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Gladysheva-Azgari M, Sharko F, Evteeva M, Kuvyrchenkova A, Boulygina E, Tsygankova S, Slobodova N, Pustovoit K, Melkina O, Nedoluzhko A, Korzhenkov A, Kudryavtseva A, Utkina A, Manukhov I, Rastorguev S, Zavilgelsky G. ArdA genes from pKM101 and from B. bifidum chromosome have a different range of regulated genes. Heliyon 2023; 9:e22986. [PMID: 38144267 PMCID: PMC10746416 DOI: 10.1016/j.heliyon.2023.e22986] [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: 04/17/2023] [Revised: 09/18/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023] Open
Abstract
The ardA genes are present in a wide variety of conjugative plasmids and play an important role in overcoming the restriction barrier. To date, there is no information on the chromosomal ardA genes. It is still unclear whether they keep their antirestriction activity and why bacterial chromosomes contain these genes. In the present study, we confirmed the antirestriction function of the ardA gene from the Bifidobacterium bifidum chromosome. Transcriptome analysis in Escherichia coli showed that the range of regulated genes varies significantly for ardA from conjugative plasmid pKM101 and from the B. bifidum chromosome. Moreover, if the targets for both ardA genes match, they often show an opposite effect on regulated gene expression. The results obtained indicate two seemingly mutually exclusive conclusions. On the one hand, the pleiotropic effect of ardA genes was shown not only on restriction-modification system, but also on expression of a number of other genes. On the other hand, the range of affected genes varies significally for ardA genes from different sources, which indicates the specificity of ardA to inhibited targets. Author Summary. Conjugative plasmids, bacteriophages, as well as transposons, are capable to transfer various genes, including antibiotic resistance genes, among bacterial cells. However, many of those genes pose a threat to the bacterial cells, therefore bacterial cells have special restriction systems that limit such transfer. Antirestriction genes have previously been described as a part of conjugative plasmids, and bacteriophages and transposons. Those plasmids are able to overcome bacterial cell protection in the presence of antirestriction genes, which inhibit bacterial restriction systems. This work unveils the antirestriction mechanisms, which play an important role in the bacterial life cycle. Here, we clearly show that antirestriction genes, which are able to inhibit cell protection, exist not only in plasmids but also in the bacterial chromosomes themselves. Moreover, antirestrictases have not only an inhibitory function but also participate in the regulation of other bacterial genes. The regulatory function of plasmid antirestriction genes also helps them to overcome the bacterial cell protection against gene transfer, whereas the regulatory function of genomic antirestrictases has no such effect.
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Affiliation(s)
| | - F.S. Sharko
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - M.A. Evteeva
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | | | - E.S. Boulygina
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | - S.V. Tsygankova
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | - N.V. Slobodova
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | - K.S. Pustovoit
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center “Kurchatov Institute”, Moscow, Russia, 115454
| | - O.E. Melkina
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center “Kurchatov Institute”, Moscow, Russia, 115454
| | - A.V. Nedoluzhko
- European University at Saint Petersburg, 191187, Saint-Petersburg, Russia
| | - A.A. Korzhenkov
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | - A.A. Kudryavtseva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - A.A. Utkina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - I.V. Manukhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
- Faculty of Physics, HSE University, 109028, Moscow, Russia
- Laboratory for Microbiology, BIOTECH University, 125080, Moscow, Russia
| | - S.M. Rastorguev
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovityanova Str. 1, Moscow, 117997, Russia
| | - G.B. Zavilgelsky
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center “Kurchatov Institute”, Moscow, Russia, 115454
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Kudryavtseva AA, Cséfalvay E, Gnuchikh EY, Yanovskaya DD, Skutel MA, Isaev AB, Bazhenov SV, Utkina AA, Manukhov IV. Broadness and specificity: ArdB, ArdA, and Ocr against various restriction-modification systems. Front Microbiol 2023; 14:1133144. [PMID: 37138625 PMCID: PMC10149784 DOI: 10.3389/fmicb.2023.1133144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/10/2023] [Indexed: 05/05/2023] Open
Abstract
ArdB, ArdA, and Ocr proteins inhibit the endonuclease activity of the type I restriction-modification enzymes (RMI). In this study, we evaluated the ability of ArdB, ArdA, and Ocr to inhibit different subtypes of Escherichia coli RMI systems (IA, IB, and IC) as well as two Bacillus licheniformis RMI systems. Furthermore we explored, the antirestriction activity of ArdA, ArdB, and Ocr against a type III restriction-modification system (RMIII) EcoPI and BREX. We found that DNA-mimic proteins, ArdA and Ocr exhibit different inhibition activity, depending on which RM system tested. This effect might be linked to the DNA mimicry nature of these proteins. In theory, DNA-mimic might competitively inhibit any DNA-binding proteins; however, the efficiency of inhibition depend on the ability to imitate the recognition site in DNA or its preferred conformation. In contrast, ArdB protein with an undescribed mechanism of action, demonstrated greater versatility against various RMI systems and provided similar antirestriction efficiency regardless of the recognition site. However, ArdB protein could not affect restriction systems that are radically different from the RMI such as BREX or RMIII. Thus, we assume that the structure of DNA-mimic proteins allows for selective inhibition of any DNA-binding proteins depending on the recognition site. In contrast, ArdB-like proteins inhibit RMI systems independently of the DNA recognition site.
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Affiliation(s)
- Anna A. Kudryavtseva
- Laboratory for Molecular Genetics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- *Correspondence: Anna A. Kudryavtseva
| | - Eva Cséfalvay
- Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology, Academy of Sciences of the Czech Republic, Nové Hrady, Czechia
| | - Evgeniy Yu Gnuchikh
- Kurchatov Genomic Center, National Research Center Kurchatov Institute, Moscow, Russia
| | - Darya D. Yanovskaya
- Center of Cellular and Molecular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Mikhail A. Skutel
- Center of Cellular and Molecular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Artem B. Isaev
- Center of Cellular and Molecular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Sergey V. Bazhenov
- Laboratory for Molecular Genetics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Laboratory for Microbiology, BIOTECH University, Moscow, Russia
- Faculty of Physics, HSE University, Moscow, Russia
| | - Anna A. Utkina
- Laboratory for Molecular Genetics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ilya V. Manukhov
- Laboratory for Molecular Genetics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Laboratory for Microbiology, BIOTECH University, Moscow, Russia
- Faculty of Physics, HSE University, Moscow, Russia
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