Skip to main content
NCBI home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1996 Oct;178(20):6006–6012. doi: 10.1128/jb.178.20.6006-6012.1996

Fis binding in the dnaA operon promoter region.

J M Froelich 1, T K Phuong 1, J W Zyskind 1
PMCID: PMC178459  PMID: 8830699

Abstract

The region between the rpmH and dnaA genes contains five promoters that divergently express the ribosomal protein L34 and the proteins of the dnaA operon, including DnaA, the beta clamp of DNA polymerase III holoenzyme, and RecF. The DNA-binding protein Fis was shown by the band shift assay to bind near the rpmHp2 and dnaAp2 promoters and by DNase I footprinting to bind to a single site in the dnaAp2 promoter overlapping the -35 and spacer sequences. There were no observable differences in Fis affinity or the angle of bending induced by Fis between methylated and unmethylated DNA fragments containing the Fis binding site in the dnaAp2 promoter. Fis directly or indirectly represses the expression of DnaA protein and the beta clamp of DNA polymerase III. A fis null mutant containing a dnaA-lacZ in-frame fusion had twofold greater beta-galactosidase activity than a fis wild-type strain, and induced expression of Fis eliminated the increase in activity of the fusion protein. A two- to threefold increase in the levels of DnaA and beta clamp proteins was found in a fis null mutant by immunoblot gel analysis.

Full Text

The Full Text of this article is available as a PDF (1.5 MB).

Selected References

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

  1. Armengod M. E., García-Sogo M., Lambíes E. Transcriptional organization of the dnaN and recF genes of Escherichia coli K-12. J Biol Chem. 1988 Aug 25;263(24):12109–12114. [PubMed] [Google Scholar]
  2. Atlung T., Hansen F. G. Three distinct chromosome replication states are induced by increasing concentrations of DnaA protein in Escherichia coli. J Bacteriol. 1993 Oct;175(20):6537–6545. doi: 10.1128/jb.175.20.6537-6545.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Augustin L. B., Jacobson B. A., Fuchs J. A. Escherichia coli Fis and DnaA proteins bind specifically to the nrd promoter region and affect expression of an nrd-lac fusion. J Bacteriol. 1994 Jan;176(2):378–387. doi: 10.1128/jb.176.2.378-387.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Ball C. A., Osuna R., Ferguson K. C., Johnson R. C. Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli. J Bacteriol. 1992 Dec;174(24):8043–8056. doi: 10.1128/jb.174.24.8043-8056.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bates D. B., Asai T., Cao Y., Chambers M. W., Cadwell G. W., Boye E., Kogoma T. The DnaA box R4 in the minimal oriC is dispensable for initiation of Escherichia coli chromosome replication. Nucleic Acids Res. 1995 Aug 25;23(16):3119–3125. doi: 10.1093/nar/23.16.3119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. 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]
  7. Campbell J. L., Kleckner N. E. coli oriC and the dnaA gene promoter are sequestered from dam methyltransferase following the passage of the chromosomal replication fork. Cell. 1990 Sep 7;62(5):967–979. doi: 10.1016/0092-8674(90)90271-f. [DOI] [PubMed] [Google Scholar]
  8. Cassler M. R., Grimwade J. E., Leonard A. C. Cell cycle-specific changes in nucleoprotein complexes at a chromosomal replication origin. EMBO J. 1995 Dec 1;14(23):5833–5841. doi: 10.1002/j.1460-2075.1995.tb00271.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Chiaramello A. E., Zyskind J. W. Coupling of DNA replication to growth rate in Escherichia coli: a possible role for guanosine tetraphosphate. J Bacteriol. 1990 Apr;172(4):2013–2019. doi: 10.1128/jb.172.4.2013-2019.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Collado-Vides J., Magasanik B., Gralla J. D. Control site location and transcriptional regulation in Escherichia coli. Microbiol Rev. 1991 Sep;55(3):371–394. doi: 10.1128/mr.55.3.371-394.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Condon C., Philips J., Fu Z. Y., Squires C., Squires C. L. Comparison of the expression of the seven ribosomal RNA operons in Escherichia coli. EMBO J. 1992 Nov;11(11):4175–4185. doi: 10.1002/j.1460-2075.1992.tb05511.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Condon C., Squires C., Squires C. L. Control of rRNA transcription in Escherichia coli. Microbiol Rev. 1995 Dec;59(4):623–645. doi: 10.1128/mr.59.4.623-645.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Diederich L., Roth A., Messer W. A versatile plasmid vector system for the regulated expression of genes in Escherichia coli. Biotechniques. 1994 May;16(5):916–923. [PubMed] [Google Scholar]
  14. Filutowicz M., Ross W., Wild J., Gourse R. L. Involvement of Fis protein in replication of the Escherichia coli chromosome. J Bacteriol. 1992 Jan;174(2):398–407. doi: 10.1128/jb.174.2.398-407.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Finkel S. E., Johnson R. C. The Fis protein: it's not just for DNA inversion anymore. Mol Microbiol. 1992 Nov;6(22):3257–3265. doi: 10.1111/j.1365-2958.1992.tb02193.x. [DOI] [PubMed] [Google Scholar]
  16. Fraser C. M., Gocayne J. D., White O., Adams M. D., Clayton R. A., Fleischmann R. D., Bult C. J., Kerlavage A. R., Sutton G., Kelley J. M. The minimal gene complement of Mycoplasma genitalium. Science. 1995 Oct 20;270(5235):397–403. doi: 10.1126/science.270.5235.397. [DOI] [PubMed] [Google Scholar]
  17. Gille H., Egan J. B., Roth A., Messer W. The FIS protein binds and bends the origin of chromosomal DNA replication, oriC, of Escherichia coli. Nucleic Acids Res. 1991 Aug 11;19(15):4167–4172. doi: 10.1093/nar/19.15.4167. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Hansen F. G., Hansen E. B., Atlung T. The nucleotide sequence of the dnaA gene promoter and of the adjacent rpmH gene, coding for the ribosomal protein L34, of Escherichia coli. EMBO J. 1982;1(9):1043–1048. doi: 10.1002/j.1460-2075.1982.tb01294.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Herendeen D. R., Kelly T. J. DNA polymerase III: running rings around the fork. Cell. 1996 Jan 12;84(1):5–8. doi: 10.1016/s0092-8674(00)80069-0. [DOI] [PubMed] [Google Scholar]
  20. Hiasa H., Marians K. J. Fis cannot support oriC DNA replication in vitro. J Biol Chem. 1994 Oct 7;269(40):24999–25003. [PubMed] [Google Scholar]
  21. Hübner P., Arber W. Mutational analysis of a prokaryotic recombinational enhancer element with two functions. EMBO J. 1989 Feb;8(2):577–585. doi: 10.1002/j.1460-2075.1989.tb03412.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Hübner P., Haffter P., Iida S., Arber W. Bent DNA is needed for recombinational enhancer activity in the site-specific recombination system Cin of bacteriophage P1. The role of FIS protein. J Mol Biol. 1989 Feb 5;205(3):493–500. doi: 10.1016/0022-2836(89)90220-9. [DOI] [PubMed] [Google Scholar]
  23. Kelman Z., O'Donnell M. DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine. Annu Rev Biochem. 1995;64:171–200. doi: 10.1146/annurev.bi.64.070195.001131. [DOI] [PubMed] [Google Scholar]
  24. Kline B. C., Kogoma T., Tam J. E., Shields M. S. Requirement of the Escherichia coli dnaA gene product for plasmid F maintenance. J Bacteriol. 1986 Oct;168(1):440–443. doi: 10.1128/jb.168.1.440-443.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Lee Y. S., Kim H., Hwang D. S. Transcriptional activation of the dnaA gene encoding the initiator for oriC replication by IciA protein, an inhibitor of in vitro oriC replication in Escherichia coli. Mol Microbiol. 1996 Jan;19(2):389–396. doi: 10.1046/j.1365-2958.1996.485902.x. [DOI] [PubMed] [Google Scholar]
  26. Macián F., Pérez-Roger I., Armengod M. E. An improved vector system for constructing transcriptional lacZ fusions: analysis of regulation of the dnaA, dnaN, recF and gyrB genes of Escherichia coli. Gene. 1994 Jul 22;145(1):17–24. doi: 10.1016/0378-1119(94)90317-4. [DOI] [PubMed] [Google Scholar]
  27. Nilsson L., Vanet A., Vijgenboom E., Bosch L. The role of FIS in trans activation of stable RNA operons of E. coli. EMBO J. 1990 Mar;9(3):727–734. doi: 10.1002/j.1460-2075.1990.tb08166.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Nilsson L., Verbeek H., Hoffmann U., Haupt M., Bosch L. Inactivation of the fis gene leads to reduced growth rate. FEMS Microbiol Lett. 1992 Nov 15;78(1):85–88. doi: 10.1016/0378-1097(92)90292-v. [DOI] [PubMed] [Google Scholar]
  29. Nilsson L., Verbeek H., Vijgenboom E., van Drunen C., Vanet A., Bosch L. FIS-dependent trans activation of stable RNA operons of Escherichia coli under various growth conditions. J Bacteriol. 1992 Feb;174(3):921–929. doi: 10.1128/jb.174.3.921-929.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Ninnemann O., Koch C., Kahmann R. The E.coli fis promoter is subject to stringent control and autoregulation. EMBO J. 1992 Mar;11(3):1075–1083. doi: 10.1002/j.1460-2075.1992.tb05146.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Ohmori H., Kimura M., Nagata T., Sakakibara Y. Structural analysis of the dnaA and dnaN genes of Escherichia coli. Gene. 1984 May;28(2):159–170. doi: 10.1016/0378-1119(84)90253-1. [DOI] [PubMed] [Google Scholar]
  32. Osuna R., Lienau D., Hughes K. T., Johnson R. C. Sequence, regulation, and functions of fis in Salmonella typhimurium. J Bacteriol. 1995 Apr;177(8):2021–2032. doi: 10.1128/jb.177.8.2021-2032.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Pan C. Q., Feng J. A., Finkel S. E., Landgraf R., Sigman D., Johnson R. C. Structure of the Escherichia coli Fis-DNA complex probed by protein conjugated with 1,10-phenanthroline copper(I) complex. Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1721–1725. doi: 10.1073/pnas.91.5.1721. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Polaczek P., Wright A. Regulation of expression of the dnaA gene in Escherichia coli: role of the two promoters and the DnaA box. New Biol. 1990 Jun;2(6):574–582. [PubMed] [Google Scholar]
  35. Pérez-Roger I., García-Sogo M., Navarro-Aviñ J. P., López-Acedo C., Macián F., Armengod M. E. Positive and negative regulatory elements in the dnaA-dnaN-recF operon of Escherichia coli. Biochimie. 1991 Feb-Mar;73(2-3):329–334. doi: 10.1016/0300-9084(91)90220-u. [DOI] [PubMed] [Google Scholar]
  36. Ross W., Thompson J. F., Newlands J. T., Gourse R. L. E.coli Fis protein activates ribosomal RNA transcription in vitro and in vivo. EMBO J. 1990 Nov;9(11):3733–3742. doi: 10.1002/j.1460-2075.1990.tb07586.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Roth A., Urmoneit B., Messer W. Functions of histone-like proteins in the initiation of DNA replication at oriC of Escherichia coli. Biochimie. 1994;76(10-11):917–923. doi: 10.1016/0300-9084(94)90016-7. [DOI] [PubMed] [Google Scholar]
  38. Segall A. M., Nash H. A. Synaptic intermediates in bacteriophage lambda site-specific recombination: integrase can align pairs of attachment sites. EMBO J. 1993 Dec;12(12):4567–4576. doi: 10.1002/j.1460-2075.1993.tb06145.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Skarstad K., Boye E. The initiator protein DnaA: evolution, properties and function. Biochim Biophys Acta. 1994 Mar 1;1217(2):111–130. doi: 10.1016/0167-4781(94)90025-6. [DOI] [PubMed] [Google Scholar]
  40. Skovgaard O., Hansen F. G. Comparison of dnaA nucleotide sequences of Escherichia coli, Salmonella typhimurium, and Serratia marcescens. J Bacteriol. 1987 Sep;169(9):3976–3981. doi: 10.1128/jb.169.9.3976-3981.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Spaeny-Dekking L., Nilsson L., von Euler A., van de Putte P., Goosen N. Effects of N-terminal deletions of the Escherichia coli protein Fis on growth rate, tRNA(2Ser) expression and cell morphology. Mol Gen Genet. 1995 Jan 20;246(2):259–265. doi: 10.1007/BF00294690. [DOI] [PubMed] [Google Scholar]
  42. Thompson J. F., Landy A. Empirical estimation of protein-induced DNA bending angles: applications to lambda site-specific recombination complexes. Nucleic Acids Res. 1988 Oct 25;16(20):9687–9705. doi: 10.1093/nar/16.20.9687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Thompson J. F., Moitoso de Vargas L., Koch C., Kahmann R., Landy A. Cellular factors couple recombination with growth phase: characterization of a new component in the lambda site-specific recombination pathway. Cell. 1987 Sep 11;50(6):901–908. doi: 10.1016/0092-8674(87)90516-2. [DOI] [PubMed] [Google Scholar]
  44. Umezu K., Chi N. W., Kolodner R. D. Biochemical interaction of the Escherichia coli RecF, RecO, and RecR proteins with RecA protein and single-stranded DNA binding protein. Proc Natl Acad Sci U S A. 1993 May 1;90(9):3875–3879. doi: 10.1073/pnas.90.9.3875. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Xu J., Johnson R. C. Fis activates the RpoS-dependent stationary-phase expression of proP in Escherichia coli. J Bacteriol. 1995 Sep;177(18):5222–5231. doi: 10.1128/jb.177.18.5222-5231.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Xu J., Johnson R. C. Identification of genes negatively regulated by Fis: Fis and RpoS comodulate growth-phase-dependent gene expression in Escherichia coli. J Bacteriol. 1995 Feb;177(4):938–947. doi: 10.1128/jb.177.4.938-947.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Xu J., Johnson R. C. aldB, an RpoS-dependent gene in Escherichia coli encoding an aldehyde dehydrogenase that is repressed by Fis and activated by Crp. J Bacteriol. 1995 Jun;177(11):3166–3175. doi: 10.1128/jb.177.11.3166-3175.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES