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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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2
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Zaworski J, Dagva O, Brandt J, Baum C, Ettwiller L, Fomenkov A, Raleigh EA. Reassembling a cannon in the DNA defense arsenal: Genetics of StySA, a BREX phage exclusion system in Salmonella lab strains. PLoS Genet 2022; 18:e1009943. [PMID: 35377874 PMCID: PMC9009780 DOI: 10.1371/journal.pgen.1009943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/14/2022] [Accepted: 03/01/2022] [Indexed: 11/18/2022] Open
Abstract
Understanding mechanisms that shape horizontal exchange in prokaryotes is a key problem in biology. A major limit on DNA entry is imposed by restriction-modification (RM) processes that depend on the pattern of DNA modification at host-specified sites. In classical RM, endonucleolytic DNA cleavage follows detection of unprotected sites on entering DNA. Recent investigation has uncovered BREX (BacteRiophage EXclusion) systems. These RM-like activities employ host protection by DNA modification, but immediate replication arrest occurs without evident of nuclease action on unmodified phage DNA. Here we show that the historical stySA RM locus of Salmonella enterica sv Typhimurium is a variant BREX system. A laboratory strain disabled for both the restriction and methylation activity of StySA nevertheless has wild type sequence in pglX, the modification gene homolog. Instead, flanking genes pglZ and brxC each carry multiple mutations (μ) in their C-terminal domains. We further investigate this system in situ, replacing the mutated pglZμ and brxCμ genes with the WT counterpart. PglZ-WT supports methylation in the presence of either BrxCμ or BrxC-WT but not in the presence of a deletion/insertion allele, ΔbrxC::cat. Restriction requires both BrxC-WT and PglZ-WT, implicating the BrxC C-terminus specifically in restriction activity. These results suggests that while BrxC, PglZ and PglX are principal components of the BREX modification activity, BrxL is required for restriction only. Furthermore, we show that a partial disruption of brxL disrupts transcription globally. Horizontal gene transfer is a major driver of evolution and adaptation in bacteria. Genes from outside may be beneficial or dangerous to the receiving cell. Benefits include new food sources such as sugars, or new homes by adhesion, or new resistances, as to antibiotics. Dangers are posed by bacteriophages--viruses that take over the cell machinery, multiply, and release progeny to kill sister cells. Host-dependent restriction-modification systems enable defense that distinguishes relatives from strangers: using a modification pattern (M) carried by DNA bases added by the host cell to prevent restriction (R). Sisters and cousin cells will have the same protective pattern on DNA, while DNA of foreign origin will have the wrong M pattern and be restricted (R, rejected). Typically, restriction involves nuclease digestion. Here we address the enigmatic StySA RM system, one of the earliest to be genetically characterized. It is a variant of the newly recognized defense mechanism, BREX. BREX systems also track DNA history via modification pattern, but restrict by a novel, uncharacterized mechanism. Like other BREX family systems, StySA-BREX modification requires multiple components. When StySA-BREX transcription is unbalanced, we find global disruption of gene transcription. The disruption pattern does not suggest SOS-inducing damage to DNA.
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Affiliation(s)
- Julie Zaworski
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Oyut Dagva
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Julius Brandt
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Chloé Baum
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Laurence Ettwiller
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Alexey Fomenkov
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Elisabeth A. Raleigh
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
- * E-mail:
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3
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Balabanov VP, Kudryavtseva AA, Melkina OE, Pustovoit KS, Khrulnova SA, Zavilgelsky GB. ArdB Protective Activity for Unmodified λ Phage Against EcoKI Restriction Decreases in UV-Treated Escherichia coli. Curr Microbiol 2019; 76:1374-1378. [PMID: 31407052 DOI: 10.1007/s00284-019-01755-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/06/2019] [Indexed: 11/28/2022]
Abstract
Anti-restriction proteins ArdB/KlcA specifically inhibit restriction (endonuclease) activity of restriction-modification (RM) type I systems. Molecular mechanisms of ArdB/KlcA-based anti-restriction remain unknown. In this study, we quantitate effects of ArdB on protection of unmodified λ phage DNA from EcoKI restriction. After UV irradiations, which produce significant amounts of unmodified chromosomal DNA in Escherichia coli K12 cells, the protective activity of ArdB decreases. Unlike ArdB, DNA-mimicking protein Ocr retains its ability to protect the unmodified λ phage regardless of UV dose. We hypothesize that the observed decrease in ArdB protective activity in UV-treated cells is due to its binding to unmodified chromosomal DNA, which decreases effective concentrations of free ArdB molecules available for λ phage protection against type I restriction enzymes.
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Affiliation(s)
- Vladimir P Balabanov
- Laboratory of Genetics of Bacteria, State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center "Kurchatov Institute", Moscow, Russia, 115454
| | - Anna A Kudryavtseva
- Molecular Genetics Lab, Moscow Institute of Physics and Technology, Dolgoprudny, Russia, 141700.
| | - Olga E Melkina
- Laboratory of Genetics of Bacteria, State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center "Kurchatov Institute", Moscow, Russia, 115454
| | - Klara S Pustovoit
- Laboratory of Genetics of Bacteria, State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center "Kurchatov Institute", Moscow, Russia, 115454
| | - Svetlana A Khrulnova
- Laboratory of Genetics of Bacteria, State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center "Kurchatov Institute", Moscow, Russia, 115454.,Laboratory of Clinical Bacteriology, Mycology, and Antibiotic Treatment, National Research Center for Hematology, Noviy Zykovskiy pr. 4, Moscow, Russia, 125167
| | - Gennadii B Zavilgelsky
- Laboratory of Genetics of Bacteria, State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center "Kurchatov Institute", Moscow, Russia, 115454
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Melkina OE, Goryanin II, Zavilgelsky GB. Histone-like protein H-NS as a negative regulator of quorum sensing systems in gram-negative bacteria. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417020065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Kanwar N, Roberts GA, Cooper LP, Stephanou AS, Dryden DTF. The evolutionary pathway from a biologically inactive polypeptide sequence to a folded, active structural mimic of DNA. Nucleic Acids Res 2016; 44:4289-303. [PMID: 27095198 PMCID: PMC4872106 DOI: 10.1093/nar/gkw234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 03/24/2016] [Indexed: 11/13/2022] Open
Abstract
The protein Ocr (overcome classical restriction) from bacteriophage T7 acts as a mimic of DNA and inhibits all Type I restriction/modification (RM) enzymes. Ocr is a homodimer of 116 amino acids and adopts an elongated structure that resembles the shape of a bent 24 bp DNA molecule. Each monomer includes 34 acidic residues and only six basic residues. We have delineated the mimicry of Ocr by focusing on the electrostatic contribution of its negatively charged amino acids using directed evolution of a synthetic form of Ocr, termed pocr, in which all of the 34 acidic residues were substituted for a neutral amino acid. In vivo analyses confirmed that pocr did not display any antirestriction activity. Here, we have subjected the gene encoding pocr to several rounds of directed evolution in which codons for the corresponding acidic residues found in Ocr were specifically re-introduced. An in vivo selection assay was used to detect antirestriction activity after each round of mutation. Our results demonstrate the variation in importance of the acidic residues in regions of Ocr corresponding to different parts of the DNA target which it is mimicking and for the avoidance of deleterious effects on the growth of the host.
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Affiliation(s)
- Nisha Kanwar
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
| | - Gareth A Roberts
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
| | - Laurie P Cooper
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
| | - Augoustinos S Stephanou
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
| | - David T F Dryden
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
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Zavilgelsky GB, Kotova VY, Melkina OE, Balabanov VP, Mindlin SZ. Proteolytic control of the antirestriction activity of Tn21, Tn5053, Tn5045, Tn501, and Tn402 non-conjugative transposons. Mol Biol 2015. [DOI: 10.1134/s0026893315020168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Zavilgelsky GB, Kotova VY, Melkina OE, Pustovoit KS. Antirestriction activity of the mercury resistance nonconjugative transposon Tn5053 is controlled by the protease ClpXP. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414090166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Roberts GA, Chen K, Bower EKM, Madrzak J, Woods A, Barker AM, Cooper LP, White JH, Blakely GW, Manfield I, Dryden DTF. Mutations of the domain forming the dimeric interface of the ArdA protein affect dimerization and antimodification activity but not antirestriction activity. FEBS J 2013; 280:4903-14. [PMID: 23910724 PMCID: PMC3906837 DOI: 10.1111/febs.12467] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 07/26/2013] [Accepted: 07/29/2013] [Indexed: 12/25/2022]
Abstract
ArdA antirestriction proteins are encoded by genes present in many conjugative plasmids and transposons within bacterial genomes. Antirestriction is the ability to prevent cleavage of foreign incoming DNA by restriction-modification (RM) systems. Antimodification, the ability to inhibit modification by the RM system, can also be observed with some antirestriction proteins. As these mobile genetic elements can transfer antibiotic resistance genes, the ArdA proteins assist their spread. The consequence of antirestriction is therefore the enhanced dissemination of mobile genetic elements. ArdA proteins cause antirestriction by mimicking the DNA structure bound by Type I RM enzymes. The crystal structure of ArdA showed it to be a dimeric protein with a highly elongated curved cylindrical shape [McMahon SA et al. (2009) Nucleic Acids Res37, 4887–4897]. Each monomer has three domains covered with negatively charged side chains and a very small interface with the other monomer. We investigated the role of the domain forming the dimer interface for ArdA activity via site-directed mutagenesis. The antirestriction activity of ArdA was maintained when up to seven mutations per monomer were made or the interface was disrupted such that the protein could only exist as a monomer. The antimodification activity of ArdA was lost upon mutation of this domain. The ability of the monomeric form of ArdA to function in antirestriction suggests, first, that it can bind independently to the restriction subunit or the modification subunits of the RM enzyme, and second, that the many ArdA homologues with long amino acid extensions, present in sequence databases, may be active in antirestriction.
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