Genomes and Genes
type i site specific deoxyribonucleases
Summary: Enzyme systems containing three different subunits and requiring ATP, S-adenosylmethionine, and magnesium for endonucleolytic activity to give random double-stranded fragments with terminal 5'-phosphates. They function also as DNA-dependent ATPases and modification methylases, catalyzing the reactions of EC 184.108.40.206 and EC 220.127.116.11 with similar site-specificity. The systems recognize specific short DNA sequences and cleave at sites remote from the recognition sequence. Enzymes from different microorganisms with the same specificity are called isoschizomers. EC 18.104.22.168.
- Sisáková E, Weiserová M, Dekker C, Seidel R, Szczelkun M. The interrelationship of helicase and nuclease domains during DNA translocation by the molecular motor EcoR124I. J Mol Biol. 2008;384:1273-86 pubmed publisher..The significance of these observations to our understanding of domain interactions in molecular machines is discussed. ..
- Sisáková E, Stanley L, Weiserová M, Szczelkun M. A RecB-family nuclease motif in the Type I restriction endonuclease EcoR124I. Nucleic Acids Res. 2008;36:3939-49 pubmed publisher..Using mutagenesis, we examined the role of the Q and Y residues in DNA binding, translocation and cleavage. Roles for the QxxxY motif in coordinating the catalytic residues or in stabilizing the nuclease domain on the DNA are discussed. ..
- Janscak P, Abadjieva A, Firman K. The type I restriction endonuclease R.EcoR124I: over-production and biochemical properties. J Mol Biol. 1996;257:977-91 pubmed..Cleavage of DNA was inhibited by an increased degree of negative supercoiling, which may reflect an increased difficulty for the enzyme to translocate the DNA. Hemi-methylated DNA was the preferred substrate for methylation. ..
- Gorbalenya A, Koonin E. Endonuclease (R) subunits of type-I and type-III restriction-modification enzymes contain a helicase-like domain. FEBS Lett. 1991;291:277-81 pubmed..17, 4713-4730]. A hypothesis is proposed that these enzymes may exert helicase activity possibly required for local unwinding of DNA in the cleavage sites. ..
- Holubova I, Vejsadová S, Firman K, Weiserova M. Cellular localization of Type I restriction-modification enzymes is family dependent. Biochem Biophys Res Commun. 2004;319:375-80 pubmed..Possible reasons for such a different organization are discussed in relation of the control of the restriction-modification activities in vivo. ..
- Makovets S, Powell L, Titheradge A, Blakely G, Murray N. Is modification sufficient to protect a bacterial chromosome from a resident restriction endonuclease?. Mol Microbiol. 2004;51:135-47 pubmed..In the absence of efficient restriction alleviation, a Type I restriction enzyme cleaves host DNA and, under these conditions, homologous recombination maintains the integrity of the bacterial chromosome. ..
- Chevalier B, Kortemme T, Chadsey M, Baker D, Monnat R, Stoddard B. Design, activity, and structure of a highly specific artificial endonuclease. Mol Cell. 2002;10:895-905 pubmed..These results indicate that it may be possible to generate novel highly specific DNA binding proteins from homing endonucleases. ..
- Kasarjian J, Kodama Y, Iida M, Matsuda K, Ryu J. Four new type I restriction enzymes identified in Escherichia coli clinical isolates. Nucleic Acids Res. 2005;33:e114 pubmed..These results suggest that type I enzymes are abundant in E.coli and many other bacteria, as has been inferred from bacterial genome sequencing projects. ..
- van Noort J, van der Heijden T, Dutta C, Firman K, Dekker C. Initiation of translocation by Type I restriction-modification enzymes is associated with a short DNA extrusion. Nucleic Acids Res. 2004;32:6540-7 pubmed
- Makovets S, Titheradge A, Murray N. ClpX and ClpP are essential for the efficient acquisition of genes specifying type IA and IB restriction systems. Mol Microbiol. 1998;28:25-35 pubmed..In the absence of either ClpX or ClpP transfer of the EcoKI genes by P1-mediated transduction was impaired, transfer of the EcoAI genes was not. ..
- Dryden D, Murray N, Rao D. Nucleoside triphosphate-dependent restriction enzymes. Nucleic Acids Res. 2001;29:3728-41 pubmed..The only well-documented GTP-dependent restriction enzyme, McrBC, requires methylated target sequences for the initiation of phosphodiester bond cleavage. ..
- Epinat J, Arnould S, Chames P, Rochaix P, Desfontaines D, Puzin C, et al. A novel engineered meganuclease induces homologous recombination in yeast and mammalian cells. Nucleic Acids Res. 2003;31:2952-62 pubmed..These results are a first step toward the generation of custom endonucleases for the purpose of targeted genome engineering. ..
- Murray N. Type I restriction systems: sophisticated molecular machines (a legacy of Bertani and Weigle). Microbiol Mol Biol Rev. 2000;64:412-34 pubmed..Finally, the review will reflect the present impact of genomic sequences on a field that has previously derived information almost exclusively from the analysis of bacteria commonly studied in the laboratory. ..
- Murray N, Daniel A, Cowan G, Sharp P. Conservation of motifs within the unusually variable polypeptide sequences of type I restriction and modification enzymes. Mol Microbiol. 1993;9:133-43 pubmed
- Bourniquel A, Bickle T. Complex restriction enzymes: NTP-driven molecular motors. Biochimie. 2002;84:1047-59 pubmed
- Seidel R, Bloom J, Dekker C, Szczelkun M. Motor step size and ATP coupling efficiency of the dsDNA translocase EcoR124I. EMBO J. 2008;27:1388-98 pubmed publisher..Our observations form a framework for understanding energy coupling in a great many other motors that translocate along dsDNA rather than ssDNA. ..
- Szczelkun M. Kinetic models of translocation, head-on collision, and DNA cleavage by type I restriction endonucleases. Biochemistry. 2002;41:2067-74 pubmed..Therefore, type I restriction enzymes can be described as having processive DNA translocation but, in some cases, nonprocessive DNA cleavage. ..
- McClelland S, Dryden D, Szczelkun M. Continuous assays for DNA translocation using fluorescent triplex dissociation: application to type I restriction endonucleases. J Mol Biol. 2005;348:895-915 pubmed..Furthermore, we demonstrated that enzymes deficient in DNA cleavage but with maximal ATPase activity showed initiation and translocation rates identical to wild-type, confirming that DNA strand breaks are not a pre-requisite of motion. ..
- Youell J, Firman K. EcoR124I: from plasmid-encoded restriction-modification system to nanodevice. Microbiol Mol Biol Rev. 2008;72:365-77, table of contents pubmed publisher..Therefore, this is a history that takes us from a plasmid isolated from (presumably) an infected source to the potential use of the plasmid-encoded R-M enzyme in bionanotechnology. ..
- Weiserova M, Dutta C, Firman K. A novel mutant of the type I restriction-modification enzyme EcoR124I is altered at a key stage of the subunit assembly pathway. J Mol Biol. 2000;304:301-10 pubmed..Therefore, HsdR acts as a chaperon allowing not only binding of the enzyme to DNA, but also restoring the methylation activity and, at sufficiently high concentrations in vitro of HsdR, restoring restriction activity. ..
- Jindrova E, Schmid Nuoffer S, Hamburger F, Janscak P, Bickle T. On the DNA cleavage mechanism of Type I restriction enzymes. Nucleic Acids Res. 2005;33:1760-6 pubmed..We conclude that Type I restriction enzymes require two restriction subunits to introduce DNA double-strand breaks, each providing one catalytic center for phosphodiester bond hydrolysis. Possible models for DNA cleavage are discussed. ..
- Doronina V, Murray N. The proteolytic control of restriction activity in Escherichia coli K-12. Mol Microbiol. 2001;39:416-28 pubmed..The molecular basis for the distinction between unmodified resident and foreign DNA remains to be determined. ..
- Chin V, Valinluck V, Magaki S, Ryu J. KpnBI is the prototype of a new family (IE) of bacterial type I restriction-modification system. Nucleic Acids Res. 2004;32:e138 pubmed..Furthermore, their identity scores to other uncharacterized putative genome type I sequences were 53% at maximum. Therefore, we propose that KpnBI is the prototype of a new 'type IE' family. ..
- Kusano K, Asami Y, Fujita A, Tanokura M, Kobayashi I. Type I restriction enzyme with RecA protein promotes illegitimate recombination. Plasmid. 2003;50:202-12 pubmed..These results are in harmony with a model in which EcoKI restriction enzyme attacks an intermediate of homologous recombination to divert it to illegitimate recombination. ..
- Taylor I, Watts D, Kneale G. Substrate recognition and selectivity in the type IC DNA modification methylase M.EcoR124I. Nucleic Acids Res. 1993;21:4929-35 pubmed..In contrast, methylation of an adenine in the recognition site which is not a target for the enzyme results in only a small decrease in both DNA binding affinity and rate of methylation by the enzyme. ..
- Titheradge A, King J, Ryu J, Murray N. Families of restriction enzymes: an analysis prompted by molecular and genetic data for type ID restriction and modification systems. Nucleic Acids Res. 2001;29:4195-205 pubmed..Implications of family relationships are discussed and evidence is presented that extends the family affiliations identified in enteric bacteria to a wide range of other genera. ..
- Seidel R, van Noort J, van der Scheer C, Bloom J, Dekker N, Dutta C, et al. Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I. Nat Struct Mol Biol. 2004;11:838-43 pubmed..This assay may be directly applicable to investigating the tracking of other DNA-translocating motors along their DNA templates. ..
- Seidel R, Bloom J, van Noort J, Dutta C, Dekker N, Firman K, et al. Dynamics of initiation, termination and reinitiation of DNA translocation by the motor protein EcoR124I. EMBO J. 2005;24:4188-97 pubmed..The dissociation/reassociation of motors during translocation allows dynamic control of the restriction process by the availability of motors. Direct evidence that this control mechanism is relevant in vivo is provided. ..
- Obarska Kosinska A, Taylor J, Callow P, Orlowski J, Bujnicki J, Kneale G. HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling. J Mol Biol. 2008;376:438-52 pubmed publisher..The model reveals an ellipsoidal shape of the enzymatic core comprising the N-terminal and central domains, and suggests conformational heterogeneity of the C-terminal region implicated in binding of HsdR to the HsdS-HsdM complex. ..
- Silva G, Belfort M, Wende W, Pingoud A. From monomeric to homodimeric endonucleases and back: engineering novel specificity of LAGLIDADG enzymes. J Mol Biol. 2006;361:744-54 pubmed..This novel endonuclease allows speculation regarding specificity of monomeric LAGLIDADG proteins, while it supports the evolutionary genesis of these proteins by a gene duplication event. ..
- Marcaida M, Prieto J, Redondo P, Nadra A, Alibés A, Serrano L, et al. Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering. Proc Natl Acad Sci U S A. 2008;105:16888-93 pubmed publisher..Our data open the door toward the generation of custom endonucleases for targeted genome engineering using the monomeric I-DmoI scaffold. ..
- Taylor I, Kneale G. A competition assay for DNA binding using the fluorescent probe ANS. Methods Mol Biol. 2009;543:577-87 pubmed publisher..These spectral changes have been used to investigate the interaction of EcoR124I with DNA target recognition sequences. ..
- Cajthamlová K, Sisáková E, Weiser J, Weiserová M. Phosphorylation of Type IA restriction-modification complex enzyme EcoKI on the HsdR subunit. FEMS Microbiol Lett. 2007;270:171-7 pubmed..coli. So far this is the first case of phosphorylation of a Type I R-M enzyme reported. ..
- Fujihara J, Hieda Y, Xue Y, Okui I, Kataoka K, Takeshita H. Single-step purification by lectin affinity and deglycosylation analysis of recombinant human and porcine deoxyribonucleases I expressed in COS-7 cells. Biotechnol Lett. 2006;28:215-21 pubmed..This study suggests that N-linked complex-type carbohydrate moieties may contribute to the enzymatic activity and/or thermal stability of recombinant DNases I. ..
- Highlander S, Garza O. The restriction-modification system of Pasteurella haemolytica is a member of a new family of type I enzymes. Gene. 1996;178:89-96 pubmed..influenzae proteins into a new group which we labeled the Type Id R-M family. Expression of the P. haemolytica R-M genes in E. coli was inefficient and is likely to be a consequence of the unusual codon usage in P. haemolytica genes. ..
- Cockfield J, Pathak S, Edgeworth J, Lindsay J. Rapid determination of hospital-acquired meticillin-resistant Staphylococcus aureus lineages. J Med Microbiol. 2007;56:614-9 pubmed..Simple and accurate typing methods will also support large scale epidemiological studies, and could lead to greater understanding of the carriage, spread and virulence of different MRSA lineages. ..
- Sitaraman R, Dybvig K. The hsd loci of Mycoplasma pulmonis: organization, rearrangements and expression of genes. Mol Microbiol. 1997;26:109-20 pubmed
- Abadjieva A, Scarlett G, Janscak P, Dutta C, Firman K. Characterization of an EcoR124I restriction-modification enzyme produced from a deleted form of the DNA-binding subunit, which results in a novel DNA specificity. Folia Microbiol (Praha). 2003;48:319-28 pubmed..We fused the hsdM and hsdS delta 50 genes and showed that the HsdM-HsdS delta 50 fusion protein is capable of dimerization confirming the model for assembly of this deletion mutant. ..
- Zavil gel skiĭ G, Letuchaia T, Rastorguev S. [Antirestriction and antimodification activities of the ArdA protein encoded by the IncI1 transmissive plasmids R-64 and ColIb-P9]. Genetika. 2006;42:331-8 pubmed..ArdA bound to the specific sK site inhibits concurrently the endonuclease and methylase activities of EcoKI (R2M2S), while ArdA bound to the nonspecific site in the R subunit blocks only its endonuclease activity. ..
- Lavigne M, Yates L, Coxhead P, Gorecki D. Nuclear-targeted chimeric vector enhancing nonviral gene transfer into skeletal muscle of Fabry mice in vivo. FASEB J. 2008;22:2097-107 pubmed publisher..Therefore, this proof-of principle result indicates that TAT (and potentially other CPP) can be used for targeting modular chimeric vectors and therapeutic nanodevices. ..
- Mathura V, Schein C, Braun W. Identifying property based sequence motifs in protein families and superfamilies: application to DNase-1 related endonucleases. Bioinformatics. 2003;19:1381-90 pubmed..MASIA WEB site: http://www.scsb.utmb.edu/masia/masia.html The dendrogram of 42 APE sequences used to derive motifs is available on http://www.scsb.utmb.edu/comp_biol.html/DNA_repair/publication.html ..
- Nguyen L, Cajthamlová K, Nguyen H, Weiser J, Holubova I, Weiserova M. Identification of the EcoKI and EcoR124I Type I restriction--modification enzyme subunits by non-equilibrium pH gradient two-dimensional gel electrophoresis. Folia Microbiol (Praha). 2002;47:641-8 pubmed..Potential application of this method for detailed studies of regulation of the function and stoichiometry of the enzyme complexes is discussed. ..
- Zhang H, Chen S. [Mapping of regulatory domain of T-protein from Escherichia coli]. Zhejiang Da Xue Xue Bao Yi Xue Ban. 2005;34:181-4 pubmed..The regulatory domain of T-protein was located in the C-terminal 270 amino acids, which was the same location as PDH domain. T-protein has no independent regulatory domain. ..
- 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. ..
- Bianco P, Xu C, Chi M. Type I restriction endonucleases are true catalytic enzymes. Nucleic Acids Res. 2009;37:3377-90 pubmed publisher..The conclusion that type I restriction enzymes are catalytic relative to DNA has important implications for the in vivo function of these previously enigmatic enzymes. ..
- 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. ..
- Laigret F, Gaurivaud P, Bove J. The unique organization of the rpoB region of Spiroplasma citri: a restriction and modification system gene is adjacent to rpoB. Gene. 1996;171:95-8 pubmed
- Moffatt B, Studier F. Entry of bacteriophage T7 DNA into the cell and escape from host restriction. J Bacteriol. 1988;170:2095-105 pubmed..T7 mutants that lack all three strong early promoters A1, A2, and A3 could grow by using a secondary promoter. ..
- Ryu J, Rowsell E. Quick identification of Type I restriction enzyme isoschizomers using newly developed pTypeI and reference plasmids. Nucleic Acids Res. 2008;36:e81 pubmed publisher..One strain EC1344 produces two Type I enzymes (EcoKI and Eco377I). ..
- Pennadam S, Lavigne M, Dutta C, Firman K, Mernagh D, Gorecki D, et al. Control of a multisubunit DNA motor by a thermoresponsive polymer switch. J Am Chem Soc. 2004;126:13208-9 pubmed..This regulation of enzyme activity arises from the coil-globule phase transitions of the polymer as shown in light scattering and gel retardation assays. ..