Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1993 Feb 25;21(4):905–911. doi: 10.1093/nar/21.4.905

The M.AluI DNA-(cytosine C5)-methyltransferase has an unusually large, partially dispensable, variable region.

B Zhang 1, T Tao 1, G G Wilson 1, R M Blumenthal 1
PMCID: PMC309223  PMID: 8451189

Abstract

The DNA methyltransferase of the AluI restriction-modification system, from Arthrobacter luteus, converts cytosine to 5-methylcytosine in the sequence AGCT. The gene for this methyltransferase, aluIM, was cloned into Escherichia coli and sequenced. A 525-codon open reading frame was found, consistent with deletion evidence, and the deduced amino acid sequence revealed all ten conserved regions common to 5-methylcytosine methyltransferases. The aluIM sequence predicts a protein of M(r) 59.0k, in agreement with the observed M(r), making M.AluI the largest known methyltransferase from a type II restriction-modification system. M.AluI also contains the largest known variable region of any monospecific DNA methyltransferase, larger than that of most multispecific methyltransferases. In other DNA methyltransferases the variable region has been implicated as the sequence-specific target recognition domain. An in-frame deletion that removes a third of this putative target-recognition region leaves the Alu I methyltransferase still fully active.

Full text

PDF
905

Selected References

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

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  2. Balganesh T. S., Reiners L., Lauster R., Noyer-Weidner M., Wilke K., Trautner T. A. Construction and use of chimeric SPR/phi 3T DNA methyltransferases in the definition of sequence recognizing enzyme regions. EMBO J. 1987 Nov;6(11):3543–3549. doi: 10.1002/j.1460-2075.1987.tb02681.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Behrens B., Noyer-Weidner M., Pawlek B., Lauster R., Balganesh T. S., Trautner T. A. Organization of multispecific DNA methyltransferases encoded by temperate Bacillus subtilis phages. EMBO J. 1987 Apr;6(4):1137–1142. doi: 10.1002/j.1460-2075.1987.tb04869.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. 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]
  5. Bocklage H., Heeger K., Müller-Hill B. Cloning and characterization of the MboII restriction-modification system. Nucleic Acids Res. 1991 Mar 11;19(5):1007–1013. doi: 10.1093/nar/19.5.1007. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. 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. Characterization of the cloned BamHI restriction modification system: its nucleotide sequence, properties of the methylase, and expression in heterologous hosts. Nucleic Acids Res. 1991 Feb 25;19(4):841–850. doi: 10.1093/nar/19.4.841. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. 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. Characterization of the cloned BamHI restriction modification system: its nucleotide sequence, properties of the methylase, and expression in heterologous hosts. Nucleic Acids Res. 1991 Feb 25;19(4):841–850. doi: 10.1093/nar/19.4.841. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. 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]
  9. Ingrosso D., Fowler A. V., Bleibaum J., Clarke S. Sequence of the D-aspartyl/L-isoaspartyl protein methyltransferase from human erythrocytes. Common sequence motifs for protein, DNA, RNA, and small molecule S-adenosylmethionine-dependent methyltransferases. J Biol Chem. 1989 Nov 25;264(33):20131–20139. [PubMed] [Google Scholar]
  10. Karreman C., de Waard A. Agmenellum quadruplicatum M.AquI, a novel modification methylase. J Bacteriol. 1990 Jan;172(1):266–272. doi: 10.1128/jb.172.1.266-272.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kiss A., Posfai G., Keller C. C., Venetianer P., Roberts R. J. Nucleotide sequence of the BsuRI restriction-modification system. Nucleic Acids Res. 1985 Sep 25;13(18):6403–6421. doi: 10.1093/nar/13.18.6403. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Lange C., Jugel A., Walter J., Noyer-Weidner M., Trautner T. A. 'Pseudo' domains in phage-encoded DNA methyltransferases. Nature. 1991 Aug 15;352(6336):645–648. doi: 10.1038/352645a0. [DOI] [PubMed] [Google Scholar]
  13. Lauster R., Trautner T. A., Noyer-Weidner M. Cytosine-specific type II DNA methyltransferases. A conserved enzyme core with variable target-recognizing domains. J Mol Biol. 1989 Mar 20;206(2):305–312. doi: 10.1016/0022-2836(89)90480-4. [DOI] [PubMed] [Google Scholar]
  14. Looney M. C., Moran L. S., Jack W. E., Feehery G. R., Benner J. S., Slatko B. E., Wilson G. G. Nucleotide sequence of the FokI restriction-modification system: separate strand-specificity domains in the methyltransferase. Gene. 1989 Aug 15;80(2):193–208. doi: 10.1016/0378-1119(89)90284-9. [DOI] [PubMed] [Google Scholar]
  15. Mauch L., Bichler V., Brandsch R. Functional analysis of the 5' regulatory region and the UUG translation initiation codon of the Arthrobacter oxidans 6-hydroxy-D-nicotine oxidase gene. Mol Gen Genet. 1990 May;221(3):427–434. doi: 10.1007/BF00259408. [DOI] [PubMed] [Google Scholar]
  16. Mi S., Roberts R. J. How M.MspI and M.HpaII decide which base to methylate. Nucleic Acids Res. 1992 Sep 25;20(18):4811–4816. doi: 10.1093/nar/20.18.4811. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. 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]
  18. Pearson W. R. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol. 1990;183:63–98. doi: 10.1016/0076-6879(90)83007-v. [DOI] [PubMed] [Google Scholar]
  19. 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]
  20. Raleigh E. A. Organization and function of the mcrBC genes of Escherichia coli K-12. Mol Microbiol. 1992 May;6(9):1079–1086. doi: 10.1111/j.1365-2958.1992.tb01546.x. [DOI] [PubMed] [Google Scholar]
  21. 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]
  22. Roberts R. J., Myers P. A., Morrison A., Murray K. A specific endonuclease from Arthrobacter luteus. J Mol Biol. 1976 Mar 25;102(1):157–165. doi: 10.1016/0022-2836(76)90079-6. [DOI] [PubMed] [Google Scholar]
  23. Sanchez-Pescador R., Urdea M. S. Use of unpurified synthetic deoxynucleotide primers for rapid dideoxynucleotide chain termination sequencing. DNA. 1984 Aug;3(4):339–343. doi: 10.1089/dna.1.1984.3.339. [DOI] [PubMed] [Google Scholar]
  24. 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]
  25. Shields S. L., Burbank D. E., Grabherr R., van Etten J. L. Cloning and sequencing the cytosine methyltransferase gene M. CviJI from Chlorella virus IL-3A. Virology. 1990 May;176(1):16–24. doi: 10.1016/0042-6822(90)90225-g. [DOI] [PubMed] [Google Scholar]
  26. Slatko B. E., Benner J. S., Jager-Quinton T., Moran L. S., Simcox T. G., Van Cott E. M., Wilson G. G. Cloning, sequencing and expression of the Taq I restriction-modification system. Nucleic Acids Res. 1987 Dec 10;15(23):9781–9796. doi: 10.1093/nar/15.23.9781. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Szomolányi E., Kiss A., Venetianer P. Cloning the modification methylase gene of Bacillus sphaericus R in Escherichia coli. Gene. 1980 Aug;10(3):219–225. doi: 10.1016/0378-1119(80)90051-7. [DOI] [PubMed] [Google Scholar]
  28. Tao T., Blumenthal R. M. Sequence and characterization of pvuIIR, the PvuII endonuclease gene, and of pvuIIC, its regulatory gene. J Bacteriol. 1992 May;174(10):3395–3398. doi: 10.1128/jb.174.10.3395-3398.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Tao T., Bourne J. C., Blumenthal R. M. A family of regulatory genes associated with type II restriction-modification systems. J Bacteriol. 1991 Feb;173(4):1367–1375. doi: 10.1128/jb.173.4.1367-1375.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. 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]
  31. Trautner T. A., Balganesh T. S., Pawlek B. Chimeric multispecific DNA methyltransferases with novel combinations of target recognition. Nucleic Acids Res. 1988 Jul 25;16(14A):6649–6658. doi: 10.1093/nar/16.14.6649. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Wilke K., Rauhut E., Noyer-Weidner M., Lauster R., Pawlek B., Behrens B., Trautner T. A. Sequential order of target-recognizing domains in multispecific DNA-methyltransferases. EMBO J. 1988 Aug;7(8):2601–2609. doi: 10.1002/j.1460-2075.1988.tb03110.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Wilson G. G. Amino acid sequence arrangements of DNA-methyltransferases. Methods Enzymol. 1992;216:259–279. doi: 10.1016/0076-6879(92)16026-g. [DOI] [PubMed] [Google Scholar]
  34. Wilson G. G., Murray N. E. Restriction and modification systems. Annu Rev Genet. 1991;25:585–627. doi: 10.1146/annurev.ge.25.120191.003101. [DOI] [PubMed] [Google Scholar]
  35. Yanisch-Perron C., Vieira J., Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103–119. doi: 10.1016/0378-1119(85)90120-9. [DOI] [PubMed] [Google Scholar]

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

RESOURCES