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. 1987 Mar;169(3):939–943. doi: 10.1128/jb.169.3.939-943.1987

N4-methylcytosine as a minor base in bacterial DNA.

M Ehrlich, G G Wilson, K C Kuo, C W Gehrke
PMCID: PMC211883  PMID: 3029036

Abstract

The DNA base composition, including the minor base content, of 26 strains of bacteria was determined. The studied bacteria are sources of widely used restriction endonucleases. Approximately 35% of the bacterial DNAs contained N4-methylcytosine, about 60% contained 5-methylcytosine, and about 90% had N6-methyladenine.

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Selected References

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  1. Adams J., Rothman E. D. Estimation of phylogenetic relationships from DNA restriction patterns and selection of endonuclease cleavage sites. Proc Natl Acad Sci U S A. 1982 Jun;79(11):3560–3564. doi: 10.1073/pnas.79.11.3560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bird A. P., Southern E. M. Use of restriction enzymes to study eukaryotic DNA methylation: I. The methylation pattern in ribosomal DNA from Xenopus laevis. J Mol Biol. 1978 Jan 5;118(1):27–47. doi: 10.1016/0022-2836(78)90242-5. [DOI] [PubMed] [Google Scholar]
  3. 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]
  4. Brooks J. E., Roberts R. J. Modification profiles of bacterial genomes. Nucleic Acids Res. 1982 Feb 11;10(3):913–934. doi: 10.1093/nar/10.3.913. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Butkus V. V., Klimasauskas S. J., Janulaitis A. A. Analysis of products of DNA modification by methylases: a procedure for the determination of 5- and N4-methylcytosines in DNA. Anal Biochem. 1985 Jul;148(1):194–198. doi: 10.1016/0003-2697(85)90645-1. [DOI] [PubMed] [Google Scholar]
  6. Butkus V., Klimasauskas S., Kersulyte D., Vaitkevicius D., Lebionka A., Janulaitis A. Investigation of restriction-modification enzymes from M. varians RFL19 with a new type of specificity toward modification of substrate. Nucleic Acids Res. 1985 Aug 26;13(16):5727–5746. doi: 10.1093/nar/13.16.5727. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. DOSKOCIL J., SORMO'VA Z. THE OCCURRENCE OF 5-METHYLCYTOSINE IN BACTERIAL DEOXYRIBONUCLEIC ACIDS. Biochim Biophys Acta. 1965 Mar 15;95:513–515. [PubMed] [Google Scholar]
  8. DUNN D. B., SMITH J. D. The occurrence of 6-methylaminopurine in deoxyribonucleic acids. Biochem J. 1958 Apr;68(4):627–636. doi: 10.1042/bj0680627. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Dubin D. T., HsuChen C. C. The 3'-terminal region of mosquito mitochondrial small ribosomal subunit RNA: sequence and localization of methylated residues. Plasmid. 1983 May;9(3):307–320. doi: 10.1016/0147-619x(83)90008-2. [DOI] [PubMed] [Google Scholar]
  10. Dybvig K., Swinton D., Maniloff J., Hattman S. Cytosine methylation of the sequence GATC in a mycoplasma. J Bacteriol. 1982 Sep;151(3):1420–1424. doi: 10.1128/jb.151.3.1420-1424.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Ehrlich M., Gama-Sosa M. A., Carreira L. H., Ljungdahl L. G., Kuo K. C., Gehrke C. W. DNA methylation in thermophilic bacteria: N4-methylcytosine, 5-methylcytosine, and N6-methyladenine. Nucleic Acids Res. 1985 Feb 25;13(4):1399–1412. doi: 10.1093/nar/13.4.1399. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Ehrlich M., Norris K. F., Wang R. Y., Kuo K. C., Gehrke C. W. DNA cytosine methylation and heat-induced deamination. Biosci Rep. 1986 Apr;6(4):387–393. doi: 10.1007/BF01116426. [DOI] [PubMed] [Google Scholar]
  13. Fellner P. Nucleotide sequences from specific areas of the 16S and 23S ribosomal RNAs of E. coli. Eur J Biochem. 1969 Nov;11(1):12–27. doi: 10.1111/j.1432-1033.1969.tb00733.x. [DOI] [PubMed] [Google Scholar]
  14. Gehrke C. W., McCune R. A., Gama-Sosa M. A., Ehrlich M., Kuo K. C. Quantitative reversed-phase high-performance liquid chromatography of major and modified nucleosides in DNA. J Chromatogr. 1984 Sep 28;301(1):199–219. doi: 10.1016/s0021-9673(01)89189-5. [DOI] [PubMed] [Google Scholar]
  15. Glickman B. W., Radman M. Escherichia coli mutator mutants deficient in methylation-instructed DNA mismatch correction. Proc Natl Acad Sci U S A. 1980 Feb;77(2):1063–1067. doi: 10.1073/pnas.77.2.1063. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hattman S., Keister T., Gottehrer A. Sequence specificity of DNA methylases from Bacillus amyloliquefaciens and Bacillus brevis. J Mol Biol. 1978 Oct 5;124(4):701–711. doi: 10.1016/0022-2836(78)90178-x. [DOI] [PubMed] [Google Scholar]
  17. Huang L. H., Farnet C. M., Ehrlich K. C., Ehrlich M. Digestion of highly modified bacteriophage DNA by restriction endonucleases. Nucleic Acids Res. 1982 Mar 11;10(5):1579–1591. doi: 10.1093/nar/10.5.1579. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Janulaitis A., Klimasauskas S., Petrusyte M., Butkus V. Cytosine modification in DNA by BcnI methylase yields N4-methylcytosine. FEBS Lett. 1983 Sep 5;161(1):131–134. doi: 10.1016/0014-5793(83)80745-5. [DOI] [PubMed] [Google Scholar]
  19. Korch C., Hagblom P., Normark S. Sequence-specific DNA modification in Neisseria gonorrhoeae. J Bacteriol. 1983 Sep;155(3):1324–1332. doi: 10.1128/jb.155.3.1324-1332.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Lacks S., Greenberg B. Complementary specificity of restriction endonucleases of Diplococcus pneumoniae with respect to DNA methylation. J Mol Biol. 1977 Jul;114(1):153–168. doi: 10.1016/0022-2836(77)90289-3. [DOI] [PubMed] [Google Scholar]
  21. Lu A. L., Clark S., Modrich P. Methyl-directed repair of DNA base-pair mismatches in vitro. Proc Natl Acad Sci U S A. 1983 Aug;80(15):4639–4643. doi: 10.1073/pnas.80.15.4639. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Lui A. C., McBride B. C., Vovis G. F., Smith M. Site specific endonuclease from Fusobacterium nucleatum. Nucleic Acids Res. 1979 Jan;6(1):1–15. doi: 10.1093/nar/6.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. 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]
  24. McClelland M. The effect of site specific methylation on restriction endonuclease cleavage (update). Nucleic Acids Res. 1983 Jan 11;11(1):r169–r173. doi: 10.1093/nar/11.1.235-c. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Nussinov R. Doublet frequencies in evolutionary distinct groups. Nucleic Acids Res. 1984 Feb 10;12(3):1749–1763. doi: 10.1093/nar/12.3.1749. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Pukkila P. J., Peterson J., Herman G., Modrich P., Meselson M. Effects of high levels of DNA adenine methylation on methyl-directed mismatch repair in Escherichia coli. Genetics. 1983 Aug;104(4):571–582. doi: 10.1093/genetics/104.4.571. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Roberts R. J. Restriction and modification enzymes and their recognition sequences. Nucleic Acids Res. 1985;13 (Suppl):r165–r200. doi: 10.1093/nar/13.suppl.r165. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Roy P. H., Smith H. O. DNA methylases of Hemophilus influenzae Rd. II. Partial recognition site base sequences. J Mol Biol. 1973 Dec 25;81(4):445–459. doi: 10.1016/0022-2836(73)90516-0. [DOI] [PubMed] [Google Scholar]
  29. Schein A., Berdahl B. J., Low M., Borek E. Deficiency of the DNA of Micrococcus radiodurans in methyladenine and methylcytosine. Biochim Biophys Acta. 1972 Jul 20;272(3):481–485. doi: 10.1016/0005-2787(72)90400-5. [DOI] [PubMed] [Google Scholar]
  30. Sternberg N. Evidence that adenine methylation influences DNA-protein interactions in Escherichia coli. J Bacteriol. 1985 Oct;164(1):490–493. doi: 10.1128/jb.164.1.490-493.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Ullrich A., Dull T. J., Gray A., Philips J. A., 3rd, Peter S. Variation in the sequence and modification state of the human insulin gene flanking regions. Nucleic Acids Res. 1982 Apr 10;10(7):2225–2240. doi: 10.1093/nar/10.7.2225. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Wang R. Y., Kuo K. C., Gehrke C. W., Huang L. H., Ehrlich M. Heat- and alkali-induced deamination of 5-methylcytosine and cytosine residues in DNA. Biochim Biophys Acta. 1982 Jun 30;697(3):371–377. doi: 10.1016/0167-4781(82)90101-4. [DOI] [PubMed] [Google Scholar]
  33. Wang R. Y., Zhang X. Y., Ehrlich M. A human DNA-binding protein is methylation-specific and sequence-specific. Nucleic Acids Res. 1986 Feb 25;14(4):1599–1614. doi: 10.1093/nar/14.4.1599. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Woese C. R., Fox G. E., Zablen L., Uchida T., Bonen L., Pechman K., Lewis B. J., Stahl D. Conservation of primary structure in 16S ribosomal RNA. Nature. 1975 Mar 6;254(5495):83–86. doi: 10.1038/254083a0. [DOI] [PubMed] [Google Scholar]
  35. Yoo O. J., Dwyer-Hallquist P., Agarwal K. L. Purification and properties of the Hpa I methylase. Nucleic Acids Res. 1982 Oct 25;10(20):6511–6519. doi: 10.1093/nar/10.20.6511. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Youssoufian H., Mulder C. Detection of methylated sequences in eukaryotic DNA with the restriction endonucleases Smai and Xmai. J Mol Biol. 1981 Jul 25;150(1):133–136. doi: 10.1016/0022-2836(81)90328-4. [DOI] [PubMed] [Google Scholar]
  37. van der Ploeg L. H., Flavell R. A. DNA methylation in the human gamma delta beta-globin locus in erythroid and nonerythroid tissues. Cell. 1980 Apr;19(4):947–958. doi: 10.1016/0092-8674(80)90086-0. [DOI] [PubMed] [Google Scholar]

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