A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes

Roberts, Richard J.; Belfort, Marlene; Bestor, Timothy H.; Bhagwat, Ashok S.; Bickle, Thomas A.; Bitinaite, Jurate; Blumenthal, Robert; Degtyarev, S. Kh.; Dryden, David T. F.; Dybvig, Kevin; Firman, Keith; Громова, Е. С.; Gumport, Richard I.; Halford, Stephen E.; Hattman, Stanley; Heitman, Joseph; Hornby, D.; Janulaitis, A.; Jeltsch, Albert; Josephsen, Jytte; Kiss, Antal; Klaenhammer, Todd R.; Kobayashi, Ichizo; Kong, Huimin; Krüger, Detlev H.; Lacks, Sanford A.; Marinus, Martin; Miyahara, Makoto; Morgan, Richard D.; Murray, Noreen E.; Nagaraja, Valakunja; Piekarowicz, Andrzej; Pingoud, Alfred; Raleigh, Elisabeth A.; Rao, Desirazu N.; Reich, Norbert O.; Repin, V. E.; Selker, Eric U.; Shaw, Pang Chui; Stein, Daniel C.; Stoddard, Barry; Szybalski, Waclaw; Trautner, Thomas A.; Etten, James L. Van; Vítor, Jorge M. B.; Wilson, Geoffrey G.; Xu, Shuai

doi:10.1093/nar/gkg274

Cited by 639 publications

(506 citation statements)

References 34 publications

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“…The AloI (13), PpiI, and TstI REases used in this study are classified as type IIB REases because of their characteristic cleavage of DNA on both sides of the recognition sequence (2). Type IIB REases are bifunctional enzymes, which either cleave or methylate DNA, depending on the nature of cofactors added.…”

Section: Characterization Of Reases Used For Domain-swapping Experimementioning

confidence: 99%

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Generation of DNA cleavage specificities of type II restriction endonucleases by reassortment of target recognition domains

Jurenaite-Urbanaviciene

Serksnaite²,

Kriukienė

et al. 2007

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

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Type II restriction endonucleases (REases) cleave double-stranded DNA at specific sites within or close to their recognition sequences. Shortly after their discovery in 1970, REases have become one of the primary tools in molecular biology. However, the list of available specificities of type II REases is relatively short despite the extensive search for them in natural sources and multiple attempts to artificially change their specificity. In this study, we examined the possibility of generating cleavage specificities of REases by swapping putative target recognition domains (TRDs) between the type IIB enzymes AloI, PpiI, and TstI. Our results demonstrate that individual TRDs recognize distinct parts of the bipartite DNA targets of these enzymes and are interchangeable. Based on these properties, we engineered a functional type IIB REase having previously undescribed DNA specificity. Our study suggests that the TRD-swapping approach may be used as a general technique for the generation of type II enzymes with predetermined specificities.hybrid ͉ AloI ͉ PpiI ͉ TstI R estriction endonucleases (REases) are parts of restrictionmodification (R-M) systems, whose primary biological function is the protection of bacterial cells from incoming foreign DNA molecules (1). There are three main groups of restriction enzymes (types I, II, and III), which differ in enzyme composition, cofactor requirements, and mode of action (2). The beststudied are type II REases, which in general recognize specific DNA targets of 4-8 bp and cleave DNA at or close to these sequences (1, 2). The exquisite accuracy of type II enzymes (3, 4) has made them indispensable tools for DNA manipulations. Although almost 3,700 type II REases with 262 different specificities have been characterized to date (5), there still is a demand for enzymes recognizing new DNA targets.During the past two decades, numerous efforts have been undertaken to engineer type II REases with altered specificities. Both rational protein design and random mutagenesis, followed by various selection procedures, have been tried (6), and several mutant enzymes with some preference for cleavage of altered DNA targets were isolated (7-10). However, projects concerned with orthodox type II REases so far have been largely unsuccessful mainly for two reasons: (i) difficulty of dealing with the observed tight coupling between DNA recognition and cleavage and (ii) absence of an efficient system for selecting enzymes with changed specificities. In this regard, unorthodox type II enzymes, such as the type IIG REase Eco57I (11), have shown more promise. Type IIG enzymes combine the catalytic centers of endonuclease and methyltransferase in one polypeptide chain, and the ability of Eco57I to methylate recognized DNA targets has been applied to isolate mutants having previously undescribed specificity (12).The discovery of AloI-like REases (13-15), classified as type IIB enzymes, opened up new opportunities for the engineering of type II REases with altered specificities. AloI-like REases ar...

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Section: Characterization Of Reases Used For Domain-swapping Experimementioning

confidence: 99%

“…There are three main groups of restriction enzymes (types I, II, and III), which differ in enzyme composition, cofactor requirements, and mode of action (2). The beststudied are type II REases, which in general recognize specific DNA targets of 4-8 bp and cleave DNA at or close to these sequences (1,2).…”

mentioning

confidence: 99%

Generation of DNA cleavage specificities of type II restriction endonucleases by reassortment of target recognition domains

Jurenaite-Urbanaviciene

Serksnaite²,

Kriukienė

et al. 2007

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

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“…Subsequent investigations of this phenomenon by Arber, Meselson and co‐workers led to the discovery of restriction‐modification (R‐M) systems, a landmark event in the history of molecular biology 4, 5. While much subsequent work focused on characterizing restriction enzymes as tools for recombinant DNA technology, the biology and biochemistry of the R‐M systems proved to be interesting in their own right 6, 7, 8. These systems are the most widespread prokaryotic biological conflict systems facilitating both discrimination of cellular “self” DNA from invasive “non‐self” DNA and destruction of the latter 6, 9, 10, 11.…”

Section: Introductionmentioning

confidence: 99%

“…1A). In classic R‐M systems, modification of DNA serves as the discriminatory tag, which prevents the restriction of self DNA, while allowing the non‐self DNA, which is not modified, to be targeted 8, 10. Several bacteriophages have evolved counter‐strategies against R‐M systems in the form of DNA modifications generated by enzymes encoded in their genomes, which inhibit restriction enzymes 10, 22, 23.…”

Section: Introductionmentioning

confidence: 99%

Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification

2015

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While N6‐methyladenosine (m6A) is a well‐known epigenetic modification in bacterial DNA, it remained largely unstudied in eukaryotes. Recent studies have brought to fore its potential epigenetic role across diverse eukaryotes with biological consequences, which are distinct and possibly even opposite to the well‐studied 5‐methylcytosine mark. Adenine methyltransferases appear to have been independently acquired by eukaryotes on at least 13 occasions from prokaryotic restriction‐modification and counter‐restriction systems. On at least four to five instances, these methyltransferases were recruited as RNA methylases. Thus, m6A marks in eukaryotic DNA and RNA might be more widespread and diversified than previously believed. Several m6A‐binding protein domains from prokaryotes were also acquired by eukaryotes, facilitating prediction of potential readers for these marks. Further, multiple lineages of the AlkB family of dioxygenases have been recruited as m6A demethylases. Although members of the TET/JBP family of dioxygenases have also been suggested to be m6A demethylases, this proposal needs more careful evaluation.Also watch the Video Abstract.

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“…Restriction endonucleases (REases) 1 provide an anti-viral protection for bacteria by degrading the foreign DNA of invading bacteriophages. The enzymes recognize specific nucleotide sequences and cleave both strands of DNA.…”

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confidence: 99%

Crystal Structures of Type II Restriction Endonuclease EcoO109I and Its Complex with Cognate DNA

Hashimoto

Shimizu

Imasaki

et al. 2005

Journal of Biological Chemistry

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EcoO109I is a type II restriction endonuclease that recognizes the DNA sequence of RGGNCCY. Here we describe the crystal structures of EcoO109I and its complex with DNA. A comparison of the two structures shows that the catalytic domain moves drastically to capture the DNA. One metal ion and two water molecules are observed near the active site of the DNA complex. The metal ion is a Lewis acid that stabilizes the pentavalent phosphorus atom in the transition state. One water molecule, activated by Lys-126, attacks the phosphorus atom in an S N 2 mechanism, whereas the other water interacts with the 3-leaving oxygen to donate a proton to the oxygen. EcoO109I is similar to EcoRI family enzymes in terms of its DNA cleavage pattern and folding topology of the common motif in the catalytic domain, but it differs in the manner of DNA recognition. Our findings propose a novel classification of the type II restriction endonucleases and lead to the suggestion that EcoO109I represents a new subclass of the EcoRI family.Bacteria have evolved a mechanism to protect themselves from viral infection. Restriction endonucleases (REases) 1 provide an anti-viral protection for bacteria by degrading the foreign DNA of invading bacteriophages. The enzymes recognize specific nucleotide sequences and cleave both strands of DNA. To date, more than 3,500 REases have been characterized and classified into four types, I, II, III, and IV (1). Of these types, type II REases are widely used in genetic technology and are the most well studied.Type II REases generally recognize 4 -8 base pairs of doublestranded DNA and hydrolyze phosphodiester bonds within the recognition sequences. The amino acid sequences are not homologous with the exception of the active site sequence. The active sites of the type II enzymes have a signature sequence PD(X) n DXK, in which four residues (Pro, Asp, Asp, and Lys; n ϭ 1 (PvuII) to ϳ49 (Bse634I) (2)) are weakly conserved and two separated acidic residues are usually followed by a basic residue. The active site structures thus share a common structural motif consisting of a five-stranded ␤-sheet flanked with ␣-helices (3-5). Specific divalent metal cations such as Mg 2ϩ are required to express the enzymatic activities and are coordinated to the conserved acidic residues during the catalytic reaction. However, details of the mechanism of the catalytic reaction are not fully understood (2).Type II REases have been classified into two families, EcoRI and EcoRV, based on their DNA cleavage pattern. The EcoRI family produces 5Ј-overhang DNA, whereas the EcoRV family produces blunt-end DNA. From a structural viewpoint, the EcoRI family approaches DNA from the major groove side, whereas the EcoRV family approaches from the minor groove side. Moreover, the folding topology of the five-stranded ␤-sheet in the common structural motif in the active site differs between the two families (7) where the topology of four ␤-strands are absolutely conserved in the common motif but the fifth ␤-strand is oppositely oriented (8).To ...

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A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes

Cited by 639 publications

References 34 publications

Generation of DNA cleavage specificities of type II restriction endonucleases by reassortment of target recognition domains

Generation of DNA cleavage specificities of type II restriction endonucleases by reassortment of target recognition domains

Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification

Crystal Structures of Type II Restriction Endonuclease EcoO109I and Its Complex with Cognate DNA

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