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Savitskaya VY, Monakhova MV, Iakushkina IV, Borovikova II, Kubareva EA. Neisseria gonorrhoeae: DNA Repair Systems and Their Role in Pathogenesis. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:965-982. [PMID: 36180987 DOI: 10.1134/s0006297922090097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 06/16/2023]
Abstract
Neisseria gonorrhoeae (a Gram-negative diplococcus) is a human pathogen and causative agent of gonorrhea, a sexually transmitted infection. The bacterium uses various approaches for adapting to environmental conditions and multiplying efficiently in the human body, such as regulation of expression of gene expression of surface proteins and lipooligosaccharides (e.g., expression of various forms of pilin). The systems of DNA repair play an important role in the bacterium ability to survive in the host body. This review describes DNA repair systems of N. gonorrhoeae and their role in the pathogenicity of this bacterium. A special attention is paid to the mismatch repair system (MMR) and functioning of the MutS and MutL proteins, as well as to the role of these proteins in regulation of the pilin antigenic variation of the N. gonorrhoeae pathogen.
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Affiliation(s)
| | - Mayya V Monakhova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Iuliia V Iakushkina
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Irina I Borovikova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Elena A Kubareva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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G-Quadruplex Formed by the Promoter Region of the hTERT Gene: Structure-Driven Effects on DNA Mismatch Repair Functions. Biomedicines 2022; 10:biomedicines10081871. [PMID: 36009419 PMCID: PMC9405553 DOI: 10.3390/biomedicines10081871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 11/17/2022] Open
Abstract
G-quadruplexes (G4s) are a unique class of noncanonical DNAs that play a key role in cellular processes and neoplastic transformation. Herein, we focused on the promoter region of human TERT oncogene, whose product is responsible for the immortality of cancer cells. It has been shown by chemical probing and spectroscopic methods that synthetic 96-nt DNAs modeling the wild-type G-rich strand of the hTERT promoter and its variants with G>A point substitutions corresponding to somatic driver mutations fold into three stacked parallel G4s with sites of local G4 destabilization caused by G>A substitutions in the G4 motif. These models were used to elucidate how the hTERT multiG4 affects the binding affinity and functional responses of two key proteins, MutS and MutL, involved in the initial stage of DNA mismatch repair (MMR) in Escherichiacoli and Neisseriagonorrhoeae with different MMR mechanisms. We have shown for the first time that (i) point substitutions do not affect the effective binding of these proteins to the hTERT G4 structure, and (ii) the endonuclease activity of MutL from N. gonorrhoeae is significantly suppressed by the stable G4 scaffold. It is likely that some of the genomic instability associated with G4 may be related to the blockage of human intrinsic methyl-independent MMR attempting to operate near G4 structures.
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Abrosimova LA, Kuznetsov NA, Astafurova NA, Samsonova AR, Karpov AS, Perevyazova TA, Oretskaya TS, Fedorova OS, Kubareva EA. Kinetic Analysis of the Interaction of Nicking Endonuclease BspD6I with DNA. Biomolecules 2021; 11:1420. [PMID: 34680052 PMCID: PMC8533099 DOI: 10.3390/biom11101420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/03/2022] Open
Abstract
Nicking endonucleases (NEs) are enzymes that incise only one strand of the duplex to produce a DNA molecule that is 'nicked' rather than cleaved in two. Since these precision tools are used in genetic engineering and genome editing, information about their mechanism of action at all stages of DNA recognition and phosphodiester bond hydrolysis is essential. For the first time, fast kinetics of the Nt.BspD6I interaction with DNA were studied by the stopped-flow technique, and changes of optical characteristics were registered for the enzyme or DNA molecules. The role of divalent metal cations was estimated at all steps of Nt.BspD6I-DNA complex formation. It was demonstrated that divalent metal ions are not required for the formation of a non-specific complex of the protein with DNA. Nt.BspD6I bound five-fold more efficiently to its recognition site in DNA than to a random DNA. DNA bending was confirmed during the specific binding of Nt.BspD6I to a substrate. The optimal size of Nt.BspD6I's binding site in DNA as determined in this work should be taken into account in methods of detection of nucleic acid sequences and/or even various base modifications by means of NEs.
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Affiliation(s)
- Liudmila A. Abrosimova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (N.A.A.); (A.S.K.)
| | - Nikita A. Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Lavrentiev Avenue 8, 630090 Novosibirsk, Russia;
| | - Natalia A. Astafurova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (N.A.A.); (A.S.K.)
| | | | - Andrey S. Karpov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (N.A.A.); (A.S.K.)
| | - Tatiana A. Perevyazova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya Str. 3, 142290 Puschino, Russia;
| | - Tatiana S. Oretskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (T.S.O.); (E.A.K.)
| | - Olga S. Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Lavrentiev Avenue 8, 630090 Novosibirsk, Russia;
| | - Elena A. Kubareva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (T.S.O.); (E.A.K.)
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Responses of DNA Mismatch Repair Proteins to a Stable G-Quadruplex Embedded into a DNA Duplex Structure. Int J Mol Sci 2020; 21:ijms21228773. [PMID: 33233554 PMCID: PMC7699706 DOI: 10.3390/ijms21228773] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 12/26/2022] Open
Abstract
DNA mismatch repair (MMR) plays a crucial role in the maintenance of genomic stability. The main MMR protein, MutS, was recently shown to recognize the G-quadruplex (G4) DNA structures, which, along with regulatory functions, have a negative impact on genome integrity. Here, we studied the effect of G4 on the DNA-binding activity of MutS from Rhodobacter sphaeroides (methyl-independent MMR) in comparison with MutS from Escherichia coli (methyl-directed MMR) and evaluated the influence of a G4 on the functioning of other proteins involved in the initial steps of MMR. For this purpose, a new DNA construct was designed containing a biologically relevant intramolecular stable G4 structure flanked by double-stranded regions with the set of DNA sites required for MMR initiation. The secondary structure of this model was examined using NMR spectroscopy, chemical probing, fluorescent indicators, circular dichroism, and UV spectroscopy. The results unambiguously showed that the d(GGGT)4 motif, when embedded in a double-stranded context, adopts a G4 structure of a parallel topology. Despite strong binding affinities of MutS and MutL for a G4, the latter is not recognized by E. coli MMR as a signal for repair, but does not prevent MMR processing when a G4 and G/T mismatch are in close proximity.
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Minobe A, Fukui K, Yonezu H, Ohshita K, Mizobuchi S, Morisawa T, Hakumai Y, Yano T, Ashiuchi M, Wakamatsu T. Biochemical characterization of mismatch-binding protein MutS1 and nicking endonuclease MutL from a euryarchaeon Methanosaeta thermophila. DNA Repair (Amst) 2019; 75:29-38. [PMID: 30711824 DOI: 10.1016/j.dnarep.2019.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 01/21/2019] [Accepted: 01/21/2019] [Indexed: 12/20/2022]
Abstract
In eukaryotes and most bacteria, the MutS1/MutL-dependent mismatch repair system (MMR) corrects DNA mismatches that arise as replication errors. MutS1 recognizes mismatched DNA and stimulates the nicking endonuclease activity of MutL to incise mismatch-containing DNA. In archaea, there has been no experimental evidence to support the existence of the MutS1/MutL-dependent MMR. Instead, it was revealed that a large part of archaea possess mismatch-specific endonuclease EndoMS, indicating that the EndoMS-dependent MMR is widely adopted in archaea. However, some archaeal genomes encode MutS1 and MutL homologs, and their molecular functions have not been revealed. In this study, we purified and characterized recombinant MutS1 and the C-terminal endonuclease domain of MutL from a methanogenic archaeon Methanosaeta thermophila (mtMutS1 and the mtMutL CTD, respectively). mtMutS1 bound to mismatched DNAs with a higher affinity than to perfectly-matched and other structured DNAs, which resembles the DNA-binding specificities of eukaryotic and bacterial MutS1 homologs. The mtMutL CTD showed a Mn2+/Ni2+/Co2+-dependent nicking endonuclease activity that introduces single-strand breaks into a circular double-stranded DNA. The nicking endonuclease activity of the mtMutL CTD was impaired by mutagenizing the metal-binding motif that is identical to those of eukaryotic and bacterial MutL endonucleases. These results raise the possibility that not only the EndoMS-dependent MMR but also the traditional MutS1/MutL-dependent MMR exist in archaea.
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Affiliation(s)
- Ai Minobe
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Kenji Fukui
- Department of Biochemistry, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Osaka, 569-8686, Japan
| | - Hitomi Yonezu
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Koki Ohshita
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Saki Mizobuchi
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Takashi Morisawa
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Yuichi Hakumai
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Takato Yano
- Department of Biochemistry, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Osaka, 569-8686, Japan
| | - Makoto Ashiuchi
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Taisuke Wakamatsu
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan.
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