1. Microbial Structure and Function MI720 Fall 2007 DNA Replication Andrew J. Pierce Department of Microbiology, Immunology and Molecular Genetics University of Kentucky

2. FEMS Microbiol Rev. 2002 Nov;26(4):355-74. The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. Messer W. E. coli origin structure

3. DnaA boxes are shown as red arrows AT-rich regions are shown in yellow Replication origins of different bacteria FEMS Microbiol Rev. 2002 Nov;26(4):355-74. The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. Messer W.

4. FEMS Microbiol Rev. 2002 Nov;26(4):355-74. The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. Messer W. 5'-TT A / T TNCACA-3' A-box: K D ~25 nM initial unwinding:DnaA: 28 bp DnaA+SSB: 44-52 bp Initial origin melting

5. Origin proteins dnaAmelt duplex dnaBmain replicative helicase commitment step for replication fork formation dnaCload dnaB dnaGprimase

6. FEMS Microbiol Rev. 2002 Nov;26(4):355-74. The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. Messer W. Initiating DNA replication

7. Annu Rev Biochem. 1995;64:171-200 DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine Kelman Z, O'Donnell M. 2 DNA polymerase molecules and 9 other accessory factors E. coli DNA polymerase III holoenzyme

8. Principles of Biochemistry, 3rd Edition Horton HR, Moran LA, Ochs RS, Rawn DJ, Scrimgeour KG Prentice Hall 2002

9. replication fork replication fork Principles of Biochemistry, 3rd Edition Horton HR, Moran LA, Ochs RS, Rawn DJ, Scrimgeour KG Prentice Hall 2002 Replicating E. coli genome

10. Other E. coli DNA polymerases DNA pol Iremove RNA primers and join Okazaki fragments DNA pol IIaka: dinA (damage inducible), polB proofread terminal mismatches extend terminal mismatches DNA pol IVaka: dinB (damage inducible) extend terminal mismatches without proofreading DNA pol Vaka: umuD' 2 C translesion synthesis

11. When Pol III goes wrong… mismatches Mol Microbiol. 2005 Oct;58(1):61-70 DNA polymerase II as a fidelity factor in chromosomal DNA synthesis in Escherichia coli Banach-Orlowska M, Fijalkowska IJ, Schaaper RM, Jonczyk P pol IV also used for template slippage

12. Trends Biochem Sci. 2000 Apr;25(4):189-95 Coping with replication 'train wrecks' in Escherichia coli using PolV, Pol II and RecA proteins Goodman MF. Bigger problems for DNA replication abasic site UV 6-4 photoproductUV cyclobutane dimer

13. SOS response TT RecA RecA * LexA Genetics, Vol. 158, 41-64, May 2001 Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli Courcells J, Khodursky A, Peter B, Borwn PO, Hanawalt PC uvrA nucleotide uvrB excision uvrD repair dinA = polB = pol II dinB = pol IV sulA block cell division lexA recA ruvA resistance ruvB to UV umuC UV umuD'umuD mutagenesis RecA * 1 2 3

14. Proc Natl Acad Sci USA 2001 Jul 17;98(15):8350-4 Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli Pham P, Rangarajan S, Woodgate R, Goodman MF Pol II helping out

15. Proc Natl Acad Sci USA 2001 Jul 17;98(15):8350-4 Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli Pham P, Rangarajan S, Woodgate R, Goodman MF Translesion synthesis polV: umuD' 2 C

16. E. coli genome Microbiol Mol Biol Rev. 2005 Sep;69(3):501-26 Replication termination in Escherichia coli: structure and antihelicase activity of the Tus-Ter complex Neylon C, Kralicek AV, Hill TM, Dixon NE

17. Mol Microbiol. 1999 Mar;31(6):1611-8 Termination of DNA replication of bacterial and plasmid chromosomes Bussiere DE, Bastia D Replication termination TerFTerBTerCTerATerDTerE

18. Tus - Ter Mol Microbiol. 1999 Mar;31(6):1611-8 Termination of DNA replication of bacterial and plasmid chromosomes Bussiere DE, Bastia D 5'-TTAGTTACAACATNCA-3'

19. Tus - Ter and DNA polymerase III Microbiol Mol Biol Rev. 2005 Sep;69(3):501-26 Replication termination in Escherichia coli: structure and antihelicase activity of the Tus-Ter complex Neylon C, Kralicek AV, Hill TM, Dixon NE

20. Replication fork disassembly Microbiol Mol Biol Rev. 2005 Sep;69(3):501-26 Replication termination in Escherichia coli: structure and antihelicase activity of the Tus-Ter complex Neylon C, Kralicek AV, Hill TM, Dixon NE