Abstract
Initiation of DNA synthesis is triggered by the binding of proteins to replication origins. However, little is known about the order in which specific proteins associate with origin sites during the cell cycle. We show that in cycling cells there are at least two different nucleoprotein complexes at oriC. A factor for inversion stimulation (FIS)-bound nucleoprotein complex, present throughout the majority of the cell cycle, switches to an integration host factor (IHF)-bound form as cells initiate DNA replication. Coincident with binding of IHF, initiator DnaA binds to its previously unoccupied R3 site. In stationary phase, a third nucleoprotein complex forms. FIS is absent and inactive oriC forms a nucleoprotein structure containing IHF that is not observed in cycling cells. We propose that interplay between FIS and IHF aids assembly of initiation nucleoprotein complexes during the cell cycle and blocks initiation at inappropriate times. This exchange of components at replication origins is reminiscent of switching between pre- and post-replicative chromatin states at yeast ARS1.
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- 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]
- Bonnefoy E., Rouvière-Yaniv J. HU, the major histone-like protein of E. coli, modulates the binding of IHF to oriC. EMBO J. 1992 Dec;11(12):4489–4496. doi: 10.1002/j.1460-2075.1992.tb05550.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Borowiec J. A., Gralla J. D. High-resolution analysis of lac transcription complexes inside cells. Biochemistry. 1986 Sep 9;25(18):5051–5057. doi: 10.1021/bi00366a012. [DOI] [PubMed] [Google Scholar]
- Bramhill D., Kornberg A. A model for initiation at origins of DNA replication. Cell. 1988 Sep 23;54(7):915–918. doi: 10.1016/0092-8674(88)90102-x. [DOI] [PubMed] [Google Scholar]
- Bramhill D., Kornberg A. Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome. Cell. 1988 Mar 11;52(5):743–755. doi: 10.1016/0092-8674(88)90412-6. [DOI] [PubMed] [Google Scholar]
- 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]
- Cartwright I. L., Kelly S. E. Probing the nature of chromosomal DNA-protein contacts by in vivo footprinting. Biotechniques. 1991 Aug;11(2):188-90, 192-4, 196 passim. [PubMed] [Google Scholar]
- Craig N. L., Nash H. A. E. coli integration host factor binds to specific sites in DNA. Cell. 1984 Dec;39(3 Pt 2):707–716. doi: 10.1016/0092-8674(84)90478-1. [DOI] [PubMed] [Google Scholar]
- Crooke E., Thresher R., Hwang D. S., Griffith J., Kornberg A. Replicatively active complexes of DnaA protein and the Escherichia coli chromosomal origin observed in the electron microscope. J Mol Biol. 1993 Sep 5;233(1):16–24. doi: 10.1006/jmbi.1993.1481. [DOI] [PubMed] [Google Scholar]
- Diffley J. F., Cocker J. H., Dowell S. J., Rowley A. Two steps in the assembly of complexes at yeast replication origins in vivo. Cell. 1994 Jul 29;78(2):303–316. doi: 10.1016/0092-8674(94)90299-2. [DOI] [PubMed] [Google Scholar]
- Ditto M. D., Roberts D., Weisberg R. A. Growth phase variation of integration host factor level in Escherichia coli. J Bacteriol. 1994 Jun;176(12):3738–3748. doi: 10.1128/jb.176.12.3738-3748.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Drlica K., Rouviere-Yaniv J. Histonelike proteins of bacteria. Microbiol Rev. 1987 Sep;51(3):301–319. doi: 10.1128/mr.51.3.301-319.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Filutowicz M., Roll J. The requirement of IHF protein for extrachromosomal replication of the Escherichia coli oriC in a mutant deficient in DNA polymerase I activity. New Biol. 1990 Sep;2(9):818–827. [PubMed] [Google Scholar]
- 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]
- 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]
- Friedman D. I. Integration host factor: a protein for all reasons. Cell. 1988 Nov 18;55(4):545–554. doi: 10.1016/0092-8674(88)90213-9. [DOI] [PubMed] [Google Scholar]
- Funnell B. E., Baker T. A., Kornberg A. In vitro assembly of a prepriming complex at the origin of the Escherichia coli chromosome. J Biol Chem. 1987 Jul 25;262(21):10327–10334. [PubMed] [Google Scholar]
- 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]
- Gille H., Messer W. Localized DNA melting and structural pertubations in the origin of replication, oriC, of Escherichia coli in vitro and in vivo. EMBO J. 1991 Jun;10(6):1579–1584. doi: 10.1002/j.1460-2075.1991.tb07678.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Granston A. E., Alessi D. M., Eades L. J., Friedman D. I. A point mutation in the Nul gene of bacteriophage lambda facilitates phage growth in Escherichia coli with himA and gyrB mutations. Mol Gen Genet. 1988 Apr;212(1):149–156. doi: 10.1007/BF00322458. [DOI] [PubMed] [Google Scholar]
- Hansen F. G., Christensen B. B., Atlung T. The initiator titration model: computer simulation of chromosome and minichromosome control. Res Microbiol. 1991 Feb-Apr;142(2-3):161–167. doi: 10.1016/0923-2508(91)90025-6. [DOI] [PubMed] [Google Scholar]
- Helmstetter C. E., Krajewski C. A. Initiation of chromosome replication in dnaA and dnaC mutants of Escherichia coli B/r F. J Bacteriol. 1982 Feb;149(2):685–693. doi: 10.1128/jb.149.2.685-693.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- 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]
- Hwang D. S., Kornberg A. Opening of the replication origin of Escherichia coli by DnaA protein with protein HU or IHF. J Biol Chem. 1992 Nov 15;267(32):23083–23086. [PubMed] [Google Scholar]
- Leonard A. C., Helmstetter C. E. Cell cycle-specific replication of Escherichia coli minichromosomes. Proc Natl Acad Sci U S A. 1986 Jul;83(14):5101–5105. doi: 10.1073/pnas.83.14.5101. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Løbner-Olesen A., Skarstad K., Hansen F. G., von Meyenburg K., Boye E. The DnaA protein determines the initiation mass of Escherichia coli K-12. Cell. 1989 Jun 2;57(5):881–889. doi: 10.1016/0092-8674(89)90802-7. [DOI] [PubMed] [Google Scholar]
- Marians K. J. Prokaryotic DNA replication. Annu Rev Biochem. 1992;61:673–719. doi: 10.1146/annurev.bi.61.070192.003325. [DOI] [PubMed] [Google Scholar]
- Marszalek J., Kaguni J. M. DnaA protein directs the binding of DnaB protein in initiation of DNA replication in Escherichia coli. J Biol Chem. 1994 Feb 18;269(7):4883–4890. [PubMed] [Google Scholar]
- Mukhopadhyay G., Carr K. M., Kaguni J. M., Chattoraj D. K. Open-complex formation by the host initiator, DnaA, at the origin of P1 plasmid replication. EMBO J. 1993 Dec;12(12):4547–4554. doi: 10.1002/j.1460-2075.1993.tb06143.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Newlon C. S. Two jobs for the origin replication complex. Science. 1993 Dec 17;262(5141):1830–1831. doi: 10.1126/science.8266070. [DOI] [PubMed] [Google Scholar]
- 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]
- Nordström K., Austin S. J. Cell-cycle-specific initiation of replication. Mol Microbiol. 1993 Nov;10(3):457–463. doi: 10.1111/j.1365-2958.1993.tb00918.x. [DOI] [PubMed] [Google Scholar]
- Ogata R. T., Gilbert W. An amino-terminal fragment of lac repressor binds specifically to lac operator. Proc Natl Acad Sci U S A. 1978 Dec;75(12):5851–5854. doi: 10.1073/pnas.75.12.5851. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Polaczek P. Bending of the origin of replication of E. coli by binding of IHF at a specific site. New Biol. 1990 Mar;2(3):265–271. [PubMed] [Google Scholar]
- 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]
- 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]
- Rowley A., Cocker J. H., Harwood J., Diffley J. F. Initiation complex assembly at budding yeast replication origins begins with the recognition of a bipartite sequence by limiting amounts of the initiator, ORC. EMBO J. 1995 Jun 1;14(11):2631–2641. doi: 10.1002/j.1460-2075.1995.tb07261.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Samitt C. E., Hansen F. G., Miller J. F., Schaechter M. In vivo studies of DnaA binding to the origin of replication of Escherichia coli. EMBO J. 1989 Mar;8(3):989–993. doi: 10.1002/j.1460-2075.1989.tb03462.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sasse-Dwight S., Gralla J. D. Footprinting protein-DNA complexes in vivo. Methods Enzymol. 1991;208:146–168. doi: 10.1016/0076-6879(91)08012-7. [DOI] [PubMed] [Google Scholar]
- Skarstad K., Baker T. A., Kornberg A. Strand separation required for initiation of replication at the chromosomal origin of E.coli is facilitated by a distant RNA--DNA hybrid. EMBO J. 1990 Jul;9(7):2341–2348. doi: 10.1002/j.1460-2075.1990.tb07406.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Skarstad K., Thöny B., Hwang D. S., Kornberg A. A novel binding protein of the origin of the Escherichia coli chromosome. J Biol Chem. 1993 Mar 15;268(8):5365–5370. [PubMed] [Google Scholar]
- Theisen P. W., Grimwade J. E., Leonard A. C., Bogan J. A., Helmstetter C. E. Correlation of gene transcription with the time of initiation of chromosome replication in Escherichia coli. Mol Microbiol. 1993 Nov;10(3):575–584. doi: 10.1111/j.1365-2958.1993.tb00929.x. [DOI] [PubMed] [Google Scholar]
- Woelker B., Messer W. The structure of the initiation complex at the replication origin, oriC, of Escherichia coli. Nucleic Acids Res. 1993 Nov 11;21(22):5025–5033. doi: 10.1093/nar/21.22.5025. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Yang C. C., Nash H. A. The interaction of E. coli IHF protein with its specific binding sites. Cell. 1989 Jun 2;57(5):869–880. doi: 10.1016/0092-8674(89)90801-5. [DOI] [PubMed] [Google Scholar]





