Specificity Changes in the Evolution of Type II Restriction Endonucleases

Pingoud, Vera; Sudina, Anna; Geyer, Hildegard; Bujnicki, Janusz M.; Lüder, Gerhild; Morgan, Richard D.; Кубарева, Е. А.; Pingoud, Alfred

doi:10.1074/jbc.m409020200

Cited by 31 publications

(18 citation statements)

References 57 publications

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“…For example, SsoII (Type IIP; |CCNGG), EcoRII (Type IIE; |CCWGG) and NgoMIV (Type IIF; G|CCGGC) have remarkably similar DNA-binding sites and catalytic centers (234). Specificities for partly related, and even unrelated, sequences can nevertheless depend upon the same structural framework: CCNGG (SsoII), CCWGG (PspGI/EcoRII), GCCGGC (NgoMIV), RCCGGY (Cfr10I), GATC (MboI) (243). …”

Section: Introductionmentioning

confidence: 99%

Type II restriction endonucleases—a historical perspective and more

2014

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This article continues the series of Surveys and Summaries on restriction endonucleases (REases) begun this year in Nucleic Acids Research. Here we discuss ‘Type II’ REases, the kind used for DNA analysis and cloning. We focus on their biochemistry: what they are, what they do, and how they do it. Type II REases are produced by prokaryotes to combat bacteriophages. With extreme accuracy, each recognizes a particular sequence in double-stranded DNA and cleaves at a fixed position within or nearby. The discoveries of these enzymes in the 1970s, and of the uses to which they could be put, have since impacted every corner of the life sciences. They became the enabling tools of molecular biology, genetics and biotechnology, and made analysis at the most fundamental levels routine. Hundreds of different REases have been discovered and are available commercially. Their genes have been cloned, sequenced and overexpressed. Most have been characterized to some extent, but few have been studied in depth. Here, we describe the original discoveries in this field, and the properties of the first Type II REases investigated. We discuss the mechanisms of sequence recognition and catalysis, and the varied oligomeric modes in which Type II REases act. We describe the surprising heterogeneity revealed by comparisons of their sequences and structures.

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Section: Introductionmentioning

confidence: 99%

Type II restriction endonucleases—a historical perspective and more

2014

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“…Methanobrevibacter ruminantium (Euryarchaeota) forms a clade with 2 Prevotella (Bacteroidales) sequences. Methanobrevibacter ruminantium is a rumen bacterium of cattle and Prevotella is involved in periodontal infections2ixs37DpnII, MboIPF04556(91)Type II Restriction Endonuclease (91)++Prokaryota Carboxydothermus hydrogeniformans in a Mycoplasma clade. Extremophilic Dictyoglomus thermophilum (Dictyoglomi) with M. smithii & Methanosphaera stadtmanae (Euryarchaeota)38Ecl18kI, EcoRII, PspGIPF09019(92)Type II Restriction Endonuclease (92){2}+{1}Bacteria Photobacterium damselae subsp.…”

Section: Resultsmentioning

confidence: 99%

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily

Steczkiewicz¹,

Muszewska²,

Kniżewski³

et al. 2012

Nucleic Acids Research

141

146

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Proteins belonging to PD-(D/E)XK phosphodiesterases constitute a functionally diverse superfamily with representatives involved in replication, restriction, DNA repair and tRNA–intron splicing. Their malfunction in humans triggers severe diseases, such as Fanconi anemia and Xeroderma pigmentosum. To date there have been several attempts to identify and classify new PD-(D/E)KK phosphodiesterases using remote homology detection methods. Such efforts are complicated, because the superfamily exhibits extreme sequence and structural divergence. Using advanced homology detection methods supported with superfamily-wide domain architecture and horizontal gene transfer analyses, we provide a comprehensive reclassification of proteins containing a PD-(D/E)XK domain. The PD-(D/E)XK phosphodiesterases span over 21 900 proteins, which can be classified into 121 groups of various families. Eleven of them, including DUF4420, DUF3883, DUF4263, COG5482, COG1395, Tsp45I, HaeII, Eco47II, ScaI, HpaII and Replic_Relax, are newly assigned to the PD-(D/E)XK superfamily. Some groups of PD-(D/E)XK proteins are present in all domains of life, whereas others occur within small numbers of organisms. We observed multiple horizontal gene transfers even between human pathogenic bacteria or from Prokaryota to Eukaryota. Uncommon domain arrangements greatly elaborate the PD-(D/E)XK world. These include domain architectures suggesting regulatory roles in Eukaryotes, like stress sensing and cell-cycle regulation. Our results may inspire further experimental studies aimed at identification of exact biological functions, specific substrates and molecular mechanisms of reactions performed by these highly diverse proteins.

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“…However, their amino acid sequences are strongly divergent. Typically, only enzymes that recognize identical or very similar DNA sequences may display similarity at the amino acid level (4). Recent bioinformatics analyses suggested that REases belong also to at least three other folds, GIY-YIG, HNH, and PLD (5-7).…”

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Mva1269I: A Monomeric Type IIS Restriction Endonuclease from Micrococcus Varians with Two EcoRI- and FokI-like Catalytic Domains

Armalyte¹,

Bujnicki

Giedriene³

et al. 2005

Journal of Biological Chemistry

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Type II restriction endonuclease Mva1269I recognizes an asymmetric DNA sequence 5-GAATGCN2-3/5-NG2CATTC-3 and cuts top and bottom DNA strands at positions, indicated by the "2" symbol. Most restriction endonucleases require dimerization to cleave both strands of DNA. We found that Mva1269I is a monomer both in solution and upon binding of cognate DNA. Protein fold-recognition analysis revealed that Mva1269I comprises two "PD-(D/E)XK" domains. The N-terminal domain is related to the 5-GAATTC-3-specific restriction endonuclease EcoRI, whereas the C-terminal one resembles the nonspecific nuclease domain of restriction endonuclease FokI. Inactivation of the C-terminal catalytic site transformed Mva1269I into a very active bottom strandnicking enzyme, whereas mutants in the N-terminal domain nicked the top strand, but only at elevated enzyme concentrations. We found that the cleavage of the bottom strand is a prerequisite for the cleavage of the top strand. We suggest that Mva1269I evolved the ability to recognize and to cleave its asymmetrical target by a fusion of an EcoRI-like domain, which incises the bottom strand within the target, and a FokI-like domain that completes the cleavage within the nonspecific region outside the target sequence. Our results have implications for the molecular evolution of restriction endonucleases, as well as for perspectives of engineering new restriction and nicking enzymes with asymmetric target sites.Type II restriction enzymes (REases) 5 are one of the largest groups of endonucleases. They recognize short double-stranded DNA sequences and specifically cleave both strands of DNA at fixed positions within or near these sites (1), a property that has made them indispensable for DNA engineering. All structurally characterized REases have been found to share a common three-dimensional fold harboring a bipartite PD-X n -(D/E)XK pattern of three moderately conserved charged catalytic/Mg 2ϩ binding residues (2, 3). However, their amino acid sequences are strongly divergent. Typically, only enzymes that recognize identical or very similar DNA sequences may display similarity at the amino acid level (4). Recent bioinformatics analyses suggested that REases belong also to at least three other folds, GIY-YIG, HNH, and PLD (5-7). Therefore, identification of the catalytic and DNA recognition residues of REases is extremely challenging.Most of type II REases (type IIP) recognize palindromic DNA sequences and cleave both DNA strands within the target at symmetrical positions. They usually act as homodimers, in which each of two identical subunits interacts symmetrically with the same part of the DNA sequence (3). Type II REases that recognize asymmetric targets are classified as type IIA (8). Of these, there are nine prototypes that cleave both DNA strands within the recognition sequence. Two of them, BbvCI and Bpu10I, have been characterized (9, 10). Both enzymes are composed of two mutually homologous, but non-identical subunits. This feature suggests that Bpu10I and BbvCI recognize and cl...

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Specificity Changes in the Evolution of Type II Restriction Endonucleases

Cited by 31 publications

References 57 publications

Type II restriction endonucleases—a historical perspective and more

Type II restriction endonucleases—a historical perspective and more

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily

Mva1269I: A Monomeric Type IIS Restriction Endonuclease from Micrococcus Varians with Two EcoRI- and FokI-like Catalytic Domains

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