Abstract
A novel gene encoding a cytosine-5-DNA methyltransferase recognizing the dinucleotide GpC was cloned from Chlorella virus NYs-1 and expressed in both Escherichia coli and Saccharomyces cerevisiae . The gene was sequenced and a predicted polypeptide of 362 amino acids with a molecular weight of 41.903 kDa was identified. The protein contains several amino acid motifs with high similarity to those of other known 5-methylcytosine-forming methyltransferases. In addition, this enzyme, named M. Cvi PI, shares 66% identity and 76% similarity with M. Cvi JI, the only other cytosine-5-DNA methyltransferase cloned from a Chlorella virus. The short, frequently occurring recognition sequence of the new methyltransferase will be very useful for in vivo chromatin structure studies in both yeast and higher organisms.
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- Backman K. A cautionary note on the use of certain restriction endonucleases with methylated substrates. Gene. 1980 Oct;11(1-2):169–171. doi: 10.1016/0378-1119(80)90097-9. [DOI] [PubMed] [Google Scholar]
- Bussey H., Kaback D. B., Zhong W., Vo D. T., Clark M. W., Fortin N., Hall J., Ouellette B. F., Keng T., Barton A. B. The nucleotide sequence of chromosome I from Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1995 Apr 25;92(9):3809–3813. doi: 10.1073/pnas.92.9.3809. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cheng X., Kumar S., Posfai J., Pflugrath J. W., Roberts R. J. Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine. Cell. 1993 Jul 30;74(2):299–307. doi: 10.1016/0092-8674(93)90421-l. [DOI] [PubMed] [Google Scholar]
- Dujon B., Alexandraki D., André B., Ansorge W., Baladron V., Ballesta J. P., Banrevi A., Bolle P. A., Bolotin-Fukuhara M., Bossier P. Complete DNA sequence of yeast chromosome XI. Nature. 1994 Jun 2;369(6479):371–378. doi: 10.1038/369371a0. [DOI] [PubMed] [Google Scholar]
- Dy L., Chalasani S., Essani K. Isolation of Escherichia coli mutants lacking methylcytosine-dependent restriction systems for cloning extensively methylated frog virus 3 DNA. Gene. 1993 Sep 6;131(1):87–91. doi: 10.1016/0378-1119(93)90673-q. [DOI] [PubMed] [Google Scholar]
- Finnegan E. J., Dennis E. S. Isolation and identification by sequence homology of a putative cytosine methyltransferase from Arabidopsis thaliana. Nucleic Acids Res. 1993 May 25;21(10):2383–2388. doi: 10.1093/nar/21.10.2383. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Frommer M., McDonald L. E., Millar D. S., Collis C. M., Watt F., Grigg G. W., Molloy P. L., Paul C. L. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A. 1992 Mar 1;89(5):1827–1831. doi: 10.1073/pnas.89.5.1827. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Giniger E., Varnum S. M., Ptashne M. Specific DNA binding of GAL4, a positive regulatory protein of yeast. Cell. 1985 Apr;40(4):767–774. doi: 10.1016/0092-8674(85)90336-8. [DOI] [PubMed] [Google Scholar]
- Jacq C., Alt-Mörbe J., Andre B., Arnold W., Bahr A., Ballesta J. P., Bargues M., Baron L., Becker A., Biteau N. The nucleotide sequence of Saccharomyces cerevisiae chromosome IV. Nature. 1997 May 29;387(6632 Suppl):75–78. [PubMed] [Google Scholar]
- Johnston M., Flick J. S., Pexton T. Multiple mechanisms provide rapid and stringent glucose repression of GAL gene expression in Saccharomyces cerevisiae. Mol Cell Biol. 1994 Jun;14(6):3834–3841. doi: 10.1128/mcb.14.6.3834. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kim Y., Geiger J. H., Hahn S., Sigler P. B. Crystal structure of a yeast TBP/TATA-box complex. Nature. 1993 Oct 7;365(6446):512–520. doi: 10.1038/365512a0. [DOI] [PubMed] [Google Scholar]
- Kladde M. P., Xu M., Simpson R. T. Direct study of DNA-protein interactions in repressed and active chromatin in living cells. EMBO J. 1996 Nov 15;15(22):6290–6300. [PMC free article] [PubMed] [Google Scholar]
- Maas R. An improved colony hybridization method with significantly increased sensitivity for detection of single genes. Plasmid. 1983 Nov;10(3):296–298. doi: 10.1016/0147-619x(83)90045-8. [DOI] [PubMed] [Google Scholar]
- Mann M. B., Smith H. O. Specificity of Hpa II and Hae III DNA methylases. Nucleic Acids Res. 1977 Dec;4(12):4211–4221. doi: 10.1093/nar/4.12.4211. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Nelson M., Zhang Y., Van Etten J. L. DNA methyltransferases and DNA site-specific endonucleases encoded by chlorella viruses. EXS. 1993;64:186–211. doi: 10.1007/978-3-0348-9118-9_9. [DOI] [PubMed] [Google Scholar]
- Oliver S. G., van der Aart Q. J., Agostoni-Carbone M. L., Aigle M., Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J. P., Benit P. The complete DNA sequence of yeast chromosome III. Nature. 1992 May 7;357(6373):38–46. doi: 10.1038/357038a0. [DOI] [PubMed] [Google Scholar]
- 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]
- Raleigh E. A. Restriction and modification in vivo by Escherichia coli K12. Methods Enzymol. 1987;152:130–141. doi: 10.1016/0076-6879(87)52015-8. [DOI] [PubMed] [Google Scholar]
- 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]
- Renbaum P., Abrahamove D., Fainsod A., Wilson G. G., Rottem S., Razin A. Cloning, characterization, and expression in Escherichia coli of the gene coding for the CpG DNA methylase from Spiroplasma sp. strain MQ1(M.SssI). Nucleic Acids Res. 1990 Mar 11;18(5):1145–1152. doi: 10.1093/nar/18.5.1145. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schuster A. M., Burbank D. E., Meister B., Skrdla M. P., Meints R. H., Hattman S., Swinton D., Van Etten J. L. Characterization of viruses infecting a eukaryotic Chlorella-like green alga. Virology. 1986 Apr 15;150(1):170–177. doi: 10.1016/0042-6822(86)90276-x. [DOI] [PubMed] [Google Scholar]
- 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]
- Studier F. W., Rosenberg A. H., Dunn J. J., Dubendorff J. W. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 1990;185:60–89. doi: 10.1016/0076-6879(90)85008-c. [DOI] [PubMed] [Google Scholar]
- Tazi J., Bird A. Alternative chromatin structure at CpG islands. Cell. 1990 Mar 23;60(6):909–920. doi: 10.1016/0092-8674(90)90339-g. [DOI] [PubMed] [Google Scholar]
- Thompson J. D., Higgins D. G., Gibson T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov 11;22(22):4673–4680. doi: 10.1093/nar/22.22.4673. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Xu M., Simpson R. T., Kladde M. P. Gal4p-mediated chromatin remodeling depends on binding site position in nucleosomes but does not require DNA replication. Mol Cell Biol. 1998 Mar;18(3):1201–1212. doi: 10.1128/mcb.18.3.1201. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zhang Y., Nelson M., Van Etten J. L. A single amino acid change restores DNA cytosine methyltransferase activity in a cloned chlorella virus pseudogene. Nucleic Acids Res. 1992 Apr 11;20(7):1637–1642. doi: 10.1093/nar/20.7.1637. [DOI] [PMC free article] [PubMed] [Google Scholar]