A Nomenclature for Restriction Enzymes, DNA Methyltransferases, Homing Endonucleases, and Their Genes

Rj, Roberts; Belford, M; Bester, T; Bhagwat, A M; Bickle, TA; Bitinaite, Jurate; Rm, Blumenthal; Sk, Degtyarev; Dryden, Dtf; Dybvig, Kevin; Firman, Keith; Es, Gromova; Ri, Gumport; Halford, SE; Hattman, Stanley; Heitman, Joseph; Hornby, D. P.; Janulaitis, A.; Jeltsch, Albert; Josephsen, Jytte; Kiss, Antal; Klaenhammer, TR; Kobayashi, Ichizo; Kong, Huimin; Dh, Krüger; Lacks, Sanford A.; Mg, Marinus; Miyahara, Makoto; Morgan, RD; Murray, NE; Nagaraja, Valakunja; Piekarowicz, Andrzej; Pingoud, Alfred; Raleigh, Elisabeth A.; Rao, D.; Reich, Norbert O.; Repin, V I; Selker, EU; Shaw, Priyanka; Stein, DC; Bl, Stoddard; Szybalski, Waclaw; Trautner, TA; Etten, J. Van; Vitor, Jmb; Wilson, GG; Xu, S.

doi:10.1007/978-3-642-18851-0_1

Cited by 88 publications

(136 citation statements)

References 37 publications

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“…In addition, the initiating incisions for DDAI may have been catalyzed by restriction-modification systems in place of the transposases in replicative inversion. The following considerations favor this possibility: (i) restrictionmodification genes are abundant in H. pylori genomes (19); (ii) some restriction-modification enzymes show a nicking activity (29); (iii) some restriction enzymes are similar to transposases in structure and function (30); and (iv) some restriction-modification units are similar to DNA transposons in organization (23).…”

Section: Discussionmentioning

confidence: 99%

Birth and death of genes linked to chromosomal inversion

Furuta

Kawai

Yahara

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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The birth and death of genes is central to adaptive evolution, yet the underlying genome dynamics remain elusive. The availability of closely related complete genome sequences helps to follow changes in gene contents and clarify their relationship to overall genome organization. Helicobacter pylori , bacteria in our stomach, are known for their extreme genome plasticity through mutation and recombination and will make a good target for such an analysis. In comparing their complete genome sequences, we found that gain and loss of genes (loci) for outer membrane proteins, which mediate host interaction, occurred at breakpoints of chromosomal inversions. Sequence comparison there revealed a unique mechanism of DNA duplication: DNA duplication associated with inversion. In this process, a DNA segment at one chromosomal locus is copied and inserted, in an inverted orientation, into a distant locus on the same chromosome, while the entire region between these two loci is also inverted. Recognition of this and three more inversion modes, which occur through reciprocal recombination between long or short sequence similarity or adjacent to a mobile element, allowed reconstruction of synteny evolution through inversion events in this species. These results will guide the interpretation of extensive DNA sequencing results for understanding long- and short-term genome evolution in various organisms and in cancer cells.

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Section: Discussionmentioning

confidence: 99%

Birth and death of genes linked to chromosomal inversion

Furuta

Kawai

Yahara

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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“…For example, R.MboII recognizes the asymmetric sequence 5=-GAAGA-3=/3=-CTTCT-5=. M1.MboII modifies the last adenine of the top-strand recognition sequence, and M2.MboII transfers the methyl group to the internal cytosine in the bottom strand (4,78). In contrast, type III R-M systems utilize only one MTase to discriminate self from nonself (e.g., hemimethylation of the internal adenine in the sequence 5=-AGACC-3= by M.EcoP1I) (14).…”

Section: Strategies Against R-m Systemsmentioning

confidence: 99%

“…R-M systems are classified mainly into four different types based on their subunit composition, sequence recognition, cleavage position, cofactor requirements, and substrate specificity (4). Type I enzymes consist of a hetero-oligomeric protein complex encompassing both restriction and modification activities.…”

Section: Introductionmentioning

confidence: 99%

“…Typical examples are EcoP1I and EcoP15I (5,14). In contrast to the above-described three groups, the type IV systems cleave only DNA substrates containing methylated, hydroxymethylated, or glucosyl-hydroxymethylated bases at specific sequences (4). For example, EcoKMcrBC, a well-studied type IV enzyme, targets A/G m C (methylated cytosine, either m 4 C or m 5 C) separated by ϳ40 to 3,000 bases (15).…”

Section: Introductionmentioning

confidence: 99%

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Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

Vasu

Nagaraja

2013

Microbiol Mol Biol Rev

507

462

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SUMMARY Restriction-modification (R-M) systems are ubiquitous and are often considered primitive immune systems in bacteria. Their diversity and prevalence across the prokaryotic kingdom are an indication of their success as a defense mechanism against invading genomes. However, their cellular defense function does not adequately explain the basis for their immaculate specificity in sequence recognition and nonuniform distribution, ranging from none to too many, in diverse species. The present review deals with new developments which provide insights into the roles of these enzymes in other aspects of cellular function. In this review, emphasis is placed on novel hypotheses and various findings that have not yet been dealt with in a critical review. Emerging studies indicate their role in various cellular processes other than host defense, virulence, and even controlling the rate of evolution of the organism. We also discuss how R-M systems could have successfully evolved and be involved in additional cellular portfolios, thereby increasing the relative fitness of their hosts in the population.

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“…The MTase modifies DNA by methylation of cytosine and adenine residues within the REase recognition sequence so that the host DNA is protected from the REase activity ( Figure 1A). RM systems are classifi ed according to the recognition site, cleavage position, subunit composition, and cofactor requirements into four groups (types I-IV) (Roberts 2003). Since the discovery of RM systems about 50 years ago, almost 5,000 restriction endonucleases, representing more than 300 modes of activity have been discovered in bacterial and archaeal genomes, 66 of which are cyanobacterial.…”

Section: Restriction-modifi Cation Systemsmentioning

confidence: 99%

Cyanobacterial defense mechanisms against foreign DNA transfer and their impact on genetic engineering

2013

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SUMMARYCyanobacteria display a large diversity of cellular forms ranging from unicellular to complex multicellular fi laments or aggregates. Species in the group present a wide range of metabolic characteristics including the fi xation of atmospheric nitrogen, resistance to extreme environments, production of hydrogen, secondary metabolites and exopolysaccharides. These characteristics led to the growing interest in cyanobacteria across the fi elds of ecology, evolution, cell biology and biotechnology. The number of available cyanobacterial genome sequences has increased considerably in recent years, with more than 140 fully sequenced genomes to date. Genetic engineering of cyanobacteria is widely applied to the model unicellular strains Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942. However the establishment of transformation protocols in many other cyanobacterial strains is challenging. One obstacle to the development of these novel model organisms is that many species have doubling times of 48 h or more, much longer than the bacterial models E. coli or B. subtilis. Furthermore, cyanobacterial defense mechanisms against foreign DNA pose a physical and biochemical barrier to DNA insertion in most strains. Here we review the various barriers to DNA uptake in the context of lateral gene transfer among microbes and the various mechanisms for DNA acquisition within the prokaryotic domain. Understanding the cyanobacterial defense mechanisms is expected to assist in the development and establishment of novel transformation protocols that are specifi cally suitable for this group.

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A Nomenclature for Restriction Enzymes, DNA Methyltransferases, Homing Endonucleases, and Their Genes

Cited by 88 publications

References 37 publications

Birth and death of genes linked to chromosomal inversion

Birth and death of genes linked to chromosomal inversion

Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

Cyanobacterial defense mechanisms against foreign DNA transfer and their impact on genetic engineering

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