DNA cleavage and methylation specificity of the single polypeptide restriction-modification enzyme LlaGI

Nucleic Acids Research

Volumn 37, Issue 21, 2009, Pages 7206-7218

  Smith, Rachel M ^a   Diffin, Fiona M ^a   Savery, Nigel J ^a   Josephsen, Jytte ^b   Szczelkun, Mark D ^a  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; ADENOSINE TRIPHOSPHATE; CYTOSINE; DEOXYADENOSINE TRIPHOSPHATE; DNA; DNA ADENINE METHYLTRANSFERASE; DOUBLE STRANDED DNA; ENDONUCLEASE; GUANINE; HELICASE; LLAGI PROTEIN; RESTRICTION ENDONUCLEASE; THYMINE; TYPE I SITE SPECIFIC DEOXYRIBONUCLEASE; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE; TYPE III SITE SPECIFIC DEOXYRIBONUCLEASE; UNCLASSIFIED DRUG; LLAGI RESTRICTION MODIFICATION SYSTEM; LLAGI RESTRICTION-MODIFICATION SYSTEM; NUCLEOTIDE;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CONTROLLED STUDY; DNA CLEAVAGE; DNA METHYLATION; DNA NICK TRANSLATION; DNA SEQUENCE; DOUBLE STRANDED DNA BREAK; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME PURIFICATION; GENE FUNCTION; GENE TRANSLOCATION; IN VITRO STUDY; MOLECULAR CLONING; MOLECULAR INTERACTION; NUCLEOTIDE BINDING SITE; NUCLEOTIDE REPEAT; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN EXPRESSION; CLASSIFICATION; ENZYME SPECIFICITY; KINETICS; METABOLISM;

LACTOCOCCUS LACTIS;

DNA CLEAVAGE; DNA METHYLATION; DNA RESTRICTION-MODIFICATION ENZYMES; KINETICS; NUCLEOTIDES; SUBSTRATE SPECIFICITY;

EID: 75349094529     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp790     Document Type: Article

References (45)

1. Madsen, A. and Josephsen, J. (2001) The LlaGI restriction and modification system of Lactococcus lactis W10 consists of only one single polypeptide. FEMS Microbiol. Lett., 200, 91-96.
2. Roberts, R.J., Vincze, T., Posfai, J. and Macelis, D. (2007) REBASE-enzymes and genes for DNA restriction and modification. NucleicAcids Res., 35, D269-D270.
3. Aravind, L., Makarova, K.S. and Koonin, E.V. (2000) SURVEY AND SUMMARY: Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res., 28, 3417-3432.
4. Bujnicki, J.M. and Rychlewski, L. (2001) Identification of a PD-(D/E)XK-like domain with a novel configuration of the endonuclease active site in the methyl-directed restriction enzyme Mrr and itshomologs. Gene., 267, 183-191.
5. Bourniquel, A.A. and Bickle, T.A. (2002) Complex restriction enzymes: NTP-driven molecular motors. Biochimie., 84, 1047-1059.
6. McClelland, S.E. and Szczelkun, M.D. (2004) Molecular motors thatprocess DNA in Restriction Enzymes. In Pingound, A. (ed.), Nucleic Acids and Molecular Biology, Vol. 14. Springer, Germany,pp. 111-135.
7. Cesnaviciene, E., Petrusyte, M., Kazlauskiene, R., Maneliene, Z., Timinskas, A., Lubys, A. and Janulaitis, A. (2001) Characterization of AloI, a restriction-modification system of a new type. J. Mol.Biol., 314, 205-216.
8. Marshall, J.J., Gowers, D.M. and Halford, S.E. (2007) Restriction endonucleases that bridge and excise two recognition sites from DNA. J. Mol. Biol., 367, 419-431.
9. Morgan, R.D., Bhatia, T.K.., Lovasco, L. and Davis, T.B. (2008)MmeI: a minimal Type II restriction-modification system that only modifies one DNA strand for host protection. Nucleic Acids Res., 36, 6558-6570.
10. Smith, R.M., Josephsen, J. and Szczelkun, M.D. (2009) The single polypeptide Restriction Modification enzyme LlaGI is a self-contained molecular motor that translocates DNA loops.
11. Smith, R.M., Josephsen, J. and Szczelkun, M.D. (2009) An Mrr-family nuclease motif in the single polypeptide Restriction-Modification enzyme LlaGI.
12. Yanisch-Perron, C., Vieira, J. and Messing, J. (1985) Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene, 33, 103-119.
13. Vipond, I.B., Baldwin, G.S., Oram, M., Erskine, S.G., Wentzell, L.M., Szczelkun, M.D., Nobbs, T.J. and Halford, S.E. (1995) A general assay for restriction endonucleases and other DNA-modifying enzymes with plasmid substrates. Mol. Biotechnol., 4, 259-268.
14. McClelland, S.E., Dryden, D.T. and Szczelkun, M.D. (2005) Continuous assays for DNA translocation using fluorescent triplex dissociation: application to type I restriction endonucleases. J. Mol.Biol., 348, 895-915.
15. de Daruvar, A., Collado-Vides, J. and Valencia, A. (2002) Analysis of the cellular functions of Escherichia coli operons and their conservation in Bacillus subtilis. J. Mol. Evol., 55, 211-221.
16. Price, M.N., Arkin, A.P. and Alm, E.J. (2006) The life-cycle of operons. PLoS Genet., 2, e96.
17. Khan, S.A. (1997) Rolling-circle replication of bacterial plasmids.Microbiol. Mol. Biol. Rev., 61, 442-455.
18. Gravesen, A., Josephsen, J., von Wright, A. and Vogensen, F.K.(1995) Characterization of the replicon from the lactococcal theta-replicating plasmid pJW563. Plasmid, 34, 105-118.
19. Sánchez, C., Hernández de Rojas, A., Martínez, B., Argüelles, M.E., Suárez, J.E., Rodríguez, A. and Mayo, B. (2000) Nucleotide sequenceand analysis of pBL1, a bacteriocin-producing plasmid fromLactococcus lactis IPLA 972. Plasmid, 44, 239-249.
20. Alvarez-Martín, P., O'Connell-Motherway, M., van Sinderen, D. andMayo, B. (2007) Functional analysis of the pBC1 replicon from Bifidobacterium catenulatum L48. Appl. Microbiol. Biotechnol., 76,1395-1402.
21. Fre' re, J., Novel, M. and Novel, G. (1993) Molecular analysis of the Lactococcus lactis subsp. lactis CNRZ270 bidirectional theta replicating lactose plasmid pUCL22. Mol. Microbiol., 10,1113-1124.
22. Kiewiet, R., Bron, S., de Jonge, K., Venema, G. and Seegers, J.F.(1993) Theta replication of the lactococcal plasmid pWVO2.Mol. Microbiol., 10, 319-327.
23. van Kranenburg, R. and de Vos, W.M. (1998) Characterization of multiple regions involved in replication and mobilization of plasmid pNZ4000 coding for exopolysaccharide production in Lactococcus lactis. J. Bacteriol., 180, 5285-5290.
24. Sears, A., Peakman, L.J., Wilson, G.G. and Szczelkun, M.D. (2005)Characterization of the Type III restriction endonuclease PstII from Providencia stuartii. Nucleic Acids Res., 33, 4775-4787.
25. Palmer, B.R. and Marinus, M.G. (1994) The dam and dcm strainsof Escherichia coli - a review. Gene, 143, 1-12.
26. Studier, F.W. and Bandyopadhyay, P.K. (1988) Model for how type I restriction enzymes select cleavage sites in DNA. Proc. Natl Acad.Sci. USA, 85, 4677-4681.
27. Szczelkun, M.D., Janscak, P., Firman, K. and Halford, S.E. (1997)Selection of non-specific DNA cleavage sites by the type IC restriction endonuclease EcoR124I. J. Mol. Biol., 271, 112-123.
28. Szczelkun, M.D. (2002) Kinetic models of translocation, head-on collision, and DNA cleavage by type I restriction endonucleases.Biochemistry, 41, 2067-2074.
29. Sistla, S. and Rao, D.N. (2004) S-Adenosyl-L-methionine-dependent restriction enzymes. Crit. Rev. Biochem. Mol. Biol., 39, 1-19.
30. Peakman, L.J., Antognozzi, M., Bickle, T.A., Janscak, P. andSzczelkun, M.D. (2003) S-adenosyl methionine prevents promiscuous DNA cleavage by the EcoP1I type III restriction enzyme. J. Mol. Biol., 333, 321-335.
31. Malone, T., Blumenthal, R.M. and Cheng, X. (1995) Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes. J. Mol. Biol., 253, 618-632.
32. Meisel, A., Bickle, T.A., Krüger, D.H. and Schroeder, C. (1992) Type III restriction enzymes need two inversely oriented recognition sites for DNA cleavage. Nature, 355, 467-469.
33. Meisel, A., Mackeldanz, P., Bickle, T.A., Kruger, D.H. andSchroeder, C. (1995) Type III restriction endonucleases translocate DNA in a reaction driven by recognition site-specific ATP hydrolysis. EMBO J., 14, 2958-2966.
34. Morgan, R.D., Dwinell, E.A., Bhatia, T.K., Lang, E.M. andLuyten, Y.A. (2009) The MmeI family: type II restriction modificationenzymes that employ single-strand modification for host protection. Nucleic Acids Res., doi:10.1093/nar/gkp534.
35. Szczelkun, M.D., Dillingham, M.S., Janscak, P., Firman, K. andHalford, S.E. (1996) Repercussions of DNA tracking by the type IC restriction endonuclease EcoR124I on linear, circular and catenated substrates. EMBO J., 15, 6335-6347.
36. McGlynn, P. and Lloyd, R.G. (2002) Recombinational repair and restart of damaged replication forks. Nat. Rev. Mol. Cell Biol., 3,859-870.
37. Firman, K. and Szczelkun, M.D. (2000) Measuring motion on DNA by the type I restriction endonuclease EcoR124I using triplex displacement. EMBO J., 19, 2094-2102.
38. Roberts, R.J., Belfort, M., Bestor, T., Bhagwat, A.S., Bickle, T.A., Bitinaite, J., Blumenthal, R.M., Degtyarev, S.Kh., Dryden, D.T., Dybvig, K. et al. (2003) A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes.Nucleic Acids Res., 31, 1805-1812.
39. Janscak, P., Abadjieva, A. and Firman, K. (1996) The type Irestriction endonuclease R. EcoR124I: over-production and biochemical properties. J. Mol. Biol., 257, 977-991.
40. Seidel, R., van Noort, J., van der Scheer, C., Bloom, J.G., Dekker, N.H., Dutta, C.F., Blundell, A., Robinson, T., Firman, K.and Dekker, C. (2004) Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I. Nat.Struct. Mol. Biol., 11, 838-843.
41. Seidel, R., Bloom, J.G., Dekker, C. and Szczelkun, M.D. (2008)Motor step size and ATP coupling efficiency of the dsDNA translocase EcoR124I. EMBO J., 27, 1388-1398.
42. Bachi, B., Reiser, J. and Pirrotta, V. (1979) Methylation and cleavage sequences of the EcoP1 restriction-modification enzyme. J. Mol.Biol., 128, 143-163.
43. Humbelin, M., Suri, B., Rao, D.N., Hornby, D.P., Eberle, H., Pripfl, T., Kenel, S. and Bickle, T.A. (1988) Type III DNA restriction and modification systems EcoP1 and EcoP15. J. Mol. Biol., 200,23-29.
44. Saha, S. and Rao, D.N. (1995) ATP hydrolysis is required for DNA cleavage by EcoPI restriction enzyme. J. Mol. Biol., 247, 559-567.
45. Janscak, P., Sandmeier, U., Szczelkun, M.D. and Bickle, T.A. (2001)Subunit assembly and mode of DNA cleavage of the type III restriction endonucleases EcoP1I and EcoP15I. J. Mol. Biol., 306,417-431.