Posttranscriptional regulation of EcoP1I and EcoP15I restriction activity

Journal of Molecular Biology

Volumn 257, Issue 4, 1996, Pages 790-803

  Redaschi, Nicole ^a   Bickle, Thomas A ^a  

^a UNIVERSITY OF BASEL   (Switzerland)

Author keywords

DNA restriction; Posttranscriptional control; Ribosomal ambiguity; Streptomycin; Type III restriction enzymes

Indexed keywords

RESTRICTION ENDONUCLEASE; TYPE III SITE SPECIFIC DEOXYRIBONUCLEASE;

ARTICLE; DNA METHYLATION; DNA MODIFICATION; DNA RESTRICTION; ENZYME ACTIVATION; ENZYME ACTIVITY; GENE EXPRESSION; IMMUNOBLOTTING; PRIORITY JOURNAL; PROTEIN PROCESSING;

ESCHERICHIA COLI;

EID: 0029979544     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0202     Document Type: Article

References (67)

1. Ahmad, I. & Rao, D. N. (1994). Interaction of EcoP15I DNA methyltransferase with oligonucleotides containing the asymmetric sequence 5′-CAGCAG-3′. J. Mol. Biol. 242, 378-388.
2. Andersson, D. I., Andersson, G. E. & Kurland, C. G. (1986). Functional interactions between mutated forms of ribosomal proteins S4, S5 and S12. Biochimie, 68, 705-713.
3. Arber, W. (1974). DNA modification and restriction. Prog. Nucl Acid Res. Mol. Biol. 14, 1-37.
4. Arber, W. & Dussoix, D. (1962). Host specificity of DNA produced by Escherichia coli. I. Host controlled modification of bacteriophage lambda. J. Mol. Biol. 5, 18-36.
5. Arber, W. & Wauters-Willems, D. (1970). Host specificity of DNA produced by Escherichia coli. XII. The two restriction and modification systems of strain 15T-. Mol. Gen. Genet. 108, 203-217.
6. Arber, W., Yuan, R. & Bickle, T. A. (1974). Strain-specific modification and restriction of DNA in bacteria. In Post Synthetic Modification of Macromolecules (Antoni, F. & Farago, A., eds), pp. 3-22, Elsevier, New York.
7. Arber, W., Iida, S., Jütte, H., Caspers, P., Meyer, J. & Hänni, C. (1978). Rearrangements of genetic material in Escherichia coli as observed on the bacteriophage P1 plasmid. Cold Spring Harbor Symp. Quant. Biol. 43, 1197-1208.
8. Berman, M. L. & Beckwith, J. R. (1979). Use of gene fusions to isolate promoter mutants in the transfer RNA gene tyrT of Escherichia coli. J. Mol. Biol. 130, 303-315.
9. Bjare, U. & Gorini, L. (1971). Drug dependence reversed by a ribosomal ambiguity mutation, ram, in Escherichia coli. J. Mol. Biol. 57, 423-435.
10. Bohman, J., Ruusala, T., Jelenc, P. C. & Kurland, C. G. (1984). Kinetic impairment of restrictive streptomycin-resistant ribosomes. Mol. Gen. Genet. 198, 90-99.
11. Bolivar, F., Rodriguez, R. L., Greene, P. J., Betlach, M. C., Heyneker, H. L. & Boyer, H. W. (1977). Construction and characterization of new cloning vehicles II. A multipurpose cloning system. Gene, 2, 95-113.
12. Brooks, J. E., Nathan, P. D., Landry, D., Sznyter, L. A., Waite-Rees, P., Ives, C. L., Moran, L. S., Slatko, B. E. & Benner, J. S. (1991). Characterization of the cloned BamHI restriction modification system: its nucleotide sequence, properties of the methylase, and expression in heterologous hosts. Nucl. Acids Res. 19, 841-850.
13. Chang, A. C. Y. & Cohen, S. N. (1978). Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J. Bacteriol. 134, 1141-1156.
14. Dartois, V., De Backer, O. & Colson, C. (1993). Sequence of the Salmonella typhimurium StyLT1 restriction-modification genes: homologies with EcoP1 and EcoP15 type-III R-M systems and presence of helicase domains. Gene, 127, 105-110.
15. Davies, J. & Nomura, M. (1972). The genetics of bacterial ribosomes. Annu. Rev. Genet. 6, 203-234.
16. De Backer, O. & Colson, C. (1991a). Identification of the recognition sequence for the M.StyLTI methyltransferase of Salmonella typhimurium LT7: an asymmetric site ttypical of type-III enzymes. Gene, 97, 103-107.
17. De Backer, O. & Colson, C. (1991b). Transfer of the genes for the StyLTI restriction-modification system of Salmonella typhimurium to strains lacking modification ability results in death of the recipient cells and degradation of their DNA. J. Bacteriol. 173, 1328-1330.
18. De Backer, O. & Colson, C. (1991c). Two-step cloning and expression in Escherichia coli of the DNA restriction-modification system StyLTI of Salmonella typhimurium. J. Bacteriol. 173, 1321-1327.
19. Devereux, J., Haeberli, P. & Smithies, O. (1984). A comprehensive set of sequence analysis programs for the VAX. Nucl. Acids Res. 12, 387-395.
20. Ditta, G., Stanfield, S., Corbin, D. & Helinski, D. R. (1980). Broad host range DNA cloning system for Gram-negative bacteria: construction of a gene bank of Rhizobium meliloti. Proc. Natl Acad. Sci. USA, 77, 7347-7351.
21. Dussoix, D. & Arber, W. (1962). Host specificity of DNA produced by Escherichia coli II. Control over acceptance of DNA from infecting phage lambda. J. Mol. Biol. 5, 37-49.
22. Engelberg-Kulka, H., Dekel, L. & Israeli-Reches, M. (1977). Streptomycin-resistant Escherichia coli mutant temperature-sensitive for the production of Qβ-infective particles. J. Virol. 21, 1-6.
23. Engelberg-Kulka, H., Amiel, A., Dekel, L., Raveh, B. & Schoulaker-Schwarz, R. (1982). Genetic analysis of a streptomycin-resistant Escherichia coli mutant temperature-sensitive for nonsense suppression. Mol. Gen. Genet. 188, 149-155.
24. Funatsu, G. & Wittmann, H. G. (1972). Location of amino-acid replacements in protein S12 isolated from Escherichia coli mutants resistant to streptomycin. J. Mol. Biol. 68, 547-550.
25. Gorini, L. (1974). Streptomycin and misreading of the genetic code. In Ribosomes (Nomura, M., Tissières, A. & Lengyel, P., eds.), pp. 791-804, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
26. Gottesman, S. & Maurizi, M. R. (1992). Regulation by proteolysis: energy-dependent proteases and their targets. Microbiol. Rev. 56, 592-621.
27. Hadi, S. M., Bächi, B., Iida, S. & Bickle, T. A. (1983). DNA restriction-modification enzymes of phage P1 and plasmid p15B. J. Mol. Biol. 165, 19-34.
28. Hornby, D. P., Muller, M. & Bickle, T. A. (1987). High level expression of the EcoPI modification methylase gene and characterization of the gene product. Gene, 54, 239-245.
29. Humbelin, M., Suri, B., Rao, D. N., Hornby D. P., Eberle, H., Pripfl, T., Kenel, S. & Bickle, T. A. (1988). Type III DNA restriction and modification systems EcoP1 and EcoP15. Nucleotide sequence of the EcoP1 operon, the EcoP15 mod gene and some EcoP1 mod mutants. J. Mol. Biol. 200, 23-29.
30. Iida, S., Meyer, J. & Arber, W. (1980). Genesis and natural history of IS-mediated transposons. Cold Spring Harbor Symp. Quant. Biol. 45, 27-43.
31. Iida, S., Meyer, J., Kennedy, K. E. & Arber, W. (1982). A site-specific, conservative recombination system carried by bacteriophage P1. Mapping the recombinase gene cin for the inversion of the C segment. EMBO J. 1, 1445-1453.
32. Iida, S., Meyer, J., Bächi, B., Stålhammar-Carlemalm, M., Schrickel, S., Bickle, T. A. & Arber, W. (1983). DNA restriction-modification genes of phage P1 and plasmid p15B. J. Mol. Biol. 165, 1-18.
33. Ikeda, H., Inuzuka, M. & Tomizawa, J. (1970). P1-like plasmid in Escherichia coli 15. J. Mol. Biol. 50, 457-470.
34. Ives, C. L., Nathan, P. D. & Brooks, J. E. (1992). Regulation of the BamHI restriction modification system by a small intergenic ORF, bamHIC, in both Escherichia coli and Bacillus subtilis. J. Bacteriol. 174, 7194-7201.
35. Jacob, F. & Wollman, E. L. (1954). Etude génétique d'un bactériophage tempéré d'Escherichia coli I. Le système génétique du bactériophage λ. Ann. Inst. Pasteur, 87, 653-673.
36. Kurland, C. G. (1992). Translational accuracy and the fitness of bacteria. Annu. Rev. Genet. 26, 29-50.
37. Kurland, C. G. (1993). Major codon preference: theme and variations. Biochem. Soc. Trans. 21, 841-846.
38. Kurland, C. G., Jörgensen, F., Richter, A., Ehrenberg, M., Bilgin, N. & Rojas, A.-M. (1990). Through the accuracy window. In The Ribosome: Structure, Function, and Evolution (Hill, W. E., Dahlberg, A., Garrett, R. A., Moore, P. B., Schlessinger, D. & Warner, J. R., eds), pp. 513-526, American Societty for Microbiology, Washington, DC.
39. Laemmli, U. K. (1970). Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature, 227, 680-685.
40. McCabe, P C. (1990). Production of single-stranded DNA by asymmetric PCR. In PCR Protocols: A Guide to Methods and Applications (Innis, M. A., Gelfand, D. H., Sninsky, J. J. & White, T. J., eds), pp. 76-83, Academic Press, Inc., San Diego, CA.
41. Meister, J., MacWilliams, M., Hubner, P., Jutte, H., Skrzypek, E., Piekarowicz, A. & Bickle, T. A. (1993). Macroevolution by transposition: drastic modification of DNA recognition by the type I restriction enzyme following Tn5 transposition. EMBO J. 12, 4585-4591.
42. Meyer, J., Iida, S. & Arber, W. (1983). Physical analysis of the genomes of hybrid phages between phage P1 and plasmid p15B. J. Mol. Biol. 165, 191-195.
43. Meyer, J., Stalhammar-Carlemalm, M., Streiff, M., Iida, S. & Arber, W. (1986). Sequence relations among the IncY plasmid p15B, P1 and P7 prophages. Plasmid, 16, 81-89.
44. Miller, J. H. (1992). A Short Course in Bacterial Genetics: A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
45. Minton, N. F. (1984). Improved plasmid vectors for the isolation of translational lac gene fusions. Gene, 31, 269-273.
46. Mise, K. & Arber, W. (1976). Plaque-forming transducing bacteriophage P1 derivatives and their behaviour in lysogenic conditions. Virology, 69, 191-205.
47. Parker, J. (1989). Errors and alternatives in reading the universal genetic code. Microbiol. Rev. 53, 273-298.
48. Prakash-Cheng, A., Chung, S. S. & Ryu, J.-I. (1993). The expression and regulation of hsdK genes after conjugative transfer. Mol. Gen. Genet. 241, 491-496.
49. Rosset, R. & Gorini, L. (1969). A ribosomal ambiguity mutation. J. Mol. Biol. 39, 95-112.
50. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
51. Ruusala, T., Andersson, D., Ehrenberg, M. & Kurland, C. G. (1984). Hyper-accurate ribosomes inhibit growth. EMBO J. 3, 2575-2580.
52. Sanger, F., Nicklen, S. & Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors, Proc. Natl Acad. Sci. USA, 74, 5463-5467.
53. Simon, R., Priefer, U. & Puehler, A. (1983). A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in Gram negative bacteria. Biotechnology, 1, 784-791.
54. Sipley, J. & Goldman, E. (1993). Increased ribosomal accuracy increases a programmed translational frameshift in Escherichia coli. Proc. Natl Acad. Sci. USA, 90, 2315-2319.
55. Tao, T. & Blumenthal, R. M. (1992). Sequence and characterization of pvuIIR, the PvuII endonuclease gene, and of pvuIIC, its regulatory gene. J. Bacteriol. 174, 3395-3398.
56. Tao, T., Bourne, J. C. & Blumenthal, R. M. (1991). A family of regulatory genes associated with Type II restriction-modification systems. J. Bacteriol. 173, 1367-1375.
57. Taylor, G. R. (1991). Polymerase chain reaction: basic principles and automation. In PCR: A Practical Approach (McPherson, M. J., Quirke, P. & Taylor, G. R., eds), pp. 1-14, IRL Press, Oxford.
58. Towbin, H., Staehelin, T. & Gordon, J. (1979). Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications. Proc. Natl Acad. Sci. USA, 76, 4350-4353.
59. van Acken, U. (1975). Proteinchemical studies on ribosomal proteins S4 and S12 from ram (ribosomal ambiguity) mutants of Escherichia coli. Mol. Gen. Genet. 140, 61-68.
60. Watson, N. (1988). A new revision of the sequence of plasmid pBR322. Gene, 70, 399-403.
61. Wertman, K. F., Wyman, A. R. & Botstein, D. (1986). Host/vector interactions which affect the viability of recombinant phage lambda clones. Gene, 49, 253-262.
62. Wilson, G. G. & Murray, N. E. (1991). Restriction and modification systems. Annu. Rev. Genet. 25, 585-627.
63. Wood, W. B. (1966). Host specificity of DNA produced by Escherichia coli: bacterial mutations affecting the restriction and modification of DNA. J. Mol. Biol. 16, 118-133.
64. Woodcock, D. M., Crowther, P. J., Doherty, J., Jefferson, S., DeCruz, E., Noyer-Weidner, M., Smith, S. S., Michael, M. Z. & Graham, M. W. (1989). Quantitative evaluation of Escherichia coli strains for tolerance to cytosine methylation in plasmid and phage recombinants. Nucl. Acids Res. 17, 3469-3478.
65. Yamamoto, K. R., Alberts, B. M., Benzinger, R., Lawhorne, L. & Treiber, G. (1970). Rapid bacteriophage sedimentation in the presence of polyethylene glycol and its application to large scale virus purification. Virology, 40, 734-744.
66. Yanish-Perron, C., Viera, J. & Messing, J. (1985). Improved M13 phage vectors and host strains. Nucleotide sequence of the M13mp18 and pUC19 vectors. Gene, 33, 103-199.
67. Yarmolinsky, M. B. & Sternberg, N. (1988). Bacteriophage P1. In The Bacteriophages (Calendar, R., ed.), pp. 291-438, Plenum Press, New York.