Genomes and Genes
dna restriction enzymes
Summary: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
- Smith R, Josephsen J, Szczelkun M. The single polypeptide restriction-modification enzyme LlaGI is a self-contained molecular motor that translocates DNA loops. Nucleic Acids Res. 2009;37:7219-30 pubmed publisher..LlaGI is therefore an example of a polypeptide that is a completely self-contained, multi-functional molecular machine. ..
- Wang H, Guan S, Quimby A, Cohen Karni D, Pradhan S, Wilson G, et al. Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine. Nucleic Acids Res. 2011;39:9294-305 pubmed publisher..Our study offers unique tools for determining more accurate hydroxymethylomes in mammalian cells. ..
- Serfiotis Mitsa D, Herbert A, Roberts G, Soares D, White J, Blakely G, et al. The structure of the KlcA and ArdB proteins reveals a novel fold and antirestriction activity against Type I DNA restriction systems in vivo but not in vitro. Nucleic Acids Res. 2010;38:1723-37 pubmed publisher..We also present the structure determined by NMR spectroscopy of the pBP136 KlcA protein. The structure shows a novel protein fold and it is clearly not a DNA structural mimic. ..
- Grizot S, Epinat J, Thomas S, Duclert A, Rolland S, Pâques F, et al. Generation of redesigned homing endonucleases comprising DNA-binding domains derived from two different scaffolds. Nucleic Acids Res. 2010;38:2006-18 pubmed publisher..The DmoCre based meganucleases can therefore offer new possibilities for various genome engineering applications. ..
- Sukackaite R, Grazulis S, Tamulaitis G, Siksnys V. The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine. Nucleic Acids Res. 2012;40:7552-62 pubmed publisher..The mechanism for 5mC recognition employed by McrB-N is highly reminiscent of that for eukaryotic SRA domains, despite the differences in their protein folds...
- Ishikawa K, Handa N, Sears L, Raleigh E, Kobayashi I. Cleavage of a model DNA replication fork by a methyl-specific endonuclease. Nucleic Acids Res. 2011;39:5489-98 pubmed publisher..This process might serve to maintain an epigenetic status along the genome through programmed cell death. ..
- Tesfazgi Mebrhatu M, Wywial E, Ghosh A, Michiels C, Lindner A, Taddei F, et al. Evidence for an evolutionary antagonism between Mrr and Type III modification systems. Nucleic Acids Res. 2011;39:5991-6001 pubmed publisher..This apparent evolutionary antagonism is further discussed in the light of a possible role for Mrr as defense mechanism against the establishment of epigenetic regulation by foreign DNA methyltransferases. ..
- Sisáková E, van Aelst K, Diffin F, Szczelkun M. The Type ISP Restriction-Modification enzymes LlaBIII and LlaGI use a translocation-collision mechanism to cleave non-specific DNA distant from their recognition sites. Nucleic Acids Res. 2013;41:1071-80 pubmed publisher..In their favoured in vitro buffer, both LlaGI and LlaBIII produce a normal distribution of random cleavage loci centred midway between the sites. In contrast, LlaGI in K(+) ions produces a far more distributive cleavage profile. ..
- Sitaraman R, Leppla S. Methylation-dependent DNA restriction in Bacillus anthracis. Gene. 2012;494:44-50 pubmed publisher..anthracis remain unidentified, and we suggest that poor transformation by such DNA could in part be a consequence of the inefficient replication of hemimethylated DNA in B. anthracis. ..
- Muñoz I, Prieto J, Subramanian S, Coloma J, Redondo P, Villate M, et al. Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus. Nucleic Acids Res. 2011;39:729-43 pubmed publisher..Our analysis illustrates the key features for à la carte procedure in protein-DNA recognition design, opening new possibilities for SCID patients whose illness can be treated ex vivo. ..
- Prinsen P, Schiessel H. Nucleosome stability and accessibility of its DNA to proteins. Biochimie. 2010;92:1722-8 pubmed publisher..We follow the lecture as closely as possible which is why we spend more time than usual on issues that are already well-known in the field, and why we discuss some well-known results from a different perspective. ..
- Zahran M, Daidone I, Smith J, Imhof P. Mechanism of DNA recognition by the restriction enzyme EcoRV. J Mol Biol. 2010;401:415-32 pubmed publisher..In the third step, the flexibility of the center base pair is probed, and in the case of the full cognate sequence the DNA bends, the complex strengthens and the protein and DNA interact more closely, allowing cleavage. ..
- Cohen Karni D, Xu D, Apone L, Fomenkov A, Sun Z, Davis P, et al. The MspJI family of modification-dependent restriction endonucleases for epigenetic studies. Proc Natl Acad Sci U S A. 2011;108:11040-5 pubmed publisher..Altogether, the MspJI family of enzymes represent appealing tools of choice for method development in DNA epigenetic studies. ..
- Nestor C, Ruzov A, Meehan R, Dunican D. Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA. Biotechniques. 2010;48:317-9 pubmed publisher..Potential differential enrichment of 5mC and hmC DNA sequences may be facilitated using a 5mC monoclonal antibody. ..
- Naumova N, Smith E, Zhan Y, Dekker J. Analysis of long-range chromatin interactions using Chromosome Conformation Capture. Methods. 2012;58:192-203 pubmed publisher..This paper represents a complete resource and detailed guide for anyone who desires to perform 3C. ..
- Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Nucleic Acids Res. 2012;40:7016-45 pubmed publisher..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. ..
- Cardenas P, Carzaniga T, Zangrossi S, Briani F, Garcia Tirado E, Dehò G, et al. Polynucleotide phosphorylase exonuclease and polymerase activities on single-stranded DNA ends are modulated by RecN, SsbA and RecA proteins. Nucleic Acids Res. 2011;39:9250-61 pubmed publisher..subtilis PNPase might also contribute to repair via NHEJ. ..
- Chan S, Opitz L, Higgins L, O loane D, Xu S. Cofactor requirement of HpyAV restriction endonuclease. PLoS ONE. 2010;5:e9071 pubmed publisher..A survey of sequenced microbial genomes uncovered 10 putative R-M systems that show high sequence similarity to the HpyAV system, suggesting lateral transfer of a prototypic HpyAV-like R-M system among these microorganisms. ..
- Stern A, Sorek R. The phage-host arms race: shaping the evolution of microbes. Bioessays. 2011;33:43-51 pubmed publisher..The commonalities between defense mechanisms suggest avenues for the discovery of novel forms of these mechanisms based on their evolutionary traits. ..
- Zylicz Stachula A, Zolnierkiewicz O, Lubys A, Ramanauskaite D, Mitkaite G, Bujnicki J, et al. Related bifunctional restriction endonuclease-methyltransferase triplets: TspDTI, Tth111II/TthHB27I and TsoI with distinct specificities. BMC Mol Biol. 2012;13:13 pubmed publisher..The characterization of TspDTI, a prototype member of this group, extends our understanding of sequence-function relationships among multifunctional restriction-modification enzymes. ..
- Zheng Y, Cohen Karni D, Xu D, Chin H, Wilson G, Pradhan S, et al. A unique family of Mrr-like modification-dependent restriction endonucleases. Nucleic Acids Res. 2010;38:5527-34 pubmed publisher..The MspJI enzyme family, with their different recognition specificities and cleavage properties, provides a basis on which many future methods can build to decode the epigenomes of different organisms. ..
- Alonso J, Cardenas P, Sanchez H, Hejna J, Suzuki Y, Takeyasu K. Early steps of double-strand break repair in Bacillus subtilis. DNA Repair (Amst). 2013;12:162-76 pubmed publisher..Here we review recent findings that shed light on the early stages of DSB repair in Firmicutes. ..
- Etter P, Bassham S, HOHENLOHE P, Johnson E, Cresko W. SNP discovery and genotyping for evolutionary genetics using RAD sequencing. Methods Mol Biol. 2011;772:157-78 pubmed publisher..Despite considerable progress, the development of analytical tools remains in its infancy, and further work is needed to fully quantify sampling variance and biases in these data types. ..
- Krauss V, Eisenhardt C, Unger T. The genome of the stick insect Medauroidea extradentata is strongly methylated within genes and repetitive DNA. PLoS ONE. 2009;4:e7223 pubmed publisher..Both repetitive DNA and coding genes appear to contain high levels of methylcytosines. These results argue for similar functions of DNA methylation in stick insects as those already known for vertebrates. ..
- Kennaway C, Taylor J, Song C, Potrzebowski W, Nicholson W, White J, et al. Structure and operation of the DNA-translocating type I DNA restriction enzymes. Genes Dev. 2012;26:92-104 pubmed publisher..The path followed by DNA through the complexes is revealed by using a DNA mimic anti-restriction protein. The structures reveal an evolutionary link between type I RM enzymes and type II RM enzymes. ..
- Mulligan E, Hatchwell E, McCorkle S, Dunn J. Differential binding of Escherichia coli McrA protein to DNA sequences that contain the dinucleotide m5CpG. Nucleic Acids Res. 2010;38:1997-2005 pubmed publisher..These results provide the first systematic analysis of McrA's in vitro binding specificity. ..
- Horton J, Mabuchi M, Cohen Karni D, Zhang X, Griggs R, Samaranayake M, et al. Structure and cleavage activity of the tetrameric MspJI DNA modification-dependent restriction endonuclease. Nucleic Acids Res. 2012;40:9763-73 pubmed publisher..Both cleavage events require binding of at least a second recognition site either in cis or in trans. ..
- Rand K, Molloy P. Sensitive measurement of unmethylated repeat DNA sequences by end-specific PCR. Biotechniques. 2010;49:xiii-xvii pubmed publisher..Because amplification only occurs if suitable ends have been generated in the target DNA, we have called this method end-specific PCR (ESPCR). ESPCR avoids the bisulfite treatment step that is usually required to measure methylation. ..
- Marshall J, Halford S. The type IIB restriction endonucleases. Biochem Soc Trans. 2010;38:410-6 pubmed publisher..Our current knowledge of the Type IIB systems is reviewed in the present paper. ..
- González Cerón G, Miranda Olivares O, Servín Gonzalez L. Characterization of the methyl-specific restriction system of Streptomyces coelicolor A3(2) and of the role played by laterally acquired nucleases. FEMS Microbiol Lett. 2009;301:35-43 pubmed publisher..Cloning of these genes in the close relative Streptomyces lividans increased the restriction of methylated DNA by this species, confirming their role as part of the methyl-specific restriction system of S. coelicolor...
- Kumar R, Rao D. A nucleotide insertion between two adjacent methyltransferases in Helicobacter pylori results in a bifunctional DNA methyltransferase. Biochem J. 2011;433:487-95 pubmed publisher..pylori to evolve genes with unique functions and thus generate variability. For organisms such as H. pylori, which have a small genome, these adaptations could be important for their survival in the hostile host environment. ..
- Ishikawa K, Fukuda E, Kobayashi I. Conflicts targeting epigenetic systems and their resolution by cell death: novel concepts for methyl-specific and other restriction systems. DNA Res. 2010;17:325-42 pubmed publisher..These restriction systems clearly demonstrate the presence of conflicts between epigenetic systems. ..
- Bacman S, Williams S, Garcia S, Moraes C. Organ-specific shifts in mtDNA heteroplasmy following systemic delivery of a mitochondria-targeted restriction endonuclease. Gene Ther. 2010;17:713-20 pubmed publisher..These results show the potential of systemic delivery of viral vectors to specific organs for the therapeutic application of mitochondria-targeted restriction enzymes in mtDNA disorders. ..
- Bae J, Sohn J. Template-blocking PCR: an advanced PCR technique for genome walking. Anal Biochem. 2010;398:112-6 pubmed publisher..The method was successfully applied for the cloning of the PGK1 promoter from Pichia ciferrii and two novel cellulase genes from Penicillium sp. ..
- Smith R, Josephsen J, Szczelkun M. An Mrr-family nuclease motif in the single polypeptide restriction-modification enzyme LlaGI. Nucleic Acids Res. 2009;37:7231-8 pubmed publisher..Cleavage by LlaGI is not targeted to methylated DNA, suggesting that the conserved motifs in the Mrr domain are a conventional sub-family of the PD-(D/E)XK superfamily of DNA nucleases. ..
- Seshasayee A, Singh P, Krishna S. Context-dependent conservation of DNA methyltransferases in bacteria. Nucleic Acids Res. 2012;40:7066-73 pubmed publisher..Despite their sporadic occurrence, conserved R-M systems are present in strength in two highly transformable genera, in which they may contribute to selection against integration of foreign DNA. ..
- Borgaro J, Zhu Z. Characterization of the 5-hydroxymethylcytosine-specific DNA restriction endonucleases. Nucleic Acids Res. 2013;41:4198-206 pubmed publisher..Lastly, we envision that the unique properties of select PvuRts1I homologues will permit their use as an additive or alternative tool to map the hydroxymethylome. ..
- Barchi L, Lanteri S, Portis E, Acquadro A, Valè G, Toppino L, et al. Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics. 2011;12:304 pubmed publisher..We have combined the recently developed Restriction-site Associated DNA (RAD) approach with Illumina DNA sequencing for rapid and mass discovery of both SNP and SSR markers for eggplant...
- O Connell Motherway M, O Driscoll J, Fitzgerald G, van Sinderen D. Overcoming the restriction barrier to plasmid transformation and targeted mutagenesis in Bifidobacterium breve UCC2003. Microb Biotechnol. 2009;2:321-32 pubmed publisher..breve UCC2003 we successfully increased the transformation efficiency to a level that allows the reliable generation of mutants by homologous recombination using a non-replicative plasmid. ..
- Liu G, Ou H, Wang T, Li L, Tan H, Zhou X, et al. Cleavage of phosphorothioated DNA and methylated DNA by the type IV restriction endonuclease ScoMcrA. PLoS Genet. 2010;6:e1001253 pubmed publisher..This is the first report of in vitro endonuclease activity of a McrA homologue and also the first demonstration of an enzyme that specifically cleaves S-modified DNA. ..
- Pingoud V, Wende W, Friedhoff P, Reuter M, Alves J, Jeltsch A, et al. On the divalent metal ion dependence of DNA cleavage by restriction endonucleases of the EcoRI family. J Mol Biol. 2009;393:140-60 pubmed publisher..Our conclusions are supported by molecular dynamics simulations and are consistent with the structural observations of both one and two Me(2+) binding to these enzymes. ..
- Zylicz Stachula A, Zołnierkiewicz O, Jezewska Frackowiak J, Skowron P. Chemically-induced affinity star restriction specificity: a novel TspGWI/sinefungin endonuclease with theoretical 3-bp cleavage frequency. Biotechniques. 2011;50:397-406 pubmed publisher..8 bp, corresponding to a putative 3-bp long recognition site. Thus, the combination of sinefungin and TspGWI represents a novel frequent cutter, next only to CviJI/CviJI*, that should prove useful in DNA cloning methodologies. ..
- Ji J, Braam J. Restriction site extension PCR: a novel method for high-throughput characterization of tagged DNA fragments and genome walking. PLoS ONE. 2010;5:e10577 pubmed publisher..RSE-PCR has high potential application in identifying tagged (T-DNA or transposon) sequence or walking from known DNA toward unknown regions in large-genome plants, with likely application in other organisms as well. ..
- Zhang P, Too P, Samuelson J, Chan S, Vincze T, Doucette S, et al. Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA. Protein Expr Purif. 2010;69:226-34 pubmed publisher..Restriction mapping and run-off DNA sequencing of digested products from the partially purified enzyme indicated that it is an EarI isoschizomer with 6-bp recognition, which we named CatHI (CTCTTC N1/N4). ..
- Xu S, Corvaglia A, Chan S, Zheng Y, Linder P. A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300. Nucleic Acids Res. 2011;39:5597-610 pubmed publisher..aureus strain SA564, and in restricting phage ? infection when the endonuclease is expressed in E. coli. ..
- Cardenas P, Carrasco B, Sanchez H, Deikus G, Bechhofer D, Alonso J. Bacillus subtilis polynucleotide phosphorylase 3'-to-5' DNase activity is involved in DNA repair. Nucleic Acids Res. 2009;37:4157-69 pubmed publisher..Our data suggest that PNPase is involved in various nucleic acid metabolic pathways, and its limited ssDNA exonuclease activity plays an important role in RecA-dependent and RecA-independent repair pathways. ..
- Skoglund A, Björkholm B, Nilsson C, Andersson A, Jernberg C, Schirwitz K, et al. Functional analysis of the M.HpyAIV DNA methyltransferase of Helicobacter pylori. J Bacteriol. 2007;189:8914-21 pubmed..HpyAIV gene mutant compared to the wild-type strain. This demonstrates the influence of M.HpyAIV methylation in gene expression. ..
- Xu S, Zhu Z, Zhang P, Chan S, Samuelson J, Xiao J, et al. Discovery of natural nicking endonucleases Nb.BsrDI and Nb.BtsI and engineering of top-strand nicking variants from BsrDI and BtsI. Nucleic Acids Res. 2007;35:4608-18 pubmed..Top-strand specific nicking variants, Nt.BsrDI and Nt.BtsI, were successfully engineered by combining the catalytic-deficient B subunit with wild-type A subunit. ..
- Aertsen A, Michiels C. Upstream of the SOS response: figure out the trigger. Trends Microbiol. 2006;14:421-3 pubmed..We suggest that these endogenous triggers have been recruited by bacteria to enable adaptation to various types of stresses. ..
- Daujotyte D, Liutkeviciute Z, Tamulaitis G, Klimasauskas S. Chemical mapping of cytosines enzymatically flipped out of the DNA helix. Nucleic Acids Res. 2008;36:e57 pubmed publisher..Ecl18kI and R.PspGI, which represent a novel class of base-flipping enzymes. Our results thus offer a simple and convenient laboratory tool for detection and mapping of flipped-out cytosines in protein-DNA complexes. ..
- Mruk I, Rajesh P, Blumenthal R. Regulatory circuit based on autogenous activation-repression: roles of C-boxes and spacer sequences in control of the PvuII restriction-modification system. Nucleic Acids Res. 2007;35:6935-52 pubmed..Any changes in that spacer reduced the stability of C.PvuII-operator complexes and abolished activation...