Cited by 714Genomics and Phylogenetic StudiesChromosomal and Genetic VariationsGenome Rearrangement Algorithms

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RESTRICTION AND MODIFICATION SYSTEMS

Wilson, Geoffrey G., Murray, Noreen E.·1991·Annual Review of Genetics

DOI 10.1146/annurev.ge.25.120191.003101

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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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Crossref · 10.1146/annurev.ge.25.120191.003101

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DNA Restriction Enzyme from E. coli
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A motif conserved among the type I restriction-modification enzymes and antirestriction proteins: a possible basis for mechanism of action of plasmid-encoded antirestriction functions
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Single amino acid substitutions in the HsdR subunit of the type IB restriction enzyme EcoAI uncouple the DNA translocation and DNA cleavage activities of the enzyme
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“It is not part of an R-M system (Wilson and Murray, 1991; Modrich 1991; Wilson, 1991; Barras and Marinus, 1989) but methylates DMA after replication, with a lag time (Ogden ef a/.”
Background
Evolution of Sequence Recognition by Restriction-Modification Enzymes: Selective Pressure for Specificity Decrease
Chinen, A., Naito, Y., Handa, N., & Kobayashi, I. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026260 · Cited by 28
“A cognate modification enzyme methylates the same recognition sequence to protect it from cleavage (Wilson and Murray 1991; Roberts and Halford 1993).”
Background
Cloning and sequence analysis of the Stsl restriction-modification gene: presence of homology to Fokl restriction-modification enzymes
Kita, K., Suisha, M., Kotani, H., Yanase, H., & Kato, N. (1992) · Nucleic Acids Research · doi:10.1093/nar/20.16.4167 · Cited by 28
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Lubys, A., Lubiene, J., Kulakauskas, S., Stankevicius, K., Timinskas, A., & Janulaitis, A. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.14.2760 · Cited by 28
Bacterial Shedu immune nucleases share a common enzymatic core regulated by diverse sensor domains
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Characterization of Type II and III Restriction-Modification Systems from Bacillus cereus Strains ATCC 10987 and ATCC 14579
Xu, S.-Y., Nugent, R. L., Kasamkattil, J., Fomenkov, A. I., Gupta, Y. K., Aggarwal, A. K., Wang, X., Li, Z., Zheng, Y., & Morgan, R. (2011) · Journal of Bacteriology · doi:10.1128/jb.06248-11 · Cited by 27
“Type I restriction enzymes are multisubunit complexes consisting of M2R2S subunits that recognize an asymmetric, bipartite sequence and require ATP hydrolysis to direct cleavage at a distant site following DNA translocations (43) (4).”
Background
Novel m4C modification in type I restriction-modification systems
Morgan, R., Luyten, Y. A., Johnson, S. A., Clough, E. M., Clark, T. A., & Roberts, R. J. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw743 · Cited by 27
“Restriction-Modification (R-M) systems are widespread in bacteria and archaea, where they function as a barrier to invasive DNA (1,2).”
Background
Restriction–Modification Systems as a Barrier for Genetic Manipulation of Staphylococcus aureus
Sadykov, M. R. (2014) · Methods in molecular biology · doi:10.1007/7651_2014_180 · Cited by 26
Tyr212: A Key Residue Involved in Strand Discrimination by the DNA Mismatch Repair Endonuclease MutH
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Dam methylase fromEscherichia coli: kinetic studies using modified DNA oligomers: hemimethylated substrates
Marzabal, S., DuBois, S., Thielking, V., Cano, A., Eritja, R., & Guschlbauer, W. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.18.3648 · Cited by 27
Restriction endonuclease cleavage of 5-methyl-deoxycytosine hemimethylated DNA at high enzyme-to-substrate ratios
Nelson, P. S., Papas, T. S., & Schweinfest, C. W. (1993) · Nucleic Acids Research · doi:10.1093/nar/21.3.681 · Cited by 27
Mechanisms and Biological Roles of DNA Methyltransferases and DNA Methylation: From Past Achievements to Future Challenges
Jurkowska, R. Z., & Jeltsch, A. (2022) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-11454-0_1 · Cited by 27
Genome DNA Sequence Variation, Evolution, and Function in Bacteria and Archaea
Nishida, H. (2013) · Current Issues in Molecular Biology · doi:10.21775/cimb.015.019 · Cited by 26
“However, when palindromic DNA sequences are methylated by a DNA methylase, restriction enzymes can no longer digest them (Wilson and Murray, 1991; Bickle and Krüger, 1993).”
Background
Gene Cloning and Manipulation
Howe, C. J. (2007) · Cambridge University Press eBooks · doi:10.1017/cbo9780511807343 · Cited by 26
DNA methylation in mycobacteria: Absence of methylation at GATC (Dam) and CCA/TGG (Dcm) sequences
Hemavathy, K. C., & Nagaraja, V. (1995) · FEMS Immunology & Medical Microbiology · doi:10.1016/0928-8244(95)00037-8 · Cited by 26
M.SpyI, a DNA Methyltransferase Encoded on a mefA Chimeric Element, Modifies the Genome of Streptococcus pyogenes
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“A CLUSTALW alignment of the amino acid sequences from the BLASTP search showed that M.SpyI contains the 10 conserved motifs that are present in the 5-methylcytosine MTases, in the proper order, and significant homology within the variable region making up the target recognition domain of these enzymes (Fig.”
BackgroundResultInfluential
Localization of a protein‐DNA interface by random mutagenesis
O'Neill, M. P., Dryden, D., & Murray, N. E. (1998) · EMBO Journal · doi:10.1093/emboj/17.23.7118 · Cited by 31
“The methyltransferase modifies hemimethylated target sequences produced after each round of DNA replication, while the endonuclease cleaves unmethylated DNA from foreign sources such as viruses (for review see Wilson and Murray, 1991; Redaschi and Bickle, 1996).”
BackgroundSelf-citation
The LlaGI restriction and modification system of Lactococcus lactis W10 consists of only one single polypeptide
Madsen, A., & Josephsen, J. (2001) · FEMS Microbiology Letters · doi:10.1016/s0378-1097(01)00199-9 · Cited by 26
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“Methylation-sensitive restriction enzyme based microarray (MRE- microarray) DNA with 5mC mark may be immune or non-immune to certain classes of restriction enzymes (Wilson & Murray, 1991).”
Background
Building a genome engineering toolbox in nonmodel prokaryotic microbes
Freed, E. F., Fenster, J. A., Smolinski, S. L., Walker, J. E., Henard, C. A., Gill, R. T., & Eckert, C. A. (2018) · Biotechnology and Bioengineering · doi:10.1002/bit.26727 · Cited by 24
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“Bacterial RM systems are classified into four types based on components, sequence specificity, cofactors, and cleavage position (7, 8).”
Background
Restriction-modification mediated barriers to exogenous DNA uptake and incorporation employed by Prevotella intermedia
Johnston, C. D., Skeete, C. A., Fomenkov, A. I., Roberts, R. J., & Rittling, S. R. (2017) · PLoS ONE · doi:10.1371/journal.pone.0185234 · Cited by 25
Detection and analysis of enzymatic DNA methylation of oligonucleotide substrates by matrix-assisted laser desorption ionization time-of-flight mass spectrometry
Humeny, A., Beck, C., Becker, C., & Jeltsch, A. (2003) · Analytical Biochemistry · doi:10.1016/s0003-2697(02)00568-7 · Cited by 25
“In most bacteria, restriction/modification systems are involved in the protection of the bacteria against bacteriophage infections, serving as a kind of immune system (review: [8]).”
Background
Identification of the CTAG-recognizing restriction-modification systemsMthZI andMthFI fromMethanobacterium thermoformicicumand characterization of the plasmid-encodedmthZIMgene
Nölling, J., & de Vos, W. M. (1992) · Nucleic Acids Research · doi:10.1093/nar/20.19.5047 · Cited by 25
Gene structure and expression of theMbolrestriction − modification system
Ueno, T., Ito, H., Kimizuka, F., Kotani, H., & Nakajima, K. (1993) · Nucleic Acids Research · doi:10.1093/nar/21.10.2309 · Cited by 25
Cloning, Expression, and Purification of a Thermostable Nonhomodimeric Restriction Enzyme, Bsl I
Hsieh, P.-C., Xiao, J.-P., O'loane, D., & Xu, S.-Y. (2000) · Journal of Bacteriology · doi:10.1128/jb.182.4.949-955.2000 · Cited by 25
Organization and sequence of the HpaII restriction-modification system and adjacent genes
Kulakauskas, S., Barsomian, J. M., Lubys, A., Roberts, R. J., & Wilson, G. G. (1994) · Gene · doi:10.1016/0378-1119(94)90348-4 · Cited by 25
“R-M genes usually occur side-by-side (Wilson and Murray, 1991) and since the hpaZZM gene was located in the middle of the PstI fragment, the approx.”
BackgroundSelf-citation
S-adenosyl methionine alters the DNA contacts of theEcoKI methyltransferase
Powell, L. M., & Murray, N. E. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.6.967 · Cited by 25
Self-citation
Tyrosine 27 of the specificity polypeptide ofEcoKI can be UV crosslinked to a bromodeoxyuridine-substituted DNA target sequence
Chen, A., Powell, L. M., Dryden, D. T. F., Murray, N. E., & Brown, T. P. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.7.1177 · Cited by 25
Self-citation
Generation of biologically contained, readily transformable, and genetically manageable mutants of the biotechnologically important Bacillus pumilus
Wemhoff, S., & Meinhardt, F. (2013) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-013-4935-5 · Cited by 23
“…medium overnight and spotted on agar plates containing M9 minimal medium with 10 μM 5-FU Appl Microbiol Biotechnol (2013) 97:7805–7819 7813 play equivalent roles in different bacteria, they exhibit a remarkable genetic diversity (Chandrasegaran and Smith 1988; Murray 2000; Wilson and Murray 1991).”
Biology and engineering of integrative and conjugative elements: Construction and analyses of hybrid ICEs reveal element functions that affect species-specific efficiencies
Bean, E. L., Herman, C., Anderson, M. E., & Grossman, A. D. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1009998 · Cited by 24
Site-specific restriction endonucleases in cyanobacteria
Lyra, C., Halme, T., Torsti, A.-M., Tenkanen, T., & Sivonen, K. (2000) · Journal of Applied Microbiology · doi:10.1046/j.1365-2672.2000.01206.x · Cited by 24
“Only few exceptions of amino acid sequence similarities between isoschizomers have been reported (Aiken and Gumport 1988; Stepheson et al. 1989; Sullivan and Saunders 1989; Erdmann et al. 1991; Wilson and Murray 1991; Barany et al. 1992).”
Background
The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity
Uyen, N. T., Park, S., Choi, J.-W., Lee, H., Nishi, K., & Kim, J. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp603 · Cited by 24
“Upon identification of specific DNA sequences containing a hemi-methylation, a methyl group is transferred from S-adenosylmethionine to the non-methylated adenine base in the remnant strand (4).”
Background
The Type IIB restriction endonucleases
Marshall, J. J. T., & Halford, S. E. (2010) · Biochemical Society Transactions · doi:10.1042/bst0380410 · Cited by 24
The Bacterial Guide to Designing a Diversified Gene Portfolio
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“This is in contrast to type II RM systems, where the protein that directs methylation is distinct from the protein that directs endonuclease activity, such that changes in specificity require mutations in more than one protein (Wilson and Murray 2003).”
Result
Methanopterin biosynthesis: methylation of the biosynthetic intermediates
White, R. H. (1998) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/s0304-4165(97)00148-7 · Cited by 24
M1.MboII and M2.MboII type IIS methyltransferases: different specificities, the same target
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“Methylation of adenosyl or cytosyl residues by the modifying enzyme results in the protection of cellular DNA against cleavage by restriction endonucleases ( Wilson & Murray, 1991; Bickle & Kruger, 1993).”
Background
The specificity of StySKI, a type I restriction enzyme, implies a structure with rotational symmetry
Thorpe, P. H., Ternent, D., & Murray, N. E. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.9.1694 · Cited by 24
Self-citation
Characterization of LlaCI, a New Restriction-Modification System from Lactococcus lactis subsp. cremoris W15
Madsen, A., & Josephsen, J. (1998) · Biological Chemistry · doi:10.1515/bchm.1998.379.4-5.443 · Cited by 24
Cloning of the BssHII restriction-modification system in Escherichia coli : BssHII methyltransferase contains circularly permuted cytosine-5 methyltransferase motifs
Xu, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.20.3991 · Cited by 24
The corrected nucleotide sequences of the TaqI restriction and modification enzymes reveal a thirteen-codon overlap
Barany, F., Slatko, B. E., Danzitz, M. J., Cowburn, D., Schildkraut, I., & Wilson, G. G. (1992) · Gene · doi:10.1016/0378-1119(92)90307-b · Cited by 24
Self-citation
A model for the evolution of prokaryotic DNA restriction-modification systems based upon the structural malleability of Type I restriction-modification enzymes
Bower, E. K. M., Cooper, L. P., Roberts, G. A., White, J. H., Luyten, Y. A., Morgan, R., & Dryden, D. T. F. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky760 · Cited by 25
“The relative locations of the TRD with respect to the motifs for SAM binding subdivide all SAMdependent MTases into six groups, to , with the group predominating (17,43).”
BackgroundMethodInfluential
THE EVOLUTION OF CONFLICT RESOLUTION BETWEEN PLASMIDS AND THEIR BACTERIAL HOSTS
Ginty, S. É. M., & Rankin, D. J. (2011) · Evolution · doi:10.1111/j.1558-5646.2011.01549.x · Cited by 23
“…system, where an infecting plasmid would be removed from the bacterial host (Sorek et al. 2008; van der Oost et al. 2009; Vale and Little 2010) or a restriction modification system whereby foreign DNA is degraded by a restriction endonuclease (Wilson and Murray 1991; Stern and Sorek 2011).”
Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006
Ouellette, M., Jackson, L. K., Chimileski, S., & Papke, R. T. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00251 · Cited by 23
“Methyltransferases catalyze a reaction that transfers a methyl group from a cofactor, S-adenosyl-L-methoinine (AdoMet), and modifies a specific nucleotide base (Wilson and Murray, 1991; Blumenthal and Cheng, 2002).”
Development of an in vivo methylation system for the solventogen Clostridium saccharobutylicum NCP 262 and analysis of two endonuclease mutants
Lesiak, J. M., Liebl, W., & Ehrenreich, A. (2014) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2014.07.005 · Cited by 23
DNA structural deformations in the interaction of the controller protein C.AhdI with its operator sequence
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“The methyltransferase (MTase) methylates specific bases within the DNA recognition sequence; the restriction endonuclease (ENase) cleaves DNA that is unmethylated at these sites, whilst host DNA is methylated and avoids restriction (1).”
Background
Bacteria-Phage Antagonistic Coevolution and the Implications for Phage Therapy
Brockhurst, M. A., Koskella, B. L., & Zhang, Q. (2017) · Springer eBooks · doi:10.1007/978-3-319-40598-8_7-1 · Cited by 23
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BsuBI—an isospecific restriction and modification system ofPstI: characterization of theBsuBI genes and enzymes
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Cloning of Nt.CviQII nicking endonuclease and its cognate methyltransferase: M.CviQII methylates AG sequences
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“Members of m6A γ MTases typically have relatively low sequence identity to each other [13, 14].”
DNA methyltransferases and DNA site-specific endonucleases encoded by chlorella viruses
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DNA restriction dependent on two recognition sites: activities of the Sfi I restriction–modification system in Escherichia coli
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“The 2900 restriction–modification (R/M) systems identified to date (Roberts and Macelis, 1998) are classified into three main types, based on their protein compositions and cofactor requirements (Wilson and Murray, 1991).”
BackgroundMethodInfluential
Biochemical Properties and Roles of DprA Protein in Bacterial Natural Transformation, Virulence, and Pilin Variation
Sharma, D. K., Misra, H. S., Bihani, S. C., & Rajpurohit, Y. S. (2023) · Journal of Bacteriology · doi:10.1128/jb.00465-22 · Cited by 22
Do‐or‐die life cycles and diverse post‐infection resistance mechanisms limit the evolution of parasite host ranges
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“One such strategy is recognition and cleavage of the phage genome by intracellular resistance mechanisms, such as restriction/modification (Wilson & Murray, 1991) and CRISPR systems (Horvath & Barrangou, 2010).”
Method
Structure and evolution of theXcylrestriction-modification system
Withers, B. E., Ambroso, L. A., & Dunbar, J. C. (1992) · Nucleic Acids Research · doi:10.1093/nar/20.23.6267 · Cited by 22
High Resolution Footprinting of a Type I Methyltransferase Reveals a Large Structural Distortion within the DNA Recognition Site
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Mapping the ‘breaker’ element of the gametocidal locus proximal to a block of sub-telomeric heterochromatin on the long arm of chromosome 4Ssh of Aegilops sharonensis
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“These include a dual-function model (breaker and inhibitor), in which the locus is similar to a restriction-modification system in bacteria (Wilson and Murray 1991; Tsujimoto 2005).”
Background
5-methylcytosine-sensitive variants ofThermococcus kodakaraensisDNA polymerase
Huber, C., von Watzdorf, J., & Marx, A. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw812 · Cited by 21
“Firstly, in the restriction–modification system that enables prokaryotes to distinguish between their own and foreign DNA (for extensive review see (12) and (13); also within the mismatch repair pathway that is best understood in the E.”
Background
A positive perspective on DNA methylation: regulatory functions of DNA methylation outside of host defense in Gram-positive bacteria
Nye, T. M., Fernandez, N. L., & Simmons, L. A. (2020) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2020.1828257 · Cited by 21
The structural basis of differential DNA sequence recognition by restriction–modification controller proteins
Ball, N. J., McGeehan, J. E., Streeter, S. D., Thresh, S.-J., & Kneale, G. G. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks718 · Cited by 21
“The DNA MTase protects the host DNA from cleavage by the associated restriction enzyme, while digesting (restricting) foreign DNA (2).”
Background
Specificity of DNA binding and methylation by the M.FokI DNA methyltransferase
Friedrich, T., Fatemi, M., Gowhar, H., Leismann, O., & Jeltsch, A. (2000) · Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology · doi:10.1016/s0167-4838(00)00065-0 · Cited by 21
Probing the Protein-DNA Interface of the EcoRV Modification Methyltransferase Bound to Its Recognition Sequence, GATATC
Szczelkun, M. D., Jones, H., & Connolly, B. A. (1995) · Biochemistry · doi:10.1021/bi00034a005 · Cited by 21
Expression and Characterisation of the N-Terminal Fragment of the HsdS Subunit of M.EcoR124I
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Probing the Domain Structure of the Type IC DNA Methyltransferase M.EcoR124I by Limited Proteolysis
Webb, M., Taylor, I. A., Firman, K., & Kneale, G. G. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1995.0369 · Cited by 21
Identification of a subdomain within DNA‐(cytosine‐C5)‐methyltransferases responsible for the recognition of the 5′ part of their DNA target.
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Effects of Extracellular Self- and Nonself-DNA on the Freshwater Microalga Chlamydomonas reinhardtii and on the Marine Microalga Nannochloropsis gaditana
Palomba, E., Chiaiese, P., Termolino, P., Paparo, R., Filippone, E., Mazzoleni, S., & Chiusano, M. L. (2022) · Plants · doi:10.3390/plants11111436 · Cited by 20
“Usually unmethylated or differently methylated DNA of exogenous DNA are recognized through the DNA restriction– modification [97] and/or by the CRISPR–Cas systems [98–100].”
Background
Quantification of Propionibacterium acidipropionici P169 Bacteria in Environmental Samples by Use of Strain-Specific Primers Derived by Suppressive Subtractive Hybridization
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“DNA from digestion (30), slightly more than an SSH compar-”
Background
Whole genome sequencing provides possible explanations for the difference in phage susceptibility among two Salmonella Typhimurium phage types (DT8 and DT30) associated with a single foodborne outbreak
Mohammed, M., & Cormican, M. (2015) · BMC Research Notes · doi:10.1186/s13104-015-1687-6 · Cited by 20
“RMS allows bacteria to recognize and destroy viral DNA by restriction endonucleases (REases) that have the ability to cut foreign DNA at certain sequence (restriction sites) while bacterial DNA is protected by the aid of DNA MTase that modifies restriction sites within the bacterial genome [28, 29].”
Background
Modulation of Escherichia coli DNA Methyltransferase Activity by Biologically Derived GATC-flanking Sequences
Coffin, S. R., & Reich, N. O. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m802502200 · Cited by 20
Bacteriophage and antiphage mechanisms of lactic acid bacteria.
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Complex transcription of an operon encoding the Sail restriction‐modification system of Streptomyces albus G
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The Neisseria gonorrhoeae S.NgoVIII restriction/modification system: a type IIs system homologous to the Haemophilus parahaemolyticus HphI restriction/modification system
Gunn, J. S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.20.4147 · Cited by 20
Identification of large cryptic plasmids in Clostridioides (Clostridium) difficile
Amy, J., Bulach, D., Knight, D. R., Riley, T., Johanesen, P., & Lyras, D. (2018) · Plasmid · doi:10.1016/j.plasmid.2018.04.001 · Cited by 19
Genetic Addiction: a Principle of Gene Symbiosis in a Genome
Kobayashi, I. (2014) · ASM Press eBooks · doi:10.1128/9781555817732.ch6 · Cited by 19
Information integration in evolutionary processes
Pagie, L. (1999) · Cited by 19
Functional cooperation between exonucleases and endonucleases--basis for the evolution of restriction enzymes
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The ever-expanding tcp conjugation locus of pCW3 from Clostridium perfringens
Revitt‐Mills, S. A., Watts, T. D., Lyras, D., Adams, V., & Rood, J. I. (2020) · Plasmid · doi:10.1016/j.plasmid.2020.102516 · Cited by 18
A cell-free transcription-translation pipeline for recreating methylation patterns boosts DNA transformation in bacteria
Vento, J. M., Durmusoglu, D., Li, T., Patinios, C., Sullivan, S., Ttofali, F., van Schaik, J., Yu, Y., Wang, Y., Barquist, L., et al. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.06.003 · Cited by 18
Diversity, evolution, and therapeutic applications of small RNAs in prokaryotic and eukaryotic immune systems
Cooper, E. L., & Overstreet, N. (2013) · Physics of Life Reviews · doi:10.1016/j.plrev.2013.11.002 · Cited by 18
“Around 25% of known bacteria possess RM systems [137].”
Background
Protoplast Transformation of Recalcitrant Alkaliphilic Bacillus sp. with Methylated Plasmid DNA and a Developed Hard Agar Regeneration Medium
Gao, C., Xue, Y., & Ma, Y. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028148 · Cited by 18
“The sequence alignment of the DNA fragments with plasmid pUC18 or pMK4 revealed only one kind of cleavage site with a palindromic sequence of 59-CGCG-39, which suggested there was a type II REase in Bacillus sp. N16-5 [20].”
Influential
Complete Genome Sequence of Geobacillus thermodenitrificans T12, A Potential Host for Biotechnological Applications
Daas, M. J. A., Vriesendorp, B., van de Weijer, A. H. P., John van der, O. O. S. T., & van Kranenburg, R. (2017) · Current Microbiology · doi:10.1007/s00284-017-1349-0 · Cited by 19
“Detected motif sequence for this site such as ‘‘GATC’’ Position in motif of modification (0-based) Type of restriction modification system [35] N6-Methyladenosine (m6A) refers to a type of methyltransferase that prefers to methylate the adenosine base at the nitrogen-6 position The percent of time this motif is detect…”
Background
Mesophilic cyanobacteria producing thermophilic restriction endonucleases
Piechula, S., Waleron, K., Światek, W., Biedrzycka, I., & Podhajska, A. J. (2001) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2001.tb10632.x · Cited by 18
Adenine Methylation in Eukaryotic DNA
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“Methylation is responsible for DNA host specificity [14], the choice of the DNA strand in mismatch repair [15], the control of replication and chromosome segregation [16], positive transcriptional regulation of phage Mu mom [17], and expression of numerous bacterial genes [18].”
Background
Individual- and Population-based Diversity in Restriction-modification Systems
Pagie, L. (2000) · Bulletin of Mathematical Biology · doi:10.1006/bulm.2000.0177 · Cited by 18
“Studies of natural bacterium populations show that RM systems in bacterium populations are highly diverse and that many bacteria carry RM systems, and often more than one (Wilson and Murray, 1991; Barcus and Murray, 1995).”
Inference of relationships in the 'twilight zone' of homology using a combination of bioinformatics and site-directed mutagenesis: a case study of restriction endonucleases Bsp6I and PvuII
Pawlak, S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki213 · Cited by 18
“enzymes that exhibit identical recognition and cleavage specificities (2,3).”
BackgroundMethod
Converting MlyI endonuclease into a nicking enzyme by changing its oligomerization state
Besnier, C., & Kong, H. (2001) · EMBO Reports · doi:10.1093/embo-reports/kve175 · Cited by 18
“Most of the Type II and Type IIs restriction endonucleases catalyze double-stranded cleavage by forming dimers (Wilson and Murray, 1991).”
Background
The tendency to recreate ancestral CG dinucleotides in the human genome
Li, M., & Chen, S. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-3 · Cited by 18
“DNA methylation is central to important biological processes, including X chromosome inactivation[1], genetic imprinting [2], gene-expression regulation [3-5], and the defense mechanisms against parasitic DNA and transposons [6,7].”
Background
The M·AluI DNA-(cytosineC5)-methyltransferase has an unusually large, partially dispensable, variable region
Zhang, B., Tao, T., Wilson, G. G., & Blumenthal, R. (1993) · Nucleic Acids Research · doi:10.1093/nar/21.4.905 · Cited by 18
Self-citation
Probing the General Base Catalysis in the First Step of BamHI Action by Computer Simulations
Fuxreiter, M., & Osman, R. (2001) · Biochemistry · doi:10.1021/bi010987x · Cited by 18
Cloning and expression of the Apa LI, Nsp I, Nsp HI, Sac I, Sca I, and Sap I restriction-modification systems in Escherichia coli
Xu, S.-Y., Xiao, J.-P., Ettwiller, L. M., Holden, M., Aliotta, J. M., Poh, C. L., Dalton, M. W., Robinson, D., Petronzio, T., Moran, L., et al. (1998) · Molecular and General Genetics MGG · doi:10.1007/s004380050890 · Cited by 18
“amongst dierent restriction enzymes, except for some isoschizomers (Wilson and Murray 1991).”
BackgroundInfluential
Short Communication
Ramchandani, S., Bigey, P., & Moshe Szyf, A. (1998) · Biological Chemistry · doi:10.1515/bchm.1998.379.4-5.535 · Cited by 18
Sequence of the gene encoding a second ScrFI m5C methyltransferase of Lactococcus lactis
Twomey, D. P., Davis, R., Daly, C., & Fitzgerald, G. F. (1993) · Gene · doi:10.1016/0378-1119(93)90465-f · Cited by 18
Discovery of an Unnatural DNA Modification Derived from a Natural Secondary Metabolite
Wang, T., & Kohli, R. M. (2020) · Cell chemical biology · doi:10.1016/j.chembiol.2020.09.006 · Cited by 17
“Methylation of these bases primarily serves rudimentary functions to distinguish self from non-self in the arms race against bacteriophages (Nabel et al., 2012; Wilson and Murray, 1991), although emerging models suggest that some modifications may impact genome regulation (Sánchez-Romero and Casadesús, 2020).”
Background
Evolutionary relationship of Alw26I, Eco31I and Esp3I, restriction endonucleases that recognise overlapping sequences
Bitinaite, J., Mitkaite, G., Dauksaite, V., Jakubauskas, A., Timinskas, A., Vaisvila, R., Lubys, A., & Janulaitis, A. (2002) · Molecular Genetics and Genomics · doi:10.1007/s00438-002-0701-6 · Cited by 17
“enzymes that recognise identical nucleotide sequences, show little, if any, similarity at the level of the amino acid sequence (Wilson and Murray 1991).”
Background
A theoretical model of restriction endonuclease NlaIV in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis and circular dichroism spectroscopy
Chmiel, A. A., Radlińska, M., Pawlak, S., Krowarsch, D., Bujnicki, J. M., & Skowronek, K. J. (2005) · Protein Engineering Design and Selection · doi:10.1093/protein/gzi019 · Cited by 17

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
DOI: 10.1146/annurev.ge.25.120191.003101
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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