Coupling chromosomal replication to cell growth by the initiator protein DnaA in Escherichia coli

Journal of Theoretical Biology

Volumn 314, Issue , 2012, Pages 164-172

  Zhang, Qing ^a   Shi, Hualin ^a  

^a INSTITUTE OF THEORETICAL PHYSICS   (China)

Author keywords

Cell cycle; Cell growth; DnaA; Replication initiation; RNA polymerase

Indexed keywords

REPLICATION INITIATOR PROTEIN DNAA; RNA POLYMERASE;

CHROMOSOME; COLIFORM BACTERIUM; CYTOLOGY; DNA; PROTEIN; RNA;

ARTICLE; CELL CYCLE; CELL GROWTH; CHROMOSOME REPLICATION; ESCHERICHIA COLI; MATHEMATICAL ANALYSIS; NONHUMAN; OSCILLATION; PRIORITY JOURNAL; REGULATORY MECHANISM; SIMULATION;

BACTERIAL PROTEINS; CELL CYCLE; CELL PROLIFERATION; CHROMOSOMES, BACTERIAL; DNA REPLICATION; DNA-BINDING PROTEINS; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; MODELS, BIOLOGICAL;

ESCHERICHIA COLI;

EID: 84866516123     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2012.08.045     Document Type: Article

References (55)

1. Atlung T., Clausen E.S., Hansen F.G. Autoregulation of the dnaA gene of Escherichia coli K12. Mol. Gen. Genet. 1985, 200:442-450.
2. Boeneman K., Crooke E. Chromosomal replication and the cell membrane. Curr. Opin. Microbiol. 2005, 8:143-148.
3. Braun R.E., O'Day K., Wright A. Autoregulation of the DNA replication gene dnaA in E. coli K-12. Cell 1985, 40:159-169.
4. Bremer H., Dennis P.P. Modulation of chemical composition and other parameters of the cell by growth rate. Escherichia coli and Salmonella. Cellular and Molecular Biology 1996, 1553-1569. ASM Press, Washington, DC. second ed. F.C. Neidhardt (Ed.).
5. Browning S.T., Castellanos M., Shuler M.L. Robust control of initiation of prokaryotic chromosome replication. essential considerations for a minimal cell. Biotechnol. Bioeng. 2004, 88:575-584.
6. Campbell J.L., Kleckner N. E. coli oriC and the dnaA gene promoter are sequestered from dam methyltransfferase following the passage of the chromosomal replication fork. Cell 1990, 62:967-979.
7. Chiaramello A.E., Zyskind J.W. Expression of Escherichia coli dnaA and mioC genes as a function of growth rate. J. Bacteriol. 1989, 171:4272-4280.
8. 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, 172:2013-2019.
9. Churchward G., Estiva E., Bremer H. Growth rate-dependent control of chromosome replication initiation in Escherichia coli. J. Bacteriol. 1981, 145:1232-1238.
10. Cooper S., Helmstetter C.E. Chromosome replication and the division cycle of Escherichia coli B/r. J. Mol. Biol. 1968, 31:519-540.
11. Donachie W.D. Relationship between cell size and time of initiation of DNA replication. Nature 1968, 219:1077-1079.
12. Fang L., Davey M.J., O'Donnell M. Replisome assembly at oriC, the replication origin of E. coli, reveals an explanation for initiation sites outside an origin. Mol. Cell 1999, 4:541-553.
13. Freiesleben U.v., Krekling M.A., Hansen F.G., Løbner-Olesen A. The eclipse period of Escherichia coli. EMBO J. 2000, 19:6240-6248.
14. Fujimitsu K., Senriuchi T., Katayama T. Specific genomic sequences of E. coli promote replicational initiation by directly reactivating ADP-DnaA. Genes Dev. 2009, 23:1221-1233.
15. 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, 38:889-900.
16. 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, 1:1043-1048.
17. Hansen F.G., Christensen B.B., Atlung T. The initiator titration model. computer simulation of chromosome and minichromosome control. Res. Microbiol. 1991, 142:161-167.
18. Helmstetter C.E., Cooper S. DNA synthesis during the division cycle of rapidly growing Escherichia coli B/r. J. Mol. Biol. 1968, 31(1968):507-518.
19. 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, 1:381-387.
20. Hughes P., Landoulsi A., Kohiyama M. A novel role for cAMP in the control of the activity of the E. coli chromosome replication initiator protein, DnaA. Cell 1988, 55:343-350.
21. Kaguni J.M. DnaA. controlling the initiation of bacterial DNA replication and more. Annu. Rev. Microbiol. 2006, 60:351-371.
22. Katayama T., Kubota T., Kurokawa K., Crooke E., Sekimizu K. The initiator function of DnaA protein is negatively regulated by the sliding clamp of the E. coli chromosomal replicase. Cell 1998, 94:61-71.
23. Katayama T., Ozaki S., Keyamura K., Fujimitsu K. Regulation of the replication cycle. conserved and diverse regulatory systems for DnaA and oriC. Nat. Rev. Microbiol. 2010, 8:163-170.
24. Kato J. Regulatory network of the initiation of chromosomal replication in Escherichia coli. Crit. Rev. Biochem. Mol. Biol. 2005, 40:331-342.
25. Kato J., Katayama T. Hda, a novel DnaA-related protein, regulates the replication cycle in Escherichia coli. EMBO J. 2001, 20:4253-4262.
26. Kitagawa R., Mitsuki H., Okazaki T., Ogawa T. A novel DnaA protein-binding site at 94.7min on the Escherichia coli chromosome. Mol. Microbiol. 1996, 19:1137-1147.
27. Klumpp S., Hwa T. Growth-rate-dependent partitioning of RNA polymerases in bacteria. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:20245-20250.
28. Kücherer C., Lother H., Kölling S., Schauzu M., Messer W. Regulation of transcription of the chromosomal dnaA gene of Escherichia coli. Mol. Gen. Genet. 1986, 205:115-121.
29. Kurokawa K., Nishida S., Emoto A., Sekimizu K., Katayama T. Replication cycle-coordinated change of the adenine nucleotide-bound forms of DnaA protein in Escherichia coli. EMBO J. 1999, 18:6642-6652.
30. Leonard A.C., Grimwade J.E. Building a bacterial orisome. emergence of new regulatory features for replication origin unwinding. Mol. Microbiol. 2005, 55:978-985.
31. Levine A., Vannier F., Dehbi M., Henckes G., Seror S.J. The stringent response blocks DNA replication outside the ori region in Bacillus subtilis and at the origin in Escherichia coli. J. Mol. Biol. 1991, 219:605-613.
32. Løbner-Olesen A., Skovgaard O., Marinus M.G. Dam methylation. coordinating cellular processes. Curr. Opin. Microbiol. 2005, 8:154-160.
33. Lu M., Campbell J.L., Boye E., Kleckner N. SeqA. a negative modulator of replication initiation in E. coli. Cell 1994, 77:413-426.
34. Mahaffy J.M., Zyskind J.W. A model for the initiation of replication in Escherichia coli. J. Theor. Biol. 1989, 140:453-477.
35. Margulies C., Kaguni J.M. Ordered and sequential binding of DnaA protein to oriC, the chromosomal origin of Escherichia coli. J. Biol. Chem. 1996, 271:17035-17040.
36. Matsui M., Oka A., Takanami M., Yasuda S., Hirota Y. Sites of dnaA protein-binding in the replication origin of the Escherichia coli K-12 chromosome. J. Mol. Biol. 1985, 184:529-533.
37. McGarry K.C., Ryan V.T., Grimwade J.E., Leonard A.C. Two discriminatory binding sites in the Escherichia coli replication origin are required for DNA strand opening by initiator DnaA-ATP. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:2811-2816.
38. Messer W. The bacterial replication initiator DnaA. DnaA, and oriC, the bacterial mode to initiate DNA replication. FEMS Microbiol. Rev. 2002, 26:355-374.
39. Miller D.T., Grimwade J.E., Betteridge T., Rozgaja T., Torgue J.J., Leonard A.C. Bacterial origin recognition complexes direct assembly of higher-order DnaA oligomeric structures. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:18479-18484.
40. Mott M.L., Berger J.M. DNA replication initiation. mechanisms and regulation in bacteria. Nat. Rev. Microbiol. 2007, 5:343-354.
41. Neidhardt F.C., Ingraham J.L., Schaechter M. Physiology of the Bacterial Cell. A Molecular Approach 1990, Sinauer Associates, Inc., Sunderland, Massachusetts, pp. 390-391.
42. Nozaki S., Niki H., Ogawa T. Replication initiator DnaA of Escherichia coli changes its assembly form on the replication origin during the cell cycle. J. Bacteriol. 2009, 191:4807-4814.
43. Ogawa T., Yamada Y., Kuroda T., Kishi T., Moriya S. The datA locus predominantly contributes to the initiator titration mechanism in the control of replication initiation in Escherichia coli. Mol. Microbiol. 2002, 44:1367-1375.
44. Potrykus K., Cashel M. (p)ppGpp. still magical?. Annu. Rev. Microbiol. 2008, 62:35-51.
45. Roth A., Messer W. High-affinity binding sites for the initiator protein DnaA on the chromosome of Escherichia coli. Mol. Microbiol. 1998, 28:395-401.
46. Schaper S., Messer W. Interaction of the initiator protein DnaA of Escherichia coli with its DNA target. J. Biol. Chem. 1995, 270:17622-17626.
47. Schreiber G., Ron E.Z., Glaser G. ppGpp-mediated regulation of DNA replication and cell division in Escherichia coli. Curr. Microbiol. 1995, 30:27-32.
48. Sekimizu K., Bramhill D., Kornberg A. ATP activates DnaA protein in initiating replication of plasmids bearing the origin of the Escherichia coli chromosome. Cell 1987, 50:259-265.
49. Skarstad K., Boye E. The initiator protein DnaA. evolution, properties and function. Biochim. Biophys. Acta 1994, 1217:111-130.
50. Sompayrac L., Maaløe O. Autorepressor model for control of DNA replication. Nat. New Biol. (Loud.) 1973, 241:133-135.
51. Speck C., Messer W. Mechanism of origin unwinding. sequential binding of DnaA to double- and single-stranded DNA. EMBO J. 2001, 20:1469-1476.
52. Speck C., Weigel C., Messer W. ATP- and ADP-DnaA protein, a molecular switch in gene regulation. EMBO J. 1999, 18:6169-6176.
53. Srivatsan A., Wang J.D. Control of bacterial transcription, translation and replication by (p)ppGpp. Curr. Opin. Microbiol. 2008, 11:100-105.
54. Torheim N.K., Skarstad K. Escherichia coli SeqA protein affects DNA topology and inhibits open complex formation at oriC. EMBO J. 1999, 18:4882-4888.
55. Wold S., Skarstad K., Steen H.B., Stokke T., Boye E. The initiation mass for DNA replication in Escherichia coli K-12 is dependent on growth rate. EMSO J. 1994, 13:2097-2102.