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. 1987 Mar 25;15(6):2479–2497. doi: 10.1093/nar/15.6.2479

Transcripts within the replication origin, oriC, of Escherichia coli.

M A Schauzu, C Kücherer, R Kölling, W Messer, H Lother
PMCID: PMC340664  PMID: 3031600

Abstract

Transcription start and termination sites were mapped in the E. coli replication origin, oriC. Outward transcription from within oriC (promoters Pori-r and Pori-l) was found to start in vivo at position 178 for Pori-l and at positions 294 and 304 for Pori-r, respectively. These transcripts were terminated after 100-150 bases, at terminators designated Tori-l and Tori-r. Transcription from the 16 kd promoter, which lies clockwise adjacent to oriC and promotes transcription toward oriC, started at position 757 and gave transcripts with 3' ends at several positions within and to the left of the minimal replication origin. However, the majority of transcripts traversed the whole oriC region, and were not terminated within the DNA segment tested. Transcription of the chromosomal 16 kd gene was negatively regulated by DnaA protein and positively affected by dam methylation. The possible function of these transcripts is discussed.

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Selected References

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  1. Amann E., Brosius J., Ptashne M. Vectors bearing a hybrid trp-lac promoter useful for regulated expression of cloned genes in Escherichia coli. Gene. 1983 Nov;25(2-3):167–178. doi: 10.1016/0378-1119(83)90222-6. [DOI] [PubMed] [Google Scholar]
  2. Atlung T. Allele-specific suppression of dnaA(Ts) mutations by rpoB mutations in Escherichia coli. Mol Gen Genet. 1984;197(1):125–128. doi: 10.1007/BF00327932. [DOI] [PubMed] [Google Scholar]
  3. Atlung T., Clausen E. S., Hansen F. G. Autoregulation of the dnaA gene of Escherichia coli K12. Mol Gen Genet. 1985;200(3):442–450. doi: 10.1007/BF00425729. [DOI] [PubMed] [Google Scholar]
  4. Backman K., Ptashne M., Gilbert W. Construction of plasmids carrying the cI gene of bacteriophage lambda. Proc Natl Acad Sci U S A. 1976 Nov;73(11):4174–4178. doi: 10.1073/pnas.73.11.4174. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bagdasarian M. M., Izakowska M., Bagdasarian M. Suppression of the DnaA phenotype by mutations in the rpoB cistron of ribonucleic acid polymerase in Salmonella typhimurium and Escherichia coli. J Bacteriol. 1977 May;130(2):577–582. doi: 10.1128/jb.130.2.577-582.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Berk A. J., Sharp P. A. Structure of the adenovirus 2 early mRNAs. Cell. 1978 Jul;14(3):695–711. doi: 10.1016/0092-8674(78)90252-0. [DOI] [PubMed] [Google Scholar]
  7. Braun R. E., O'Day K., Wright A. Autoregulation of the DNA replication gene dnaA in E. coli K-12. Cell. 1985 Jan;40(1):159–169. doi: 10.1016/0092-8674(85)90319-8. [DOI] [PubMed] [Google Scholar]
  8. 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]
  9. 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]
  10. Brosius J., Cate R. L., Perlmutter A. P. Precise location of two promoters for the beta-lactamase gene of pBR322. S1 mapping of ribonucleic acid isolated from Escherichia coli or synthesized in vitro. J Biol Chem. 1982 Aug 10;257(15):9205–9210. [PubMed] [Google Scholar]
  11. Buhk H. J., Messer W. The replication origin region of Escherichia coli: nucleotide sequence and functional units. Gene. 1983 Oct;24(2-3):265–279. doi: 10.1016/0378-1119(83)90087-2. [DOI] [PubMed] [Google Scholar]
  12. Fuller R. S., Funnell B. E., Kornberg A. The dnaA protein complex with the E. coli chromosomal replication origin (oriC) and other DNA sites. Cell. 1984 Oct;38(3):889–900. doi: 10.1016/0092-8674(84)90284-8. [DOI] [PubMed] [Google Scholar]
  13. Fuller R. S., Kaguni J. M., Kornberg A. Enzymatic replication of the origin of the Escherichia coli chromosome. Proc Natl Acad Sci U S A. 1981 Dec;78(12):7370–7374. doi: 10.1073/pnas.78.12.7370. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hansen E. B., Hansen F. G., von Meyenburg K. The nucleotide sequence of the dnaA gene and the first part of the dnaN gene of Escherichia coli K-12. Nucleic Acids Res. 1982 Nov 25;10(22):7373–7385. doi: 10.1093/nar/10.22.7373. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hansen F. G., Rasmussen K. V. Regulation of the dnaA product in Escherichia coli. Mol Gen Genet. 1977 Oct 20;155(2):219–225. doi: 10.1007/BF00393163. [DOI] [PubMed] [Google Scholar]
  16. Hirose S., Hiraga S., Okazaki T. Initiation site of deoxyribonucleotide polymerization at the replication origin of the Escherichia coli chromosome. Mol Gen Genet. 1983;189(3):422–431. doi: 10.1007/BF00325904. [DOI] [PubMed] [Google Scholar]
  17. Holmes W. M., Platt T., Rosenberg M. Termination of transcription in E. coli. Cell. 1983 Apr;32(4):1029–1032. doi: 10.1016/0092-8674(83)90287-8. [DOI] [PubMed] [Google Scholar]
  18. Junker D. E., Jr, Rokeach L. A., Ganea D., Chiaramello A., Zyskind J. W. Transcription termination within the Escherichia coli origin of DNA replication, oriC. Mol Gen Genet. 1986 Apr;203(1):101–109. doi: 10.1007/BF00330390. [DOI] [PubMed] [Google Scholar]
  19. Kohara Y., Tohdoh N., Jiang X. W., Okazaki T. The distribution and properties of RNA primed initiation sites of DNA synthesis at the replication origin of Escherichia coli chromosome. Nucleic Acids Res. 1985 Oct 11;13(19):6847–6866. doi: 10.1093/nar/13.19.6847. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. 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]
  21. Lark K. G. Evidence for the direct involvement of RNA in the initiation of DNA replication in Escherichia coli 15T. J Mol Biol. 1972 Feb 28;64(1):47–60. doi: 10.1016/0022-2836(72)90320-8. [DOI] [PubMed] [Google Scholar]
  22. Lother H., Kölling R., Kücherer C., Schauzu M. dnaA protein-regulated transcription: effects on the in vitro replication of Escherichia coli minichromosomes. EMBO J. 1985 Feb;4(2):555–560. doi: 10.1002/j.1460-2075.1985.tb03664.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Lother H., Messer W. Promoters in the E. coli replication origin. Nature. 1981 Nov 26;294(5839):376–378. doi: 10.1038/294376a0. [DOI] [PubMed] [Google Scholar]
  24. Marinus M. G., Morris N. R. Isolation of deoxyribonucleic acid methylase mutants of Escherichia coli K-12. J Bacteriol. 1973 Jun;114(3):1143–1150. doi: 10.1128/jb.114.3.1143-1150.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  26. Meijer M., Beck E., Hansen F. G., Bergmans H. E., Messer W., von Meyenburg K., Schaller H. Nucleotide sequence of the origin of replication of the Escherichia coli K-12 chromosome. Proc Natl Acad Sci U S A. 1979 Feb;76(2):580–584. doi: 10.1073/pnas.76.2.580. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Meijer M., Messer W. Functional analysis of minichromosome replication: bidirectional and unidirectional replication from the Escherichia coli replication origin, oriC. J Bacteriol. 1980 Aug;143(2):1049–1053. doi: 10.1128/jb.143.2.1049-1053.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. 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]
  29. Messer W. Initiation of deoxyribonucleic acid replication in Escherichia coli B-r: chronology of events and transcriptional control of initiation. J Bacteriol. 1972 Oct;112(1):7–12. doi: 10.1128/jb.112.1.7-12.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Ogawa T., Baker T. A., van der Ende A., Kornberg A. Initiation of enzymatic replication at the origin of the Escherichia coli chromosome: contributions of RNA polymerase and primase. Proc Natl Acad Sci U S A. 1985 Jun;82(11):3562–3566. doi: 10.1073/pnas.82.11.3562. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Oka A., Sugimoto K., Takanami M., Hirota Y. Replication origin of the Escherichia coli K-12 chromosome: the size and structure of the minimum DNA segment carrying the information for autonomous replication. Mol Gen Genet. 1980 Apr;178(1):9–20. doi: 10.1007/BF00267207. [DOI] [PubMed] [Google Scholar]
  32. Polaczek P., Cieśla Z. Effect of altered efficiency of the RNA I and RNA II promoters on in vivo replication of ColE1-like plasmids in Escherichia coli. Mol Gen Genet. 1984;194(1-2):227–231. doi: 10.1007/BF00383521. [DOI] [PubMed] [Google Scholar]
  33. Rak B., von Reutern M. Insertion element IS5 contains a third gene. EMBO J. 1984 Apr;3(4):807–811. doi: 10.1002/j.1460-2075.1984.tb01889.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Rasmussen K. V., Atlung T., Kerszman G., Hansen G. E., Hansen F. G. Conditional change of DNA replication control in an RNA polymerase mutant of Escherichia coli. J Bacteriol. 1983 Apr;154(1):443–451. doi: 10.1128/jb.154.1.443-451.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Rokeach L. A., Zyskind J. W. RNA terminating within the E. coli origin of replication: stringent regulation and control by DnaA protein. Cell. 1986 Aug 29;46(5):763–771. doi: 10.1016/0092-8674(86)90352-1. [DOI] [PubMed] [Google Scholar]
  36. Schaus N., O'Day K., Peters W., Wright A. Isolation and characterization of amber mutations in gene dnaA of escherichia coli K-12. J Bacteriol. 1981 Feb;145(2):904–913. doi: 10.1128/jb.145.2.904-913.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Seiler A., Blöcker H., Frank R., Kahmann R. The mom gene of bacteriophage Mu: the mechanism of methylation-dependent expression. EMBO J. 1986 Oct;5(10):2719–2728. doi: 10.1002/j.1460-2075.1986.tb04556.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Seufert W., Messer W. Initiation of Escherichia coli minichromosome replication at oriC and at protein n' recognition sites. Two modes for initiating DNA synthesis in vitro. EMBO J. 1986 Dec 1;5(12):3401–3406. doi: 10.1002/j.1460-2075.1986.tb04656.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. 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]
  40. 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]
  41. Stueber D., Bujard H. Transcription from efficient promoters can interfere with plasmid replication and diminish expression of plasmid specified genes. EMBO J. 1982;1(11):1399–1404. doi: 10.1002/j.1460-2075.1982.tb01329.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Stuitje A. R., Meijer M. Maintenance and incompatibility of plasmids carrying the replication origin of the Escherichia coli chromosome: evidence for a control region of replication between oriC and asnA. Nucleic Acids Res. 1983 Aug 25;11(16):5775–5791. doi: 10.1093/nar/11.16.5775. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Stuitje A. R., de Wind N., van der Spek J. C., Pors T. H., Meijer M. Dissection of promoter sequences involved in transcriptional activation of the Escherichia coli replication origin. Nucleic Acids Res. 1986 Mar 11;14(5):2333–2344. doi: 10.1093/nar/14.5.2333. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Tanaka M., Ohmori H., Hiraga S. A novel type of E. coli mutants with increased chromosomal copy number. Mol Gen Genet. 1983;192(1-2):51–60. doi: 10.1007/BF00327646. [DOI] [PubMed] [Google Scholar]
  45. Tippe-Schindler R., Zahn G., Messer W. Control of the initiation of DNA replication in Escherichia coli. I. Negative control of initiation. Mol Gen Genet. 1979 Jan 10;168(2):185–195. doi: 10.1007/BF00431444. [DOI] [PubMed] [Google Scholar]
  46. Tomizawa J., Itoh T. Plasmid ColE1 incompatibility determined by interaction of RNA I with primer transcript. Proc Natl Acad Sci U S A. 1981 Oct;78(10):6096–6100. doi: 10.1073/pnas.78.10.6096. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Yamaguchi K., Yamaguchi M., Tomizawa J. Incompatibility of plasmids containing the replication origin of the Escherichia coli chromosome. Proc Natl Acad Sci U S A. 1982 Sep;79(17):5347–5351. doi: 10.1073/pnas.79.17.5347. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Zyskind J. W., Deen L. T., Smith D. W. Temporal sequence of events during the initiation process in Escherichia coli deoxyribonucleic acid replication: roles of the dnaA and dnaC gene products and ribonucleic acid polymerase. J Bacteriol. 1977 Mar;129(3):1466–1475. doi: 10.1128/jb.129.3.1466-1475.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. van der Ende A., Baker T. A., Ogawa T., Kornberg A. Initiation of enzymatic replication at the origin of the Escherichia coli chromosome: primase as the sole priming enzyme. Proc Natl Acad Sci U S A. 1985 Jun;82(12):3954–3958. doi: 10.1073/pnas.82.12.3954. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. von Meyenburg K., Hansen F. G., Riise E., Bergmans H. E., Meijer M., Messer W. Origin of replication, oriC, of the Escherichia coli K12 chromosome: genetic mapping and minichromosome replication. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):121–128. doi: 10.1101/sqb.1979.043.01.018. [DOI] [PubMed] [Google Scholar]

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