Binding of SeqA protein to DNA requires interaction between two or more complexes bound to separate hemimethylated GATC sequences (original) (raw)

Abstract

The SeqA protein binds to the post-replicative forms of the origins of replication of the Escherichia coli chromosome (oriC) and the P1 plasmid (P1oriR) at hemimethylated GATC adenine methylation sites. It appears to regulate replication by preventing premature reinitiation. However, SeqA binding is not exclusive to replication origins: different fragments with hemimethylated GATC sites can bind SeqA in vitro when certain rules apply. Most notably, more than one such site must be present on a bound fragment. The protein appears to recognize individual hemimethylated sites, but must undergo an obligate cooperative interaction with a nearby bound protein for stable binding. SeqA contacts both DNA strands in a discrete patch at each hemimethylated GATC sequence. All four GATC bases are contacted and are essential for binding. Although the recognized sequence is symmetrical, the footprint on the methylated strand is always broader, suggesting that the bound protein is positioned asymmetrically with its orientation dictated by the position of the unique methyl group. Studies of alternative spacings and relative orientations of adjacent sites suggest that each site may be recognized by a symmetrical dimer with an induced asymmetry in one of the subunits similar to that seen with certain type II restriction endonucleases.

Full Text

The Full Text of this article is available as a PDF (242.0 KB).

Selected References

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

  1. Bakker A., Smith D. W. Methylation of GATC sites is required for precise timing between rounds of DNA replication in Escherichia coli. J Bacteriol. 1989 Oct;171(10):5738–5742. doi: 10.1128/jb.171.10.5738-5742.1989. [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. Boye E., Løbner-Olesen A. The role of dam methyltransferase in the control of DNA replication in E. coli. Cell. 1990 Sep 7;62(5):981–989. doi: 10.1016/0092-8674(90)90272-g. [DOI] [PubMed] [Google Scholar]
  4. Brendler T., Abeles A., Austin S. A protein that binds to the P1 origin core and the oriC 13mer region in a methylation-specific fashion is the product of the host seqA gene. EMBO J. 1995 Aug 15;14(16):4083–4089. doi: 10.1002/j.1460-2075.1995.tb00080.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. 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]
  6. Herrick J., Kern R., Guha S., Landoulsi A., Fayet O., Malki A., Kohiyama M. Parental strand recognition of the DNA replication origin by the outer membrane in Escherichia coli. EMBO J. 1994 Oct 3;13(19):4695–4703. doi: 10.1002/j.1460-2075.1994.tb06793.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Hiraga S., Ichinose C., Niki H., Yamazoe M. Cell cycle-dependent duplication and bidirectional migration of SeqA-associated DNA-protein complexes in E. coli. Mol Cell. 1998 Feb;1(3):381–387. doi: 10.1016/s1097-2765(00)80038-6. [DOI] [PubMed] [Google Scholar]
  8. Kuwabara M. D., Sigman D. S. Footprinting DNA-protein complexes in situ following gel retardation assays using 1,10-phenanthroline-copper ion: Escherichia coli RNA polymerase-lac promoter complexes. Biochemistry. 1987 Nov 17;26(23):7234–7238. doi: 10.1021/bi00397a006. [DOI] [PubMed] [Google Scholar]
  9. Landoulsi A., Malki A., Kern R., Kohiyama M., Hughes P. The E. coli cell surface specifically prevents the initiation of DNA replication at oriC on hemimethylated DNA templates. Cell. 1990 Nov 30;63(5):1053–1060. doi: 10.1016/0092-8674(90)90508-c. [DOI] [PubMed] [Google Scholar]
  10. Lu M., Campbell J. L., Boye E., Kleckner N. SeqA: a negative modulator of replication initiation in E. coli. Cell. 1994 May 6;77(3):413–426. doi: 10.1016/0092-8674(94)90156-2. [DOI] [PubMed] [Google Scholar]
  11. Newman M., Strzelecka T., Dorner L. F., Schildkraut I., Aggarwal A. K. Structure of Bam HI endonuclease bound to DNA: partial folding and unfolding on DNA binding. Science. 1995 Aug 4;269(5224):656–663. doi: 10.1126/science.7624794. [DOI] [PubMed] [Google Scholar]
  12. 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]
  13. Pingoud A., Jeltsch A. Recognition and cleavage of DNA by type-II restriction endonucleases. Eur J Biochem. 1997 May 15;246(1):1–22. doi: 10.1111/j.1432-1033.1997.t01-6-00001.x. [DOI] [PubMed] [Google Scholar]
  14. Reshetnyak E., d'Alençon E., Kern R., Taghbalout A., Guillaud P., Kohiyama M. Hemi-methylated oriC DNA binding activity found in non-specific acid phosphatase. Mol Microbiol. 1999 Jan;31(1):167–175. doi: 10.1046/j.1365-2958.1999.01156.x. [DOI] [PubMed] [Google Scholar]
  15. 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]
  16. Shakibai N., Ishidate K., Reshetnyak E., Gunji S., Kohiyama M., Rothfield L. High-affinity binding of hemimethylated oriC by Escherichia coli membranes is mediated by a multiprotein system that includes SeqA and a newly identified factor, SeqB. Proc Natl Acad Sci U S A. 1998 Sep 15;95(19):11117–11121. doi: 10.1073/pnas.95.19.11117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Sigman D. S., Kuwabara M. D., Chen C. H., Bruice T. W. Nuclease activity of 1,10-phenanthroline-copper in study of protein-DNA interactions. Methods Enzymol. 1991;208:414–433. doi: 10.1016/0076-6879(91)08022-a. [DOI] [PubMed] [Google Scholar]
  18. Slater S., Wold S., Lu M., Boye E., Skarstad K., Kleckner N. E. coli SeqA protein binds oriC in two different methyl-modulated reactions appropriate to its roles in DNA replication initiation and origin sequestration. Cell. 1995 Sep 22;82(6):927–936. doi: 10.1016/0092-8674(95)90272-4. [DOI] [PubMed] [Google Scholar]
  19. 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]
  20. Tabor S., Richardson C. C. A single residue in DNA polymerases of the Escherichia coli DNA polymerase I family is critical for distinguishing between deoxy- and dideoxyribonucleotides. Proc Natl Acad Sci U S A. 1995 Jul 3;92(14):6339–6343. doi: 10.1073/pnas.92.14.6339. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. von Freiesleben U., Rasmussen K. V., Schaechter M. SeqA limits DnaA activity in replication from oriC in Escherichia coli. Mol Microbiol. 1994 Nov;14(4):763–772. doi: 10.1111/j.1365-2958.1994.tb01313.x. [DOI] [PubMed] [Google Scholar]