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Gohil D, Sarker AH, Roy R. Base Excision Repair: Mechanisms and Impact in Biology, Disease, and Medicine. Int J Mol Sci 2023; 24:14186. [PMID: 37762489 PMCID: PMC10531636 DOI: 10.3390/ijms241814186] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Base excision repair (BER) corrects forms of oxidative, deamination, alkylation, and abasic single-base damage that appear to have minimal effects on the helix. Since its discovery in 1974, the field has grown in several facets: mechanisms, biology and physiology, understanding deficiencies and human disease, and using BER genes as potential inhibitory targets to develop therapeutics. Within its segregation of short nucleotide (SN-) and long patch (LP-), there are currently six known global mechanisms, with emerging work in transcription- and replication-associated BER. Knockouts (KOs) of BER genes in mouse models showed that single glycosylase knockout had minimal phenotypic impact, but the effects were clearly seen in double knockouts. However, KOs of downstream enzymes showed critical impact on the health and survival of mice. BER gene deficiency contributes to cancer, inflammation, aging, and neurodegenerative disorders. Medicinal targets are being developed for single or combinatorial therapies, but only PARP and APE1 have yet to reach the clinical stage.
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Affiliation(s)
- Dhara Gohil
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA;
| | - Altaf H. Sarker
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA;
| | - Rabindra Roy
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA;
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Turgimbayeva A, Zein U, Zharkov DO, Ramankulov Y, Saparbaev M, Abeldenov S. Cloning and characterization of the major AP endonuclease from Staphylococcus aureus. DNA Repair (Amst) 2022; 119:103390. [DOI: 10.1016/j.dnarep.2022.103390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/19/2022] [Accepted: 08/20/2022] [Indexed: 11/03/2022]
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3
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Srivastava PN, Narwal SK, Mishra S. Mitochondrial apurinic/apyrimidinic endonuclease Apn1 is not critical for the completion of the Plasmodium berghei life cycle. DNA Repair (Amst) 2021; 101:103078. [PMID: 33711786 DOI: 10.1016/j.dnarep.2021.103078] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/14/2022]
Abstract
Mitochondrion is an essential organelle in malaria parasite and its DNA must be maintained for optimal function during its complex life cycle. Base excision repair is one of the major pathways by which this is achieved. Apurinic/apyrimidinic (AP) endonucleases are important components of this pathway as they create a nick at the 5'-phosphodiester bond in the AP site and generate free 5'-phosphate and 3'-hydroxyl groups. Two class II AP endonucleases (Apn1 and Ape1) have been annotated in the Plasmodium berghei genome. Using reverse genetic approaches, we provide direct evidence that Apn1 is exclusively localized to the mitochondria of P. berghei. Surprisingly, our gene deletion study revealed a completely dispensable role of Apn1 for the entirety of the P. berghei life cycle. Apn1- parasites were found to successfully grow in the blood. They were transmitted normally to the mosquito midguts and salivary glands. Sporozoites obtained from the salivary glands were infective and achieved similar patency as WT. Our results help emphasize the non-availability of this enzyme as a plausible drug target. We also emphasize the importance of genetic validation of antimalarial drug targets before furthering them down the drug discovery pipeline.
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Affiliation(s)
- Pratik Narain Srivastava
- Division of Molecular Parasitology and Immunology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Sunil Kumar Narwal
- Division of Molecular Parasitology and Immunology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Satish Mishra
- Division of Molecular Parasitology and Immunology, CSIR-Central Drug Research Institute, Lucknow, 226031, India; Academy of Scientific and Innovative Research, Ghaziabad, India.
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Krumkacheva OA, Shevelev GY, Lomzov AA, Dyrkheeva NS, Kuzhelev AA, Koval VV, Tormyshev VM, Polienko YF, Fedin MV, Pyshnyi DV, Lavrik OI, Bagryanskaya EG. DNA complexes with human apurinic/apyrimidinic endonuclease 1: structural insights revealed by pulsed dipolar EPR with orthogonal spin labeling. Nucleic Acids Res 2019; 47:7767-7780. [PMID: 31329919 PMCID: PMC6735896 DOI: 10.1093/nar/gkz620] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/04/2019] [Accepted: 07/11/2019] [Indexed: 12/19/2022] Open
Abstract
A DNA molecule is under continuous influence of endogenous and exogenous damaging factors, which produce a variety of DNA lesions. Apurinic/apyrimidinic sites (abasic or AP sites) are among the most common DNA lesions. In this work, we applied pulse dipolar electron paramagnetic resonance (EPR) spectroscopy in combination with molecular dynamics (MD) simulations to investigate in-depth conformational changes in DNA containing an AP site and in a complex of this DNA with AP endonuclease 1 (APE1). For this purpose, triarylmethyl (TAM)-based spin labels were attached to the 5' ends of an oligonucleotide duplex, and nitroxide spin labels were introduced into APE1. In this way, we created a system that enabled monitoring the conformational changes of the main APE1 substrate by EPR. In addition, we were able to trace substrate-to-product transformation in this system. The use of different (orthogonal) spin labels in the enzyme and in the DNA substrate has a crucial advantage allowing for detailed investigation of local damage and conformational changes in AP-DNA alone and in its complex with APE1.
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Affiliation(s)
- Olesya A Krumkacheva
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentiev ave, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk 630090, Russia
| | - Georgiy Yu Shevelev
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Alexander A Lomzov
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Nadezhda S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Andrey A Kuzhelev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentiev ave, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk 630090, Russia
| | - Vladimir V Koval
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Victor M Tormyshev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentiev ave, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Yuliya F Polienko
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentiev ave, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Matvey V Fedin
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Olga I Lavrik
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave, Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentiev ave, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
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Wang K, Lin Z, Zhang H, Zhang X, Zheng X, Zhao L, Yang Q, Ahima J, Boateng NAS. Investigating proteome and transcriptome response of Cryptococcus podzolicus Y3 to citrinin and the mechanisms involved in its degradation. Food Chem 2019; 283:345-352. [PMID: 30722882 DOI: 10.1016/j.foodchem.2019.01.052] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/16/2018] [Accepted: 01/13/2019] [Indexed: 11/28/2022]
Abstract
Citrinin (CIT) contamination has been reported in agricultural foods and is known to be nephrotoxic to human and animals. In the present study, the proteomes and transcriptomes of C. podzolicus Y3 treated with or without 10 μg/mL CIT were compared by two-dimensional electrophoresis (2-DE) and RNA sequencing, respectively. The proteomics results showed that there were 23 differentially expressed proteins (DEPs), 8 DEPs were up-regulated and 15 DEPs were significantly down-regulated. Transcriptomic analysis showed that 1208 genes were differentially expressed, 551 (43.05%) DEGs were up regulated and 657 (56.95%) were down-regulated. These results showed that the CIT treatment caused DNA damage, oxidative stress and cell apoptosis in C. podzolicus Y3. CIT treatment also activated the defense response (DNA repair and drug resistance biological process, antioxidative activity and TCA cycle) as well as drug metabolism (synthesize the CIT-degrading enzymes) in yeast cells to respond to CIT stress and degrade CIT.
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Affiliation(s)
- Kaili Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, People's Republic of China
| | - Zhen Lin
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, People's Republic of China
| | - Hongyin Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, People's Republic of China.
| | - Xiaoyun Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, People's Republic of China
| | - Xiangfeng Zheng
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, People's Republic of China
| | - Lina Zhao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, People's Republic of China
| | - Qiya Yang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, People's Republic of China
| | - Joseph Ahima
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, People's Republic of China
| | - Nana Adwoa Serwah Boateng
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, People's Republic of China
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Data on PAGE analysis and MD simulation for the interaction of endonuclease Apn1 from Saccharomyces cerevisiae with DNA substrates containing 5,6-dihydrouracyl and 2-aminopurine. Data Brief 2018; 20:1515-1524. [PMID: 30671502 PMCID: PMC6334592 DOI: 10.1016/j.dib.2018.09.007] [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: 07/03/2018] [Revised: 08/29/2018] [Accepted: 09/03/2018] [Indexed: 11/20/2022] Open
Abstract
This article presents new data on nucleotide incision repair
(NIR) activity of apurinic/apyrimidinic endonuclease Apn1 of Saccharomyces
cerevisiae, which is known as a key player of the base excision DNA
repair (BER) pathway, see “Yeast structural gene (APN1) for the major apurinic
endonuclease: homology to Escherichia coli endonuclease IV” [1], “Abasic sites in DNA: repair and biological
consequences in Saccharomyces cerevisiae” [2] and “Characterisation of new substrate specificities of
Escherichia coli and Saccharomyces cerevisiae AP endonucleases” [3]. The characterization of NIR activity
of wild type Apn1 and mutant form Ape1 H83A were made by denaturing PAGE analysis,
and MD simulations of Apn1 complexed with DNA containing 5,6-dihydro-2′-deoxyuridine
(DHU) and 2-aminopurine (2-aPu) residues. This data article is associated to the
manuscript titled “Apurinic/apyrimidinic endonuclease Apn1 from
Saccharomyces cerevisiae is recruited to the nucleotide
incision repair pathway: kinetic and structural features” [4]. Published by Elsevier Inc. This is an open access article under the CC BY
license (http://creativecommons.org/licenses/by/4.0/).
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