non-repair activities. In this study, we evaluate the role of serum APE1 (sAPE1) as a new diagnostic biomarker and we investigate the biological role for extracellular APE1 in HCC. sAPE1 level was quantified in 99 HCC patients, 50 non-HCC cirrhotic and 100 healthy controls. The expression level was significantly high in HCC (75.8 [67.3–87.9] pg/mL) compared to cirrhosis (29.8 [18.3–36.5] pg/mL] and controls (10.8 [7.5–13.2] pg/mL) (p < 0.001). The sAPE1 level corresponded with its protein expression in HCC tissue. sAPE1 had high diagnostic accuracy to differentiate HCC from cirrhotic (AUC = 0.87, sensitivity 88%, specificity 71%, cut-off of 36.3 pg/mL) and healthy subjects (AUC 0.98, sensibility 98% and specificity 83%, cut-off of 19.0 pg/mL). Recombinant APE1, exogenously added to JHH6 cells, significantly promotes IL-6 and IL-8 expression, suggesting a role of sAPE1 as a paracrine pro-inflammatory molecule, which may modulate the inflammatory status in cancer microenvironment. We described herein, for the first time to our knowledge, that sAPE1 might be considered as a promising diagnostic biomarker for HCC.
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Burra S, Marasco D, Malfatti MC, Antoniali G, Virgilio A, Esposito V, Demple B, Galeone A, Tell G. Human AP-endonuclease (Ape1) activity on telomeric G4 structures is modulated by acetylatable lysine residues in the N-terminal sequence. DNA Repair (Amst) 2018; 73:129-143. [PMID: 30509560 DOI: 10.1016/j.dnarep.2018.11.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 02/08/2023]
Abstract
Loss of telomeres stability is a hallmark of cancer cells. Exposed telomeres are prone to aberrant end-joining reactions leading to chromosomal fusions and translocations. Human telomeres contain repeated TTAGGG elements, in which the 3' exposed strand may adopt a G-quadruplex (G4) structure. The guanine-rich regions of telomeres are hotspots for oxidation forming 8-oxoguanine, a lesion that is handled by the base excision repair (BER) pathway. One key player of this pathway is Ape1, the main human endonuclease processing abasic sites. Recent evidences showed an important role for Ape1 in telomeric physiology, but the molecular details regulating Ape1 enzymatic activities on G4-telomeric sequences are lacking. Through a combination of in vitro assays, we demonstrate that Ape1 can bind and process different G4 structures and that this interaction involves specific acetylatable lysine residues (i.e. K27/31/32/35) present in the unstructured N-terminal sequence of the protein. The cleavage of an abasic site located in a G4 structure by Ape1 depends on the DNA conformation or the position of the lesion and on electrostatic interactions between the protein and the nucleic acids. Moreover, Ape1 mutants mimicking the acetylated protein display increased cleavage activity for abasic sites. We found that nucleophosmin (NPM1), which binds the N-terminal sequence of Ape1, plays a role in modulating telomere length and Ape1 activity at abasic G4 structures. Thus, the Ape1 N-terminal sequence is an important relay site for regulating the enzyme's activity on G4-telomeric sequences, and specific acetylatable lysine residues constitute key regulatory sites of Ape1 enzymatic activity dynamics at telomeres.
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Affiliation(s)
- Silvia Burra
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Daniela Marasco
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Antonella Virgilio
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Veronica Esposito
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Bruce Demple
- Department of Pharmacological Sciences, Stony Brook University, School of Medicine, Stony Brook, NY, 11794-8651, USA
| | - Aldo Galeone
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine (DAME), University of Udine, Udine, Italy.
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38
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Ilina ES, Khodyreva SN, Lavrik OI. Unusual interaction of human apurinic/apyrimidinic endonuclease 1 (APE1) with abasic sites via the Schiff-base-dependent mechanism. Biochimie 2018; 150:88-99. [PMID: 29730300 DOI: 10.1016/j.biochi.2018.04.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 04/30/2018] [Indexed: 12/12/2022]
Abstract
Clustered apurinic/apyrimidinic (AP) sites are more cytotoxic than isolated AP lesions because double strand breaks (DSB) can be formed during repair of closely positioned bistranded AP sites. Formation of DSB due to simultaneous cleavage of bistranded AP sites may be regulated by proteins specifically interacting with this complex lesion. A set of AP DNA duplexes containing AP sites in both strands in different mutual orientation (BS-AP DNAs) was used for search in the extracts of human cells proteins specifically recognizing clustered AP sites. A protein, which formed the Schiff-base-dependent covalent products having an apparent molecular mass of 50 kDa with the subset of BS-AP DNAs, was identified by mass spectrometry as apurinic/apyrimidinic endonuclease 1 (APE1). The identity of trapped protein was confirmed by Western blot analysis with anti-APE1 antibodies. Purified recombinant human APE1 is also capable of forming the 50 kDa-adducts with efficiency of BS-AP DNAs cross-linking to APE1 being dependent on the mutual orientation of AP sites. In spite of formation of the Schiff-base-dependent intermediate, which is prerequisite for the β-elimination mechanism, APE1 is unable to cleave AP sites. APE1 lacking the first 34 amino acids at the N-terminus, unlike wild type enzyme, is unable to form cross-links with BS-AP DNAs that testifies to the involvement of disordered N-terminal extension, which is enriched in lysine residues, in the interaction with AP sites. The yield of APE1-AP DNA cross-links was found to correlate with the enzyme amount in the extracts estimated by the immunochemical approach; therefore the BS-AP DNA-probes can be useful for comparative analysis of APE1 content in cell extracts.
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Affiliation(s)
- Ekaterina S Ilina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Svetlana N Khodyreva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia.
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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.
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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.
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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.
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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.
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Alemasova EE, Naumenko KN, Moor NA, Lavrik OI. Y-Box-Binding Protein 1 Stimulates Abasic Site Cleavage. BIOCHEMISTRY (MOSCOW) 2018; 82:1521-1528. [PMID: 29486702 DOI: 10.1134/s0006297917120112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Apurinic/apyrimidinic (AP) sites are among the most frequent DNA lesions. The first step in the AP site repair involves the magnesium-dependent enzyme AP endonuclease 1 (APE1) that catalyzes hydrolytic cleavage of the DNA phosphodiester bond at the 5' side of the AP site, thereby generating a single-strand DNA break flanked by the 3'-OH and 5'-deoxyribose phosphate (dRP) groups. Increased APE1 activity in cancer cells might correlate with tumor chemoresistance to DNA-damaging treatment. It has been previously shown that the multifunctional oncoprotein Y-box-binding protein 1 (YB-1) interacts with APE1 and inhibits APE1-catalyzed hydrolysis of AP sites in single-stranded DNAs. In this work, we demonstrated that YB-1 stabilizes the APE1 complex with double-stranded DNAs containing the AP sites and stimulates cleavage of these AP sites at low magnesium concentrations.
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Affiliation(s)
- E E Alemasova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
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Kladova OA, Bazlekowa-Karaban M, Baconnais S, Piétrement O, Ishchenko AA, Matkarimov BT, Iakovlev DA, Vasenko A, Fedorova OS, Le Cam E, Tudek B, Kuznetsov NA, Saparbaev M. The role of the N-terminal domain of human apurinic/apyrimidinic endonuclease 1, APE1, in DNA glycosylase stimulation. DNA Repair (Amst) 2018; 64:10-25. [PMID: 29475157 DOI: 10.1016/j.dnarep.2018.02.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 01/09/2018] [Accepted: 02/06/2018] [Indexed: 12/25/2022]
Abstract
The base excision repair (BER) pathway consists of sequential action of DNA glycosylase and apurinic/apyrimidinic (AP) endonuclease necessary to remove a damaged base and generate a single-strand break in duplex DNA. Human multifunctional AP endonuclease 1 (APE1, a.k.a. APEX1, HAP-1, or Ref-1) plays essential roles in BER by acting downstream of DNA glycosylases to incise a DNA duplex at AP sites and remove 3'-blocking sugar moieties at DNA strand breaks. Human 8-oxoguanine-DNA glycosylase (OGG1), methyl-CpG-binding domain 4 (MBD4, a.k.a. MED1), and alkyl-N-purine-DNA glycosylase (ANPG, a.k.a. Aag or MPG) excise a variety of damaged bases from DNA. Here we demonstrated that the redox-deficient truncated APE1 protein lacking the first N-terminal 61 amino acid residues (APE1-NΔ61) cannot stimulate DNA glycosylase activities of OGG1, MBD4, and ANPG on duplex DNA substrates. Electron microscopy imaging of APE1-DNA complexes revealed oligomerization of APE1 along the DNA duplex and APE1-mediated DNA bridging followed by DNA aggregation. APE1 polymerizes on both undamaged and damaged DNA in cooperative mode. Association of APE1 with undamaged DNA may enable scanning for damage; however, this event reduces effective concentration of the enzyme and subsequently decreases APE1-catalyzed cleavage rates on long DNA substrates. We propose that APE1 oligomers on DNA induce helix distortions thereby enhancing molecular recognition of DNA lesions by DNA glycosylases via a conformational proofreading/selection mechanism. Thus, APE1-mediated structural deformations of the DNA helix stabilize the enzyme-substrate complex and promote dissociation of human DNA glycosylases from the AP site with a subsequent increase in their turnover rate. SIGNIFICANCE STATEMENT The major human apurinic/apyrimidinic (AP) endonuclease, APE1, stimulates DNA glycosylases by increasing their turnover rate on duplex DNA substrates. At present, the mechanism of the stimulation remains unclear. We report that the redox domain of APE1 is necessary for the active mode of stimulation of DNA glycosylases. Electron microscopy revealed that full-length APE1 oligomerizes on DNA possibly via cooperative binding to DNA. Consequently, APE1 shows DNA length dependence with preferential repair of short DNA duplexes. We propose that APE1-catalyzed oligomerization along DNA induces helix distortions, which in turn enable conformational selection and stimulation of DNA glycosylases. This new biochemical property of APE1 sheds light on the mechanism of redox function and its role in DNA repair.
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Affiliation(s)
- Olga A Kladova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Milena Bazlekowa-Karaban
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR8200, Université Paris-Sud, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France; Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Sonia Baconnais
- CNRS UMR8126, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy, F-94805 Villejuif Cedex, France
| | - Olivier Piétrement
- CNRS UMR8126, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy, F-94805 Villejuif Cedex, France
| | - Alexander A Ishchenko
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR8200, Université Paris-Sud, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Bakhyt T Matkarimov
- National laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Danila A Iakovlev
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Andrey Vasenko
- National Research University Higher School of Economics, 101000 Moscow, Russia
| | - Olga S Fedorova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Eric Le Cam
- CNRS UMR8126, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy, F-94805 Villejuif Cedex, France
| | - Barbara Tudek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Nikita A Kuznetsov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia.
| | - Murat Saparbaev
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR8200, Université Paris-Sud, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France.
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APE1 polymorphic variants cause persistent genomic stress and affect cancer cell proliferation. Oncotarget 2018; 7:26293-306. [PMID: 27050370 PMCID: PMC5041981 DOI: 10.18632/oncotarget.8477] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 03/12/2016] [Indexed: 01/15/2023] Open
Abstract
Apurinic/apyrimidinic endonuclease 1 (APE1) is the main mammalian AP-endonuclease responsible for the repair of endogenous DNA damage through the base excision repair (BER) pathway. Molecular epidemiological studies have identified several genetic variants associated with human diseases, but a well-defined functional connection between mutations in APE1 and disease development is lacking. In order to understand the biological consequences of APE1 genetic mutations, we examined the molecular and cellular consequences of the selective expression of four non-synonymous APE1 variants (L104R, R237C, D148E and D283G) in human cells. We found that D283G, L104R and R237C variants have reduced endonuclease activity and impaired ability to associate with XRCC1 and DNA polymerase β, which are enzymes acting downstream of APE1 in the BER pathway. Complementation experiments performed in cells, where endogenous APE1 had been silenced by shRNA, showed that the expression of these variants resulted in increased phosphorylation of histone H2Ax and augmented levels of poly(ADP-ribosyl)ated (PAR) proteins. Persistent activation of DNA damage response markers was accompanied by growth defects likely due to combined apoptotic and autophagic processes. These phenotypes were observed in the absence of exogenous stressors, suggesting that chronic replication stress elicited by the BER defect may lead to a chronic activation of the DNA damage response. Hence, our data reinforce the concept that non-synonymous APE1 variants present in the human population may act as cancer susceptibility alleles.
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44
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Molecules that target nucleophosmin for cancer treatment: an update. Oncotarget 2018; 7:44821-44840. [PMID: 27058426 PMCID: PMC5190137 DOI: 10.18632/oncotarget.8599] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/28/2016] [Indexed: 11/25/2022] Open
Abstract
Nucleophosmin is a highly and ubiquitously expressed protein, mainly localized in nucleoli but able to shuttle between nucleus and cytoplasm. Nucleophosmin plays crucial roles in ribosome maturation and export, centrosome duplication, cell cycle progression, histone assembly and response to a variety of stress stimuli. Much interest in this protein has arisen in the past ten years, since the discovery of heterozygous mutations in the terminal exon of the NPM1 gene, which are the most frequent genetic alteration in acute myeloid leukemia. Nucleophosmin is also frequently overexpressed in solid tumours and, in many cases, its overexpression correlates with mitotic index and metastatization. Therefore it is considered as a promising target for the treatment of both haematologic and solid malignancies. NPM1 targeting molecules may suppress different functions of the protein, interfere with its subcellular localization, with its oligomerization properties or drive its degradation. In the recent years, several such molecules have been described and here we review what is currently known about them, their interaction with nucleophosmin and the mechanistic basis of their toxicity. Collectively, these molecules exemplify a number of different strategies that can be adopted to target nucleophosmin and we summarize them at the end of the review.
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45
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Regulation of limited N-terminal proteolysis of APE1 in tumor via acetylation and its role in cell proliferation. Oncotarget 2017; 7:22590-604. [PMID: 26981776 PMCID: PMC5008384 DOI: 10.18632/oncotarget.8026] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 11/25/2022] Open
Abstract
Mammalian apurinic/apyrimidinic (AP) endonuclease 1 (APE1), a ubiquitous and multifunctional protein, plays an essential role in the repair of both endogenous and drug-induced DNA damages in the genome. Unlike its E.coli counterpart Xth, mammalian APE1 has a unique N-terminal domain and possesses both DNA damage repair and transcriptional regulatory functions. Although the overexpression of APE1 in diverse cancer types and the association of APE1 expression with chemotherapy resistance and poor prognosis are well documented, the cellular and molecular mechanisms that alter APE1 functions during tumorigenesis are largely unknown. Here, we show the presence of full-length APE1 and N-terminal truncated isoforms of APE1 in tumor tissue samples of various cancer types. However, primary tumor tissue has higher levels of acetylated APE1 (AcAPE1) as well as full-length APE1 compared to adjacent non-tumor tissue. We found that APE1 is proteolytically cleaved by an unknown serine protease at its N-terminus following residue lysine (Lys) Lys6 and/or Lys7 and after Lys27 and Lys31 or Lys32. Acetylation of these Lys residues in APE1 prevents this proteolysis. The N-terminal domain of APE1 and its acetylation are required for modulation of the expression of hundreds of genes. Importantly, we found that AcAPE1 is essential for sustained cell proliferation. Together, our study demonstrates that increased acetylation levels of APE1 in tumor cells inhibit the limited N-terminal proteolysis of APE1 and thereby maintain the functions of APE1 to promote tumor cells' sustained proliferation and survival.
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46
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Scott DD, Trahan C, Zindy PJ, Aguilar LC, Delubac MY, Van Nostrand EL, Adivarahan S, Wei KE, Yeo GW, Zenklusen D, Oeffinger M. Nol12 is a multifunctional RNA binding protein at the nexus of RNA and DNA metabolism. Nucleic Acids Res 2017; 45:12509-12528. [PMID: 29069457 PMCID: PMC5716212 DOI: 10.1093/nar/gkx963] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 10/01/2017] [Accepted: 10/09/2017] [Indexed: 12/29/2022] Open
Abstract
To counteract the breakdown of genome integrity, eukaryotic cells have developed a network of surveillance pathways to prevent and resolve DNA damage. Recent data has recognized the importance of RNA binding proteins (RBPs) in DNA damage repair (DDR) pathways. Here, we describe Nol12 as a multifunctional RBP with roles in RNA metabolism and genome maintenance. Nol12 is found in different subcellular compartments-nucleoli, where it associates with ribosomal RNA and is required for efficient separation of large and small subunit precursors at site 2; the nucleoplasm, where it co-localizes with the RNA/DNA helicase Dhx9 and paraspeckles; as well as GW/P-bodies in the cytoplasm. Loss of Nol12 results in the inability of cells to recover from DNA stress and a rapid p53-independent ATR-Chk1-mediated apoptotic response. Nol12 co-localizes with DNA repair proteins in vivo including Dhx9, as well as with TOPBP1 at sites of replication stalls, suggesting a role for Nol12 in the resolution of DNA stress and maintenance of genome integrity. Identification of a complex Nol12 interactome, which includes NONO, Dhx9, DNA-PK and Stau1, further supports the protein's diverse functions in RNA metabolism and DNA maintenance, establishing Nol12 as a multifunctional RBP essential for genome integrity.
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Affiliation(s)
- Daniel D. Scott
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
| | - Christian Trahan
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Pierre J. Zindy
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
| | - Lisbeth C. Aguilar
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
| | - Marc Y. Delubac
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Eric L. Van Nostrand
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA; Stem Cell Program, University of California at San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Srivathsan Adivarahan
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Karen E. Wei
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA; Stem Cell Program, University of California at San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Molecular Engineering Laboratory, A*STAR, Singapore
| | - Daniel Zenklusen
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Marlene Oeffinger
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
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47
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Malfatti MC, Balachander S, Antoniali G, Koh KD, Saint-Pierre C, Gasparutto D, Chon H, Crouch RJ, Storici F, Tell G. Abasic and oxidized ribonucleotides embedded in DNA are processed by human APE1 and not by RNase H2. Nucleic Acids Res 2017; 45:11193-11212. [PMID: 28977421 PMCID: PMC5737539 DOI: 10.1093/nar/gkx723] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 08/11/2017] [Indexed: 12/13/2022] Open
Abstract
Ribonucleoside 5′-monophosphates (rNMPs) are the most common non-standard nucleotides found in DNA of eukaryotic cells, with over 100 million rNMPs transiently incorporated in the mammalian genome per cell cycle. Human ribonuclease (RNase) H2 is the principal enzyme able to cleave rNMPs in DNA. Whether RNase H2 may process abasic or oxidized rNMPs incorporated in DNA is unknown. The base excision repair (BER) pathway is mainly responsible for repairing oxidized and abasic sites into DNA. Here we show that human RNase H2 is unable to process an abasic rNMP (rAP site) or a ribose 8oxoG (r8oxoG) site embedded in DNA. On the contrary, we found that recombinant purified human apurinic/apyrimidinic endonuclease-1 (APE1) and APE1 from human cell extracts efficiently process an rAP site in DNA and have weak endoribonuclease and 3′-exonuclease activities on r8oxoG substrate. Using biochemical assays, our results provide evidence of a human enzyme able to recognize and process abasic and oxidized ribonucleotides embedded in DNA.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, Udine, Italy
| | - Sathya Balachander
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, Udine, Italy
| | - Kyung Duk Koh
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,University of California, San Francisco, UCSF, School of Medicine, San Francisco, CA, USA
| | - Christine Saint-Pierre
- Chimie Reconnaissance & Etude Assemblages Biologiques, Université Grenoble Alpes, SPrAM UMR5819 CEA CNRS UGA, INAC/CEA, Grenoble, France
| | - Didier Gasparutto
- Chimie Reconnaissance & Etude Assemblages Biologiques, Université Grenoble Alpes, SPrAM UMR5819 CEA CNRS UGA, INAC/CEA, Grenoble, France
| | - Hyongi Chon
- Developmental Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Robert J Crouch
- Developmental Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, Udine, Italy
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48
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Antoniali G, Serra F, Lirussi L, Tanaka M, D'Ambrosio C, Zhang S, Radovic S, Dalla E, Ciani Y, Scaloni A, Li M, Piazza S, Tell G. Mammalian APE1 controls miRNA processing and its interactome is linked to cancer RNA metabolism. Nat Commun 2017; 8:797. [PMID: 28986522 PMCID: PMC5630600 DOI: 10.1038/s41467-017-00842-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 07/28/2017] [Indexed: 01/31/2023] Open
Abstract
Mammalian apurinic/apyrimidinic endonuclease 1 is a DNA repair enzyme involved in genome stability and expression of genes involved in oxidative stress responses, tumor progression and chemoresistance. However, the molecular mechanisms underlying the role of apurinic/apyrimidinic endonuclease 1 in these processes are still unclear. Recent findings point to a novel role of apurinic/apyrimidinic endonuclease 1 in RNA metabolism. Through the characterization of the interactomes of apurinic/apyrimidinic endonuclease 1 with RNA and other proteins, we demonstrate here a role for apurinic/apyrimidinic endonuclease 1 in pri-miRNA processing and stability via association with the DROSHA-processing complex during genotoxic stress. We also show that endonuclease activity of apurinic/apyrimidinic endonuclease 1 is required for the processing of miR-221/222 in regulating expression of the tumor suppressor PTEN. Analysis of a cohort of different cancers supports the relevance of our findings for tumor biology. We also show that apurinic/apyrimidinic endonuclease 1 participates in RNA-interactomes and protein-interactomes involved in cancer development, thus indicating an unsuspected post-transcriptional effect on cancer genes. APE1 plays an important role in the cellular response to oxidative stress, and mutations are linked to tumor progression and chemoresistance. Here, the authors characterize the interactions of APE1 with RNA and demonstrate a role in microRNA processing.
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Affiliation(s)
- Giulia Antoniali
- Department of Medicine, Laboratory of Molecular Biology and DNA repair, University of Udine, p.le M. Kolbe 4, Udine, 33100, Italy
| | - Fabrizio Serra
- Department of Medicine, Laboratory of Molecular Biology and DNA repair, University of Udine, p.le M. Kolbe 4, Udine, 33100, Italy.,Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, I.R.C.C.S., via Franco Gallini 2, Aviano (PN), 33081, Italy
| | - Lisa Lirussi
- Department of Medicine, Laboratory of Molecular Biology and DNA repair, University of Udine, p.le M. Kolbe 4, Udine, 33100, Italy.,Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Sykehusveien 27, Nordbyhagen, 1474, Norway
| | - Mikiei Tanaka
- Laboratory of Biochemistry, National Heart Lung and Blood Institute, National Institutes of Health, 50 South Drive, MSC-8012, Bethesda, MD, 20892-8012, USA
| | - Chiara D'Ambrosio
- Proteomics and Mass Spectrometry Laboratory, Institute for the Animal Production System in the Mediterranean Environment (ISPAAM) National Research Council (CNR) of Italy, via Argine 1085, Naples, 80147, Italy
| | - Shiheng Zhang
- Cancer Center of Daping Hospital, Third Military Medical University, Chongqing, 400042, China
| | | | - Emiliano Dalla
- Laboratorio Nazionale CIB, Area Science Park Padriciano, Trieste, 34149, Italy
| | - Yari Ciani
- Laboratorio Nazionale CIB, Area Science Park Padriciano, Trieste, 34149, Italy
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry Laboratory, Institute for the Animal Production System in the Mediterranean Environment (ISPAAM) National Research Council (CNR) of Italy, via Argine 1085, Naples, 80147, Italy
| | - Mengxia Li
- Cancer Center of Daping Hospital, Third Military Medical University, Chongqing, 400042, China.
| | - Silvano Piazza
- Laboratorio Nazionale CIB, Area Science Park Padriciano, Trieste, 34149, Italy. .,Bioinformatics Core Facility, Centre for Integrative Biology, CIBIO, University of Trento, via Sommarive 18, Povo, Trento, TN, 38123, Italy.
| | - Gianluca Tell
- Department of Medicine, Laboratory of Molecular Biology and DNA repair, University of Udine, p.le M. Kolbe 4, Udine, 33100, Italy.
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49
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Di Matteo A, Franceschini M, Paiardini A, Grottesi A, Chiarella S, Rocchio S, Di Natale C, Marasco D, Vitagliano L, Travaglini-Allocatelli C, Federici L. Structural investigation of nucleophosmin interaction with the tumor suppressor Fbw7γ. Oncogenesis 2017; 6:e379. [PMID: 28920929 PMCID: PMC5623904 DOI: 10.1038/oncsis.2017.78] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 07/17/2017] [Accepted: 07/19/2017] [Indexed: 02/07/2023] Open
Abstract
Nucleophosmin (NPM1) is a multifunctional nucleolar protein implicated in ribogenesis, centrosome duplication, cell cycle control, regulation of DNA repair and apoptotic response to stress stimuli. The majority of these functions are played through the interactions with a variety of protein partners. NPM1 is frequently overexpressed in solid tumors of different histological origin. Furthermore NPM1 is the most frequently mutated protein in acute myeloid leukemia (AML) patients. Mutations map to the C-terminal domain and lead to the aberrant and stable localization of the protein in the cytoplasm of leukemic blasts. Among NPM1 protein partners, a pivotal role is played by the tumor suppressor Fbw7γ, an E3-ubiquitin ligase that degrades oncoproteins like c-MYC, cyclin E, Notch and c-jun. In AML with NPM1 mutations, Fbw7γ is degraded following its abnormal cytosolic delocalization by mutated NPM1. This mechanism also applies to other tumor suppressors and it has been suggested that it may play a key role in leukemogenesis. Here we analyse the interaction between NPM1 and Fbw7γ, by identifying the protein surfaces implicated in recognition and key aminoacids involved. Based on the results of computational methods, we propose a structural model for the interaction, which is substantiated by experimental findings on several site-directed mutants. We also extend the analysis to two other NPM1 partners (HIV Tat and CENP-W) and conclude that NPM1 uses the same molecular surface as a platform for recognizing different protein partners. We suggest that this region of NPM1 may be targeted for cancer treatment.
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Affiliation(s)
- A Di Matteo
- Istituto di Biologia e Patologia Molecolari - Consiglio Nazionale delle ricerche, Roma, Italy
| | - M Franceschini
- Dipartimento di Scienze Mediche, Orali e Biotecnologiche, Chieti, Italy.,CeSI-Met - Università di Chieti-Pescara 'G d'Annunzio', Chieti, Italy
| | - A Paiardini
- Dipartimento di Biologia e Biotecnologie 'C Darwin' - Sapienza Università di Roma, Roma, Italy
| | - A Grottesi
- CINECA Consorzio Interuniversitario, Sede di Roma, Roma, Italy
| | - S Chiarella
- Dipartimento di Scienze Mediche, Orali e Biotecnologiche, Chieti, Italy.,CeSI-Met - Università di Chieti-Pescara 'G d'Annunzio', Chieti, Italy
| | - S Rocchio
- Dipartimento di Scienze Biochimiche 'A Rossi Fanelli' - Sapienza Università di Roma, Roma, Italy
| | - C Di Natale
- Dipartimento di Farmacia,- Università di Napoli 'Federico II', Napoli, Italy
| | - D Marasco
- Dipartimento di Farmacia,- Università di Napoli 'Federico II', Napoli, Italy
| | - L Vitagliano
- Istituto di Biostrutture e Bioimmagini - Consiglio Nazionale delle Ricerche, Napoli, Italy
| | - C Travaglini-Allocatelli
- Dipartimento di Scienze Biochimiche 'A Rossi Fanelli' - Sapienza Università di Roma, Roma, Italy
| | - L Federici
- Dipartimento di Scienze Mediche, Orali e Biotecnologiche, Chieti, Italy.,CeSI-Met - Università di Chieti-Pescara 'G d'Annunzio', Chieti, Italy
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50
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DNA repair enzyme APE1 from evolutionarily ancient Hydra reveals redox activity exclusively found in mammalian APE1. DNA Repair (Amst) 2017; 59:44-56. [PMID: 28946035 DOI: 10.1016/j.dnarep.2017.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/10/2017] [Accepted: 09/15/2017] [Indexed: 01/12/2023]
Abstract
Only mammalian apurinic/apyrimidinic endonuclease1 (APE1) has been reported to possess both DNA repair and redox activities. C terminal of the protein is required for base excision repair, while the redox activity resides in the N terminal due to cysteine residues at specific positions. APE1s from other organisms studied so far lack the redox activity in spite of having the N terminal domain. We find that APE1 from the Cnidarian Hydra exhibits both endonuclease and redox activities similar to mammalian APE1. We further show the presence of the three indispensable cysteines in Hydra APE1 for redox activity by site directed mutagenesis. Importance of redox domain but not the repair domain of APE1 in regeneration has been demonstrated by using domain-specific inhibitors. Our findings clearly demonstrate that the redox function of APE1 evolved very early in metazoan evolution and is not a recent acquisition in mammalian APE1 as believed so far.
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