Four New Type I Restriction Enzymes Identified in Escherichia Coli Clinical Isolates

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2005 Jul 26

PMID 16040596

Citations 4

Authors

Julie K A Kasarjian

Yoshiaki Kodama

Masatake Iida

Katsura Matsuda

Junichi Ryu

Affiliations

Soon will be listed here.

Abstract

Using a plasmid transformation method and the RM search computer program, four type I restriction enzymes with new recognition sites and two isoschizomers (EcoBI and Eco377I) were identified in a collection of clinical Escherichia coli isolates. These new enzymes were designated Eco394I, Eco826I, Eco851I and Eco912I. Their recognition sequences were determined to be GAC(5N)RTAAY, GCA(6N)CTGA, GTCA(6N)TGAY and CAC(5N)TGGC, respectively. A methylation sensitivity assay, using various synthetic oligonucleotides, was used to identify the adenines that prevent cleavage when methylated (underlined). 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.

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References

Kan N, Lautenberger J, Edgell M, HUTCHISON 3rd C . The nucleotide sequence recognized by the Escherichia coli K12 restriction and modification enzymes. J Mol Biol. 1979; 130(2):191-209. DOI: 10.1016/0022-2836(79)90426-1. View

Lautenberger J, Kan N, Lackey D, Linn S, Edgell M, HUTCHISON 3rd C . Recognition site of Escherichia coli B restriction enzyme on phi XsB1 and simian virus 40 DNAs: an interrupted sequence. Proc Natl Acad Sci U S A. 1978; 75(5):2271-5. PMC: 392534. DOI: 10.1073/pnas.75.5.2271. View

Nagaraja V, Stieger M, Nager C, Hadi S, Bickle T . The nucleotide sequence recognised by the Escherichia coli D type I restriction and modification enzyme. Nucleic Acids Res. 1985; 13(2):389-99. PMC: 341003. DOI: 10.1093/nar/13.2.389. View

Nagaraja V, Shepherd J, Pripfl T, Bickle T . Two type I restriction enzymes from Salmonella species. Purification and DNA recognition sequences. J Mol Biol. 1985; 182(4):579-87. DOI: 10.1016/0022-2836(85)90243-8. View

Nagaraja V, Shepherd J, Bickle T . A hybrid recognition sequence in a recombinant restriction enzyme and the evolution of DNA sequence specificity. Nature. 1985; 316(6026):371-2. DOI: 10.1038/316371a0. View

Piekarowicz A, Goguen J . The DNA sequence recognized by the EcoDXX1 restriction endonuclease. Eur J Biochem. 1986; 154(2):295-8. DOI: 10.1111/j.1432-1033.1986.tb09396.x. View

Cowan G, Gann A, Murray N . Conservation of complex DNA recognition domains between families of restriction enzymes. Cell. 1989; 56(1):103-9. DOI: 10.1016/0092-8674(89)90988-4. View

Kannan P, Cowan G, Daniel A, Gann A, Murray N . Conservation of organization in the specificity polypeptides of two families of type I restriction enzymes. J Mol Biol. 1989; 209(3):335-44. DOI: 10.1016/0022-2836(89)90001-6. View

Gubler M, Braguglia D, Meyer J, Piekarowicz A, Bickle T . Recombination of constant and variable modules alters DNA sequence recognition by type IC restriction-modification enzymes. EMBO J. 1992; 11(1):233-40. PMC: 556444. DOI: 10.1002/j.1460-2075.1992.tb05046.x. View

10.

Bickle T, Kruger D . Biology of DNA restriction. Microbiol Rev. 1993; 57(2):434-50. PMC: 372918. DOI: 10.1128/mr.57.2.434-450.1993. View

11.

Meister J, MacWilliams M, Hubner P, Jutte H, Skrzypek E, Piekarowicz A . Macroevolution by transposition: drastic modification of DNA recognition by a type I restriction enzyme following Tn5 transposition. EMBO J. 1993; 12(12):4585-91. PMC: 413889. DOI: 10.1002/j.1460-2075.1993.tb06147.x. View

12.

Abadjieva A, Patel J, Webb M, Zinkevich V, Firman K . A deletion mutant of the type IC restriction endonuclease EcoR1241 expressing a novel DNA specificity. Nucleic Acids Res. 1993; 21(19):4435-43. PMC: 311173. DOI: 10.1093/nar/21.19.4435. View

13.

Tyndall C, Meister J, Bickle T . The Escherichia coli prr region encodes a functional type IC DNA restriction system closely integrated with an anticodon nuclease gene. J Mol Biol. 1994; 237(3):266-74. DOI: 10.1006/jmbi.1994.1230. View

14.

Thomson J, Parrott W . pMECA: a cloning plasmid with 44 unique restriction sites that allows selection of recombinants based on colony size. Biotechniques. 1998; 24(6):922-4, 926, 928. DOI: 10.2144/98246bm04. View

15.

Roberts R, Vincze T, Posfai J, Macelis D . REBASE--restriction enzymes and DNA methyltransferases. Nucleic Acids Res. 2004; 33(Database issue):D230-2. PMC: 539983. DOI: 10.1093/nar/gki029. View

16.

Gann A, Campbell A, Collins J, Coulson A, Murray N . Reassortment of DNA recognition domains and the evolution of new specificities. Mol Microbiol. 1987; 1(1):13-22. DOI: 10.1111/j.1365-2958.1987.tb00521.x. View

17.

Piekarowicz A, Klyz A, Kwiatek A, Stein D . Analysis of type I restriction modification systems in the Neisseriaceae: genetic organization and properties of the gene products. Mol Microbiol. 2001; 41(5):1199-210. DOI: 10.1046/j.1365-2958.2001.02587.x. View

18.

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(20):4195-205. PMC: 60208. DOI: 10.1093/nar/29.20.4195. View

19.

Murray N . 2001 Fred Griffith review lecture. Immigration control of DNA in bacteria: self versus non-self. Microbiology (Reading). 2002; 148(Pt 1):3-20. DOI: 10.1099/00221287-148-1-3. View

20.

Ellrott K, Kasarjian J, Jiang T, Ryu J . Restriction enzyme recognition sequence search program. Biotechniques. 2002; 33(6):1322-6. DOI: 10.2144/02336bc02. View