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RESTRICTION AND MODIFICATION SYSTEMS
Abstract
Orthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics. A ...Read More
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“The RM system, an important immune system for bacteria that prevents the uptake of exogenous DNA, is largely variable in terms of copy number and constitution.45 , 46”
From Whole genomic DNA sequencing and comparative genomic analysis of Arthrospira platensis: high genome plasticity and genetic diversity (2016) · cites this paper as [46]
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“Cytosine methylation at the internal GATC sites was confirmed by the fact that the DNAs were resistant to digestion with Sau3AI, which is unable to cut GATC sequences with methylated cytosine, whereas they were digested by MboI, which cuts the GATC sites regardless of cytosine methylation (data not shown) [11].”
BackgroundThe Dawn of In Vivo Gene Editing Era: A Revolution in the Making
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Phage Milagro: a platform for engineering a broad host range virulent phage for Burkholderia
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“In related temperate phages Full-Length Text such as coliphages P2 and 186, operator binding sites are recognizable as repeated DNA sequence motifs in or near phage promoters.”
BackgroundInfluentialMolecular medical microbiology—from bench to bedside
Tang, Y., Hindiyeh, M. Y., Liu, D., Sails, A. D., Spearman, P. W., & Zhang, J.-R. (2024) · Elsevier eBooks · doi:10.1016/b978-0-12-818619-0.00027-7 · Cited by 18
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“influenzae, and in Salmonella and Citrobacter (Wilson and Murray 1991).”
BackgroundInfluentialStructure of the restriction–modification controller protein C.Esp1396I
Ball, N. J., Streeter, S. D., Kneale, G. G., & McGeehan, J. E. (2009) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909020514 · Cited by 16
“M system allows the discrimination of ‘self’ from ‘nonself’ DNA (Wilson & Murray, 1991).”
BackgroundCharacterization of a Novel Plasmid-Encoded HsdS Subunit, S.LlaW12I, from Lactococcus lactis W12
Madsen, A., Westphal, C., & Josephsen, J. (2000) · Plasmid · doi:10.1006/plas.2000.1478 · Cited by 16
POLYMORPHISM OF BACTERIAL RESTRICTION‐MODIFICATION SYSTEMS: THE ADVANTAGE OF DIVERSITY
Frank, S. A. (1994) · Evolution · doi:10.1111/j.1558-5646.1994.tb02189.x · Cited by 16
DNA Binding and Subunit Interactions in the Type I Methyltransferase M.EcoR124I
Mernagh, D., Reynolds, L. A., & Kneale, G. G. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.5.987 · Cited by 16
Taylor, I. A., Webb, M., & Kneale, G. G. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0234 · Cited by 16
“Type I methyltransferases (MTases) are more complex enzymes ( Wilson & Murray, 1991; Bickle & Kruger, 1993), having separate subunits for DNA recognition (HsdS) and methyltransferase activity (HsdM).”
BackgroundLee, C., Shaw, P., Picone, S. J., Wilson, G. G., & Lunnen, K. D. (1998) · Biological Chemistry · doi:10.1515/bchm.1998.379.4-5.437 · Cited by 16
“In contrast, DNA methyltransferases (MTases) share conserved motifs (Posfai ef a/., 1989; Wilson and Murray, 1991).”
BackgroundSelf-citationCloning and sequence comparison of
Ruan, H., Lunnen, K. D., Scott, M. E., Moran, L. S., Slatko, B. E., Pelletier, J. J., Hess, E. J., Benner, J. S., Wilson, G. G., & Xu, S.-Y. (1996) · Molecular and General Genetics MGG · doi:10.1007/s004380050278 · Cited by 16
Self-citationThe vibriophage-encoded inhibitor OrbA abrogates BREX-mediated defense through the ATPase BrxC
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Processing DNA molecules as text
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“A common technique is the use of restriction enzymes to cut the DNA molecule at specific sites which enables the joining of DNA fragments that contains matching sites on their ends (Wilson 1988; Wilson and Murray 1991).”
MethodInfluentialScreeningHelicobacter pylorigenes induced during infection of mouse stomachs
Singh, A. (2012) · World Journal of Gastroenterology · doi:10.3748/wjg.v18.i32.4323 · Cited by 16
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“To reduce the risk of acquisition of exogenous DNA, prokaryotes have evolved both innate immunity that is mediated by restriction-modification systems (4) and adaptive immunity that is mediated by CRISPR-Cas systems (5–13).”
BackgroundEvolution of animal Piwi-interacting RNAs and prokaryotic CRISPRs
Kumar, M., & Chen, K. C. (2012) · Briefings in Functional Genomics · doi:10.1093/bfgp/els016 · Cited by 16
“Several such defense mechanisms have been discussed in the literature, including the restriction–modification system (RM) [79] and envelope resistance [80].”
BackgroundBacteriophages Infecting Lactic Acid Bacteria
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“They are usually accompanied by DNA methyltransferases (MTases) of similar specificity, which methylate the DNA of the host, thereby rendering it resistant to the cleavage (Wilson and Murray 1991).”
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“The simplest systems are type II R-M systems, which usually consist of two separate enzymes, a restriction endonuclease and a methyltransferase (4, 40).”
BackgroundSmith, R. M., Marshall, J. J. T., Jacklin, A. J., Retter, S. E., Halford, S. E., & Sobott, F. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1023 · Cited by 14
“Restriction-Modification (RM) systems use two enzyme activities to defend bacteria against foreign DNA, a restriction endonuclease (REase) and a modification methyltransferase (MTase) (1,2).”
BackgroundDawoud, T. M. S., Jiang, T., Mandal, R. K., Ricke, S. C., & Kwon, Y. M. (2014) · Molecular Biotechnology · doi:10.1007/s12033-014-9779-4 · Cited by 14
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“Type II restriction–modification (R–M) systems encode a restriction endonuclease that recognizes and cleaves specific DNA sequences and a methyltransferase that recognizes the same DNA sequence and methylates it first on one DNA strand - to produce hemimethylated DNA - and then on the other strand to produce fully met…”
BackgroundProbing the Role of Cysteine Residues in the EcoP15I DNA Methyltransferase
Reddy, Y. V. R., & Rao, D. N. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.37.23866 · Cited by 14
Molecular Scale Architecture: Engineered Three- And Four-Way Junctions
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Functional Analysis of BamHI DNA Cytosine-N4 Methyltransferase
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Restriction and Modification Systems
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Comparative genomics analysis of Mycoplasma capricolum subsp. capripneumoniae 87001
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“Most of the enzymes of this group recognize palindromic sequence which generally vary between four to eight base pairs in length ( Wilson and Murray 1991 ).”
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“1989) are typically found within a polypeptide ranging from 228 to 587 amino acids in length (Wilson and Murray 1991).”
BackgroundInfluentialIn Vivo Mutational Characterization of DndE Involved in DNA Phosphorothioate Modification
Lai, C., Wu, X., Chen, C., Huang, T., Xiong, X., Wu, S., Gu, M., Deng, Z., Chen, X., Chen, S., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0107981 · Cited by 14
“This system displays similarities to methylation-based R-M systems [9,10,11,12].”
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“The Restriction–Modification (RM) enzymes play an important role in bacteria and archaea by preventing infection by bacteriophages and other foreign DNA elements (1,2).”
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Sequence-specific DNA Recognition by the SmaI Endonuclease
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Cellular localization of Type I restriction–modification enzymes is family dependent
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“, StySBLI), based on genetic complementation, cross-hybridization of genes, and antibody cross-reactivity [6,7].”
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“The sequencespecific DNA methyltransferase protects the host DNA from cleavage by the associated restriction enzyme, and the specific methylation pattern of the host RM system allows the discrimination of ‘self’ from ‘non-self’ DNA (2).”
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“Historically, restriction-modification endonucleases have been and continue to be used as tools for gene cloning (Wilson and Murray 1991 ) and have enabled many of the achievements of modern biology, while whole bacteriophages have become biotechnological tools in their own right (Elois et al.…”
Gupta, Y. K., Yang, L., Chan, S., Samuelson, J. C., Xu, S.-Y., & Aggarwal, A. K. (2012) · Journal of Molecular Biology · doi:10.1016/j.jmb.2012.04.026 · Cited by 12
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AFM protein–protein interactions within the EcoR124I molecular motor
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“In prokaryotes, DNA methylation plays an essential role in the host defense mechanism against foreign DNA invasion as part of the restriction modification systems ( Wilson and Murray, 1991 ).”
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“Possibly, these strains possess a highly efficient protection system against foreign DNA, such as restriction–modification (R–M) systems (Wilson and Murray 1991), a histonelike nucleoid structure-like (H-NS) protein repression system (Navarre et al.”
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[23] Characterization of type II DNA-methyltransferases
Landry, D., Barsomian, J. M., Feehery, G. R., & Wilson, G. G. (1992) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(92)16025-f · Cited by 12
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“In conventional R-M systems, this domain plays a key role in the recognition of their target DNA sequence motifs ( 3 , 4 , 70 , 71 ).”
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“Bacterial restriction–modification (R–M) systems employ a range of mechanisms for the temporal regulation of methylase and restriction endonuclease.(1) In many type II systems, this is achieved at the transcriptional level by the action of a small helix–turn–helix controller protein, or C-protein.”
Forensics: Food Authentication Using MtDNA
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“Three types of restriction modification RM (type I, II and III) have been found and were classified according to their subunit composition, cofactor requirement and mode of action [94].”
EcoR124I: from Plasmid-Encoded Restriction-Modification System to Nanodevice
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Isolation and Characterization of a HpyC1I Restriction-Modification System in Helicobacter pylori
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“In contrast, Type II RM systems generally feature two separate proteins, for restriction and modification respectively (6).”
Chmuzh, E. V., Kashirina, Y. G., Tomilova, Y. E., Chernukhin, V. A., Okhapkina, S. S., Gonchar, D. A., Dedkov, V. S., Abdurashitov, M. A., & Degtyarev, S. K. (2007) · Molecular Biology · doi:10.1134/s0026893307010062 · Cited by 10
“MT modifies certain bases within the recognition sites of the host DNA, thereby protecting it from digestion by cognate RE [1, 2].”
BackgroundDifferences in Methylation at GATC Sites in Genomic DNA of Campylobacter coli from Turkeys and Swine
Wright, S., Simone, W., Miller, W. G., Mandrell, R. E., Siletzky, R. M., & Kathariou, S. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.00934-10 · Cited by 10
“bacterial genomes and is frequently associated with restrictionmodification systems (30).”
BackgroundSmith, R. M., Jacklin, A. J., Marshall, J. J. T., Sobott, F., & Halford, S. E. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1000 · Cited by 10
“Many Type II systems have palindromic recognition sites, with the same 50–30 sequence in both strands (3).”
BackgroundInfluentialApplication of methylation in improving plasmid transformation into Helicobacter pylori
Zhao, H., Xu, L., Rong, Q., Xu, Z., Ding, Y., Zhang, Y., Wu, Y., Li, B., & Ji, X. (2018) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2018.05.016 · Cited by 10
Bacteria-Phage Antagonistic Coevolution and the Implications for Phage Therapy
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Dimeric/oligomeric DNA methyltransferases: an unfinished story
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“Thus, the paradigm was extended to include all DNA MTases except the more complex bifunctional type I and type III enzymes (Wilson and Murray, 1991; Noyer-Weidner and Trautner, 1993), which will not be considered in this review.”
BackgroundStarter Cultures: Bacteriophage
McGrath, S., Fitzgerald, G. F., & van Sinderen, D. (2004) · Cheese · doi:10.1016/s1874-558x(04)80067-8 · Cited by 10
Domain structure and subunit interactions in the type I DNA methyltransferase M.EcoR124I
Smith, M. A., Read, C. M., & Kneale, G. G. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.5123 · Cited by 10
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Horizontal transfer and phylogenetic distribution of the immune evasion factor tarP
Gerlach, D., Sieber, R. N., Larsen, J., Krusche, J., Castro, C. D., Baumann, J., Molinaro, A., & Peschel, A. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.951333 · Cited by 9
“aureus (Waldron and Lindsay, 2006); the DNA methyltransferase HsdM; and HsdS that confers specificity via two DNA target recognition domains to HsdR, and HsdM in a clonal complex-specific manner (Wilson and Murray, 1991).”
BackgroundHistorical Aspects of Restriction Endonucleases as Intelligent Scissors for Genetic Engineering
Alekseeva, I. V., & Kuznetsov, N. A. (2023) · Fermentation · doi:10.3390/fermentation9100874 · Cited by 10
“In contrast, their amino acid sequences are only 19% identical [11].”
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Cloning and characterization of the TneDI restriction–modification system of Thermotoga neapolitana
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“(Wilson and Murray 1991; Roberts et al. 2003).”
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“Type I enzymes have been difficult to characterize [43], because the cleave at a sites remote the recognition site [33, 39, 44, 45].”
BackgroundMcGeehan, J. E., Streeter, S. A., Cooper, J. B., Mohammed, F., Fox, G. C., & Kneale, G. G. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444903026143 · Cited by 9
“Bacterial restriction-modi®cation (RM) systems are gene complexes that allow bacteria to methylate and protect their own DNA whilst cleaving and eliminating unmethylated, i.e. foreign, DNA (Wilson & Murray, 1991; Roberts et al., 2003).”
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“The most common DNA MTases are associated with a cognate restriction endonuclease ( Wilson & Murray, 1991 ).”
BackgroundPhotolabeling of the EcoP15 DNA methyltransferase with
Ahmad, I., & Rao, D. N. (1994) · Gene · doi:10.1016/0378-1119(94)90356-5 · Cited by 9
Organization and sequence of the SalI restriction-modification system
Rodicio, M. R., Quinton-Jager, T., Moran, L. S., Slatko, B. E., & Wilson, G. G. (1994) · Gene · doi:10.1016/0378-1119(94)90650-5 · Cited by 9
“(c) Comparison with other R-M systems The gene organization of the Sal1 system is similar to many type-II R-M systems, including AccI, BanI, BsuFI, D&I, EcoRI, HgiCI and DI, HindIII, HpuI, MwoI, NulIII, NgoPII, Sau3A1, SmaI and XbuI (Wilson and Murray, 1991).”
ResultSelf-citationSkowronek, K. J., Kosiński, J., & Bujnicki, J. M. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20920 · Cited by 9
“among REases has lead to speculations that they may be products of convergent evolution.(7) Crystallographic analy-”
BackgroundModulation of EcoKI restriction in vivo: role of the lambda Gam protein and plasmid metabolism
Salaj-Šmic, E., Maršić, N., Trgovčević, Ž., & Lloyd, R. G. (1997) · Journal of Bacteriology · doi:10.1128/jb.179.6.1852-1856.1997 · Cited by 9
“, in foreign DNA), it acts as a restriction endonuclease (46, 47).”
BackgroundMechanism of Action of Restriction Endonuclease EcoRV
Halford, S. E., Taylor, J. D., Vermote, C. L. M., & Vipond, I. B. (1993) · Nucleic acids and molecular biology · doi:10.1007/978-3-642-77950-3_4 · Cited by 9
Martínez, M., Rizzuto, I., & Molina, R. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25094929 · Cited by 8
“Restriction–modification systems serve to distinguish self from non-self, cleaving phage-invading nucleic acids based on epigenetic modifications [44].”
BackgroundConcerted action at eight phosphodiester bonds by the BcgI restriction endonuclease
Marshall, J. J. T., Smith, R. M., Ganguly, S., & Halford, S. E. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr453 · Cited by 8
“Most restriction–modification (R–M) systems display two activities that act in response to a specific DNA sequence: a modification methyltransferase (MTase) that methylates a specific base within the sequence; and a restriction endonuclease (REase) that cleaves the DNA provided neither strand is modified (1).”
BackgroundEstablishing genetic manipulation for novel strains of human gut bacteria
Sheridan, P. O., Al-Odat, M. A., & Scott, K. P. (2023) · Microbiome Research Reports · doi:10.20517/mrr.2022.13 · Cited by 8
Two different restriction-modification systems for degrading exogenous DNA in Paenibacillus polymyxa
Shen, M., Chen, Z., Mao, X., Wang, L., Liang, J., Huo, Q., Yin, X., Qiu, J., & Sun, D. (2018) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2018.09.016 · Cited by 8
Narayanan, N., Banerjee, A. K., Jain, D., Kulkarni, D. S., Sharma, R., Nirwal, S., Rao, D. N., & Nair, D. T. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.10.001 · Cited by 8
Roles for Helicases as ATP-Dependent Molecular Switches
Szczelkun, M. D. (2012) · Advances in experimental medicine and biology · doi:10.1007/978-1-4614-5037-5_11 · Cited by 7
Lasek, R., Dziewit, Ł., & Bartosik, D. (2012) · Extremophiles · doi:10.1007/s00792-012-0435-2 · Cited by 8
“The aforementioned tail to tail organization of the ORFs of the pP62BP1 R-M1 and R-M2 systems with overlapping of their 30 ends is rather uncommon among the restrictionmodification systems (Wilson and Murray 1991).”
BackgroundEvolutionary change and phylogenetic relationships in light of horizontal gene transfer
Boto, L. (2015) · Journal of Biosciences · doi:10.1007/s12038-015-9514-8 · Cited by 9
“In bacteria, restriction/modification systems (Wilson and Murray 1991), the CRISPRs/Cas system (Horvath and J. Biosci.”
Lian, C., Zhu, F.-C., Wei, Z., & He, L. (2021) · Deep Sea Research Part I Oceanographic Research Papers · doi:10.1016/j.dsr.2021.103488 · Cited by 8
Crystal structure of a putative DNA methylase TTHA0409 from Thermus thermophilus HB8
Morita, R., Ishikawa, H., Nakagawa, N., Kuramitsu, S., & Masui, R. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22158 · Cited by 8
Hubáček, J., Holubová, I., & Weiserová, M. (1998) · Folia Microbiologica · doi:10.1007/bf02818573 · Cited by 8
Ruan, H., Lunnen, K. D., Pelletier, J. J., & Xu, S.-Y. (1997) · Gene · doi:10.1016/s0378-1119(96)00773-1 · Cited by 8
Metadata
- Authors
- Wilson, G. G., & Murray, N. E.
- Affiliations
- New England Biolabs (United States) (US)
- Venue
- Annual Review of Genetics
- Publisher
- Annual Reviews
- Published
- 1991-12
- Volume
- 25
- Issue
- 1
- Pages
- 585-627
- ISSN
- 0066-4197 (ISSN-L)
- 1545-2948
- OpenAlex
- W2179631201
- Cited by
- 714
- References
- 94
- Citations by year
- 2026: 11 · 2025: 13 · 2024: 14 · 2023: 22 · 2022: 15 · 2021: 13 · 2020: 18 · 2019: 20 · 2018: 18 · 2017: 14 · 2016: 22 · 2015: 18 · 2014: 30 · 2013: 22 · 2012: 33
- FWCI
- 9.78
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Annual Review of Genetics (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- restriction-modification systems, restriction enzymes, DNA methylation, DNA methyltransferases, bacterial defense against foreign DNA, gene duplication, homologous genes, orthology, paralogy
- MeSH terms
- Cloning, Molecular, DNA, Bacterial, DNA, Viral, Genes, Bacterial, Methylation, Terminology as Topic, Substrate Specificity, DNA Restriction-Modification Enzymes, Gene Expression Regulation, Bacterial
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