1
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Kruchinin AA, Kamzeeva PN, Zharkov DO, Aralov AV, Makarova AV. 8-Oxoadenine: A «New» Player of the Oxidative Stress in Mammals? Int J Mol Sci 2024; 25:1342. [PMID: 38279342 PMCID: PMC10816367 DOI: 10.3390/ijms25021342] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024] Open
Abstract
Numerous studies have shown that oxidative modifications of guanine (7,8-dihydro-8-oxoguanine, 8-oxoG) can affect cellular functions. 7,8-Dihydro-8-oxoadenine (8-oxoA) is another abundant paradigmatic ambiguous nucleobase but findings reported on the mutagenicity of 8-oxoA in bacterial and eukaryotic cells are incomplete and contradictory. Although several genotoxic studies have demonstrated the mutagenic potential of 8-oxoA in eukaryotic cells, very little biochemical and bioinformatics data about the mechanism of 8-oxoA-induced mutagenesis are available. In this review, we discuss dual coding properties of 8-oxoA, summarize historical and recent genotoxicity and biochemical studies, and address the main protective cellular mechanisms of response to 8-oxoA. We also discuss the available structural data for 8-oxoA bypass by different DNA polymerases as well as the mechanisms of 8-oxoA recognition by DNA repair enzymes.
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Affiliation(s)
- Alexander A. Kruchinin
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., 119334 Moscow, Russia; (A.A.K.); (P.N.K.)
- National Research Center, Kurchatov Institute, Kurchatov sq. 2, 123182 Moscow, Russia
| | - Polina N. Kamzeeva
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., 119334 Moscow, Russia; (A.A.K.); (P.N.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia;
| | - Dmitry O. Zharkov
- Department of Natural Sciences, Novosibirsk State University, 1 Pirogova St., 630090 Novosibirsk, Russia;
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Andrey V. Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia;
| | - Alena V. Makarova
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., 119334 Moscow, Russia; (A.A.K.); (P.N.K.)
- National Research Center, Kurchatov Institute, Kurchatov sq. 2, 123182 Moscow, Russia
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2
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Yudkina AV, Endutkin AV, Diatlova EA, Zharkov DO. A non-canonical nucleotide from viral genomes interferes with the oxidative DNA damage repair system. DNA Repair (Amst) 2024; 133:103605. [PMID: 38042029 DOI: 10.1016/j.dnarep.2023.103605] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/09/2023] [Accepted: 11/15/2023] [Indexed: 12/04/2023]
Abstract
Oxidative damage is a major source of genomic instability in all organisms with the aerobic metabolism. 8-Oxoguanine (8-oxoG), an abundant oxidized purine, is mutagenic and must be controlled by a dedicated DNA repair system (GO system) that prevents G:C→T:A transversions through an easily formed 8-oxoG:A mispair. In some forms, the GO system is present in nearly all cellular organisms. However, recent studies uncovered many instances of viruses possessing non-canonical nucleotides in their genomes. The features of genome damage and maintenance in such cases of alternative genetic chemistry remain barely explored. In particular, 2,6-diaminopurine (Z nucleotide) completely substitutes for A in the genomes of some bacteriophages, which have evolved pathways for dZTP synthesis and specialized polymerases that prefer dZTP over dATP. Here we address the ability of the GO system enzymes to cope with oxidative DNA damage in the presence of Z in DNA. DNA polymerases of two different structural families (Klenow fragment and RB69 polymerase) were able to incorporate dZMP opposite to 8-oxoG in the template, as well as 8-oxodGMP opposite to Z in the template. Fpg, a 8-oxoguanine-DNA glycosylase that discriminates against 8-oxoG:A mispairs, also did not remove 8-oxoG from 8-oxoG:Z mispairs. However, MutY, a DNA glycosylase that excises A from pairs with 8-oxoG, had a significantly lower activity on Z:8-oxoG mispairs. Similar preferences were observed for Fpg and MutY from different bacterial species (Escherichia coli, Staphylococcus aureus and Lactococcus lactis). Overall, the relaxed control of 8-oxoG in the presence of the Z nucleotide may be a source of additional mutagenesis in the genomes of bacteriophages or bacteria that have survived the viral invasion.
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Affiliation(s)
- Anna V Yudkina
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Anton V Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Evgeniia A Diatlova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia.
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3
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Kim DV, Diatlova EA, Zharkov TD, Melentyev VS, Yudkina AV, Endutkin AV, Zharkov DO. Back-Up Base Excision DNA Repair in Human Cells Deficient in the Major AP Endonuclease, APE1. Int J Mol Sci 2023; 25:64. [PMID: 38203235 PMCID: PMC10778768 DOI: 10.3390/ijms25010064] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Apurinic/apyrimidinic (AP) sites are abundant DNA lesions generated both by spontaneous base loss and as intermediates of base excision DNA repair. In human cells, they are normally repaired by an essential AP endonuclease, APE1, encoded by the APEX1 gene. Other enzymes can cleave AP sites by either hydrolysis or β-elimination in vitro, but it is not clear whether they provide the second line of defense in living cells. Here, we studied AP site repairs in APEX1 knockout derivatives of HEK293FT cells using a reporter system based on transcriptional mutagenesis in the enhanced green fluorescent protein gene. Despite an apparent lack of AP site-processing activity in vitro, the cells efficiently repaired the tetrahydrofuran AP site analog resistant to β-elimination. This ability persisted even when the second AP endonuclease homolog, APE2, was also knocked out. Moreover, APEX1 null cells were able to repair uracil, a DNA lesion that is removed via the formation of an AP site. If AP site hydrolysis was chemically blocked, the uracil repair required the presence of NTHL1, an enzyme that catalyzes β-elimination. Our results suggest that human cells possess at least two back-up AP site repair pathways, one of which is NTHL1-dependent.
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Affiliation(s)
- Daria V. Kim
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Evgeniia A. Diatlova
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
| | - Timofey D. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
| | - Vasily S. Melentyev
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Anna V. Yudkina
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Anton V. Endutkin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
| | - Dmitry O. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
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Beskrovnaia M, Agapov A, Makasheva K, Zharkov DO, Esyunina D, Kulbachinskiy A. Sensing of DNA modifications by pAgo proteins in vitro. Biochimie 2023; 220:39-47. [PMID: 38128776 DOI: 10.1016/j.biochi.2023.12.006] [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: 10/11/2023] [Revised: 12/09/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Many prokaryotic Argonaute (pAgo) proteins act as programmable nucleases that use small guide DNAs for recognition and cleavage of complementary target DNA. Recent studies suggested that pAgos participate in cell defense against invader DNA and may also be involved in other genetic processes, including DNA replication and repair. The ability of pAgos to recognize specific targets potentially make them an invaluable tool for DNA manipulations. Here, we demonstrate that DNA-guided DNA-targeting pAgo nucleases from three bacterial species, DloAgo from Dorea longicatena, CbAgo from Clostridium butyricum and KmAgo from Kurthia massiliensis, can sense site-specific modifications in the target DNA, including 8-oxoguanine, thymine glycol, ethenoadenine and pyrimidine dimers. The effects of DNA modifications on the activity of pAgos strongly depend on their positions relative to the site of cleavage and are comparable to or exceed the effects of guide-target mismatches at corresponding positions. For all tested pAgos, the strongest effects are observed when DNA lesions are located at the cleavage position. The results demonstrate that DNA cleavage by pAgos is strongly affected by DNA modifications, thus making possible their use as sensors of DNA damage.
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Affiliation(s)
| | - Aleksei Agapov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Kristina Makasheva
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, 630090, Russia
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, 630090, Russia
| | - Daria Esyunina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
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5
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Eroshenko DA, Diatlova EA, Golyshev VM, Endutkin AV, Zharkov DO. Aberrant Repair of 8-Oxoguanine in Short DNA Bulges. DOKL BIOCHEM BIOPHYS 2023; 513:S82-S86. [PMID: 38337103 DOI: 10.1134/s1607672923600355] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 11/25/2023] [Accepted: 11/25/2023] [Indexed: 02/12/2024]
Abstract
The presence of DNA damage can increase the likelihood of DNA replication errors and promote mutations. In particular, pauses of DNA polymerase at the site of damage can lead to polymerase slippage and the formation of 1-2-nucleotide bulges. Repair of such structures using an undamaged DNA template leads to small deletions. One of the most abundant oxidative DNA lesions, 8-oxoguanine (oxoG), was shown to induce small deletions, but the mechanism of this phenomenon is currently unknown. We studied the aberrant repair of oxoG located in one- and two-nucleotide bulges by the Escherichia coli and human base excision repair systems. Our results indicate that the repair in such substrates can serve as a mechanism for fixing small deletions in bacteria but not in humans.
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Affiliation(s)
- D A Eroshenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - E A Diatlova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - V M Golyshev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - A V Endutkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - D O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.
- Novosibirsk State University, Novosibirsk, Russia.
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6
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Maltseva EA, Vasil’eva IA, Moor NA, Kim DV, Dyrkheeva NS, Kutuzov MM, Vokhtantsev IP, Kulishova LM, Zharkov DO, Lavrik OI. Cas9 is mostly orthogonal to human systems of DNA break sensing and repair. PLoS One 2023; 18:e0294683. [PMID: 38019812 PMCID: PMC10686484 DOI: 10.1371/journal.pone.0294683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023] Open
Abstract
CRISPR/Cas9 system is а powerful gene editing tool based on the RNA-guided cleavage of target DNA. The Cas9 activity can be modulated by proteins involved in DNA damage signalling and repair due to their interaction with double- and single-strand breaks (DSB and SSB, respectively) generated by wild-type Cas9 or Cas9 nickases. Here we address the interplay between Streptococcus pyogenes Cas9 and key DNA repair factors, including poly(ADP-ribose) polymerase 1 (SSB/DSB sensor), its closest homolog poly(ADP-ribose) polymerase 2, Ku antigen (DSB sensor), DNA ligase I (SSB sensor), replication protein A (DNA duplex destabilizer), and Y-box binding protein 1 (RNA/DNA binding protein). None of those significantly affected Cas9 activity, while Cas9 efficiently shielded DSBs and SSBs from their sensors. Poly(ADP-ribosyl)ation of Cas9 detected for poly(ADP-ribose) polymerase 2 had no apparent effect on the activity. In cellulo, Cas9-dependent gene editing was independent of poly(ADP-ribose) polymerase 1. Thus, Cas9 can be regarded as an enzyme mostly orthogonal to the natural regulation of human systems of DNA break sensing and repair.
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Affiliation(s)
| | - Inna A. Vasil’eva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Nina A. Moor
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Daria V. Kim
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | | | - Mikhail M. Kutuzov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Ivan P. Vokhtantsev
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Lilya M. Kulishova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Dmitry O. Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Olga I. Lavrik
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
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Gromova AS, Boldinova EO, Kim DV, Chuprov-Netochin RN, Leonov SV, Pustovalova MV, Zharkov DO, Makarova AV. Response of PRIMPOL-Knockout Human Lung Adenocarcinoma A549 Cells to Genotoxic Stress. Biochemistry (Mosc) 2023; 88:1933-1943. [PMID: 38105210 DOI: 10.1134/s0006297923110214] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 08/08/2023] [Accepted: 09/15/2023] [Indexed: 12/19/2023]
Abstract
Human DNA primase/polymerase PrimPol synthesizes DNA primers de novo after replication fork stalling at the sites of DNA damage, thus contributing to the DNA damage tolerance. The role of PrimPol in response to the different types of DNA damage is poorly understood. We knocked out the PRIMPOL gene in the lung carcinoma A549 cell line and characterized the response of the obtained cells to the DNA damage caused by hydrogen peroxide, methyl methanesulfonate (MMS), cisplatin, bleomycin, and ionizing radiation. The PRIMPOL knockout reduced the number of proliferating cells and cells in the G2 phase after treatment with MMS and caused a more pronounced delay of the S phase in the cisplatin-treated cells. Ionizing radiation at a dose of 10 Gy significantly increased the content of apoptotic cells among the PRIMPOL-deficient cells, while the proportion of cells undergoing necroptosis increased in both parental and knockout cells at any radiation dose. The viability of PRIMPOL-deficient cells upon the hydrogen peroxide-induced oxidative stress increased compared to the control cells, as determined by the methyl tetrazolium (MTT) assay. The obtained data indicate the involvement of PRIMPOL in the modulation of adaptive cell response to various types of genotoxic stress.
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Affiliation(s)
- Anastasia S Gromova
- Institute of Molecular Genetics, Kurchatov Institute National Research Center, Moscow, 123182, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Elizaveta O Boldinova
- Institute of Molecular Genetics, Kurchatov Institute National Research Center, Moscow, 123182, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Daria V Kim
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Roman N Chuprov-Netochin
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
| | - Sergey V Leonov
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
- Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Margarita V Pustovalova
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Alena V Makarova
- Institute of Molecular Genetics, Kurchatov Institute National Research Center, Moscow, 123182, Russia.
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
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Grin IR, Petrova DV, Endutkin AV, Ma C, Yu B, Li H, Zharkov DO. Base Excision DNA Repair in Plants: Arabidopsis and Beyond. Int J Mol Sci 2023; 24:14746. [PMID: 37834194 PMCID: PMC10573277 DOI: 10.3390/ijms241914746] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Base excision DNA repair (BER) is a key pathway safeguarding the genome of all living organisms from damage caused by both intrinsic and environmental factors. Most present knowledge about BER comes from studies of human cells, E. coli, and yeast. Plants may be under an even heavier DNA damage threat from abiotic stress, reactive oxygen species leaking from the photosynthetic system, and reactive secondary metabolites. In general, BER in plant species is similar to that in humans and model organisms, but several important details are specific to plants. Here, we review the current state of knowledge about BER in plants, with special attention paid to its unique features, such as the existence of active epigenetic demethylation based on the BER machinery, the unexplained diversity of alkylation damage repair enzymes, and the differences in the processing of abasic sites that appear either spontaneously or are generated as BER intermediates. Understanding the biochemistry of plant DNA repair, especially in species other than the Arabidopsis model, is important for future efforts to develop new crop varieties.
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Affiliation(s)
- Inga R. Grin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Daria V. Petrova
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
| | - Anton V. Endutkin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
| | - Chunquan Ma
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Harbin 150080, China; (C.M.); (B.Y.); (H.L.)
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, Harbin 150080, China
- School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Bing Yu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Harbin 150080, China; (C.M.); (B.Y.); (H.L.)
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, Harbin 150080, China
- School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Haiying Li
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Harbin 150080, China; (C.M.); (B.Y.); (H.L.)
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, Harbin 150080, China
- School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Dmitry O. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
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9
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Shilkin ES, Petrova DV, Zharkov DO, Makarova AV. [Alternative Mechanisms of Mutagenesis at mCpG Sites during Replication and Repair]. Mol Biol (Mosk) 2023; 57:587-596. [PMID: 37528779 DOI: 10.31857/s0026898423040195, edn: qlyepa] [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] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/08/2023] [Indexed: 08/03/2023]
Abstract
5-Methyl-2'-deoxycytidine (mC) at CpG sites plays a key role in the epigenetic gene regulation, cell differentiation, and carcinogenesis. Despite the importance of mC for normal cell function, CpG dinucleotides are known as mutagenesis hotspots. Deamination of mC yields T, causing C→T transitions. However, several recent studies demonstrated the effect of epigenetic modifications of C on the fidelity and efficiency of DNA polymerases and excision repair enzymes. The review summarizes the available data that indicate the existence of deamination-independent mechanisms of mutagenesis at CpG sites.
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Affiliation(s)
- E S Shilkin
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, 123182 Russia
| | - D V Petrova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
- Novosibirsk State University, Novosibirsk, 630090 Russia
| | - D O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
- Novosibirsk State University, Novosibirsk, 630090 Russia
| | - A V Makarova
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, 123182 Russia
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10
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Yudkina AV, Barmatov AE, Bulgakov NA, Boldinova EO, Shilkin ES, Makarova AV, Zharkov DO. Bypass of Abasic Site-Peptide Cross-Links by Human Repair and Translesion DNA Polymerases. Int J Mol Sci 2023; 24:10877. [PMID: 37446048 DOI: 10.3390/ijms241310877] [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: 04/30/2023] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
DNA-protein cross-links remain the least-studied type of DNA damage. Recently, their repair was shown to involve proteolysis; however, the fate of the peptide remnant attached to DNA is unclear. Particularly, peptide cross-links could interfere with DNA polymerases. Apurinuic/apyrimidinic (AP) sites, abundant and spontaneously arising DNA lesions, readily form cross-links with proteins. Their degradation products (AP site-peptide cross-links, APPXLs) are non-instructive and should be even more problematic for polymerases. Here, we address the ability of human DNA polymerases involved in DNA repair and translesion synthesis (POLβ, POLλ, POLη, POLκ and PrimPOL) to carry out synthesis on templates containing AP sites cross-linked to the N-terminus of a 10-mer peptide (APPXL-I) or to an internal lysine of a 23-mer peptide (APPXL-Y). Generally, APPXLs strongly blocked processive DNA synthesis. The blocking properties of APPXL-I were comparable with those of an AP site, while APPXL-Y constituted a much stronger obstruction. POLη and POLκ demonstrated the highest bypass ability. DNA polymerases mostly used dNTP-stabilized template misalignment to incorporate nucleotides when encountering an APPXL. We conclude that APPXLs are likely highly cytotoxic and mutagenic intermediates of AP site-protein cross-link repair and must be quickly eliminated before replication.
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Affiliation(s)
- Anna V Yudkina
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Alexander E Barmatov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Nikita A Bulgakov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Elizaveta O Boldinova
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | - Evgeniy S Shilkin
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | - Alena V Makarova
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
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11
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Wu Z, Zhang T, Li J, Chen S, Grin IR, Zharkov DO, Yu B, Li H. Genome-wide analysis of WD40 protein family and functional characterization of BvWD40-82 in sugar beet. Front Plant Sci 2023; 14:1185440. [PMID: 37332716 PMCID: PMC10272600 DOI: 10.3389/fpls.2023.1185440] [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] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/10/2023] [Indexed: 06/20/2023]
Abstract
Sugar beet is one of the most important sugar crops in the world. It contributes greatly to the global sugar production, but salt stress negatively affects the crop yield. WD40 proteins play important roles in plant growth and response to abiotic stresses through their involvement in a variety of biological processes, such as signal transduction, histone modification, ubiquitination, and RNA processing. The WD40 protein family has been well-studied in Arabidopsis thaliana, rice and other plants, but the systematic analysis of the sugar beet WD40 proteins has not been reported. In this study, a total of 177 BvWD40 proteins were identified from the sugar beet genome, and their evolutionary characteristics, protein structure, gene structure, protein interaction network and gene ontology were systematically analyzed to understand their evolution and function. Meanwhile, the expression patterns of BvWD40s under salt stress were characterized, and a BvWD40-82 gene was hypothesized as a salt-tolerant candidate gene. Its function was further characterized using molecular and genetic methods. The result showed that BvWD40-82 enhanced salt stress tolerance in transgenic Arabidopsis seedlings by increasing the contents of osmolytes and antioxidant enzyme activities, maintaining intracellular ion homeostasis and increasing the expression of genes related to SOS and ABA pathways. The result has laid a foundation for further mechanistic study of the BvWD40 genes in sugar beet tolerance to salt stress, and it may inform biotechnological applications in improving crop stress resilience.
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Affiliation(s)
- Zhirui Wu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Tingyue Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Jinna Li
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Sixue Chen
- Department of Biology, University of Mississippi, Oxford, MS, United States
| | - Inga R. Grin
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Dmitry O. Zharkov
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Bing Yu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Haiying Li
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
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12
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Diatlova EA, Mechetin GV, Yudkina AV, Zharkov VD, Torgasheva NA, Endutkin AV, Shulenina OV, Konevega AL, Gileva IP, Shchelkunov SN, Zharkov DO. Correlated Target Search by Vaccinia Virus Uracil-DNA Glycosylase, a DNA Repair Enzyme and a Processivity Factor of Viral Replication Machinery. Int J Mol Sci 2023; 24:ijms24119113. [PMID: 37298065 DOI: 10.3390/ijms24119113] [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: 04/20/2023] [Revised: 05/13/2023] [Accepted: 05/21/2023] [Indexed: 06/12/2023] Open
Abstract
The protein encoded by the vaccinia virus D4R gene has base excision repair uracil-DNA N-glycosylase (vvUNG) activity and also acts as a processivity factor in the viral replication complex. The use of a protein unlike PolN/PCNA sliding clamps is a unique feature of orthopoxviral replication, providing an attractive target for drug design. However, the intrinsic processivity of vvUNG has never been estimated, leaving open the question whether it is sufficient to impart processivity to the viral polymerase. Here, we use the correlated cleavage assay to characterize the translocation of vvUNG along DNA between two uracil residues. The salt dependence of the correlated cleavage, together with the similar affinity of vvUNG for damaged and undamaged DNA, support the one-dimensional diffusion mechanism of lesion search. Unlike short gaps, covalent adducts partly block vvUNG translocation. Kinetic experiments show that once a lesion is found it is excised with a probability ~0.76. Varying the distance between two uracils, we use a random walk model to estimate the mean number of steps per association with DNA at ~4200, which is consistent with vvUNG playing a role as a processivity factor. Finally, we show that inhibitors carrying a tetrahydro-2,4,6-trioxopyrimidinylidene moiety can suppress the processivity of vvUNG.
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Affiliation(s)
- Evgeniia A Diatlova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Grigory V Mechetin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Anna V Yudkina
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Vasily D Zharkov
- Biology Department, Tomsk State University, 634050 Tomsk, Russia
| | - Natalia A Torgasheva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Anton V Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Olga V Shulenina
- NRC "Kurchatov Institute"-B. P. Konstantinov Petersburg Nuclear Physics Institute, Leningrad Region, 188300 Gatchina, Russia
| | - Andrey L Konevega
- NRC "Kurchatov Institute"-B. P. Konstantinov Petersburg Nuclear Physics Institute, Leningrad Region, 188300 Gatchina, Russia
| | - Irina P Gileva
- State Research Center of Virology and Biotechnology Vector, Novosibirsk Region, 630559 Koltsovo, Russia
| | - Sergei N Shchelkunov
- State Research Center of Virology and Biotechnology Vector, Novosibirsk Region, 630559 Koltsovo, Russia
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
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13
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Yuyukina SK, Barmatov AE, Bizyaev SN, Stetsenko DA, Sergeeva OV, Zatsepin TS, Zharkov DO. Activity of nsp14 Exonuclease from SARS-CoV-2 towards RNAs with Modified 3'-Termini. DOKL BIOCHEM BIOPHYS 2023; 509:65-69. [PMID: 37340295 DOI: 10.1134/s1607672923700102] [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: 11/25/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 06/22/2023]
Abstract
The COVID-19 pandemic has shown the urgent need for new treatments for coronavirus infections. Nucleoside analogs were successfully used to inhibit replication of some viruses through the incorporation into the growing DNA or RNA chain. However, the replicative machinery of coronaviruses contains nsp14, a non-structural protein with a 3'→5'-exonuclease activity that removes misincorporated and modified nucleotides from the 3' end of the growing RNA chain. Here, we studied the efficiency of hydrolysis of RNA containing various modifications in the 3'-terminal region by SARS-CoV-2 nsp14 exonuclease and its complex with the auxiliary protein nsp10. Single-stranded RNA was a preferable substrate compared to double-stranded RNA, which is consistent with the model of transfer of the substrate strand to the exonuclease active site, which was proposed on the basis of structural analysis. Modifications of the phosphodiester bond between the penultimate and last nucleotides had the greatest effect on nsp14 activity.
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Affiliation(s)
- S K Yuyukina
- Novosibirsk State University, Novosibirsk, Russia.
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.
| | - A E Barmatov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - S N Bizyaev
- Novosibirsk State University, Novosibirsk, Russia
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - D A Stetsenko
- Novosibirsk State University, Novosibirsk, Russia
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - O V Sergeeva
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - T S Zatsepin
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Moscow State University, Moscow, Russia
| | - D O Zharkov
- Novosibirsk State University, Novosibirsk, Russia.
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.
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14
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Ovcherenko SS, Shernyukov AV, Nasonov DM, Endutkin AV, Zharkov DO, Bagryanskaya EG. Dynamics of 8-Oxoguanine in DNA: Decisive Effects of Base Pairing and Nucleotide Context. J Am Chem Soc 2023; 145:5613-5617. [PMID: 36867834 DOI: 10.1021/jacs.2c11230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
8-Oxo-7,8-dihydroguanine (oxoG), an abundant DNA lesion, can mispair with adenine and induce mutations. To prevent this, cells possess DNA repair glycosylases that excise either oxoG from oxoG:C pairs (bacterial Fpg, human OGG1) or A from oxoG:A mispairs (bacterial MutY, human MUTYH). Early lesion recognition steps remain murky and may include enforced base pair opening or capture of a spontaneously opened pair. We adapted the CLEANEX-PM NMR protocol to detect DNA imino proton exchange and analyzed the dynamics of oxoG:C, oxoG:A, and their undamaged counterparts in nucleotide contexts with different stacking energy. Even in a poorly stacking context, the oxoG:C pair did not open easier than G:C, arguing against extrahelical base capture by Fpg/OGG1. On the contrary, oxoG opposite A significantly populated the extrahelical state, which may assist recognition by MutY/MUTYH.
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Affiliation(s)
- Sergey S Ovcherenko
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Andrey V Shernyukov
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Dmitry M Nasonov
- Vorozhtsov Novosibirsk Institute of Organic Chemistry 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
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
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15
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Yudkina AV, Kovalenko EA, Endutkin AV, Panferova EP, Kirilenko AA, Kokhanenko AA, Zharkov DO. [Factors Affecting the Stability of the Trimer of 2'-Deoxyuridine 5'-Triphosphate Nucleotide Hydrolase from Escherichia coli]. Mol Biol (Mosk) 2023; 57:330-339. [PMID: 37000660 DOI: 10.31857/s0026898423020246, edn: eejrnt] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 04/01/2023]
Abstract
2'-Deoxyuridine 5'-triphosphate nucleotide hydrolase (Dut) hydrolyzes dUTP to dUMP and pyrophosphate to prevent erroneous incorporation of dUMP from the dUTP metabolic pool into DNA. Dut is considered as a promising pharmacological target for antimetabolite therapy. Enzymatically active Dut is a trimer that binds the substrate at the interface between the subunits. High-speed nanoscale differential scanning fluorimetry (nanoDSF) was used to study how various physicochemical factors affect the stability of the Escherichia coli Dut trimer. Unlike with monomeric proteins, thermal unfolding of Dut occurred in two steps, the first one corresponding to dissociation of the trimer into monomeric subunits. Hydrophobic interactions and hydrogen bonds at the interfaces between the subunits were found to contribute most to trimer stabilization. The binding of nucleotide ligands partly stabilized the Dut trimer. In general, nanoDSF is a convenient assay for screening low-molecular-weight compounds for their ability to destabilize the active Dut trimer.
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Affiliation(s)
- A V Yudkina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
- Novosibirsk State University, Novosibirsk, 630090 Russia
| | | | - A V Endutkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - E P Panferova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | | | | | - D O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
- Novosibirsk State University, Novosibirsk, 630090 Russia
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16
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Kulishova LM, Vokhtantsev IP, Kim DV, Zharkov DO. [Mechanisms of the Specificity of the CRISPR/Cas9 System in Genome Editing]. Mol Biol (Mosk) 2023; 57:269-284. [PMID: 37000655 DOI: 10.31857/s0026898423020155, edn: efdqpq] [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] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/06/2022] [Indexed: 04/01/2023]
Abstract
The CRISPR/Cas9 system, which was discovered recently, utilizes nucleases targeted by sequence complementarity and is originally intended to protect bacteria from foreign genetic elements. The system provided a convenient tool for manipulating the genomes of living cells. The CRISPR/Cas9 genomic editing technology moved beyond the laboratory and already found application in biotechnology and agriculture. However, off-target activity of the CRISPR/Cas9 system can cause oncogenic mutations and thus limits its use for genome editing in human cells for medical purposes. Many studies are therefore aimed at developing variants of the CRISPR/Cas9 system with improved accuracy. The review considers the mechanisms of precise and erroneous actions of Cas9 RNA-guided nuclease, natural and artificial variants of RNA-targeted nucleases, possibilities to modulate their specificity through guide RNA modifications, and other approaches to increasing the accuracy of the CRISPR/Cas9 system in genome editing.
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Affiliation(s)
- L M Kulishova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - I P Vokhtantsev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - D V Kim
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
- Novosibirsk State University, Novosibirsk, 630090 Russia
| | - D O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
- Novosibirsk State University, Novosibirsk, 630090 Russia
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17
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Mechetin GV, Zharkov DO. DNA Damage Response and Repair in Boron Neutron Capture Therapy. Genes (Basel) 2023; 14:127. [PMID: 36672868 PMCID: PMC9859301 DOI: 10.3390/genes14010127] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Boron neutron capture therapy (BNCT) is an approach to the radiotherapy of solid tumors that was first outlined in the 1930s but has attracted considerable attention recently with the advent of a new generation of neutron sources. In BNCT, tumor cells accumulate 10B atoms that react with epithermal neutrons, producing energetic α particles and 7Li atoms that damage the cell's genome. The damage inflicted by BNCT appears not to be easily repairable and is thus lethal for the cell; however, the molecular events underlying the action of BNCT remain largely unaddressed. In this review, the chemistry of DNA damage during BNCT is outlined, the major mechanisms of DNA break sensing and repair are summarized, and the specifics of the repair of BNCT-induced DNA lesions are discussed.
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Affiliation(s)
- Grigory V. Mechetin
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Dmitry O. Zharkov
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
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18
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Prokhorova DV, Vokhtantsev IP, Tolstova PO, Zhuravlev ES, Kulishova LM, Zharkov DO, Stepanov GA. Natural Nucleoside Modifications in Guide RNAs Can Modulate the Activity of the CRISPR-Cas9 System In Vitro. CRISPR J 2022; 5:799-812. [PMID: 36350691 DOI: 10.1089/crispr.2022.0069] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
At the present time, the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system has been widely adopted as an efficient genomic editing tool. However, there are some actual problems such as the off-target effects, cytotoxicity, and immunogenicity. The incorporation of modifications into guide RNAs permits enhancing both the efficiency and the specificity of the CRISPR-Cas9 system. In this study, we demonstrate that the inclusion of N6-methyladenosine, 5-methylcytidine, and pseudouridine in trans-activating RNA (tracrRNA) or in single guide RNA (sgRNA) enables efficient gene editing in vitro. We found that the complexes of modified guide RNAs with Cas9 protein promoted cleavage of the target short/long duplexes and plasmid substrates. In addition, the modified monomers in guide RNAs allow increasing the specificity of CRISPR-Cas9 system in vitro and promote diminishing both the immunostimulating and the cytotoxic effects of sgRNAs.
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Affiliation(s)
- Daria V Prokhorova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Ivan P Vokhtantsev
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Polina O Tolstova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Evgenii S Zhuravlev
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Lilia M Kulishova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Grigory A Stepanov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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19
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Endutkin AV, Yudkina AV, Zharkov TD, Kim DV, Zharkov DO. Recognition of a Clickable Abasic Site Analog by DNA Polymerases and DNA Repair Enzymes. Int J Mol Sci 2022; 23:ijms232113353. [PMID: 36362137 PMCID: PMC9655677 DOI: 10.3390/ijms232113353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/27/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022] Open
Abstract
Azide–alkyne cycloaddition (“click chemistry”) has found wide use in the analysis of molecular interactions in living cells. 5-ethynyl-2-(hydroxymethyl)tetrahydrofuran-3-ol (EAP) is a recently developed apurinic/apyrimidinic (AP) site analog functionalized with an ethynyl moiety, which can be introduced into cells in DNA constructs to perform labeling or cross-linking in situ. However, as a non-natural nucleoside, EAP could be subject to removal by DNA repair and misreading by DNA polymerases. Here, we investigate the interaction of this clickable AP site analog with DNA polymerases and base excision repair enzymes. Similarly to the natural AP site, EAP was non-instructive and followed the “A-rule”, directing residual but easily detectable incorporation of dAMP by E. coli DNA polymerase I Klenow fragment, bacteriophage RB69 DNA polymerase and human DNA polymerase β. On the contrary, EAP was blocking for DNA polymerases κ and λ. EAP was an excellent substrate for the major human AP endonuclease APEX1 and E. coli AP exonucleases Xth and Nfo but was resistant to the AP lyase activity of DNA glycosylases. Overall, our data indicate that EAP, once within a cell, would represent a replication block and would be removed through an AP endonuclease-initiated long-patch base excision repair pathway.
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Affiliation(s)
- Anton V. Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
- Correspondence: (A.V.E.); (D.O.Z.)
| | - Anna V. Yudkina
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Timofey D. Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Daria V. Kim
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia
| | - Dmitry O. Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia
- Correspondence: (A.V.E.); (D.O.Z.)
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20
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Diatlova EA, Mechetin GV, Zharkov DO. Distinct Mechanisms of Target Search by Endonuclease VIII-like DNA Glycosylases. Cells 2022; 11:cells11203192. [PMID: 36291061 PMCID: PMC9600533 DOI: 10.3390/cells11203192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/08/2022] [Accepted: 10/09/2022] [Indexed: 12/02/2022] Open
Abstract
Proteins that recognize specific DNA sequences or structural elements often find their cognate DNA lesions in a processive mode, in which an enzyme binds DNA non-specifically and then slides along the DNA contour by one-dimensional diffusion. Opposite to the processive mechanism is distributive search, when an enzyme binds, samples and releases DNA without significant lateral movement. Many DNA glycosylases, the repair enzymes that excise damaged bases from DNA, use processive search to find their cognate lesions. Here, using a method based on correlated cleavage of multiply damaged oligonucleotide substrates we investigate the mechanism of lesion search by three structurally related DNA glycosylases—bacterial endonuclease VIII (Nei) and its mammalian homologs NEIL1 and NEIL2. Similarly to another homologous enzyme, bacterial formamidopyrimidine–DNA glycosylase, NEIL1 seems to use a processive mode to locate its targets. However, the processivity of Nei was notably lower, and NEIL2 exhibited almost fully distributive action on all types of substrates. Although one-dimensional diffusion is often regarded as a universal search mechanism, our results indicate that even proteins sharing a common fold may be quite different in the ways they locate their targets in DNA.
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Affiliation(s)
- Evgeniia A. Diatlova
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Grigory V. Mechetin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Dmitry O. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Correspondence:
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21
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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] [What about the content of this article? (0)] [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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22
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Torgasheva NA, Diatlova EA, Grin IR, Endutkin AV, Mechetin GV, Vokhtantsev IP, Yudkina AV, Zharkov DO. Noncatalytic Domains in DNA Glycosylases. Int J Mol Sci 2022; 23:ijms23137286. [PMID: 35806289 PMCID: PMC9266487 DOI: 10.3390/ijms23137286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 02/04/2023] Open
Abstract
Many proteins consist of two or more structural domains: separate parts that have a defined structure and function. For example, in enzymes, the catalytic activity is often localized in a core fragment, while other domains or disordered parts of the same protein participate in a number of regulatory processes. This situation is often observed in many DNA glycosylases, the proteins that remove damaged nucleobases thus initiating base excision DNA repair. This review covers the present knowledge about the functions and evolution of such noncatalytic parts in DNA glycosylases, mostly concerned with the human enzymes but also considering some unique members of this group coming from plants and prokaryotes.
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Affiliation(s)
- Natalia A. Torgasheva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
| | - Evgeniia A. Diatlova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Street, 630090 Novosibirsk, Russia
| | - Inga R. Grin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
| | - Anton V. Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
| | - Grigory V. Mechetin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
| | - Ivan P. Vokhtantsev
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Street, 630090 Novosibirsk, Russia
| | - Anna V. Yudkina
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
| | - Dmitry O. Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, 630090 Novosibirsk, Russia; (N.A.T.); (E.A.D.); (I.R.G.); (A.V.E.); (G.V.M.); (I.P.V.); (A.V.Y.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Street, 630090 Novosibirsk, Russia
- Correspondence:
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23
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Kakhkharova ZI, Zharkov DO, Grin IR. A Low-Activity Polymorphic Variant of Human NEIL2 DNA Glycosylase. Int J Mol Sci 2022; 23:ijms23042212. [PMID: 35216329 PMCID: PMC8879280 DOI: 10.3390/ijms23042212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 01/05/2023] Open
Abstract
Human NEIL2 DNA glycosylase (hNEIL2) is a base excision repair protein that removes oxidative lesions from DNA. A distinctive feature of hNEIL2 is its preference for the lesions in bubbles and other non-canonical DNA structures. Although a number of associations of polymorphisms in the hNEIL2 gene were reported, there is little data on the functionality of the encoded protein variants, as follows: only hNEIL2 R103Q was described as unaffected, and R257L, as less proficient in supporting the repair in a reconstituted system. Here, we report the biochemical characterization of two hNEIL2 variants found as polymorphisms in the general population, R103W and P304T. Arg103 is located in a long disordered segment within the N-terminal domain of hNEIL2, while Pro304 occupies a position in the β-turn of the DNA-binding zinc finger motif. Similar to the wild-type protein, both of the variants could catalyze base excision and nick DNA by β-elimination but demonstrated a lower affinity for DNA. Steady-state kinetics indicates that the P304T variant has its catalytic efficiency (in terms of kcat/KM) reduced ~5-fold compared with the wild-type hNEIL2, whereas the R103W enzyme is much less affected. The P304T variant was also less proficient than the wild-type, or R103W hNEIL2, in the removal of damaged bases from single-stranded and bubble-containing DNA. Overall, hNEIL2 P304T could be worthy of a detailed epidemiological analysis as a possible cancer risk modifier.
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Affiliation(s)
- Zarina I. Kakhkharova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia;
| | - Dmitry O. Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia;
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence: (D.O.Z.); (I.R.G.)
| | - Inga R. Grin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia;
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence: (D.O.Z.); (I.R.G.)
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24
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Abstract
Apurinic/apyrimidinic (AP) sites appear in DNA spontaneously and as intermediates of base excision DNA repair. AP sites are noninstructive lesions: they strongly block DNA polymerases, and if bypassed, the nature of the incorporated dNMP is mostly guided by the interactions within the polymerase-DNA active site. Many DNA polymerases follow the "A-rule", preferentially incorporating dAMP opposite to natural AP sites. Methoxyamine (MX), a small molecule, efficiently reacts with the aldehyde moiety of natural AP sites, thereby preventing their cleavage by APEX1, the major human AP endonuclease. MX is currently regarded as a possible sensitizer of cancer cells toward DNA-damaging drugs. To evaluate the mutagenic potential of MX, we have studied the utilization of various dNTPs by five DNA polymerases of different families encountering MX-AP adducts in the template in comparison with the natural aldehydic AP site. The Klenow fragment of Escherichia coli DNA polymerase I strictly followed the A-rule with both natural AP and MX-adducted AP sites. Phage RB69 DNA polymerase, a close relative of human DNA polymerases δ and ε, efficiently incorporated both dAMP and dGMP. DNA polymerase β mostly incorporated dAMP and dCMP, preferring dCMP opposite to the natural AP site and dAMP opposite to the MX-AP site, while DNA polymerase λ was selective for dGMP, apparently via the primer misalignment mechanism. Finally, translesion DNA polymerase κ also followed the A-rule for MX-AP and additionally incorporated dCMP opposite to a natural AP site. Overall, the MX-AP site, despite structural differences, was similar to the natural AP site in terms of the dNMP misincorporation preference but was bypassed less efficiently by all polymerases except for Pol κ.
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Affiliation(s)
- Anna V Yudkina
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, Novosibirsk 630090, Russia
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, Novosibirsk 630090, Russia.,Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia
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25
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Endutkin AV, Yatsenko DD, Zharkov DO. Effect of DNA Methylation on the 3'→5' Exonuclease Activity of Major Human Abasic Site Endonuclease APEX1. Biochemistry (Mosc) 2022; 87:10-20. [PMID: 35491018 DOI: 10.1134/s0006297922010023] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
Apurinic/apyrimidinic (AP) endonucleases are the key enzymes in the DNA base excision repair, as they hydrolyze the phosphodiester bond in the AP site formed after removal of the damaged base. Major human AP endonuclease APEX1 also possesses the 3'-phosphodiesterase and 3'→5' exonuclease activities. The biological role of the latter has not been established yet; it is assumed that it corrects DNA synthesis errors during DNA repair. If DNA is damaged at the 3'-side of 5-methylcytosine (mC) residue, the 3'→5' exonuclease activity can change the epigenetic methylation status of the CpG dinucleotide. It remains unclear whether the 3'→5' exonuclease activity of APEX1 contributes to the active epigenetic demethylation or, on the contrary, is limited in the case of methylated CpG dinucleotides in order to preserve the epigenetic status upon repair of accidental DNA damage. Here, we report the results of the first systematic study on the efficiency of removal of 3'-terminal nucleotides from the substrates modeling DNA repair intermediates in the CpG dinucleotides. The best substrates for the 3'→5' exonuclease activity of APEX1 were oligonucleotides with the 3'-terminal bases non-complementary to the template, while the worst substrates contained mC. The presence of mC in the complementary strand significantly reduced the reaction rate even for the non-complementary 3'-ends. Therefore, the efficiency of the 3'→5' exonuclease reaction catalyzed by APEX1 is limited in the case of the methylated CpG dinucleotides, which likely reflects the need to preserve the epigenetic status during DNA repair.
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Affiliation(s)
- Anton V Endutkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Darya D Yatsenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, 630090, Russia
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26
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Zhdanova PV, Ishchenko AA, Chernonosov AA, Zharkov DO, Koval VV. Dynamics and Conformational Changes in Human NEIL2 DNA Glycosylase Analyzed by Hydrogen/Deuterium Exchange Mass Spectrometry. J Mol Biol 2021; 434:167334. [PMID: 34757057 DOI: 10.1016/j.jmb.2021.167334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/20/2021] [Revised: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 12/31/2022]
Abstract
Base excision DNA repair (BER) is necessary for removal of damaged nucleobases from the genome and their replacement with normal nucleobases. BER is initiated by DNA glycosylases, the enzymes that cleave the N-glycosidic bonds of damaged deoxynucleotides. Human endonuclease VIII-like protein 2 (hNEIL2), belonging to the helix-two-turn-helix structural superfamily of DNA glycosylases, is an enzyme uniquely specific for oxidized pyrimidines in non-canonical DNA substrates such as bubbles and loops. The structure of hNEIL2 has not been solved; its closest homologs with known structures are NEIL2 from opossum and from giant mimivirus. Here we analyze the conformational dynamics of free hNEIL2 using a combination of hydrogen/deuterium exchange mass spectrometry, homology modeling and molecular dynamics simulations. We show that a prominent feature of vertebrate NEIL2 - a large insert in its N-terminal domain absent from other DNA glycosylases - is unstructured in solution. It was suggested that helix-two-turn-helix DNA glycosylases undergo open-close transition upon DNA binding, with the large movement of their N- and C-terminal domains, but the open conformation has been elusive to capture. Our data point to the open conformation as favorable for free hNEIL2 in solution. Overall, our results are consistent with the view of hNEIL2 as a conformationally flexible protein, which may be due to its participation in the repair of non-canonical DNA structures and/or to the involvement in functional and regulatory protein-protein interactions.
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Affiliation(s)
- Polina V Zhdanova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibisk, Russia; Novosibirsk State University, Novosibisk, Russia
| | - Alexander A Ishchenko
- Groupe "Réparation de lADN", Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, Villejuif F-94805, France; Gustave Roussy, Université Paris-Saclay, Villejuif F-94805, France
| | | | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibisk, Russia; Novosibirsk State University, Novosibisk, Russia
| | - Vladimir V Koval
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibisk, Russia; Novosibirsk State University, Novosibisk, Russia.
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27
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Zharkov DO, Yudkina AV, Riesebeck T, Loshchenova PS, Mostovich EA, Dianov GL. Boron-containing nucleosides as tools for boron-neutron capture therapy. Am J Cancer Res 2021; 11:4668-4682. [PMID: 34765286 PMCID: PMC8569357] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023] Open
Abstract
Despite the significant progress in cancer cure, the development of new approaches to cancer therapy is still of great importance since many deadly tumors remain untreatable. Boron neutron capture therapy (BNCT), proposed more than eighty years ago, is still considered a potentially advantageous approach. Irradiation of cells containing 10B isotopes with epithermal neutrons and the consequent decay of boron nuclei releases particles that deposit high energy along a very short path, inflicting heavy damage on the target cells but sparing the neighbouring tissue. Delivery and preferential accumulation of boron in cancer cells are the major obstacles that slow down the clinical use of BNCT. Since DNA damage caused by irradiation is the major reason for cell death, the incorporation of boron-containing nucleotides into the DNA of cancer cells may significantly increase the efficacy of BNCT. In this review, we discuss the current state of knowledge in the synthesis of boron-containing nucleosides and their application for BNCT with a special focus on their possible incorporation into genomic DNA.
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Affiliation(s)
- Dmitry O Zharkov
- Novosibirsk State University2 Pirogova Street, Novosibirsk 630090, Russia
- SB RAS Institute of Chemical Biology and Fundamental Medicine8 Lavrentieva Avenue, Novosibirsk 630090, Russia
| | - Anna V Yudkina
- Novosibirsk State University2 Pirogova Street, Novosibirsk 630090, Russia
- SB RAS Institute of Chemical Biology and Fundamental Medicine8 Lavrentieva Avenue, Novosibirsk 630090, Russia
| | - Tim Riesebeck
- Novosibirsk State University2 Pirogova Street, Novosibirsk 630090, Russia
| | - Polina S Loshchenova
- Novosibirsk State University2 Pirogova Street, Novosibirsk 630090, Russia
- SB RAS Institute of Cytology and Genetics10 Lavrentieva Avenue, Novosibirsk 630090, Russia
| | - Evgeny A Mostovich
- Novosibirsk State University2 Pirogova Street, Novosibirsk 630090, Russia
| | - Grigory L Dianov
- Novosibirsk State University2 Pirogova Street, Novosibirsk 630090, Russia
- SB RAS Institute of Cytology and Genetics10 Lavrentieva Avenue, Novosibirsk 630090, Russia
- Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research BuildingOxford OX3 7DQ, United Kingdom
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28
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Kim DV, Kulishova LM, Torgasheva NA, Melentyev VS, Dianov GL, Medvedev SP, Zakian SM, Zharkov DO. Mild phenotype of knockouts of the major apurinic/apyrimidinic endonuclease APEX1 in a non-cancer human cell line. PLoS One 2021; 16:e0257473. [PMID: 34529719 PMCID: PMC8445474 DOI: 10.1371/journal.pone.0257473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/01/2021] [Indexed: 12/26/2022] Open
Abstract
The major human apurinic/apyrimidinic (AP) site endonuclease, APEX1, is a central player in the base excision DNA repair (BER) pathway and has a role in the regulation of DNA binding by transcription factors. In vertebrates, APEX1 knockouts are embryonic lethal, and only a handful of knockout cell lines are known. To facilitate studies of multiple functions of this protein in human cells, we have used the CRISPR/Cas9 system to knock out the APEX1 gene in a widely used non-cancer hypotriploid HEK 293FT cell line. Two stable knockout lines were obtained, one carrying two single-base deletion alleles and one single-base insertion allele in exon 3, another homozygous in the single-base insertion allele. Both mutations cause a frameshift that leads to premature translation termination before the start of the protein's catalytic domain. Both cell lines totally lacked the APEX1 protein and AP site-cleaving activity, and showed significantly lower levels of the APEX1 transcript. The APEX1-null cells were unable to support BER on uracil- or AP site-containing substrates. Phenotypically, they showed a moderately increased sensitivity to methyl methanesulfonate (MMS; ~2-fold lower EC50 compared with wild-type cells), and their background level of natural AP sites detected by the aldehyde-reactive probe was elevated ~1.5-2-fold. However, the knockout lines retained a nearly wild-type sensitivity to oxidizing agents hydrogen peroxide and potassium bromate. Interestingly, despite the increased MMS cytotoxicity, we observed no additional increase in AP sites in knockout cells upon MMS treatment, which could indicate their conversion into more toxic products in the absence of repair. Overall, the relatively mild cell phenotype in the absence of APEX1-dependent BER suggests that mammalian cells possess mechanisms of tolerance or alternative repair of AP sites. The knockout derivatives of the extensively characterized HEK 293FT cell line may provide a valuable tool for studies of APEX1 in DNA repair and beyond.
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Affiliation(s)
- Daria V. Kim
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Liliya M. Kulishova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | | | - Vasily S. Melentyev
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- SB RAS Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Grigory L. Dianov
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- SB RAS Institute of Cytology and Genetics, Novosibirsk, Russia
- Department of Oncology, MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | | | - Suren M. Zakian
- SB RAS Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Dmitry O. Zharkov
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
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29
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Boldinova EO, Yudkina AV, Shilkin ES, Gagarinskaya DI, Baranovskiy AG, Tahirov TH, Zharkov DO, Makarova AV. Translesion activity of PrimPol on DNA with cisplatin and DNA-protein cross-links. Sci Rep 2021; 11:17588. [PMID: 34475447 PMCID: PMC8413282 DOI: 10.1038/s41598-021-96692-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 07/26/2021] [Indexed: 12/24/2022] Open
Abstract
Human PrimPol belongs to the archaeo-eukaryotic primase superfamily of primases and is involved in de novo DNA synthesis downstream of blocking DNA lesions and non-B DNA structures. PrimPol possesses both DNA/RNA primase and DNA polymerase activities, and also bypasses a number of DNA lesions in vitro. In this work, we have analyzed translesion synthesis activity of PrimPol in vitro on DNA with an 1,2-intrastrand cisplatin cross-link (1,2-GG CisPt CL) or a model DNA–protein cross-link (DpCL). PrimPol was capable of the 1,2-GG CisPt CL bypass in the presence of Mn2+ ions and preferentially incorporated two complementary dCMPs opposite the lesion. Nucleotide incorporation was stimulated by PolDIP2, and yeast Pol ζ efficiently extended from the nucleotides inserted opposite the 1,2-GG CisPt CL in vitro. DpCLs significantly blocked the DNA polymerase activity and strand displacement synthesis of PrimPol. However, PrimPol was able to reach the DpCL site in single strand template DNA in the presence of both Mg2+ and Mn2+ ions despite the presence of the bulky protein obstacle.
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Affiliation(s)
- Elizaveta O Boldinova
- Institute of Molecular Genetics, National Research Center «Kurchatov Institute», Kurchatov sq. 2, Moscow, Russia, 123182
| | - Anna V Yudkina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk, Russia, 630090
| | - Evgeniy S Shilkin
- Institute of Molecular Genetics, National Research Center «Kurchatov Institute», Kurchatov sq. 2, Moscow, Russia, 123182
| | - Diana I Gagarinskaya
- Institute of Molecular Genetics, National Research Center «Kurchatov Institute», Kurchatov sq. 2, Moscow, Russia, 123182
| | - Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk, Russia, 630090.,Novosibirsk State University, 2 Pirogova St., Novosibirsk, Russia, 630090
| | - Alena V Makarova
- Institute of Molecular Genetics, National Research Center «Kurchatov Institute», Kurchatov sq. 2, Moscow, Russia, 123182.
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30
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Dymova MA, Endutkin AV, Polunovsky VV, Zakabunin AI, Khrapov EA, Torgasheva NA, Yudkina AV, Mechetin GV, Filipenko ML, Zharkov DO. [Characterization of Recombinant Endonuclease IV from Mycobacterium tuberculosis]. Mol Biol (Mosk) 2021; 55:258-268. [PMID: 33871439 DOI: 10.31857/s002689842102004x] [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: 09/04/2020] [Accepted: 10/20/2020] [Indexed: 11/24/2022]
Abstract
Mycobacterium tuberculosis cells contain two apurinic/apyrimidinic (AP) endonucleases, endonuclease IV (MtbEnd) and exonuclease III (MtbXthA), the former playing a dominant role in protecting mycobacterial DNA from oxidative stress. Mycobacterial endonuclease IV substantially differs from its homologs found in Escherichia coli and other proteobacteria in a number of conserved positions important for DNA binding and AP site recognition. The M. tuberculosis end gene was cloned, and recombinant MtbEnd purified and characterized. The protein efficiently hydrolyzed DNA at the natural AP site and its 1'-deoxy analog in the presence of divalent cations, of which Ca^(2+), Mn^(2+), and Co^(2+) supported the highest activity. Exonuclease activity was not detected in MtbEnt preparations. The pH optimum was estimated at 7.0-8.0; the ionic strength optimum, at ~50 mM NaCl. Enzymatic activity of MtbEnd was suppressed in the presence of methoxyamine, a chemotherapeutic agent that modifies AP sites. Based on the results, MtbEnd was assumed to provide a possible target for new anti-tuberculosis drugs.
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Affiliation(s)
- M A Dymova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - A V Endutkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - V V Polunovsky
- Novosibirsk State University, Novosibirsk, 630090 Russia
| | - A I Zakabunin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - E A Khrapov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - N A Torgasheva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - A V Yudkina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - G V Mechetin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - M L Filipenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - D O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia.,Novosibirsk State University, Novosibirsk, 630090 Russia.,
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31
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Shilkin ES, Petrova DV, Poltorachenko VA, Boldinova EO, Zharkov DO, Makarova AV. [Template Properties of 5-Methyl-2'-Deoxycytidine and 5-Hydroxymethyl-2'-Deoxycytidine in Reactions with Human Translesion and Reparative DNA Polymerases]. Mol Biol (Mosk) 2021; 55:305-311. [PMID: 33871443 DOI: 10.31857/s0026898421020130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 08/30/2020] [Accepted: 09/24/2020] [Indexed: 11/24/2022]
Abstract
5-Methyl-2'-deoxycytidine (mC) and the product of its controlled oxidation, 5-hydroxymethyl-2'-cytidine (hmC), play a key role in the epigenetic regulation of gene expression, the cell differentiation, and the carcinogenesis. Due to spontaneious deamination, genomic CpG sites containing mC and hmC serve as mutagenesis hotspots. In addition, error-prone translesion and reparative DNA polymerases may serve as additional source of mutations in the lesion-containing regions with CpG sites. In the present work, we performed in vitro analysis of the accuracy of nucleotide incorporation opposite to mC and hmC by human DNA polymerases Polβ, Polλ, Polη, Polι, PoIκ and primase polymerase PrimPol. The results of the study show a high accuracy of copying mC and hmC by the reparative DNA polymerases polymerases Polβ and Polλ, while Polη, Polι, PoIκ, and PrimPol copied mC and hmC with less accuracy evident by incorporation of dAMP and dTMP. The same spectrum of error-prone dNMP incorporation was also noted at sites with unmodified cytosines.
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Affiliation(s)
- E S Shilkin
- Institute of Molecular Genetics, Kurchatov Institute Research Center, Moscow, 123182 Russia
| | - D V Petrova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - V A Poltorachenko
- Institute of Molecular Genetics, Kurchatov Institute Research Center, Moscow, 123182 Russia
| | - E O Boldinova
- Institute of Molecular Genetics, Kurchatov Institute Research Center, Moscow, 123182 Russia
| | - D O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia.,Novosibirsk State University, Novosibirsk, 630090 Russia.,
| | - A V Makarova
- Institute of Molecular Genetics, Kurchatov Institute Research Center, Moscow, 123182 Russia.,
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Abstract
The GO system is part of the DNA base excision repair pathway and is required for the error-free repair of 8-oxoguanine (oxoG), one of the most common oxidative DNA lesions. Due to the ability of oxoG to form oxoG:A mispairs, this base is highly mutagenic. Its repair requires the action of two enzymes: 8-oxoguanine DNA glycosylase (Fpg or MutM in bacteria and OGG1 in eukaryotes), which removes oxoG from oxoG:C pairs, and adenine DNA glycosylase (MutY in bacteria and MUTYH in eukaryotes), which removes A from oxoG:A mispairs to prevent mutations. The third enzyme of the system (MutT in bacteria and MTH1 or NUDT1 in eukaryotes) hydrolyzes 8-oxo-2'-deoxyguanosine triphosphate, thus preventing its incorporation into DNA. Recent data point to the proteins of the GO system as promising targets for the therapy of cancer, autoimmune diseases, and bacterial infections. This review highlights the structure and specificity of the GO system in bacteria and eukaryotes and its unique role in mutation avoidance.
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Affiliation(s)
- A V Endutkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia.,
| | - D O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia.,Novosibirsk State University, Novosibirsk, 630090 Russia.,
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33
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Makasheva KA, Endutkin AV, Zharkov DO. Requirements for DNA bubble structure for efficient cleavage by helix-two-turn-helix DNA glycosylases. Mutagenesis 2021; 35:119-128. [PMID: 31784740 DOI: 10.1093/mutage/gez047] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022] Open
Abstract
Oxidative DNA lesions, constantly generated by both endogenous and environmentally induced reactive oxygen species, are removed via the base excision repair pathway. In bacteria, Fpg and Nei DNA glycosylases, belonging to the helix-two-turn-helix (H2TH) structural superfamily, remove oxidised purines and pyrimidines, respectively. Interestingly, the human H2TH family glycosylases, NEIL1, NEIL2 and NEIL3, have been reported to prefer oxidative lesions in DNA bubbles or single-stranded DNA. It had been hypothesised that NEIL2 might be involved in the repair of lesions in transcription bubbles; however, bubble-like structures may appear in other cellular contexts such as displacement loops (D-loops) associated with transcription, recombination or telomere maintenance. The activities of bacterial Fpg and Nei on bubble substrates were not addressed. Also, it is not known whether H2TH enzymes process bubbles containing the third DNA or RNA strand, and how the bubble length and position of the lesion within a bubble affect the excision. We have investigated the removal of 8-oxoguanine (8-oxoG) and 5,6-dihydrouracil (DHU) by Escherichia coli Fpg and Nei and human NEIL1 and NEIL2 from single-strand oligonucleotides, perfect duplexes, bubbles with different numbers of unpaired bases (6-30), bubbles containing the lesion in different positions and D-loops with the third strand made of DNA or RNA. Fpg, NEIL1 and NEIL2 efficiently excised lesions located within bubbles, with NEIL1 and NEIL2 being specific for DHU, and Fpg removing both 8-oxoG and DHU. Nei, in contrast, was significantly active only on DHU located in double-stranded DNA. Fpg and NEIL1 also tolerated the presence of the third strand of either DNA or RNA in D-loops if the lesion was in the single-stranded part, and Fpg, Nei and NEIL1 excised lesions from the double-stranded DNA part of D-loops. The presence of an additional unpaired 5'-tail of DNA or RNA did not affect the activity. No significant position preference for lesions in a 12-mer bubble was found. Overall, the activities of Fpg, NEIL1 and NEIL2 on these non-canonical substrates are consistent with the possibility that these enzymes may participate in the repair in structures arising during transcription or homologous recombination.
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Affiliation(s)
| | - Anton V Endutkin
- Novosibirsk State University, Novosibirsk, Russia.,SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Dmitry O Zharkov
- Novosibirsk State University, Novosibirsk, Russia.,SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
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Popov AV, Endutkin AV, Yatsenko DD, Yudkina AV, Barmatov AE, Makasheva KA, Raspopova DY, Diatlova EA, Zharkov DO. Molecular dynamics approach to identification of new OGG1 cancer-associated somatic variants with impaired activity. J Biol Chem 2021; 296:100229. [PMID: 33361155 PMCID: PMC7948927 DOI: 10.1074/jbc.ra120.014455] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 01/02/2023] Open
Abstract
DNA of living cells is always exposed to damaging factors. To counteract the consequences of DNA lesions, cells have evolved several DNA repair systems, among which base excision repair is one of the most important systems. Many currently used antitumor drugs act by damaging DNA, and DNA repair often interferes with chemotherapy and radiotherapy in cancer cells. Tumors are usually extremely genetically heterogeneous, often bearing mutations in DNA repair genes. Thus, knowledge of the functionality of cancer-related variants of proteins involved in DNA damage response and repair is of great interest for personalization of cancer therapy. Although computational methods to predict the variant functionality have attracted much attention, at present, they are mostly based on sequence conservation and make little use of modern capabilities in computational analysis of 3D protein structures. We have used molecular dynamics (MD) to model the structures of 20 clinically observed variants of a DNA repair enzyme, 8-oxoguanine DNA glycosylase. In parallel, we have experimentally characterized the activity, thermostability, and DNA binding in a subset of these mutant proteins. Among the analyzed variants of 8-oxoguanine DNA glycosylase, three (I145M, G202C, and V267M) were significantly functionally impaired and were successfully predicted by MD. Alone or in combination with sequence-based methods, MD may be an important functional prediction tool for cancer-related protein variants of unknown significance.
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Affiliation(s)
- Aleksandr V Popov
- Laboratory of Genome and Protein Engineering, SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.
| | - Anton V Endutkin
- Laboratory of Genome and Protein Engineering, SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Darya D Yatsenko
- Laboratory of Genome and Protein Engineering, SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia; Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Anna V Yudkina
- Laboratory of Genome and Protein Engineering, SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Alexander E Barmatov
- Laboratory of Genome and Protein Engineering, SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Kristina A Makasheva
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Darya Yu Raspopova
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Evgeniia A Diatlova
- Laboratory of Genome and Protein Engineering, SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Dmitry O Zharkov
- Laboratory of Genome and Protein Engineering, SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia; Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia.
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35
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Mechetin GV, Endutkin AV, Diatlova EA, Zharkov DO. Inhibitors of DNA Glycosylases as Prospective Drugs. Int J Mol Sci 2020; 21:ijms21093118. [PMID: 32354123 PMCID: PMC7247160 DOI: 10.3390/ijms21093118] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 12/22/2022] Open
Abstract
DNA glycosylases are enzymes that initiate the base excision repair pathway, a major biochemical process that protects the genomes of all living organisms from intrinsically and environmentally inflicted damage. Recently, base excision repair inhibition proved to be a viable strategy for the therapy of tumors that have lost alternative repair pathways, such as BRCA-deficient cancers sensitive to poly(ADP-ribose)polymerase inhibition. However, drugs targeting DNA glycosylases are still in development and so far have not advanced to clinical trials. In this review, we cover the attempts to validate DNA glycosylases as suitable targets for inhibition in the pharmacological treatment of cancer, neurodegenerative diseases, chronic inflammation, bacterial and viral infections. We discuss the glycosylase inhibitors described so far and survey the advances in the assays for DNA glycosylase reactions that may be used to screen pharmacological libraries for new active compounds.
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Affiliation(s)
- Grigory V. Mechetin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (G.V.M.); (A.V.E.); (E.A.D.)
| | - Anton V. Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (G.V.M.); (A.V.E.); (E.A.D.)
| | - Evgeniia A. Diatlova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (G.V.M.); (A.V.E.); (E.A.D.)
| | - Dmitry O. Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (G.V.M.); (A.V.E.); (E.A.D.)
- Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Correspondence: ; Tel.: +7-383-363-5187
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36
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Popov AV, Yudkina AV, Vorobjev YN, Zharkov DO. Catalytically Competent Conformation of the Active Site of Human 8-Oxoguanine-DNA Glycosylase. Biochemistry (Mosc) 2020; 85:192-204. [PMID: 32093595 DOI: 10.1134/s0006297920020066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
8-Oxoguanine-DNA N-glycosylase (OGG1) is a eukaryotic DNA repair enzyme responsible for the removal of 8-oxoguanine (oxoG), one of the most abundant oxidative DNA lesions. OGG1 catalyzes two successive reactions - N-glycosidic bond hydrolysis (glycosylase activity) and DNA strand cleavage on the 3'-side of the lesion by β-elimination (lyase activity). The enzyme also exhibits lyase activity with substrates containing apurinic/apyrimidinic (AP) sites (deoxyribose moieties lacking the nucleobase). OGG1 is highly specific for the base opposite the lesion, efficiently excising oxoG and cleaving AP sites located opposite to C, but not opposite to A. The activity is also profoundly decreased by amino acid changes that sterically interfere with oxoG binding in the active site of the enzyme after the lesion is everted from the DNA duplex. Earlier, the molecular dynamics approach was used to study the conformational dynamics of such human OGG1 mutants in complexes with the oxoG:C-containing substrate DNA, and the population density of certain conformers of two OGG1 catalytic residues, Lys249 and Asp268, was suggested to determine the enzyme activity. Here, we report the study of molecular dynamics of human OGG1 bound to the oxoG:A-containing DNA and OGG1 mutants bound to the AP:C-containing DNA. We showed that the enzyme low activity is associated with a decrease in the populations of Lys249 and Asp268 properly configured for catalysis. The experimentally measured rate constants for the OGG1 mutants show a good agreement with the models. We conclude that the enzymatic activity of OGG1 is determined majorly by the population density of the catalytically competent conformations of the active site residues Lys249 and Asp268.
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Affiliation(s)
- A V Popov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - A V Yudkina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Yu N Vorobjev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - D O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia
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37
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Kim DV, Makarova AV, Miftakhova RR, Zharkov DO. Base Excision DNA Repair Deficient Cells: From Disease Models to Genotoxicity Sensors. Curr Pharm Des 2020; 25:298-312. [PMID: 31198112 DOI: 10.2174/1381612825666190319112930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/13/2019] [Indexed: 12/29/2022]
Abstract
Base excision DNA repair (BER) is a vitally important pathway that protects the cell genome from many kinds of DNA damage, including oxidation, deamination, and hydrolysis. It involves several tightly coordinated steps, starting from damaged base excision and followed by nicking one DNA strand, incorporating an undamaged nucleotide, and DNA ligation. Deficiencies in BER are often embryonic lethal or cause morbid diseases such as cancer, neurodegeneration, or severe immune pathologies. Starting from the early 1980s, when the first mammalian cell lines lacking BER were produced by spontaneous mutagenesis, such lines have become a treasure trove of valuable information about the mechanisms of BER, often revealing unexpected connections with other cellular processes, such as antibody maturation or epigenetic demethylation. In addition, these cell lines have found an increasing use in genotoxicity testing, where they provide increased sensitivity and representativity to cell-based assay panels. In this review, we outline current knowledge about BER-deficient cell lines and their use.
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Affiliation(s)
- Daria V Kim
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russian Federation
| | - Alena V Makarova
- RAS Institute of Molecular Genetics, 2 Kurchatova Sq., Moscow 123182, Russian Federation
| | - Regina R Miftakhova
- Kazan Federal University, 18 Kremlevsakaya St., Kazan 420008, Russian Federation
| | - Dmitry O Zharkov
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russian Federation.,SB RAS Institute of Chemical Biology and Fu ndamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russian Federation
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38
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Matkarimov BT, Zharkov DO, Saparbaev MK. Mechanistic insight into the role of Poly(ADP-ribosyl)ation in DNA topology modulation and response to DNA damage. Mutagenesis 2019; 35:107-118. [DOI: 10.1093/mutage/gez045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/12/2019] [Indexed: 12/31/2022] Open
Abstract
AbstractGenotoxic stress generates single- and double-strand DNA breaks either through direct damage by reactive oxygen species or as intermediates of DNA repair. Failure to detect and repair DNA strand breaks leads to deleterious consequences such as chromosomal aberrations, genomic instability and cell death. DNA strand breaks disrupt the superhelical state of cellular DNA, which further disturbs the chromatin architecture and gene activity regulation. Proteins from the poly(ADP-ribose) polymerase (PARP) family, such as PARP1 and PARP2, use NAD+ as a substrate to catalyse the synthesis of polymeric chains consisting of ADP-ribose units covalently attached to an acceptor molecule. PARP1 and PARP2 are regarded as DNA damage sensors that, upon activation by strand breaks, poly(ADP-ribosyl)ate themselves and nuclear acceptor proteins. Noteworthy, the regularly branched structure of poly(ADP-ribose) polymer suggests that the mechanism of its synthesis may involve circular movement of PARP1 around the DNA helix, with a branching point in PAR corresponding to one complete 360° turn. We propose that PARP1 stays bound to a DNA strand break end, but rotates around the helix displaced by the growing poly(ADP-ribose) chain, and that this rotation could introduce positive supercoils into damaged chromosomal DNA. This topology modulation would enable nucleosome displacement and chromatin decondensation around the lesion site, facilitating the access of DNA repair proteins or transcription factors. PARP1-mediated DNA supercoiling can be transmitted over long distances, resulting in changes in the high-order chromatin structures. The available structures of PARP1 are consistent with the strand break-induced PAR synthesis as a driving force for PARP1 rotation around the DNA axis.
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Affiliation(s)
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Murat K Saparbaev
- Groupe «Réparation de l’ADN», Equipe Labellisée par la Ligue Nationale Contre le Cancer, Université Paris-Sud, Gustave Roussy Cancer Campus, Villejuif Cedex, France
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39
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Gruber DR, Toner JJ, Miears HL, Shernyukov AV, Kiryutin AS, Lomzov AA, Endutkin AV, Grin IR, Petrova DV, Kupryushkin MS, Yurkovskaya AV, Johnson EC, Okon M, Bagryanskaya EG, Zharkov DO, Smirnov SL. Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation. Nucleic Acids Res 2019; 46:10827-10839. [PMID: 30289469 PMCID: PMC6237784 DOI: 10.1093/nar/gky893] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 09/20/2018] [Indexed: 01/20/2023] Open
Abstract
DNA damage can affect various regulatory elements of the genome, with the consequences for DNA structure, dynamics, and interaction with proteins remaining largely unexplored. We used solution NMR spectroscopy, restrained and free molecular dynamics to obtain the structures and investigate dominant motions for a set of DNA duplexes containing CpG sites permuted with combinations of 5-methylcytosine (mC), the primary epigenetic base, and 8-oxoguanine (oxoG), an abundant DNA lesion. Guanine oxidation significantly changed the motion in both hemimethylated and fully methylated DNA, increased base pair breathing, induced BI→BII transition in the backbone 3′ to the oxoG and reduced the variability of shift and tilt helical parameters. UV melting experiments corroborated the NMR and molecular dynamics results, showing significant destabilization of all methylated contexts by oxoG. Notably, some dynamic and thermodynamic effects were not additive in the fully methylated oxidized CpG, indicating that the introduced modifications interact with each other. Finally, we show that the presence of oxoG biases the recognition of methylated CpG dinucleotides by ROS1, a plant enzyme involved in epigenetic DNA demethylation, in favor of the oxidized DNA strand. Thus, the conformational and dynamic effects of spurious DNA oxidation in the regulatory CpG dinucleotide can have far-reaching biological consequences.
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Affiliation(s)
- David R Gruber
- Chemistry Department, Western Washington University, 516 High St., Bellingham, WA 98225-9150, USA
| | - Joanna J Toner
- Chemistry Department, Western Washington University, 516 High St., Bellingham, WA 98225-9150, USA
| | - Heather L Miears
- Chemistry Department, Western Washington University, 516 High St., Bellingham, WA 98225-9150, USA
| | - Andrey V Shernyukov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentieva Ave., Novosibirsk 630090, Russia.,Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Alexey S Kiryutin
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia.,SB RAS International Tomography Center, 3a Institutskaya St., Novosibirsk 630090, Russia
| | - Alexander A Lomzov
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia.,SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Anton V Endutkin
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia.,SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Inga R Grin
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia.,SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Darya V Petrova
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia.,SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Maxim S Kupryushkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Alexandra V Yurkovskaya
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia.,SB RAS International Tomography Center, 3a Institutskaya St., Novosibirsk 630090, Russia
| | | | - Mark Okon
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver BC, V6T 1Z3, Canada
| | - Elena G Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentieva Ave., Novosibirsk 630090, Russia.,Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Dmitry O Zharkov
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia.,SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Serge L Smirnov
- Chemistry Department, Western Washington University, 516 High St., Bellingham, WA 98225-9150, USA
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41
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Boldinova EO, Khairullin RF, Makarova AV, Zharkov DO. Isoforms of Base Excision Repair Enzymes Produced by Alternative Splicing. Int J Mol Sci 2019; 20:ijms20133279. [PMID: 31277343 PMCID: PMC6651865 DOI: 10.3390/ijms20133279] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 06/29/2019] [Accepted: 07/02/2019] [Indexed: 02/07/2023] Open
Abstract
Transcripts of many enzymes involved in base excision repair (BER) undergo extensive alternative splicing, but functions of the corresponding alternative splice variants remain largely unexplored. In this review, we cover the studies describing the common alternatively spliced isoforms and disease-associated variants of DNA glycosylases, AP-endonuclease 1, and DNA polymerase beta. We also discuss the roles of alternative splicing in the regulation of their expression, catalytic activities, and intracellular transport.
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Affiliation(s)
| | - Rafil F Khairullin
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 9 Parizhskoy Kommuny Str., 420012 Kazan, Russia
| | - Alena V Makarova
- RAS Institute of Molecular Genetics, 2 Kurchatova Sq., 123182 Moscow, Russia.
| | - Dmitry O Zharkov
- Novosibirsk State University, 1 Pirogova St., 630090 Novosibirsk, Russia.
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia.
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42
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Endutkin AV, Zharkov DO. Critical Sites of DNA Backbone Integrity for Damaged Base Removal by Formamidopyrimidine-DNA Glycosylase. Biochemistry 2019; 58:2740-2749. [PMID: 31120733 DOI: 10.1021/acs.biochem.9b00134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA glycosylases, the enzymes that initiate base excision DNA repair, recognize damaged bases through a series of precisely orchestrated movements. Most glycosylases sharply kink the DNA axis at the lesion site and extrude the target base from the DNA double helix into the enzyme's active site. Little attention has been paid so far to the role of the physical continuity of the DNA backbone in allowing the required conformational distortion. Here, we analyze base excision by formamidopyrimidine-DNA glycosylase (Fpg) from substrates keeping all phosphates but containing a nick within three nucleotides of the lesion in either DNA strand. Four phosphoester linkages at the damaged nucleotide and two nucleotides 3' to it were essential for Fpg activity, while the breakage of the others, even at the same critical phosphates, had no effect or even stimulated the reaction. Reduction of the likelihood of hydrogen bonding at the nicks by using dideoxynucleotides as their 3'-terminal groups was more detrimental for the activity. All phosphoester bonds in the complementary strand were dispensable for base excision, but nicks close to the orphaned nucleotide caused early termination of damaged strand cleavage. Elastic network analysis of Fpg-DNA structures showed that the vibrational motions of the critical phosphates are strongly correlated, in part due to the presence of the protein. Overall, our results suggest that mechanical forces propagating along the DNA backbone play a critical role in the correct conformational distortion of DNA by Fpg and possibly by other target base-everting DNA glycosylases.
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Affiliation(s)
- Anton V Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine , 8 Lavrentieva Avenue , Novosibirsk 630090 , Russia.,Novosibirsk State University , 2 Pirogova Street , Novosibirsk 630090 , Russia
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine , 8 Lavrentieva Avenue , Novosibirsk 630090 , Russia.,Novosibirsk State University , 2 Pirogova Street , Novosibirsk 630090 , Russia
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43
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Kladova OA, Grin IR, Fedorova OS, Kuznetsov NA, Zharkov DO. Conformational Dynamics of Damage Processing by Human DNA Glycosylase NEIL1. J Mol Biol 2019; 431:1098-1112. [DOI: 10.1016/j.jmb.2019.01.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 10/27/2022]
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Abstract
Transient protein-protein complexes are of great importance for organizing multiple enzymatic reactions into productive reaction pathways. Base excision repair (BER), a process of critical importance for maintaining genome stability against a plethora of DNA-damaging factors, involves several enzymes, including DNA glycosylases, AP endonucleases, DNA polymerases, DNA ligases and accessory proteins acting sequentially on the same damaged site in DNA. Rather than being assembled into one stable multisubunit complex, these enzymes pass the repair intermediates between them in a highly coordinated manner. In this review, we discuss the nature and the role of transient complexes arising during BER as deduced from structural and kinetic data. Almost all of the transient complexes are DNA-mediated, although some may also exist in solution and strengthen under specific conditions. The best-studied example, the interactions between DNA glycosylases and AP endonucleases, is discussed in more detail to provide a framework for distinguishing between stable and transient complexes based on the kinetic data. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anton V Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine , Novosibirsk , Russia.,Novosibirsk State University , Novosibirsk , Russia.,Podalirius Ltd. , Novosibirsk , Russia
| | - Anna V Yudkina
- SB RAS Institute of Chemical Biology and Fundamental Medicine , Novosibirsk , Russia.,Novosibirsk State University , Novosibirsk , Russia
| | - Viktoriya S Sidorenko
- Department of Pharmacological Sciences, Stony Brook University , Stony Brook , NY , USA
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine , Novosibirsk , Russia.,Novosibirsk State University , Novosibirsk , Russia
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45
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Zutterling C, Mursalimov A, Talhaoui I, Koshenov Z, Akishev Z, Bissenbaev AK, Mazon G, Geacintov NE, Gasparutto D, Groisman R, Zharkov DO, Matkarimov BT, Saparbaev M. Aberrant repair initiated by the adenine-DNA glycosylase does not play a role in UV-induced mutagenesis in Escherichia coli. PeerJ 2018; 6:e6029. [PMID: 30568855 PMCID: PMC6286661 DOI: 10.7717/peerj.6029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 10/30/2018] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND DNA repair is essential to counteract damage to DNA induced by endo- and exogenous factors, to maintain genome stability. However, challenges to the faithful discrimination between damaged and non-damaged DNA strands do exist, such as mismatched pairs between two regular bases resulting from spontaneous deamination of 5-methylcytosine or DNA polymerase errors during replication. To counteract these mutagenic threats to genome stability, cells evolved the mismatch-specific DNA glycosylases that can recognize and remove regular DNA bases in the mismatched DNA duplexes. The Escherichia coli adenine-DNA glycosylase (MutY/MicA) protects cells against oxidative stress-induced mutagenesis by removing adenine which is mispaired with 7,8-dihydro-8-oxoguanine (8oxoG) in the base excision repair pathway. However, MutY does not discriminate between template and newly synthesized DNA strands. Therefore the ability to remove A from 8oxoG•A mispair, which is generated via misincorporation of an 8-oxo-2'-deoxyguanosine-5'-triphosphate precursor during DNA replication and in which A is the template base, can induce A•T→C•G transversions. Furthermore, it has been demonstrated that human MUTYH, homologous to the bacterial MutY, might be involved in the aberrant processing of ultraviolet (UV) induced DNA damage. METHODS Here, we investigated the role of MutY in UV-induced mutagenesis in E. coli. MutY was probed on DNA duplexes containing cyclobutane pyrimidine dimers (CPD) and pyrimidine (6-4) pyrimidone photoproduct (6-4PP). UV irradiation of E. coli induces Save Our Souls (SOS) response characterized by increased production of DNA repair enzymes and mutagenesis. To study the role of MutY in vivo, the mutation frequencies to rifampicin-resistant (RifR) after UV irradiation of wild type and mutant E. coli strains were measured. RESULTS We demonstrated that MutY does not excise Adenine when it is paired with CPD and 6-4PP adducts in duplex DNA. At the same time, MutY excises Adenine in A•G and A•8oxoG mispairs. Interestingly, E. coli mutY strains, which have elevated spontaneous mutation rate, exhibited low mutational induction after UV exposure as compared to MutY-proficient strains. However, sequence analysis of RifR mutants revealed that the frequencies of C→T transitions dramatically increased after UV irradiation in both MutY-proficient and -deficient E. coli strains. DISCUSSION These findings indicate that the bacterial MutY is not involved in the aberrant DNA repair of UV-induced DNA damage.
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Affiliation(s)
- 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, Villejuif, France
| | - Aibek Mursalimov
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Ibtissam Talhaoui
- CNRS UMR 8200—Laboratoire «Stabilité Génétique et Oncogenèse», Université Paris Sud (Paris XI), Gustave Roussy Cancer Campus, Villejuif, France
| | - Zhanat Koshenov
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Zhiger Akishev
- Department of Molecular Biology and Genetics, al-Farabi Kazakh National University, Faculty of Biology, Almaty, Kazakhstan
| | - Amangeldy K. Bissenbaev
- Department of Molecular Biology and Genetics, al-Farabi Kazakh National University, Faculty of Biology, Almaty, Kazakhstan
| | - Gerard Mazon
- CNRS UMR 8200—Laboratoire «Stabilité Génétique et Oncogenèse», Université Paris Sud (Paris XI), Gustave Roussy Cancer Campus, Villejuif, France
| | | | - Didier Gasparutto
- CEA, CNRS, INAC, SyMMES, Université Grenoble Alpes, Grenoble, France
| | - Regina Groisman
- Groupe «Réparation de l’ADN», Equipe Labellisée par la Ligue Nationale Contre le Cancer, CNRS UMR8200, Université Paris-Sud, Gustave Roussy Cancer Campus, Villejuif, France
| | - Dmitry O. Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, 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, Villejuif, France
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46
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Endutkin AV, Koptelov SS, Popov AV, Torgasheva NA, Lomzov AA, Tsygankova AR, Skiba TV, Afonnikov DA, Zharkov DO. Residue coevolution reveals functionally important intramolecular interactions in formamidopyrimidine-DNA glycosylase. DNA Repair (Amst) 2018; 69:24-33. [DOI: 10.1016/j.dnarep.2018.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 07/04/2018] [Accepted: 07/04/2018] [Indexed: 10/28/2022]
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47
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Lukina MV, Koval VV, Lomzov AA, Zharkov DO, Fedorova OS. Global DNA dynamics of 8-oxoguanine repair by human OGG1 revealed by stopped-flow kinetics and molecular dynamics simulation. Mol Biosyst 2018; 13:1954-1966. [PMID: 28770925 DOI: 10.1039/c7mb00343a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The toxic action of different endogenous and exogenous agents leads to damage in genomic DNA. 8-Oxoguanine is one of the most often generated and highly mutagenic oxidative forms of damage in DNA. Normally, in human cells it is promptly removed by 8-oxoguanine-DNA-glycosylase hOGG1, the key DNA-repair enzyme. An association between the accumulation of oxidized guanine and an increased risk of harmful processes in organisms was already found. However, the detailed mechanism of damaged base recognition and removal is still unclear. To clarify the role of active site amino acids in the damaged base coordination and to reveal the elementary steps in the overall enzymatic process we investigated hOGG1 mutant forms with substituted amino acid residues in the enzyme base-binding pocket. Replacing the functional groups of the enzyme active site allowed us to change the rates of the individual steps of the enzymatic reaction. To gain further insight into the mechanism of hOGG1 catalysis a detailed pre-steady state kinetic study of this enzymatic process was carried out using the stopped-flow approach. The changes in the DNA structure after mixing with enzymes were followed by recording the FRET signal using Cy3/Cy5 labels in DNA substrates in the time range from milliseconds to hundreds of seconds. DNA duplexes containing non-damaged DNA, 8-oxoG, or an AP-site or its unreactive synthetic analogue were used as DNA-substrates. The kinetic parameters of DNA binding and damage processing were obtained for the mutant forms and for WT hOGG1. The analyses of fluorescence traces provided information about the DNA dynamics during damage recognition and removal. The kinetic study for the mutant forms revealed that all introduced substitutions reduced the efficiency of the hOGG1 activity; however, they played pivotal roles at certain elementary stages identified during the study. Taken together, our results gave the opportunity to restore the role of substituted amino acids and main "damaged base-amino acid" contacts, which provide an important link in the understanding the mechanism of the DNA repair process catalyzed by hOGG1.
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Affiliation(s)
- M V Lukina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia.
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48
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Talhaoui I, Matkarimov BT, Tchenio T, Zharkov DO, Saparbaev MK. Aberrant base excision repair pathway of oxidatively damaged DNA: Implications for degenerative diseases. Free Radic Biol Med 2017; 107:266-277. [PMID: 27890638 DOI: 10.1016/j.freeradbiomed.2016.11.040] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 02/06/2023]
Abstract
In cellular organisms composition of DNA is constrained to only four nucleobases A, G, T and C, except for minor DNA base modifications such as methylation which serves for defence against foreign DNA or gene expression regulation. Interestingly, this severe evolutionary constraint among other things demands DNA repair systems to discriminate between regular and modified bases. DNA glycosylases specifically recognize and excise damaged bases among vast majority of regular bases in the base excision repair (BER) pathway. However, the mismatched base pairs in DNA can occur from a spontaneous conversion of 5-methylcytosine to thymine and DNA polymerase errors during replication. To counteract these mutagenic threats to genome stability, cells evolved special DNA repair systems that target the non-damaged DNA strand in a duplex to remove mismatched regular DNA bases. Mismatch-specific adenine- and thymine-DNA glycosylases (MutY/MUTYH and TDG/MBD4, respectively) initiated BER and mismatch repair (MMR) pathways can recognize and remove normal DNA bases in mismatched DNA duplexes. Importantly, in DNA repair deficient cells bacterial MutY, human TDG and mammalian MMR can act in the aberrant manner: MutY and TDG removes adenine and thymine opposite misincorporated 8-oxoguanine and damaged adenine, respectively, whereas MMR removes thymine opposite to O6-methylguanine. These unusual activities lead either to mutations or futile DNA repair, thus indicating that the DNA repair pathways which target non-damaged DNA strand can act in aberrant manner and introduce genome instability in the presence of unrepaired DNA lesions. Evidences accumulated showing that in addition to the accumulation of oxidatively damaged DNA in cells, the aberrant DNA repair can also contribute to cancer, brain disorders and premature senescence. For example, the aberrant BER and MMR pathways for oxidized guanine residues can lead to trinucleotide expansion that underlies Huntington's disease, a severe hereditary neurodegenerative syndrome. This review summarises the present knowledge about the aberrant DNA repair pathways for oxidized base modifications and their possible role in age-related diseases.
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Affiliation(s)
- Ibtissam Talhaoui
- 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
| | - Thierry Tchenio
- LBPA, UMR8113 ENSC - CNRS, Ecole Normale Supérieure de Cachan, Cachan, France
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Murat K 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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49
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Popov AV, Endutkin AV, Vorobjev YN, Zharkov DO. Molecular dynamics simulation of the opposite-base preference and interactions in the active site of formamidopyrimidine-DNA glycosylase. BMC Struct Biol 2017; 17:5. [PMID: 28482831 PMCID: PMC5422863 DOI: 10.1186/s12900-017-0075-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 04/20/2017] [Indexed: 01/20/2023]
Abstract
Background Formamidopyrimidine-DNA glycosylase (Fpg) removes abundant pre-mutagenic 8-oxoguanine (oxoG) bases from DNA through nucleophilic attack of its N-terminal proline at C1′ of the damaged nucleotide. Since oxoG efficiently pairs with both C and A, Fpg must excise oxoG from pairs with C but not with A, otherwise a mutation occurs. The crystal structures of several Fpg–DNA complexes have been solved, yet no structure with A opposite the lesion is available. Results Here we use molecular dynamic simulation to model interactions in the pre-catalytic complex of Lactococcus lactis Fpg with DNA containing oxoG opposite C or A, the latter in either syn or anti conformation. The catalytic dyad, Pro1–Glu2, was modeled in all four possible protonation states. Only one transition was observed in the experimental reaction rate pH dependence plots, and Glu2 kept the same set of interactions regardless of its protonation state, suggesting that it does not limit the reaction rate. The adenine base opposite oxoG was highly distorting for the adjacent nucleotides: in the more stable syn models it formed non-canonical bonds with out-of-register nucleotides in both the damaged and the complementary strand, whereas in the anti models the adenine either formed non-canonical bonds or was expelled into the major groove. The side chains of Arg109 and Phe111 that Fpg inserts into DNA to maintain its kinked conformation tended to withdraw from their positions if A was opposite to the lesion. The region showing the largest differences in the dynamics between oxoG:C and oxoG:A substrates was unexpectedly remote from the active site, located near the linker joining the two domains of Fpg. This region was also highly conserved among 124 analyzed Fpg sequences. Three sites trapping water molecules through multiple bonds were identified on the protein–DNA interface, apparently helping to maintain enzyme-induced DNA distortion and participating in oxoG recognition. Conclusion Overall, the discrimination against A opposite to the lesion seems to be due to incorrect DNA distortion around the lesion-containing base pair and, possibly, to gross movement of protein domains connected by the linker. Electronic supplementary material The online version of this article (doi:10.1186/s12900-017-0075-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander V Popov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk, 630090, Russia
| | - Anton V Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk, 630090, Russia.,Novosibrsk State University, 2 Pirogova St., Novosibirsk, 630090, Russia
| | - Yuri N Vorobjev
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk, 630090, Russia. .,Novosibrsk State University, 2 Pirogova St., Novosibirsk, 630090, Russia.
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk, 630090, Russia. .,Novosibrsk State University, 2 Pirogova St., Novosibirsk, 630090, Russia.
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50
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Grosheva AS, Zharkov DO, Stahl J, Gopanenko AV, Tupikin AE, Kabilov MR, Graifer DM, Karpova GG. Recognition but no repair of abasic site in single-stranded DNA by human ribosomal uS3 protein residing within intact 40S subunit. Nucleic Acids Res 2017; 45:3833-3843. [PMID: 28334742 PMCID: PMC5397187 DOI: 10.1093/nar/gkx052] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 01/13/2017] [Accepted: 01/19/2017] [Indexed: 01/04/2023] Open
Abstract
Isolated human ribosomal protein uS3 has extra-ribosomal functions including those related to base excision DNA repair, e.g. AP lyase activity that nicks double-stranded (ds) DNA 3΄ to the abasic (AP) site. However, the ability of uS3 residing within ribosome to recognize and cleave damaged DNA has never been addressed. Here, we compare interactions of single-stranded (ss) DNA and dsDNA bearing AP site with human ribosome-bound uS3 and with the isolated protein, whose interactions with ssDNA were not yet studied. The AP lyase activity of free uS3 was much higher with ssDNA than with dsDNA, whereas ribosome-bound uS3 was completely deprived of this activity. Nevertheless, an exposed peptide of ribosome-bound uS3 located far away from the putative catalytic center previously suggested for isolated uS3 cross-linked to full-length uncleaved ssDNA, but not to dsDNA. In contrast, free uS3 cross-linked mainly to the 5΄-part of the damaged DNA strand after its cleavage at the AP site. ChIP-seq analysis showed preferential uS3 binding to nucleolus-associated chromatin domains. We conclude that free and ribosome-bound uS3 proteins interact with AP sites differently, exhibiting their non-translational functions in DNA repair in and around the nucleolus and in regulation of DNA damage response in looped DNA structures, respectively.
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Affiliation(s)
- Anastasia S. Grosheva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
| | - Dmitry O. Zharkov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Joachim Stahl
- Max-Delbrück-Center for Molecular Medicine, D-13092 Berlin, Germany
| | - Alexander V. Gopanenko
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
| | - Dmitri M. Graifer
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Galina G. Karpova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
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