Initiating chromosome replication in E. coli: It makes sense to recycle

Genes and Development

Volumn 23, Issue 10, 2009, Pages 1145-1150

  Leonard, Alan C ^a   Grimwade, Julia E ^a  

^a Florida Institute of Technology   (United States)

Author keywords

DnaA reactivation; Functional DNA sequence; Initiation regulation; Nucleotide exchange; Protein complex; Replication cycle

Indexed keywords

ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE; ORIGIN RECOGNITION COMPLEX; REPLICATION INITIATOR PROTEIN DNAA; BACTERIAL PROTEIN; DNA BINDING PROTEIN; DNAA PROTEIN, BACTERIA; NUCLEOPROTEIN; SPACER DNA;

CHROMOSOME REPLICATION; CHROMOSOME STRUCTURE; DNA REPLICATION ORIGIN; DNA REPLICATION TIMING; DNAA REACTIVATING SEQUENCE; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; REVIEW; BACTERIAL CHROMOSOME; CELL MEMBRANE; DNA REPLICATION; GENETICS; METABOLISM; NOTE; PROTEIN SYNTHESIS;

ESCHERICHIA COLI;

BACTERIAL PROTEINS; CELL MEMBRANE; CHROMOSOMES, BACTERIAL; DNA REPLICATION; DNA, INTERGENIC; DNA-BINDING PROTEINS; ESCHERICHIA COLI; NUCLEOPROTEINS; PROTEIN BIOSYNTHESIS;

EID: 66149123740     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.1809909     Document Type: Review

References (40)

1. Bell SP. 2002. The origin recognition complex: From simple origins to complex functions. Genes & Dev 16: 659-672. (Pubitemid 34274034)
2. Boeneman K, Crooke E. 2005. Chromosomal replication and the cell membrane. Curr Opin Microbiol 8: 143-148. (Pubitemid 40417954)
3. Boye E, Lobner-Olesen A, Skarstad K. 2000. Limiting DNA replication to once and only once. EMBO Rep 1: 479-483.
4. Campbell JL, Kleckner N. 1990. E. coli oriC and the dnaA gene promoter are sequestered from dam methyltransferase following the passage of the chromosomal replication fork. Cell 62: 967-979. (Pubitemid 20269143)
5. Cassler MR, Grimwade JE, Leonard AC. 1995. Cell cycle-specific changes in nucleoprotein complexes at a chromosomal replication origin. EMBO J 14: 5833-5841.
6. Crooke E. 2001. Escherichia coli DnaA protein-phospholipid interactions: In vitro and in vivo. Biochimie 83: 19-23.
7. Crooke E, Castuma CE, Kornberg A. 1992. The chromosome origin of Escherichia coli stabilizes DnaA protein during rejuvenation by phospholipids. J Biol Chem 267: 16779-16782.
8. Crooke E, Thresher R, Hwang DS, Griffith J, Kornberg A. 1993. Replicatively active complexes of DnaA protein and the Escherichia coli chromosomal origin observed in the electron microscope. J Mol Biol 233: 16-24. (Pubitemid 23288908)
9. Donachie WD, Blakely GW. 2003. Coupling the initiation of chromosome replication to cell size in Escherichia coli. Curr Opin Microbiol 6: 146-150. (Pubitemid 36628658)
10. Erzberger JP, Pirruccello MM, Berger JM. 2002. The structure of bacterial DnaA: Implications for general mechanisms underlying DNA replication initiation. EMBO J 21: 4763-4773.
11. Erzberger JP, Mott ML, Berger JM. 2006. Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling. Nat Struct Mol Biol 13: 676-683. (Pubitemid 44175159)
12. Fang L, Davey MJ, O'Donnell M. 1999. Replisome assembly at oriC, the replication origin of E. coli, reveals an explanation for initiation sites outside an origin. Mol Cell 4: 541-553. (Pubitemid 29531134)
13. Fujimitsu K, Katayama T. 2004. Reactivation of DnaA by DNA sequence-specific nucleotide exchange in vitro. Biochem Biophys Res Commun 322: 411-419. (Pubitemid 39490319)
14. Fujimitsu K, Senriuchi T, Katayama T. 2009. Specific genomic sequences of E. coli promote replicational initiation by directly reactivating ADP-DnaA. Genes & Dev. (this issue). doi: 10.1101/gad.1775809.
15. Grimwade JE, Torgue JJ, McGarry KC, Rozgaja T, Enloe ST, Leonard AC. 2007. Mutational analysis reveals Escherichia coli oriC interacts with both DnaA-ATP and DnaA-ADP during pre-RC assembly. Mol Microbiol 66: 428-439. (Pubitemid 47482384)
16. Hansen FG, Christensen BB, Atlung T. 1991. The initiator titration model: Computer simulation of chromosome and minichromosome control. Res Microbiol 142: 161-167.
17. Helmstetter CE. 1996. Timing of synthetic activities in the cell cycle. In Escherichia coli and Salmonella: Cellular and molecular biology (eds. FC Neidhardt et al.), pp. 1627-1639. ASM Press, Washington, DC.
18. Kaguni JM. 2006. DnaA: Controlling the initiation of bacterial DNA replication and more. Annu Rev Microbiol 60: 351-375.
19. Katayama T, Sekimizu K. 1999. Inactivation of Escherichia coli DnaA protein by DNA polymerase III and negative regulations for initiation of chromosomal replication. Biochimie 81: 835-840. (Pubitemid 29520609)
20. Kato J, Katayama T. 2001. Hda, a novel DnaA-related protein, regulates the replication cycle in Escherichia coli. EMBO J 20: 4253-4262. (Pubitemid 32751841)
21. Kawakami H, Keyamura K, Katayama T. 2005. Formation of an ATP-DnaA-specific initiation complex requires DnaA Arginine 285, a conserved motif in the AAA+ protein family. J Biol Chem 280: 27420-27430. (Pubitemid 41040784)
22. Kitagawa R, Mitsuki H, Okazaki T, Ogawa T. 1996. A novel DnaA protein-binding site at 94.7 min on the Escherichia coli chromosome. Mol Microbiol 19: 1137-1147. (Pubitemid 126422293)
23. Kitagawa R, Ozaki T, Moriya S, Ogawa T. 1998. Negative control of replication initiation by a novel chromosomal locus exhibiting exceptional affinity for Escherichia coli DnaA protein. Genes & Dev 12: 3032-3043. (Pubitemid 28469305)
24. Kurokawa K, Nishida S, Emoto A, Sekimizu K, Katayama T. 1999. Replication cycle-coordinated change of the adenine nucleotide-bound forms of DnaA protein in Escherichia coli. EMBO J 18: 6642-6652.
25. Leonard AC, Grimwade JE. 2005. Building a bacterial orisome: Emergence of new regulatory features for replication origin unwinding. Mol Microbiol 55: 978-985. (Pubitemid 40299170)
26. Lu M, Campbell JL, Boye E, Kleckner N. 1994. SeqA: A negative modulator of replication initiation in E. coli. Cell 77: 413-426. (Pubitemid 24145202)
27. Macian F, Perez-Roger I, Armengod ME. 1994. An improved vector system for constructing transcriptional lacZ fusions: Analysis of regulation of the dnaA, dnaN, recF and gyrB genes of Escherichia coli. Gene 145: 17-24. (Pubitemid 24224958)
28. McGarry KC, Ryan VT, Grimwade JE, Leonard AC. 2004. Two discriminatory binding sites in the Escherichia coli replication origin are required for DNA strand opening by initiator DnaA-ATP. Proc Natl Acad Sci 101: 2811-2816. (Pubitemid 38327693)
29. Messer W, Weigel C. 1997. DnaA initiator - also a transcription factor. Mol Microbiol 24: 1-6. (Pubitemid 27160833)
30. Mott ML, Berger JM. 2007. DNA replication initiation: Mechanisms and regulation in bacteria. Nat Rev Microbiol 5: 343-354. (Pubitemid 46605488)
31. Mott ML, Erzberger JP, Coons MM, Berger JM. 2008. Structural synergy and molecular crosstalk between bacterial helicase loaders and replication initiators. Cell 135: 623-634.
32. Nievera C, Torgue JJ, Grimwade JE, Leonard AC. 2006. SeqA blocking of DnaA-oriC interactions ensures staged assembly of the E. coli pre-RC. Mol Cell 24: 581-592.
33. Ogden GB, Pratt MJ, Schaechter M. 1988. The replicative origin of the E. coli chromosome binds to cell membranes only when hemimethylated. Cell 54: 127-135.
34. Samitt CE, Hansen FG, Miller JF, Schaechter M. 1989. In vivo studies of DnaA binding to the origin of replication of Escherichia coli. EMBO J 8: 989-993.
35. Sekimizu K, Bramhill D, Kornberg A. 1987. ATP activates dnaA protein in initiating replication of plasmids bearing the origin of the E. coli chromosome. Cell 50: 259-265.
36. Sekimizu K, Yung BY, Kornberg A. 1988. The dnaA protein of Escherichia coli. Abundance, improved purification, and membrane binding. J Biol Chem 263: 7136-7140. (Pubitemid 18155740)
37. Skarstad K, Boye E, Steen HB. 1986. Timing of initiation of chromosome replication in individual Escherichia coli cells. EMBO J 5: 1711-1717.
38. Stillman B. 2005. Origin recognition and the chromosome cycle. FEBS Lett 579: 877-884. (Pubitemid 40361858)
39. Xia W, Dowhan W. 1995. In vivo evidence for the involvement of anionic phospholipids in initiation of DNA replication in Escherichia coli. Proc Natl Acad Sci 92: 783-787.
40. Zheng W, Li Z, Skarstad K, Crooke E. 2001. Mutations in DnaA protein suppress the growth arrest of acidic phospholipid-deficient Escherichia coli cells. EMBO J 20: 1164-1172. (Pubitemid 32186806)