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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“endonucleases) which appear to have that role [13,14].”
Background
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Approaches for bacteriophage genome engineering
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Asymmetrical recognition and activity of the I‐SceI endonuclease on its site and on intron‐exon junctions.
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Alanylation of Teichoic Acids ProtectsStaphylococcus aureusagainst Toll‐like Receptor 2–Dependent Host Defense in a Mouse Tissue Cage Infection Model
Kristian, S. A., Lauth, X., Nizet, V., Goetz, F., Neumeister, B., Peschel, A., & Landmann, R. M. (2003) · The Journal of Infectious Diseases · doi:10.1086/376533 · Cited by 121
Epigenetic Control of Salmonella enterica O-Antigen Chain Length: A Tradeoff between Virulence and Bacteriophage Resistance
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“However, protection by restriction-modification systems can be expected to be incomplete as only a fraction of infecting phage genomes are modified [61].”
Background
Viral Diversity Threshold for Adaptive Immunity in Prokaryotes
Weinberger, A. D., Wolf, Y. I., Lobkovsky, A. E., Gilmore, M. S., & Koonin, E. V. (2012) · mBio · doi:10.1128/mbio.00456-12 · Cited by 110
“Immune encounters arise in one of two ways: (i) CRISPRCas hosts can survive viral infection by possessing spacers matching viral protospacers, or (ii) CRISPR-Cas and CRISPRCas hosts can survive through non-CRISPR-based resistance mechanisms such as restriction modification (35, 51).”
Background
The Escherichia coli Dam DNA Methyltransferase Modifies DNA in a Highly Processive Reaction
Urig, S., Gowher, H., Hermann, A., Beck, C., Fatemi, M., Humeny, A., & Jeltsch, A. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00371-6 · Cited by 113
Recognition and polymorphism in host—parasite genetics
Frank, S. A. (1994) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.1994.0145 · Cited by 113
“This reduction is probably caused by the high proportion of phage deaths that result when the phages invade and are restricted by bacteria for which the phage DNA is unmodified.”
BackgroundInfluential
Genomics of Staphylococcal Twort-like Phages - Potential Therapeutics of the Post-Antibiotic Era
Łobocka, M. B., Hejnowicz, M. S., Dąbrowski, K., Gozdek, A., Kosakowski, J., Witkowska, M., Ulatowska, M., Weber‐Dąbrowska, B., Kwiatek, M., Parasion, S., et al. (2012) · Advances in virus research · doi:10.1016/b978-0-12-394438-2.00005-0 · Cited by 112
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses
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“This strongly biased distribution of similarities and dissimilarity made comparative sequence analysis of all REases impossible with the use of standard tools for sequence alignment and raised a question whether the diversity of amino acid sequences of REases indicates polyphyletic evolution (convergence) or extreme d…”
Comparative Genomics of 12 Strains of Erwinia amylovora Identifies a Pan-Genome with a Large Conserved Core
Mann, R. A., Smits, T. H. M., Bühlmann, A., Blom, J., Goesmann, A., Frey, J. E., Plummer, K. M., Beer, S. V., Luck, J., Duffy, B., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0055644 · Cited by 112
“These modification systems generally have two primary functions; protection of host DNA (bacterial) and degradation of foreign DNA with restriction enzymes [32].”
Background
Crystal Structure of ErmC‘, an rRNA Methyltransferase Which Mediates Antibiotic Resistance in Bacteria
Bussiere, D. E., Muchmore, S. W., Dealwis, C. G., Schluckebier, G., Nienaber, V. L., Edalji, R. P., Walter, K. A., Ladror, U. S., Holzman, T. F., & Abad‐Zapatero, C. (1998) · Biochemistry · doi:10.1021/bi973113c · Cited by 109
Restriction-modification systems as genomic parasites in competition for specific sequences.
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Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences
Cao, B., Chen, C., DeMott, M. S., Cheng, Q., Clark, T. A., Xiong, X., Zheng, X., Butty, V. L., Levine, S. S., Yuan, G., et al. (2014) · Nature Communications · doi:10.1038/ncomms4951 · Cited by 107
Maintenance of species identity and controlling speciation of bacteria: a new function for restriction/modification systems?
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“Restriction/modification (RM) systems (reviews: Wilson and Murray, 1991; Bickle and Kruger, 1993; Heitman, 1993; Raleigh and Brooks, 1998) consist of two activities: a methyltransferase (reviews: Cheng, 1995; Jeltsch, 2002) that modifies adenine or cytosine residues at certain recognition sites and a restriction endon…”
Background
Review
Schmütte, C., & Jones, P. A. (1998) · Biological Chemistry · doi:10.1515/bchm.1998.379.4-5.377 · Cited by 107
Genome and evolution of the arbuscular mycorrhizal fungus Diversispora epigaea (formerly Glomus versiforme) and its bacterial endosymbionts
Sun, X., Chen, W., Ivanov, S., MacLean, A. M., Wight, H., Ramaraj, T., Mudge, J., Harrison, M., & Fei, Z. (2018) · New Phytologist · doi:10.1111/nph.15472 · Cited by 106
The fission yeast gene pmt1+encodes a DNA methyltransferase homologue
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A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300
Xu, S.-Y., Corvaglia, A., Chan, S., Zheng, Y., & Linder, P. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr098 · Cited by 105
“Type I restriction enzymes are multi-subunit complexes consisting of M2R2S subunits, and their activity requires ATP hydrolysis (3).”
Crystal structure of PvuII endonuclease reveals extensive structural homologies to EcoRV
Athanasiadis, A., Vlassi, M., Kotsifaki, D., Tucker, P. A., Wilson, K. S., & Kokkinidis, M. (1994) · Nature Structural & Molecular Biology · doi:10.1038/nsb0794-469 · Cited by 105
Restriction endonucleases and modification methylases
Anderson, J. E. (1993) · Current Opinion in Structural Biology · doi:10.1016/0959-440x(93)90197-s · Cited by 105
Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at Single-Base Resolution
Lluch‐Senar, M., Luong, K., Lloréns‐Rico, V., Delgado, J., Fang, G., Spittle, K. E., Clark, T. A., Schadt, E. E., Turner, S. W., Korlach, J., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003191 · Cited by 107
“The S subunit determines the specificity of both restriction and methylation [39].”
Background
Identification of type II restriction and modification systems in Helicobacter pylori reveals their substantial diversity among strains
Xu, Q. S., Morgan, R., Roberts, R. J., & Blaser, M. J. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.17.9671 · Cited by 101
Determinants of Phage Host Range in Staphylococcus Species
Moller, A. G., Lindsay, J. A., & Read, T. D. (2019) · Applied and Environmental Microbiology · doi:10.1128/aem.00209-19 · Cited by 101
“Sau42I is an example of a type IIS R-M system, which binds asymmetric DNA 271 sequences and cleaves outside the recognition site, unlike most type II systems (82).”
Background
The dynamic genetic repertoire of microbial communities
Wilmes, P., Simmons, S. L., Denef, V. J., & Banfield, J. F. (2008) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2008.00144.x · Cited by 99
“These include restriction-modification systems (Wilson & Murray, 1991), cell-surface manipulations (Weitz et al., 2005), exopolysaccharide production (Sutherland, 2001), biofilm formation (Sutherland et al., 2004), abortive infection systems (Sturino & Klaenhammer, 2007) and the CRISPR system…”
Method
Integrating conjugative elements of the SXT/R391 family trigger the excision and drive the mobilization of a new class of Vibrio genomic islands
Daccord, A., Ceccarelli, D., & Burrus, V. (2010) · Molecular Microbiology · doi:10.1111/j.1365-2958.2010.07364.x · Cited by 99
“Bacteria encoding restriction-modification systems are usually less susceptible to phage infection (Wilson and Murray, 1991), which would be advantageous in the aquatic environment where bacteriophages thrive.”
Background
Virion-Associated Restriction Endonucleases of Chloroviruses
Agarkova, I. V., Dunigan, D. D., & Etten, J. L. V. (2006) · Journal of Virology · doi:10.1128/jvi.00486-06 · Cited by 96
The evolving functions of DNA methylation
Zilberman, D. (2008) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2008.07.004 · Cited by 94
“The host’s genome is protected by a cognate DNA methyltransferase that modifies the same site recognized by the endonuclease [2].”
Background
Restriction-modification gene complexes as selfish gene entities: Roles of a regulatory system in their establishment, maintenance, and apoptotic mutual exclusion
Nakayama, Y., & Kobayashi, I. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.11.6442 · Cited by 91
Two-domain structure of the td intron-encoded endonuclease I-TevI correlates with the two-domain configuration of the homing site
Derbyshire, V., Kowalski, J. C., Dansereau, J. T., Hauer, C. R., & Belfort, M. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0754 · Cited by 91
On the Origins, Structures and Functions of Restriction-Modification Enzymes
Heitman, J. (1993) · Springer eBooks · doi:10.1007/978-1-4899-1666-2_4 · Cited by 89

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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