1
|
Vlachogiannis NI, Ntouros PA, Pappa M, Kravvariti E, Kostaki EG, Fragoulis GE, Papanikolaou C, Mavroeidi D, Bournia VK, Panopoulos S, Laskari K, Arida A, Gorgoulis VG, Tektonidou MG, Paraskevis D, Sfikakis PP, Souliotis VL. Chronological Age and DNA Damage Accumulation in Blood Mononuclear Cells: A Linear Association in Healthy Humans after 50 Years of Age. Int J Mol Sci 2023; 24:ijms24087148. [PMID: 37108309 PMCID: PMC10138488 DOI: 10.3390/ijms24087148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/19/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Aging is characterized by the progressive deregulation of homeostatic mechanisms causing the accumulation of macromolecular damage, including DNA damage, progressive decline in organ function and chronic diseases. Since several features of the aging phenotype are closely related to defects in the DNA damage response (DDR) network, we have herein investigated the relationship between chronological age and DDR signals in peripheral blood mononuclear cells (PBMCs) from healthy individuals. DDR-associated parameters, including endogenous DNA damage (single-strand breaks and double-strand breaks (DSBs) measured by the alkaline comet assay (Olive Tail Moment (OTM); DSBs-only by γH2AX immunofluorescence staining), DSBs repair capacity, oxidative stress, and apurinic/apyrimidinic sites were evaluated in PBMCs of 243 individuals aged 18-75 years, free of any major comorbidity. While OTM values showed marginal correlation with age until 50 years (rs = 0.41, p = 0.11), a linear relationship was observed after 50 years (r = 0.95, p < 0.001). Moreover, individuals older than 50 years showed increased endogenous DSBs levels (γH2Ax), higher oxidative stress, augmented apurinic/apyrimidinic sites and decreased DSBs repair capacity than those with age lower than 50 years (all p < 0.001). Results were reproduced when we examined men and women separately. Prospective studies confirming the value of DNA damage accumulation as a biomarker of aging, as well as the presence of a relevant agethreshold, are warranted.
Collapse
Affiliation(s)
- Nikolaos I Vlachogiannis
- First Department of Propaedeutic Internal Medicine and Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, 115 27 Athens, Greece
| | - Panagiotis A Ntouros
- First Department of Propaedeutic Internal Medicine and Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, 115 27 Athens, Greece
| | - Maria Pappa
- First Department of Propaedeutic Internal Medicine and Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, 115 27 Athens, Greece
| | - Evrydiki Kravvariti
- First Department of Propaedeutic Internal Medicine and Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, 115 27 Athens, Greece
- Postgraduate Medical Studies in Geriatric Syndromes and Physiology of Aging, National and Kapodistrian University of Athens Medical School, 115 27 Athens, Greece
| | - Evangelia Georgia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, National and Kapodistrian University of Athens Medical School, 115 27 Athens, Greece
| | - Georgios E Fragoulis
- First Department of Propaedeutic Internal Medicine and Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, 115 27 Athens, Greece
| | - Christina Papanikolaou
- Institute of Chemical Biology, National Hellenic Research Foundation, 116 35 Athens, Greece
| | - Dimitra Mavroeidi
- Institute of Chemical Biology, National Hellenic Research Foundation, 116 35 Athens, Greece
| | - Vasiliki-Kalliopi Bournia
- First Department of Propaedeutic Internal Medicine and Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, 115 27 Athens, Greece
| | - Stylianos Panopoulos
- First Department of Propaedeutic Internal Medicine and Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, 115 27 Athens, Greece
| | - Katerina Laskari
- First Department of Propaedeutic Internal Medicine and Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, 115 27 Athens, Greece
| | - Aikaterini Arida
- First Department of Propaedeutic Internal Medicine and Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, 115 27 Athens, Greece
| | - Vassilis G Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, National Kapodistrian University of Athens Medical School, 115 27 Athens, Greece
| | - Maria G Tektonidou
- First Department of Propaedeutic Internal Medicine and Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, 115 27 Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, National and Kapodistrian University of Athens Medical School, 115 27 Athens, Greece
| | - Petros P Sfikakis
- First Department of Propaedeutic Internal Medicine and Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, 115 27 Athens, Greece
- Postgraduate Medical Studies in Geriatric Syndromes and Physiology of Aging, National and Kapodistrian University of Athens Medical School, 115 27 Athens, Greece
| | - Vassilis L Souliotis
- First Department of Propaedeutic Internal Medicine and Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, 115 27 Athens, Greece
- Institute of Chemical Biology, National Hellenic Research Foundation, 116 35 Athens, Greece
| |
Collapse
|
2
|
Ilina ES, Lavrik OI, Khodyreva SN. [5'-Deoxyribose Phosphate Lyase Activity of Apurinic/Apyrimidinic Endonuclease 1]. Mol Biol (Mosk) 2021; 55:269-276. [PMID: 33871440 DOI: 10.31857/s0026898421020075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/22/2020] [Indexed: 11/24/2022]
Abstract
One of the most common DNA lesions is the appearance of apurinic/apyrimidinic (AP-) sites. The main repair pathway for AP sites is initiated by apurinic/apyrimidinic endonuclease 1 (APE1). Upon hydrolysis of the phosphodiester bond by this enzyme, a one nucleotide gap flanked by 3'-hydroxyl and 5'-deoxyribose phosphate groups on the 5'-side of the AP site is formed. After hydrolysis of the AP site, APE1 remains associated with the product for some time. In the present work, the ability of APE1 to form a product of covalent attachment of APE1 to DNA containing a gap with a 5'-deoxyribose phosphate residue was demonstrated. In addition, it was found that while in a complex with the product of hydrolysis of the AP site, APE1 exhibits 5'-deoxyribose phosphate lyase activity, cleaving off the 5'-deoxyribose phosphate residue. The presence of lyase activity in APE1 may be important for the repair of AP sites if there is a deficiency of, or mutations in DNA polymerase β, the main enzyme that removes the 5'-deoxyribose phosphate group.
Collapse
Affiliation(s)
- E S Ilina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia.,Novosibirsk State University, Novosibirsk, 630090 Russia
| | - O I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia.,Novosibirsk State University, Novosibirsk, 630090 Russia
| | - S N Khodyreva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia.,
| |
Collapse
|
3
|
Fairlamb MS, Whitaker AM, Freudenthal BD. Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches. Acta Crystallogr D Struct Biol 2018; 74:760-768. [PMID: 30082511 PMCID: PMC6079627 DOI: 10.1107/s2059798318003340] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/26/2018] [Indexed: 01/17/2023] Open
Abstract
Despite the DNA duplex being central to biological functions, many intricacies of this molecule, including the dynamic nature of mismatched base pairing, are still unknown. The unique conformations adopted by DNA mismatches can provide insight into the forces at play between nucleotides. Moreover, DNA-binding proteins apply their own individualized steric and electrochemical influences on the nucleotides that they interact with, further altering base-pairing conformations. Here, seven X-ray crystallographic structures of the human nuclease apurinic/apyrimidinic (AP) endonuclease 1 (APE1) in complex with its substrate target flanked by a 5' mismatch are reported. The structures reveal how APE1 influences the conformations of a variety of different mismatched base pairs. Purine-purine mismatches containing a guanine are stabilized by a rotation of the guanine residue about the N-glycosidic bond to utilize the Hoogsteen edge for hydrogen bonding. Interestingly, no rotation of adenine, the other purine, is observed. Mismatches involving both purine and pyrimidine bases adopt wobble conformations to accommodate the mismatch. Pyrimidine-pyrimidine mismatches also wobble; however, the smaller profile of a pyrimidine base results in a gap between the Watson-Crick faces that is reduced by a C1'-C1' compression. These results advance our understanding of mismatched base pairing and the influence of a bound protein.
Collapse
Affiliation(s)
- Max S. Fairlamb
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66016, USA
| | - Amy M. Whitaker
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66016, USA
| | - Bret D. Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66016, USA
| |
Collapse
|
4
|
Akishev Z, Taipakova S, Joldybayeva B, Zutterling C, Smekenov I, Ishchenko AA, Zharkov DO, Bissenbaev AK, Saparbaev M. The major Arabidopsis thaliana apurinic/apyrimidinic endonuclease, ARP is involved in the plant nucleotide incision repair pathway. DNA Repair (Amst) 2016; 48:30-42. [PMID: 27836324 DOI: 10.1016/j.dnarep.2016.10.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 10/25/2016] [Accepted: 10/26/2016] [Indexed: 11/18/2022]
Abstract
Apurinic/apyrimidinic (AP) endonucleases are important DNA repair enzymes involved in two overlapping pathways: DNA glycosylase-initiated base excision (BER) and AP endonuclease-initiated nucleotide incision repair (NIR). In the BER pathway, AP endonucleases cleave DNA at AP sites and 3'-blocking moieties generated by DNA glycosylases, whereas in NIR, the same AP endonucleases incise DNA 5' to a wide variety of oxidized bases. The flowering plant Arabidopsis thaliana contains three genes encoding homologues of major human AP endonuclease 1 (APE1): Arp, Ape1L and Ape2. It has been shown that all three proteins contain AP site cleavage and 3'-repair phosphodiesterase activities; however, it was not known whether the plant AP endonucleases contain the NIR activity. Here, we report that ARP proteins from Arabidopsis and common wheat (Triticum aestivum) contain NIR and 3'→5' exonuclease activities in addition to their AP endonuclease and 3'-repair phosphodiesterase functions. The steady-state kinetic parameters of reactions indicate that Arabidopsis ARP cleaves oligonucleotide duplexes containing α-anomeric 2'-deoxyadenosine (αdA) and 5,6-dihydrouridine (DHU) with efficiencies (kcat/KM=134 and 7.3 μM-1·min-1, respectively) comparable to those of the human counterpart. However, the ARP-catalyzed 3'-repair phosphodiesterase and 3'→5' exonuclease activities (kcat/KM=314 and 34 μM-1·min-1, respectively) were about 10-fold less efficient as compared to those of APE1. Interestingly, homozygous A. thaliana arp-/- mutant exhibited high sensitivity to methyl methanesulfonate and tert-butyl hydroperoxide, but not to H2O2, suggesting that ARP is a major plant AP endonuclease that removes abasic sites and specific types of oxidative DNA base damage. Taken together, these data establish the presence of the NIR pathway in plants and suggest its possible role in the repair of DNA damage generated by oxidative stress.
Collapse
Affiliation(s)
- Zhiger Akishev
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan
| | - Sabira Taipakova
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan
| | - Botagoz Joldybayeva
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan
| | - Caroline Zutterling
- 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
| | - Izat Smekenov
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan
| | - 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
| | - Dmitry O Zharkov
- Novosibirsk State University, Novosibirsk 630090, Russia; SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Amangeldy K Bissenbaev
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 0530040, Almaty, Kazakhstan.
| | - 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.
| |
Collapse
|