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. 1993 May 25;21(10):2383–2388. doi: 10.1093/nar/21.10.2383

Isolation and identification by sequence homology of a putative cytosine methyltransferase from Arabidopsis thaliana.

E J Finnegan 1, E S Dennis 1
PMCID: PMC309536  PMID: 8389441

Abstract

A plant cytosine methyltransferase cDNA was isolated using degenerate oligonucleotides, based on homology between prokaryote and mouse methyltransferases, and PCR to amplify a short fragment of a methyltransferase gene. A fragment of the predicted size was amplified from genomic DNA from Arabidopsis thaliana. Overlapping cDNA clones, some with homology to the PCR amplified fragment, were identified and sequenced. The assembled nucleic acid sequence is 4720 bp and encodes a protein of 1534 amino acids which has significant homology to prokaryote and mammalian cytosine methyltransferases. Like mammalian methylases, this enzyme has a C terminal methyltransferase domain linked to a second larger domain. The Arabidopsis methylase has eight of the ten conserved sequence motifs found in prokaryote cytosine-5 methyltransferases and shows 50% homology to the murine enzyme in the methyltransferase domain. The amino terminal domain is only 24% homologous to the murine enzyme and lacks the zinc binding region that has been found in methyltransferases from both mouse and man. In contrast to mouse where a single methyltransferase gene has been identified, a small multigene family with homology to the region amplified in PCR has been identified in Arabidopsis thaliana.

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Selected References

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  1. Adams R. L., Bryans M., Rinaldi A., Smart A., Yesufu H. M. Eukaryotic DNA methylases and their use for in vitro methylation. Philos Trans R Soc Lond B Biol Sci. 1990 Jan 30;326(1235):189–198. doi: 10.1098/rstb.1990.0003. [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. Bestor T. H. DNA methylation: evolution of a bacterial immune function into a regulator of gene expression and genome structure in higher eukaryotes. Philos Trans R Soc Lond B Biol Sci. 1990 Jan 30;326(1235):179–187. doi: 10.1098/rstb.1990.0002. [DOI] [PubMed] [Google Scholar]
  4. Bestor T. H., Gundersen G., Kolstø A. B., Prydz H. CpG islands in mammalian gene promoters are inherently resistant to de novo methylation. Genet Anal Tech Appl. 1992 Apr;9(2):48–53. doi: 10.1016/1050-3862(92)90030-9. [DOI] [PubMed] [Google Scholar]
  5. Bestor T., Laudano A., Mattaliano R., Ingram V. Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases. J Mol Biol. 1988 Oct 20;203(4):971–983. doi: 10.1016/0022-2836(88)90122-2. [DOI] [PubMed] [Google Scholar]
  6. Bezdek M., Koukalová B., Kuhrová V., Vyskot B. Differential sensitivity of CG and CCG DNA sequences to ethionine-induced hypomethylation of the Nicotiana tabacum genome. FEBS Lett. 1992 Apr 6;300(3):268–270. doi: 10.1016/0014-5793(92)80860-j. [DOI] [PubMed] [Google Scholar]
  7. Caserta M., Zacharias W., Nwankwo D., Wilson G. G., Wells R. D. Cloning, sequencing, in vivo promoter mapping, and expression in Escherichia coli of the gene for the HhaI methyltransferase. J Biol Chem. 1987 Apr 5;262(10):4770–4777. [PubMed] [Google Scholar]
  8. Chen L., MacMillan A. M., Chang W., Ezaz-Nikpay K., Lane W. S., Verdine G. L. Direct identification of the active-site nucleophile in a DNA (cytosine-5)-methyltransferase. Biochemistry. 1991 Nov 19;30(46):11018–11025. doi: 10.1021/bi00110a002. [DOI] [PubMed] [Google Scholar]
  9. Churchill M. E., Suzuki M. 'SPKK' motifs prefer to bind to DNA at A/T-rich sites. EMBO J. 1989 Dec 20;8(13):4189–4195. doi: 10.1002/j.1460-2075.1989.tb08604.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. 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]
  11. Elledge S. J., Mulligan J. T., Ramer S. W., Spottswood M., Davis R. W. Lambda YES: a multifunctional cDNA expression vector for the isolation of genes by complementation of yeast and Escherichia coli mutations. Proc Natl Acad Sci U S A. 1991 Mar 1;88(5):1731–1735. doi: 10.1073/pnas.88.5.1731. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Finnegan E. J., Brettell R. I., Dennis E. S. The role of DNA methylation in the regulation of plant gene expression. EXS. 1993;64:218–261. doi: 10.1007/978-3-0348-9118-9_11. [DOI] [PubMed] [Google Scholar]
  13. Garcia-Bustos J., Heitman J., Hall M. N. Nuclear protein localization. Biochim Biophys Acta. 1991 Mar 7;1071(1):83–101. doi: 10.1016/0304-4157(91)90013-m. [DOI] [PubMed] [Google Scholar]
  14. Giordano M., Mattachini M. E., Cella R., Pedrali-Noy G. Purification and properties of a novel DNA methyltransferase from cultured rice cells. Biochem Biophys Res Commun. 1991 Jun 14;177(2):711–719. doi: 10.1016/0006-291x(91)91846-5. [DOI] [PubMed] [Google Scholar]
  15. Grill E., Somerville C. Construction and characterization of a yeast artificial chromosome library of Arabidopsis which is suitable for chromosome walking. Mol Gen Genet. 1991 May;226(3):484–490. doi: 10.1007/BF00260662. [DOI] [PubMed] [Google Scholar]
  16. Gruenbaum Y., Naveh-Many T., Cedar H., Razin A. Sequence specificity of methylation in higher plant DNA. Nature. 1981 Aug 27;292(5826):860–862. doi: 10.1038/292860a0. [DOI] [PubMed] [Google Scholar]
  17. 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]
  18. Klimasauskas S., Nelson J. L., Roberts R. J. The sequence specificity domain of cytosine-C5 methylases. Nucleic Acids Res. 1991 Nov 25;19(22):6183–6190. doi: 10.1093/nar/19.22.6183. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. 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]
  20. Leonhardt H., Page A. W., Weier H. U., Bestor T. H. A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei. Cell. 1992 Nov 27;71(5):865–873. doi: 10.1016/0092-8674(92)90561-p. [DOI] [PubMed] [Google Scholar]
  21. Lewis J., Bird A. DNA methylation and chromatin structure. FEBS Lett. 1991 Jul 22;285(2):155–159. doi: 10.1016/0014-5793(91)80795-5. [DOI] [PubMed] [Google Scholar]
  22. 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]
  23. Pósfai J., Bhagwat A. S., Pósfai G., Roberts R. J. Predictive motifs derived from cytosine methyltransferases. Nucleic Acids Res. 1989 Apr 11;17(7):2421–2435. doi: 10.1093/nar/17.7.2421. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Razin A., Cedar H. DNA methylation and gene expression. Microbiol Rev. 1991 Sep;55(3):451–458. doi: 10.1128/mr.55.3.451-458.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Szilák L., Venetianer P., Kiss A. Cloning and nucleotide sequence of the genes coding for the Sau96I restriction and modification enzymes. Nucleic Acids Res. 1990 Aug 25;18(16):4659–4664. doi: 10.1093/nar/18.16.4659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. 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]
  27. Taylor B. H., Finnegan E. J., Dennis E. S., Peacock W. J. The maize transposable element Ac excises in progeny of transformed tobacco. Plant Mol Biol. 1989 Jul;13(1):109–118. doi: 10.1007/BF00027339. [DOI] [PubMed] [Google Scholar]
  28. Theiss G., Schleicher R., Schimpff-Weiland G., Follmann H. DNA methylation in wheat. Purification and properties of DNA methyltransferase. Eur J Biochem. 1987 Aug 17;167(1):89–96. doi: 10.1111/j.1432-1033.1987.tb13307.x. [DOI] [PubMed] [Google Scholar]
  29. 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]
  30. Walter J., Noyer-Weidner M., Trautner T. A. The amino acid sequence of the CCGG recognizing DNA methyltransferase M.BsuFI: implications for the analysis of sequence recognition by cytosine DNA methyltransferases. EMBO J. 1990 Apr;9(4):1007–1013. doi: 10.1002/j.1460-2075.1990.tb08203.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. 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]
  32. Wu J. C., Santi D. V. Kinetic and catalytic mechanism of HhaI methyltransferase. J Biol Chem. 1987 Apr 5;262(10):4778–4786. [PubMed] [Google Scholar]
  33. Wyszynski M. W., Gabbara S., Bhagwat A. S. Substitutions of a cysteine conserved among DNA cytosine methylases result in a variety of phenotypes. Nucleic Acids Res. 1992 Jan 25;20(2):319–326. doi: 10.1093/nar/20.2.319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Yen R. W., Vertino P. M., Nelkin B. D., Yu J. J., el-Deiry W., Cumaraswamy A., Lennon G. G., Trask B. J., Celano P., Baylin S. B. Isolation and characterization of the cDNA encoding human DNA methyltransferase. Nucleic Acids Res. 1992 May 11;20(9):2287–2291. doi: 10.1093/nar/20.9.2287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Yesufu H. M., Hanley A., Rinaldi A., Adams R. L. DNA methylase from Pisum sativum. Biochem J. 1991 Jan 15;273(Pt 2):469–475. doi: 10.1042/bj2730469. [DOI] [PMC free article] [PubMed] [Google Scholar]

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