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. 1997 Nov 15;25(22):4666–4673. doi: 10.1093/nar/25.22.4666

Baculovirus-mediated expression and characterization of the full-length murine DNA methyltransferase.

S Pradhan 1, D Talbot 1, M Sha 1, J Benner 1, L Hornstra 1, E Li 1, R Jaenisch 1, R J Roberts 1
PMCID: PMC147102  PMID: 9358180

Abstract

The original cDNA sequence reported for the murine DNA methyltransferase (MTase) was not full length. Recently, additional cDNA sequences have been reported that lie upstream of the original and contain an extended open reading frame with three additional ATGs in frame with the coding region [Tucker et al . (1996) Proc. Natl. Acad. Sci. USA , 93, 12920-12925; Yoder et al . (1996) J. Biol. Chem . 271, 31092-31097]. Genomic DNA upstream of this ATG contains two more ATGs in frame and no obvious splice site. We have constructed, and expressed in baculovirus, MTase clones that begin at each of these four ATGs and examined their properties. Constructs beginning with any of the first three ATGs as their initiator methionines give a predominant DNA MTase band of approximately 185 kDa on SDS-PAGE corresponding to translational initiation at the third ATG. The fourth ATG construct gives a much smaller protein band of 173 kDa. The 185 kDa protein was purified by HPLC, characterized by mass spectrometry and has a measured molecular mass of 184 +/- 0.5 kDa. All of these MTases were functional in vitro and steady state kinetic analysis showed that the recombinant proteins exhibit similar kinetic properties irrespective of their length. The homogeneous recombinant enzyme from the fourth ATG construct shows a 2.5-fold preference for a hemi-methylated DNA substrate as compared to an unmethylated substrate, whereas the 185 kDa protein is equally active on both substrates. The kinetic properties of the recombinant enzyme are similar to those reported for the native MTase derived from murine erythroleukemia cells. The new clones are capable of yielding large quantities of intact MTases for further structural and functional studies.

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Selected References

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  1. Barlow D. P. Gametic imprinting in mammals. Science. 1995 Dec 8;270(5242):1610–1613. doi: 10.1126/science.270.5242.1610. [DOI] [PubMed] [Google Scholar]
  2. Bestor T. H. Activation of mammalian DNA methyltransferase by cleavage of a Zn binding regulatory domain. EMBO J. 1992 Jul;11(7):2611–2617. doi: 10.1002/j.1460-2075.1992.tb05326.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bestor T. H., Hellewell S. B., Ingram V. M. Differentiation of two mouse cell lines is associated with hypomethylation of their genomes. Mol Cell Biol. 1984 Sep;4(9):1800–1806. doi: 10.1128/mcb.4.9.1800. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bestor T. H., Ingram V. M. Growth-dependent expression of multiple species of DNA methyltransferase in murine erythroleukemia cells. Proc Natl Acad Sci U S A. 1985 May;82(9):2674–2678. doi: 10.1073/pnas.82.9.2674. [DOI] [PMC free article] [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. Bolden A., Ward C., Siedlecki J. A., Weissbach A. DNA methylation. Inhibition of de novo and maintenance methylation in vitro by RNA and synthetic polynucleotides. J Biol Chem. 1984 Oct 25;259(20):12437–12443. [PubMed] [Google Scholar]
  7. Brown R. S., Lennon J. J. Mass resolution improvement by incorporation of pulsed ion extraction in a matrix-assisted laser desorption/ionization linear time-of-flight mass spectrometer. Anal Chem. 1995 Jul 1;67(13):1998–2003. doi: 10.1021/ac00109a015. [DOI] [PubMed] [Google Scholar]
  8. Christman J. K., Sheikhnejad G., Marasco C. J., Sufrin J. R. 5-Methyl-2'-deoxycytidine in single-stranded DNA can act in cis to signal de novo DNA methylation. Proc Natl Acad Sci U S A. 1995 Aug 1;92(16):7347–7351. doi: 10.1073/pnas.92.16.7347. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Cooper D. N., Youssoufian H. The CpG dinucleotide and human genetic disease. Hum Genet. 1988 Feb;78(2):151–155. doi: 10.1007/BF00278187. [DOI] [PubMed] [Google Scholar]
  10. Czank A., Häuselmann R., Page A. W., Leonhardt H., Bestor T. H., Schaffner W., Hergersberg M. Expression in mammalian cells of a cloned gene encoding murine DNA methyltransferase. Gene. 1991 Dec 30;109(2):259–263. doi: 10.1016/0378-1119(91)90618-l. [DOI] [PubMed] [Google Scholar]
  11. DePaoli-Roach A., Roach P. J., Zucker K. E., Smith S. S. Selective phosphorylation of human DNA methyltransferase by protein kinase C. FEBS Lett. 1986 Mar 3;197(1-2):149–153. doi: 10.1016/0014-5793(86)80316-7. [DOI] [PubMed] [Google Scholar]
  12. Engler P., Weng A., Storb U. Influence of CpG methylation and target spacing on V(D)J recombination in a transgenic substrate. Mol Cell Biol. 1993 Jan;13(1):571–577. doi: 10.1128/mcb.13.1.571. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Flynn J., Glickman J. F., Reich N. O. Murine DNA cytosine-C5 methyltransferase: pre-steady- and steady-state kinetic analysis with regulatory DNA sequences. Biochemistry. 1996 Jun 11;35(23):7308–7315. doi: 10.1021/bi9600512. [DOI] [PubMed] [Google Scholar]
  14. Gartler S. M., Riggs A. D. Mammalian X-chromosome inactivation. Annu Rev Genet. 1983;17:155–190. doi: 10.1146/annurev.ge.17.120183.001103. [DOI] [PubMed] [Google Scholar]
  15. Glickman J. F., Flynn J., Reich N. O. Purification and characterization of recombinant baculovirus-expressed mouse DNA methyltransferase. Biochem Biophys Res Commun. 1997 Jan 13;230(2):280–284. doi: 10.1006/bbrc.1996.5943. [DOI] [PubMed] [Google Scholar]
  16. Glickman J. F., Reich N. O. Baculovirus-mediated high level expression of a mammalian DNA methyltransferase. Biochem Biophys Res Commun. 1994 Nov 15;204(3):1003–1008. doi: 10.1006/bbrc.1994.2562. [DOI] [PubMed] [Google Scholar]
  17. Jones P. A., Buckley J. D. The role of DNA methylation in cancer. Adv Cancer Res. 1990;54:1–23. doi: 10.1016/s0065-230x(08)60806-4. [DOI] [PubMed] [Google Scholar]
  18. Kass S. U., Goddard J. P., Adams R. L. Inactive chromatin spreads from a focus of methylation. Mol Cell Biol. 1993 Dec;13(12):7372–7379. doi: 10.1128/mcb.13.12.7372. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Klimasauskas S., Kumar S., Roberts R. J., Cheng X. HhaI methyltransferase flips its target base out of the DNA helix. Cell. 1994 Jan 28;76(2):357–369. doi: 10.1016/0092-8674(94)90342-5. [DOI] [PubMed] [Google Scholar]
  20. Kumar S., Cheng X., Klimasauskas S., Mi S., Posfai J., Roberts R. J., Wilson G. G. The DNA (cytosine-5) methyltransferases. Nucleic Acids Res. 1994 Jan 11;22(1):1–10. doi: 10.1093/nar/22.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Kumar S., Cheng X., Pflugrath J. W., Roberts R. J. Purification, crystallization, and preliminary X-ray diffraction analysis of an M.HhaI-AdoMet complex. Biochemistry. 1992 Sep 15;31(36):8648–8653. doi: 10.1021/bi00151a035. [DOI] [PubMed] [Google Scholar]
  22. Lei H., Oh S. P., Okano M., Jüttermann R., Goss K. A., Jaenisch R., Li E. De novo DNA cytosine methyltransferase activities in mouse embryonic stem cells. Development. 1996 Oct;122(10):3195–3205. doi: 10.1242/dev.122.10.3195. [DOI] [PubMed] [Google Scholar]
  23. 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]
  24. Li E., Bestor T. H., Jaenisch R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell. 1992 Jun 12;69(6):915–926. doi: 10.1016/0092-8674(92)90611-f. [DOI] [PubMed] [Google Scholar]
  25. 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]
  26. Matsudaira P. Sequence from picomole quantities of proteins electroblotted onto polyvinylidene difluoride membranes. J Biol Chem. 1987 Jul 25;262(21):10035–10038. [PubMed] [Google Scholar]
  27. Migeon B. R. X-chromosome inactivation: molecular mechanisms and genetic consequences. Trends Genet. 1994 Jul;10(7):230–235. doi: 10.1016/0168-9525(94)90169-4. [DOI] [PubMed] [Google Scholar]
  28. Monk M. Changes in DNA methylation during mouse embryonic development in relation to X-chromosome activity and imprinting. Philos Trans R Soc Lond B Biol Sci. 1990 Jan 30;326(1235):299–312. doi: 10.1098/rstb.1990.0013. [DOI] [PubMed] [Google Scholar]
  29. Rein T., Zorbas H., DePamphilis M. L. Active mammalian replication origins are associated with a high-density cluster of mCpG dinucleotides. Mol Cell Biol. 1997 Jan;17(1):416–426. doi: 10.1128/mcb.17.1.416. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Reinisch K. M., Chen L., Verdine G. L., Lipscomb W. N. The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing. Cell. 1995 Jul 14;82(1):143–153. doi: 10.1016/0092-8674(95)90060-8. [DOI] [PubMed] [Google Scholar]
  31. SWARTZ M. N., TRAUTNER T. A., KORNBERG A. Enzymatic synthesis of deoxyribonucleic acid. XI. Further studies on nearest neighbor base sequences in deoxyribonucleic acids. J Biol Chem. 1962 Jun;237:1961–1967. [PubMed] [Google Scholar]
  32. Smith S. S., Kan J. L., Baker D. J., Kaplan B. E., Dembek P. Recognition of unusual DNA structures by human DNA (cytosine-5)methyltransferase. J Mol Biol. 1991 Jan 5;217(1):39–51. doi: 10.1016/0022-2836(91)90609-a. [DOI] [PubMed] [Google Scholar]
  33. Smith S. S., Kaplan B. E., Sowers L. C., Newman E. M. Mechanism of human methyl-directed DNA methyltransferase and the fidelity of cytosine methylation. Proc Natl Acad Sci U S A. 1992 May 15;89(10):4744–4748. doi: 10.1073/pnas.89.10.4744. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Smith S. S., Lingeman R. G., Kaplan B. E. Recognition of foldback DNA by the human DNA (cytosine-5-)-methyltransferase. Biochemistry. 1992 Jan 28;31(3):850–854. doi: 10.1021/bi00118a030. [DOI] [PubMed] [Google Scholar]
  35. Sved J., Bird A. The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4692–4696. doi: 10.1073/pnas.87.12.4692. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Tollefsbol T. O., Hutchison C. A., 3rd Mammalian DNA (cytosine-5-)-methyltransferase expressed in Escherichia coli, purified and characterized. J Biol Chem. 1995 Aug 4;270(31):18543–18550. doi: 10.1074/jbc.270.31.18543. [DOI] [PubMed] [Google Scholar]
  37. Tucker K. L., Talbot D., Lee M. A., Leonhardt H., Jaenisch R. Complementation of methylation deficiency in embryonic stem cells by a DNA methyltransferase minigene. Proc Natl Acad Sci U S A. 1996 Nov 12;93(23):12920–12925. doi: 10.1073/pnas.93.23.12920. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Vertino P. M., Yen R. W., Gao J., Baylin S. B. De novo methylation of CpG island sequences in human fibroblasts overexpressing DNA (cytosine-5-)-methyltransferase. Mol Cell Biol. 1996 Aug;16(8):4555–4565. doi: 10.1128/mcb.16.8.4555. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Waite-Rees P. A., Keating C. J., Moran L. S., Slatko B. E., Hornstra L. J., Benner J. S. Characterization and expression of the Escherichia coli Mrr restriction system. J Bacteriol. 1991 Aug;173(16):5207–5219. doi: 10.1128/jb.173.16.5207-5219.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. 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]
  41. Xu G., Flynn J., Glickman J. F., Reich N. O. Purification and stabilization of mouse DNA methyltransferase. Biochem Biophys Res Commun. 1995 Feb 15;207(2):544–551. doi: 10.1006/bbrc.1995.1222. [DOI] [PubMed] [Google Scholar]
  42. Yoder J. A., Yen R. W., Vertino P. M., Bestor T. H., Baylin S. B. New 5' regions of the murine and human genes for DNA (cytosine-5)-methyltransferase. J Biol Chem. 1996 Dec 6;271(49):31092–31097. doi: 10.1074/jbc.271.49.31092. [DOI] [PubMed] [Google Scholar]

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