Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1985 Dec 9;13(23):8441–8461. doi: 10.1093/nar/13.23.8441

Nucleotide sequence of the PaeR7 restriction/modification system and partial characterization of its protein products.

G Theriault, P H Roy, K A Howard, J S Benner, J E Brooks, A F Waters, T R Gingeras
PMCID: PMC322144  PMID: 3001639

Abstract

Bal31 deletion experiments on clones of the PaeR7 restriction-modification system from Pseudomonas aeruginosa demonstrate that it is arranged as an operon, with the methylase gene preceding the endonuclease gene. The DNA sequence of this operon agrees with in vitro transcription-translation assays which predict proteins of 532 amino acids, Mr = 59,260 daltons, and 246 amino acids, Mr = 27,280 daltons, coincident with the methylase and endonuclease genes, respectively. These predicted values coincide with the measured molecular weights of the purified, denatured PaeR7 endonuclease and methylase proteins. The first twenty amino acids from the amino-terminus of the purified endonuclease exactly match those predicted from the DNA sequence. Finally, potential regulatory mechanisms for the expression of phage restriction are described based on the properties of several PaeR7 subclones.

Full text

PDF
8443

Images in this article

8454Image
on p.8454
8455Image
on p.8455

Selected References

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

  1. Bibb M. J., Findlay P. R., Johnson M. W. The relationship between base composition and codon usage in bacterial genes and its use for the simple and reliable identification of protein-coding sequences. Gene. 1984 Oct;30(1-3):157–166. doi: 10.1016/0378-1119(84)90116-1. [DOI] [PubMed] [Google Scholar]
  2. Biggin M. D., Gibson T. J., Hong G. F. Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci U S A. 1983 Jul;80(13):3963–3965. doi: 10.1073/pnas.80.13.3963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bougueleret L., Schwarzstein M., Tsugita A., Zabeau M. Characterization of the genes coding for the Eco RV restriction and modification system of Escherichia coli. Nucleic Acids Res. 1984 Apr 25;12(8):3659–3676. doi: 10.1093/nar/12.8.3659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. 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: 10.1016/0003-2697(76)90527-3. [DOI] [PubMed] [Google Scholar]
  6. Brooks J. E., Blumenthal R. M., Gingeras T. R. The isolation and characterization of the Escherichia coli DNA adenine methylase (dam) gene. Nucleic Acids Res. 1983 Feb 11;11(3):837–851. doi: 10.1093/nar/11.3.837. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Brown N. L., Ford S. J., Pridmore R. D., Fritzinger D. C. Nucleotide sequence of a gene from the Pseudomonas transposon Tn501 encoding mercuric reductase. Biochemistry. 1983 Aug 16;22(17):4089–4095. doi: 10.1021/bi00286a015. [DOI] [PubMed] [Google Scholar]
  8. Buhk H. J., Behrens B., Tailor R., Wilke K., Prada J. J., Günthert U., Noyer-Weidner M., Jentsch S., Trautner T. A. Restriction and modification in Bacillus subtilis: nucleotide sequence, functional organization and product of the DNA methyltransferase gene of bacteriophage SPR. Gene. 1984 Jul-Aug;29(1-2):51–61. doi: 10.1016/0378-1119(84)90165-3. [DOI] [PubMed] [Google Scholar]
  9. Clewell D. B., Helinski D. R. Effect of growth conditions on the formation of the relaxation complex of supercoiled ColE1 deoxyribonucleic acid and protein in Escherichia coli. J Bacteriol. 1972 Jun;110(3):1135–1146. doi: 10.1128/jb.110.3.1135-1146.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. 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]
  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. Gingeras T. R., Milazzo J. P., Sciaky D., Roberts R. J. Computer programs for the assembly of DNA sequences. Nucleic Acids Res. 1979 Sep 25;7(2):529–545. doi: 10.1093/nar/7.2.529. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Greene P. J., Gupta M., Boyer H. W., Brown W. E., Rosenberg J. M. Sequence analysis of the DNA encoding the Eco RI endonuclease and methylase. J Biol Chem. 1981 Mar 10;256(5):2143–2153. [PubMed] [Google Scholar]
  14. Grosjean H., Fiers W. Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene. 1982 Jun;18(3):199–209. doi: 10.1016/0378-1119(82)90157-3. [DOI] [PubMed] [Google Scholar]
  15. Hawley D. K., McClure W. R. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 1983 Apr 25;11(8):2237–2255. doi: 10.1093/nar/11.8.2237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hinkle N. F., Miller R. V. pMG7-mediated restriction of Pseudomonas aeruginosa phage DNAs is determined by a class II restriction endonuclease. Plasmid. 1979 Jul;2(3):387–393. doi: 10.1016/0147-619x(79)90022-2. [DOI] [PubMed] [Google Scholar]
  17. Jacoby G. A., Sutton L. Restriction and modification determined by a Pseudomonas R plasmid. Plasmid. 1977 Nov;1(1):115–116. doi: 10.1016/0147-619x(77)90012-9. [DOI] [PubMed] [Google Scholar]
  18. Kosykh V. G., Buryanov Y. I., Bayev A. A. Molecular cloning of EcoRII endonuclease and methylase genes. Mol Gen Genet. 1980;178(3):717–718. doi: 10.1007/BF00337884. [DOI] [PubMed] [Google Scholar]
  19. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  20. Mann M. B., Rao R. N., Smith H. O. Cloning of restriction and modification genes in E. coli: the HbaII system from Haemophilus haemolyticus. Gene. 1978 Apr;3(2):97–112. doi: 10.1016/0378-1119(78)90054-9. [DOI] [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. Messing J., Crea R., Seeburg P. H. A system for shotgun DNA sequencing. Nucleic Acids Res. 1981 Jan 24;9(2):309–321. doi: 10.1093/nar/9.2.309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Minton N. P., Atkinson T., Bruton C. J., Sherwood R. F. The complete nucleotide sequence of the Pseudomonas gene coding for carboxypeptidase G2. Gene. 1984 Nov;31(1-3):31–38. doi: 10.1016/0378-1119(84)90192-6. [DOI] [PubMed] [Google Scholar]
  24. Nakai C., Kagamiyama H., Nozaki M., Nakazawa T., Inouye S., Ebina Y., Nakazawa A. Complete nucleotide sequence of the metapyrocatechase gene on the TOI plasmid of Pseudomonas putida mt-2. J Biol Chem. 1983 Mar 10;258(5):2923–2928. [PubMed] [Google Scholar]
  25. Newman A. K., Rubin R. A., Kim S. H., Modrich P. DNA sequences of structural genes for Eco RI DNA restriction and modification enzymes. J Biol Chem. 1981 Mar 10;256(5):2131–2139. [PubMed] [Google Scholar]
  26. Norrander J., Kempe T., Messing J. Construction of improved M13 vectors using oligodeoxynucleotide-directed mutagenesis. Gene. 1983 Dec;26(1):101–106. doi: 10.1016/0378-1119(83)90040-9. [DOI] [PubMed] [Google Scholar]
  27. 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]
  28. Schoner B., Kelly S., Smith H. O. The nucleotide sequence of the HhaII restriction and modification genes from Haemophilus haemolyticus. Gene. 1983 Oct;24(2-3):227–236. doi: 10.1016/0378-1119(83)90083-5. [DOI] [PubMed] [Google Scholar]
  29. Shine J., Dalgarno L. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A. 1974 Apr;71(4):1342–1346. doi: 10.1073/pnas.71.4.1342. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Siebenlist U. Nucleotide sequence of the three major early promoters of bacteriophage T7. Nucleic Acids Res. 1979;6(5):1895–1907. doi: 10.1093/nar/6.5.1895. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Smith B. R., Schleif R. Nucleotide sequence of the L-arabinose regulatory region of Escherichia coli K12. J Biol Chem. 1978 Oct 10;253(19):6931–6933. [PubMed] [Google Scholar]
  32. Sutcliffe J. G. Nucleotide sequence of the ampicillin resistance gene of Escherichia coli plasmid pBR322. Proc Natl Acad Sci U S A. 1978 Aug;75(8):3737–3741. doi: 10.1073/pnas.75.8.3737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Thériault G., Roy P. H. Cloning of Pseudomonas plasmid pMG7 and its restriction-modification system in Escherichia coli. Gene. 1982 Oct;19(3):355–359. doi: 10.1016/0378-1119(82)90026-9. [DOI] [PubMed] [Google Scholar]
  34. Wain-Hobson S., Nussinov R., Brown R. J., Sussman J. L. Preferential codon usage in genes. Gene. 1981 May;13(4):355–364. doi: 10.1016/0378-1119(81)90015-9. [DOI] [PubMed] [Google Scholar]
  35. Walder R. Y., Hartley J. L., Donelson J. E., Walder J. A. Cloning and expression of the Pst I restriction-modification system in Escherichia coli. Proc Natl Acad Sci U S A. 1981 Mar;78(3):1503–1507. doi: 10.1073/pnas.78.3.1503. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Walder R. Y., Walder J. A., Donelson J. E. The organization and complete nucleotide sequence of the PstI restriction-modification system. J Biol Chem. 1984 Jun 25;259(12):8015–8026. [PubMed] [Google Scholar]
  37. Wallace R. G., Lee N., Fowler A. V. The araC gene of Escherichia coli: transcriptional and translational start-points and complete nucleotide sequence. Gene. 1980 Dec;12(3-4):179–190. doi: 10.1016/0378-1119(80)90100-6. [DOI] [PubMed] [Google Scholar]
  38. Yuan R. Structure and mechanism of multifunctional restriction endonucleases. Annu Rev Biochem. 1981;50:285–319. doi: 10.1146/annurev.bi.50.070181.001441. [DOI] [PubMed] [Google Scholar]

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

RESOURCES