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Journal of Bacteriology logoLink to Journal of Bacteriology
. 1989 Oct;171(10):5738–5742. doi: 10.1128/jb.171.10.5738-5742.1989

Methylation of GATC sites is required for precise timing between rounds of DNA replication in Escherichia coli.

A Bakker 1, D W Smith 1
PMCID: PMC210423  PMID: 2676991

Abstract

We have used the Koppes and Nordstrøm (Cell 44:117-124, 1986) CsCl density transfer approach for analysis of DNA from exponentially growing, isogenic Escherichia coli dam+ and dam mutant cells to show that timing between DNA replication initiation events is precise in the dam+ cells but is essentially random in the dam cells. Thus, methylation of one or more GATC sites, such as those found in unusual abundance within the origin, oriC, is required for precise timing between rounds of DNA replication, and precise timing between initiation events is not required for cell viability. Both the dam-3 point mutant and the delta(dam)100 complete deletion mutant were examined. The results were independent of the mismatch repair system; E. coli mutH cells showed precise timing, whereas timing in the isogenic E. coli mutH delta(dam)100 double mutant was random. The mechanism is thus different from the role of Dam methylation in mismatch repair and probably involves conversion of hemimethylated GATC sites present in daughter origins just after initiation to a fully methylated state.

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Selected References

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

  1. Barbeyron T., Kean K., Forterre P. DNA adenine methylation of GATC sequences appeared recently in the Escherichia coli lineage. J Bacteriol. 1984 Nov;160(2):586–590. doi: 10.1128/jb.160.2.586-590.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Boye E., Løbner-Olesen A., Skarstad K. Timing of chromosomal replication in Escherichia coli. Biochim Biophys Acta. 1988 Dec 20;951(2-3):359–364. doi: 10.1016/0167-4781(88)90107-8. [DOI] [PubMed] [Google Scholar]
  3. Braun R. E., Wright A. DNA methylation differentially enhances the expression of one of the two E. coli dnaA promoters in vivo and in vitro. Mol Gen Genet. 1986 Feb;202(2):246–250. doi: 10.1007/BF00331644. [DOI] [PubMed] [Google Scholar]
  4. Geier G. E., Modrich P. Recognition sequence of the dam methylase of Escherichia coli K12 and mode of cleavage of Dpn I endonuclease. J Biol Chem. 1979 Feb 25;254(4):1408–1413. [PubMed] [Google Scholar]
  5. Glickman B. W., Rietveld K., Aaron C. S. gamma-Ray induced mutational spectrum in the lacI gene of Escherichia coli: comparison of induced and spontaneous spectra at the molecular level. Mutat Res. 1980 Jan;69(1):1–12. doi: 10.1016/0027-5107(80)90171-2. [DOI] [PubMed] [Google Scholar]
  6. Jonczyk P., Hines R., Smith D. W. The Escherichia coli dam gene is expressed as a distal gene of a new operon. Mol Gen Genet. 1989 May;217(1):85–96. doi: 10.1007/BF00330946. [DOI] [PubMed] [Google Scholar]
  7. Kogoma T. A novel Escherichia coli mutant capable of DNA replication in the absence of protein synthesis. J Mol Biol. 1978 May 5;121(1):55–69. doi: 10.1016/0022-2836(78)90262-0. [DOI] [PubMed] [Google Scholar]
  8. Koppes L., Nordström K. Insertion of an R1 plasmid into the origin of replication of the E. coli chromosome: random timing of replication of the hybrid chromosome. Cell. 1986 Jan 17;44(1):117–124. doi: 10.1016/0092-8674(86)90490-3. [DOI] [PubMed] [Google Scholar]
  9. Kücherer C., Lother H., Kölling R., Schauzu M. A., Messer W. Regulation of transcription of the chromosomal dnaA gene of Escherichia coli. Mol Gen Genet. 1986 Oct;205(1):115–121. doi: 10.1007/BF02428040. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. Lahue R. S., Modrich P. Methyl-directed DNA mismatch repair in Escherichia coli. Mutat Res. 1988 Mar;198(1):37–43. doi: 10.1016/0027-5107(88)90037-1. [DOI] [PubMed] [Google Scholar]
  12. Makris J. C., Nordmann P. L., Reznikoff W. S. Mutational analysis of insertion sequence 50 (IS50) and transposon 5 (Tn5) ends. Proc Natl Acad Sci U S A. 1988 Apr;85(7):2224–2228. doi: 10.1073/pnas.85.7.2224. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Messer W., Bellekes U., Lother H. Effect of dam methylation on the activity of the E. coli replication origin, oriC. EMBO J. 1985 May;4(5):1327–1332. doi: 10.1002/j.1460-2075.1985.tb03780.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Modrich P. Methyl-directed DNA mismatch correction. J Biol Chem. 1989 Apr 25;264(12):6597–6600. [PubMed] [Google Scholar]
  15. Murray N. E., Brammar W. J., Murray K. Lambdoid phages that simplify the recovery of in vitro recombinants. Mol Gen Genet. 1977 Jan 7;150(1):53–61. doi: 10.1007/BF02425325. [DOI] [PubMed] [Google Scholar]
  16. Nagai K., Hendrickson W., Balakrishnan R., Yamaki H., Boyd D., Schaechter M. Isolation of a replication origin complex from Escherichia coli. Proc Natl Acad Sci U S A. 1980 Jan;77(1):262–266. doi: 10.1073/pnas.77.1.262. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Nagata T., Meselson M. Periodic replication of DNA in steadily growing Escherichia coli: the localized origin of replication. Cold Spring Harb Symp Quant Biol. 1968;33:553–557. doi: 10.1101/sqb.1968.033.01.062. [DOI] [PubMed] [Google Scholar]
  18. Neidhardt F. C., Bloch P. L., Smith D. F. Culture medium for enterobacteria. J Bacteriol. 1974 Sep;119(3):736–747. doi: 10.1128/jb.119.3.736-747.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Ogden G. B., Pratt M. J., Schaechter M. The replicative origin of the E. coli chromosome binds to cell membranes only when hemimethylated. Cell. 1988 Jul 1;54(1):127–135. doi: 10.1016/0092-8674(88)90186-9. [DOI] [PubMed] [Google Scholar]
  20. 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]
  21. Russell D. W., Zinder N. D. Hemimethylation prevents DNA replication in E. coli. Cell. 1987 Sep 25;50(7):1071–1079. doi: 10.1016/0092-8674(87)90173-5. [DOI] [PubMed] [Google Scholar]
  22. Smith D. W., Garland A. M., Herman G., Enns R. E., Baker T. A., Zyskind J. W. Importance of state of methylation of oriC GATC sites in initiation of DNA replication in Escherichia coli. EMBO J. 1985 May;4(5):1319–1326. doi: 10.1002/j.1460-2075.1985.tb03779.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Yin J. C., Krebs M. P., Reznikoff W. S. Effect of dam methylation on Tn5 transposition. J Mol Biol. 1988 Jan 5;199(1):35–45. doi: 10.1016/0022-2836(88)90377-4. [DOI] [PubMed] [Google Scholar]
  24. Zyskind J. W., Cleary J. M., Brusilow W. S., Harding N. E., Smith D. W. Chromosomal replication origin from the marine bacterium Vibrio harveyi functions in Escherichia coli: oriC consensus sequence. Proc Natl Acad Sci U S A. 1983 Mar;80(5):1164–1168. doi: 10.1073/pnas.80.5.1164. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Zyskind J. W., Deen L. T., Smith D. W. Isolation and mapping of plasmids containing the Salmonella typhimurium origin of DNA replication. Proc Natl Acad Sci U S A. 1979 Jul;76(7):3097–3101. doi: 10.1073/pnas.76.7.3097. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. de Massy B., Fayet O., Kogoma T. Multiple origin usage for DNA replication in sdrA(rnh) mutants of Escherichia coli K-12. Initiation in the absence of oriC. J Mol Biol. 1984 Sep 15;178(2):227–236. doi: 10.1016/0022-2836(84)90141-4. [DOI] [PubMed] [Google Scholar]

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