An EcoRI-RsrI chimeric restriction endonuclease retains parental sequence specificity

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1774, Issue 5, 2007, Pages 583-594

  Chuluunbaatar, Tungalag ^a   Ivanenko Johnston, Tetiana ^a   Fuxreiter, Mónika ^a   Meleshko, Ruslan ^a   Raskó, Tamás ^a   Simon, István ^a   Heitman, Joseph ^b   Kiss, Antal ^a  

^a INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

^b DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Molecular dynamics simulations; Protein refolding; Restriction endonuclease; Sequence specific DNA recognition

Indexed keywords

AMINO ACID; BACTERIAL PROTEIN; CHIMERIC PROTEIN; ENDONUCLEASE; HYBRID PROTEIN; RESTRICTION ENDONUCLEASE;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; CELL VIABILITY; CHIMERA; CYTOTOXICITY; DNA BINDING; DNA SEQUENCE; ENZYME ACTIVITY; ENZYME BINDING; ESCHERICHIA COLI; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; SIMULATION;

BASE SEQUENCE; DEOXYRIBONUCLEASE ECORI; DNA PRIMERS; HYDROGEN BONDING; MODELS, MOLECULAR; RECOMBINANT FUSION PROTEINS; SITE-SPECIFIC DNA-METHYLTRANSFERASE (ADENINE-SPECIFIC); SUBSTRATE SPECIFICITY;

EID: 34247582888     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2007.02.011     Document Type: Article

References (55)

1. Roberts R.J., Belfort M., Bestor T., Bhagwat A.S., Bickle T.A., Bitinaite J., Blumenthal R.M., Degtyarev S., Dryden D.T., Dybvig K., Firman K., Gromova E.S., Gumport R.I., Halford S.E., Hattman S., Heitman J., Hornby D.P., Janulaitis A., Jeltsch A., Josephsen J., Kiss A., Klaenhammer T.R., Kobayashi I., Kong H., Kruger D.H., Lacks S., Marinus M.G., Miyahara M., Morgan R.D., Murray N.E., Nagaraja V., Piekarowicz A., Pingoud A., Raleigh E., Rao D.N., Reich N., Repin V.E., Selker E.U., Shaw P.C., Stein D.C., Stoddard B.L., Szybalski W., Trautner T.A., Van Etten J.L., Vitor J.M., Wilson G.G., and Xu S.Y. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res. 31 (2003) 1805-1812
2. Modrich P., and Zabel D. EcoRI endonuclease. Physical and catalytic properties of the homogenous enzyme. J. Biol. Chem. 251 (1976) 5866-5874
3. Lesser D.R., Kurpiewski M.R., and Jen-Jacobson L. The energetic basis of specificity in the EcoRI endonuclease-DNA interaction. Science 250 (1990) 776-786
4. Grigorescu A., Horvath M., Wilkosz P.A., Chandrasekhar K., and Rosenberg J.M. The integration of recognition and cleavage: X-ray structures of pre-transition state complex, post-reactive complex and the DNA-free endonuclease. In: Pingoud A. (Ed). Restriction Endonucleases vol. 14 (2004) 137-177
5. Hedgpeth J., Goodman H.M., and Boyer H.W. DNA nucleotide sequence restricted by the RI endonuclease. Proc. Natl. Acad. Sci. U. S. A. 69 (1972) 3448-3452
6. Greene P.J., Ballard B.T., Stephenson F., Kohr W.J., Rodriguez H., Rosenberg J.M., and Boyer H.W. Purification and characterization of the restriction endonuclease RsrI, an isoschizomer of EcoRI. Gene 68 (1988) 43-51
7. Aiken C., and Gumport R.I. Restriction endonuclease RsrI from Rhodobacter sphaeroides, an isoschizomer of EcoRI: Purification and properties. Nucleic Acids Res. 16 (1988) 7901-7916
8. Stephenson F.H., Ballard B.T., Boyer H.W., Rosenberg J.M., and Greene P.J. Comparison of the nucleotide and amino acid sequences of the RsrI and EcoRI restriction endonucleases. Gene 85 (1989) 1-13
9. Kim Y.C., Grable J.C., Love R., Greene P.J., and Rosenberg J.M. Refinement of EcoRI endonuclease crystal structure: a revised protein chain tracing. Science 249 (1990) 1307-1309
10. Siksnys V., Zareckaja N., Vaisvila R., Timinskas A., Stakenas P., Butkus V., and Janulaitis A. CAATTG-specific restriction-modification munI genes from Mycoplasma: sequence similarities between R.MunI and R.EcoRI. Gene 142 (1994) 1-8
11. Deibert M., Grazulis S., Janulaitis A., Siksnys V., and Huber R. Crystal structure of MunI restriction endonuclease in complex with cognate DNA at 1.7 A resolution. EMBO J. 18 (1999) 5805-5816
12. Thompson J.F., and Landy A. Empirical estimation of protein-induced DNA bending angles: applications to lambda site-specific recombination complexes. Nucleic Acids Res. 16 (1988) 9687-9705
13. Kim R., Modrich P., and Kim S.H. 'Interactive' recognition in EcoRI restriction enzyme-DNA complex. Nucleic Acids Res. 12 (1984) 7285-7292
14. Aiken C.R., Fisher E.W., and Gumport R.I. The specific binding, bending, and unwinding of DNA by RsrI endonuclease, an isoschizomer of EcoRI endonuclease. J. Biol. Chem. 266 (1991) 19063-19069
15. Aiken C.R., McLaughlin L.W., and Gumport R.I. The highly homologous isoschizomers RsrI endonuclease and EcoRI endonuclease do not recognize their target sequence identically. J. Biol. Chem. 266 (1991) 19070-19078
16. Heitman J., and Model P. SOS induction as an in vivo assay of enzyme-DNA interactions. Gene 103 (1991) 1-9
17. Bolivar F., Rodriguez R.L., Greene P.J., Betlach M.C., Heyneker H.L., and Boyer H.W. Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene 2 (1977) 95-113
18. Boyer H.W., and Roulland-Dussoix D. A complementation analysis of the restriction and modification of DNA in Escherichia coli. J. Mol. Biol. 41 (1969) 459-472
19. Heitman J., Zinder N.D., and Model P. Repair of the Escherichia coli chromosome after in vivo scission by the EcoRI endonuclease. Proc. Natl. Acad. Sci. U. S. A. 86 (1989) 2281-2285
20. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning: A Laboratory Manual. 2nd edn. (1989), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
21. Ivanenko T., Heitman J., and Kiss A. Mutational analysis of the function of Met137 and Ile197, two amino acids implicated in sequence-specific DNA recognition by the EcoRI endonuclease. Biol. Chem. 379 (1998) 459-465
22. Muir R.S., Flores H., Zinder N.D., Model P., Soberon X., and Heitman J. Temperature-sensitive mutants of the EcoRI endonuclease. J. Mol. Biol. 274 (1997) 722-737
23. Kaszubska W., Webb H.K., and Gumport R.I. Purification and characterization of the M.RsrI DNA methyltransferase from Escherichia coli. Gene 118 (1992) 5-11
24. Hadjeb N., and Berkowitz G.A. Preparation of T-overhang vectors with high PCR product cloning efficiency. BioTechniques 20 (1996) 20-22
25. Newman A.K., Rubin R.A., Kim S.H., and Modrich P. DNA sequences of structural genes for EcoRI DNA restriction and modification enzymes. J. Biol. Chem. 256 (1981) 2131-2139
26. Lukacsovich T., Orosz A., Baliko G., and Venetianer P. A family of expression vectors based on the rrnB P2 promoter of Escherichia coli. J. Biotechnol. 16 (1990) 49-55
27. Haring V., Scholz P., Scherzinger E., Frey J., Derbyshire K., Hatfull G., Willetts N.S., and Bagdasarian M. Protein RepC is involved in copy number control of the broad host range plasmid RSF1010. Proc. Natl. Acad. Sci. U. S. A. 82 (1985) 6090-6094
28. Schwede T., Kopp J., Guex N., and Peitsch M.C. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res. 31 (2003) 3381-3385
29. Jorgensen W.L., Chandrashekar J., Madura J.D., Impey R., and Klein M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79 (1983) 926-935
30. Spector T.I., Cheatham T.E.I., and Kollman P.A. Unrestrained molecular dynamics of photodamaged DNA in aqueous solution. J. Am. Chem. Soc. 119 (1997) 9156-9163
31. Cornell W.D., Cieplak R., Bayly C.L., Gould I.R., Merz K.M., Ferguson D.M., Spellmeyer D.G., Fox T., Caldwell J.W., and Kollman P.A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117 (1995) 5179-5197
32. Darden T.A., and York D. particle mesh Ewald Nlog (N) method for Ewald sums in large systems. J. Chem. Phys. 103 (1993) 8577-8593
33. Greene P.J., Gupta M., Boyer H.W., Brown W.E., and Rosenberg J.M. Sequence analysis of the DNA encoding the EcoRI endonuclease and methylase. J. Biol. Chem. 256 (1981) 2143-2153
34. Luke P.A., and Halford S.E. Solubility of the EcoRI restriction endonuclease and its purification from an over-producing strain. Gene 37 (1985) 241-246
35. King K., Benkovic S.J., and Modrich P. Glu-111 is required for activation of the DNA cleavage center of EcoRI endonuclease. J. Biol. Chem. 264 (1989) 11807-11815
36. Heitman J., and Model P. Mutants of the EcoRI endonuclease with promiscuous substrate specificity implicate residues involved in substrate recognition. EMBO J. 9 (1990) 3369-3378
37. Heitman J., and Model P. Substrate recognition by the EcoRI endonuclease. Proteins 7 (1990) 185-197
38. Heitman J., Ivanenko T., and Kiss A. DNA nicks inflicted by restriction endonucleases are repaired by a RecA- and RecB-dependent pathway in Escherichia coli. Mol. Microbiol. 33 (1999) 1141-1151
39. Wolfes H., Alves J., Fliess A., Geiger R., and Pingoud A. Site directed mutagenesis experiments suggest that Glu 111, Glu 144 and Arg 145 are essential for endonucleolytic activity of EcoRI. Nucleic Acids Res. 14 (1986) 9063-9080
40. Yanofsky S.D., Love R., McClarin J.A., Rosenberg J.M., Boyer H.W., and Greene P.J. Clustering of null mutations in the EcoRI endonuclease. Proteins 2 (1987) 273-282
41. Needels M.C., Fried S.R., Love R., Rosenberg J.M., Boyer H.W., and Greene P.J. Determinants of EcoRI endonuclease sequence discrimination. Proc. Natl. Acad. Sci. U. S. A. 86 (1989) 3579-3583
42. Oelgeschlager T., Geiger R., Ruter T., Alves J., Fliess A., and Pingoud A. Probing the function of individual amino acid residues in the DNA binding site of the EcoRI restriction endonuclease by analysing the toxicity of genetically engineered mutants. Gene 89 (1990) 19-27
43. Sapienza P.J., dela Torre C.A., McCoy IV W.H., Jana S.V., and Jen-Jacobson L. Thermodynamic and kinetic basis for the relaxed DNA sequence specificity of "promiscuous" mutant EcoRI endonucleases. J. Mol. Biol. 348 (2005) 307-324
44. Grabowski G., Jeltsch A., Wolfes H., Maass G., and Alves J. Site-directed mutagenesis in the catalytic center of the restriction endonuclease EcoRI. Gene 157 (1995) 113-118
45. Kurpiewski M.R., Engler L.E., Wozniak L.A., Kobylanska A., Koziolkiewicz M., Stec W.J., and Jen-Jacobson L. Mechanisms of coupling between DNA recognition specificity and catalysis in EcoRI endonuclease. Structure 12 (2004) 1775-1788
46. Venclovas C., Timinskas A., and Siksnys V. Five-stranded beta-sheet sandwiched with two alpha-helices: a structural link between restriction endonucleases EcoRI and EcoRV. Proteins 20 (1994) 279-282
47. Pingoud A., and Jeltsch A. Structure and function of type II restriction endonucleases. Nucleic Acids Res. 29 (2001) 3705-3727
48. Fuxreiter M., and Simon I. Protein stability indicates divergent evolution of PD-(D/E)XK type II restriction endonucleases. Protein Sci. 11 (2002) 1978-1983
49. Rosenberg J.M. Structure and function of restriction endonucleases. Curr. Opin. Struct. Biol. 1 (1991) 104-113
50. Wyszynski M.W., Gabbara S., and Bhagwat A.S. Substitutions of a cysteine conserved among DNA cytosine methylases result in a variety of phenotypes. Nucleic Acids Res. 20 (1992) 319-326
51. Mi S., and Roberts R.J. The DNA binding affinity of HhaI methylase is increased by a single amino acid substitution in the catalytic center. Nucleic Acids Res. 21 (1993) 2459-2464
52. Hyrien O. Mechanisms and consequences of replication fork arrest. Biochimie 82 (2000) 5-17
53. Horiuchi T., and Fujimura Y. Recombinational rescue of the stalled DNA replication fork: a model based on analysis of an Escherichia coli strain with a chromosome region difficult to replicate. J. Bacteriol. 177 (1995) 783-791
54. Jeltsch A., Alves J., Oelgeschlager T., Wolfes H., Maass G., and Pingoud A. Mutational analysis of the function of Gln115 in the EcoRI restriction endonuclease, a critical amino acid for recognition of the inner thymidine residue in the sequence -GAATTC- and for coupling specific DNA binding to catalysis. J. Mol. Biol. 229 (1993) 221-234
55. Flores H., Osuna J., Heitman J., and Soberon X. Saturation mutagenesis of His114 of EcoRI reveals relaxed-specificity mutants. Gene 157 (1995) 295-301