Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1989 Feb 11;17(3):979–997. doi: 10.1093/nar/17.3.979

Cloning the BamHI restriction modification system.

J E Brooks 1, J S Benner 1, D F Heiter 1, K R Silber 1, L A Sznyter 1, T Jager-Quinton 1, L S Moran 1, B E Slatko 1, G G Wilson 1, D O Nwankwo 1
PMCID: PMC331717  PMID: 2537955

Abstract

BamHI, a Type II restriction modification system from Bacillus amyloliquefaciensH recognizes the sequence GGATCC. The methylase and endonuclease genes have been cloned into E. coli in separate steps; the clone is able to restrict unmodified phage. Although within the clone the methylase and endonuclease genes are present on the same pACYC184 vector, the system can be maintained in E. coli only with an additional copy of the methylase gene present on a separate vector. The initial selection for BamHI methylase activity also yielded a second BamHI methylase gene which is not homologous in DNA sequence and hybridizes to different genomic restriction fragments than does the endonuclease-linked methylase gene. Finally, the interaction of the BamHI system with the E. coli Dam and the Mcr A and B functions, have been studied and are reported here.

Full text

PDF
982

Images in this article

989Image
on p.989
990Image
on p.990

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Ansorge W., Labeit S. Field gradients improve resolution on DNA sequencing gels. J Biochem Biophys Methods. 1984 Dec;10(3-4):237–243. doi: 10.1016/0165-022x(84)90043-5. [DOI] [PubMed] [Google Scholar]
  2. Blumenthal R. M., Gregory S. A., Cooperider J. S. Cloning of a restriction-modification system from Proteus vulgaris and its use in analyzing a methylase-sensitive phenotype in Escherichia coli. J Bacteriol. 1985 Nov;164(2):501–509. doi: 10.1128/jb.164.2.501-509.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bolivar F., Rodriguez R. L., Greene P. J., Betlach M. C., Heyneker H. L., Boyer H. W., Crosa J. H., Falkow S. Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene. 1977;2(2):95–113. [PubMed] [Google Scholar]
  4. Bradford M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976 May 7;72:248–254. doi: 10.1006/abio.1976.9999. [DOI] [PubMed] [Google Scholar]
  5. Chang A. C., Cohen S. N. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J Bacteriol. 1978 Jun;134(3):1141–1156. doi: 10.1128/jb.134.3.1141-1156.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Chen E. Y., Seeburg P. H. Supercoil sequencing: a fast and simple method for sequencing plasmid DNA. DNA. 1985 Apr;4(2):165–170. doi: 10.1089/dna.1985.4.165. [DOI] [PubMed] [Google Scholar]
  7. Clewell D. B., Helinski D. R. Supercoiled circular DNA-protein complex in Escherichia coli: purification and induced conversion to an opern circular DNA form. Proc Natl Acad Sci U S A. 1969 Apr;62(4):1159–1166. doi: 10.1073/pnas.62.4.1159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Cohen S. N., Chang A. C., Hsu L. Nonchromosomal antibiotic resistance in bacteria: genetic transformation of Escherichia coli by R-factor DNA. Proc Natl Acad Sci U S A. 1972 Aug;69(8):2110–2114. doi: 10.1073/pnas.69.8.2110. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Dreiseikelmann B., Eichenlaub R., Wackernagel W. The effect of differential methylation by Escherichia coli of plasmid DNA and phage T7 and lambda DNA on the cleavage by restriction endonuclease MboI from Moraxella bovis. Biochim Biophys Acta. 1979 May 24;562(3):418–428. doi: 10.1016/0005-2787(79)90105-9. [DOI] [PubMed] [Google Scholar]
  11. Gingeras T. R., Brooks J. E. Cloned restriction/modification system from Pseudomonas aeruginosa. Proc Natl Acad Sci U S A. 1983 Jan;80(2):402–406. doi: 10.1073/pnas.80.2.402. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Günthert U., Trautner T. A. DNA methyltransferases of Bacillus subtilis and its bacteriophages. Curr Top Microbiol Immunol. 1984;108:11–22. doi: 10.1007/978-3-642-69370-0_2. [DOI] [PubMed] [Google Scholar]
  13. Haltiner M., Kempe T., Tjian R. A novel strategy for constructing clustered point mutations. Nucleic Acids Res. 1985 Feb 11;13(3):1015–1025. doi: 10.1093/nar/13.3.1015. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hattman S., Brooks J. E., Masurekar M. Sequence specificity of the P1 modification methylase (M.Eco P1) and the DNA methylase (M.Eco dam) controlled by the Escherichia coli dam gene. J Mol Biol. 1978 Dec 15;126(3):367–380. doi: 10.1016/0022-2836(78)90046-3. [DOI] [PubMed] [Google Scholar]
  15. Hattman S., Keister T., Gottehrer A. Sequence specificity of DNA methylases from Bacillus amyloliquefaciens and Bacillus brevis. J Mol Biol. 1978 Oct 5;124(4):701–711. doi: 10.1016/0022-2836(78)90178-x. [DOI] [PubMed] [Google Scholar]
  16. Hattori M., Sakaki Y. Dideoxy sequencing method using denatured plasmid templates. Anal Biochem. 1986 Feb 1;152(2):232–238. doi: 10.1016/0003-2697(86)90403-3. [DOI] [PubMed] [Google Scholar]
  17. Heitman J., Model P. Site-specific methylases induce the SOS DNA repair response in Escherichia coli. J Bacteriol. 1987 Jul;169(7):3243–3250. doi: 10.1128/jb.169.7.3243-3250.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Howard K. A., Card C., Benner J. S., Callahan H. L., Maunus R., Silber K., Wilson G., Brooks J. E. Cloning the DdeI restriction-modification system using a two-step method. Nucleic Acids Res. 1986 Oct 24;14(20):7939–7951. doi: 10.1093/nar/14.20.7939. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Hunkapiller M. W., Hood L. E. Analysis of phenylthiohydantoins by ultrasensitive gradient high-performance liquid chromatography. Methods Enzymol. 1983;91:486–493. doi: 10.1016/s0076-6879(83)91045-5. [DOI] [PubMed] [Google Scholar]
  20. Keller C., Corcoran M., Roberts R. J. Computer programs for handling nucleic acid sequences. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):379–386. doi: 10.1093/nar/12.1part1.379. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  22. Nardone G., George J., Chirikjian J. G. Sequence-specific BamHI methylase. Purification and characterization. J Biol Chem. 1984 Aug 25;259(16):10357–10362. [PubMed] [Google Scholar]
  23. Noyer-Weidner M., Diaz R., Reiners L. Cytosine-specific DNA modification interferes with plasmid establishment in Escherichia coli K12: involvement of rglB. Mol Gen Genet. 1986 Dec;205(3):469–475. doi: 10.1007/BF00338084. [DOI] [PubMed] [Google Scholar]
  24. Noyer-Weidner M., Jentsch S., Pawlek B., Günthert U., Trautner T. A. Restriction and modification in Bacillus subtilis: DNA methylation potential of the related bacteriophages Z, SPR, SP beta, phi 3T, and rho 11. J Virol. 1983 May;46(2):446–453. doi: 10.1128/jvi.46.2.446-453.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Olsson A., Moks T., Uhlén M., Gaal A. B. Uniformly spaced banding pattern in DNA sequencing gels by use of field-strength gradient. J Biochem Biophys Methods. 1984 Nov;10(1-2):83–90. doi: 10.1016/0165-022x(84)90053-8. [DOI] [PubMed] [Google Scholar]
  26. Raleigh E. A., Murray N. E., Revel H., Blumenthal R. M., Westaway D., Reith A. D., Rigby P. W., Elhai J., Hanahan D. McrA and McrB restriction phenotypes of some E. coli strains and implications for gene cloning. Nucleic Acids Res. 1988 Feb 25;16(4):1563–1575. doi: 10.1093/nar/16.4.1563. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Raleigh E. A., Wilson G. Escherichia coli K-12 restricts DNA containing 5-methylcytosine. Proc Natl Acad Sci U S A. 1986 Dec;83(23):9070–9074. doi: 10.1073/pnas.83.23.9070. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Ravi R. S., Sozhamannan S., Dharmalingam K. Transposon mutagenesis and genetic mapping of the rglA and rglB loci of Escherichia coli. Mol Gen Genet. 1985;198(3):390–392. doi: 10.1007/BF00332928. [DOI] [PubMed] [Google Scholar]
  29. Rigby P. W., Dieckmann M., Rhodes C., Berg P. Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J Mol Biol. 1977 Jun 15;113(1):237–251. doi: 10.1016/0022-2836(77)90052-3. [DOI] [PubMed] [Google Scholar]
  30. Roberts R. J., Wilson G. A., Young F. E. Recognition sequence of specific endonuclease BamH.I from Bacillus amyloliquefaciens H. Nature. 1977 Jan 6;265(5589):82–84. doi: 10.1038/265082a0. [DOI] [PubMed] [Google Scholar]
  31. Ross T. K., Braymer H. D. Localization of a genetic region involved in McrB restriction by Escherichia coli K-12. J Bacteriol. 1987 Apr;169(4):1757–1759. doi: 10.1128/jb.169.4.1757-1759.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Russell D. W., Zinder N. D. Hemimethylation prevents DNA replication in E. coli. Cell. 1987 Sep 25;50(7):1071–1079. doi: 10.1016/0092-8674(87)90173-5. [DOI] [PubMed] [Google Scholar]
  33. Sanger F., Coulson A. R. The use of thin acrylamide gels for DNA sequencing. FEBS Lett. 1978 Mar 1;87(1):107–110. doi: 10.1016/0014-5793(78)80145-8. [DOI] [PubMed] [Google Scholar]
  34. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Shibata T., Ando T. The restriction endonucleases in Bacillus amyloliquefaciens N strain. Substrate specificities. Biochim Biophys Acta. 1976 Aug 18;442(2):184–196. doi: 10.1016/0005-2787(76)90489-5. [DOI] [PubMed] [Google Scholar]
  36. Smith L. A., Chirikjian J. G. Purification and characterization of the sequence-specific endonuclease Bam HI. J Biol Chem. 1979 Feb 25;254(4):1003–1006. [PubMed] [Google Scholar]
  37. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  38. Strickler J. E., Hunkapiller M. W., Wilson K. J. Utility of the gas-phase sequencer for both liquid- and solid-phase degradation of proteins and peptides at low picomole levels. Anal Biochem. 1984 Aug 1;140(2):553–566. doi: 10.1016/0003-2697(84)90207-0. [DOI] [PubMed] [Google Scholar]
  39. Suggs S. V., Wallace R. B., Hirose T., Kawashima E. H., Itakura K. Use of synthetic oligonucleotides as hybridization probes: isolation of cloned cDNA sequences for human beta 2-microglobulin. Proc Natl Acad Sci U S A. 1981 Nov;78(11):6613–6617. doi: 10.1073/pnas.78.11.6613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Sznyter L. A., Slatko B., Moran L., O'Donnell K. H., Brooks J. E. Nucleotide sequence of the DdeI restriction-modification system and characterization of the methylase protein. Nucleic Acids Res. 1987 Oct 26;15(20):8249–8266. doi: 10.1093/nar/15.20.8249. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Theriault G., Roy P. H., Howard K. A., Benner J. S., Brooks J. E., Waters A. F., Gingeras T. R. Nucleotide sequence of the PaeR7 restriction/modification system and partial characterization of its protein products. Nucleic Acids Res. 1985 Dec 9;13(23):8441–8461. doi: 10.1093/nar/13.23.8441. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Vieira J., Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982 Oct;19(3):259–268. doi: 10.1016/0378-1119(82)90015-4. [DOI] [PubMed] [Google Scholar]
  43. Wallace R. B., Johnson M. J., Hirose T., Miyake T., Kawashima E. H., Itakura K. The use of synthetic oligonucleotides as hybridization probes. II. Hybridization of oligonucleotides of mixed sequence to rabbit beta-globin DNA. Nucleic Acids Res. 1981 Feb 25;9(4):879–894. doi: 10.1093/nar/9.4.879. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Wilson G. A., Young F. E. Isolation of a sequence-specific endonuclease (BamI) from Bacillus amyloliquefaciens H. J Mol Biol. 1975 Sep 5;97(1):123–125. doi: 10.1016/s0022-2836(75)80028-3. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES