microbial structure and function mi720 fall 2007 dna replication andrew j. pierce department of...
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Microbial Structure and FunctionMI720
Fall 2007
DNA Replication
Andrew J. Pierce
Department of Microbiology, Immunology and Molecular Genetics
University of Kentucky
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
DnaA boxes are shown as red arrowsAT-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.
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'-TTA/TTNCACA-3'
A-box: KD ~25 nM
initial unwinding: DnaA: 28 bpDnaA+SSB: 44-52 bp
Initial origin melting
Origin proteins
dnaA melt duplex
dnaB main replicative helicasecommitment step for replication fork formation
dnaC load dnaB
dnaG primase
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
Annu Rev Biochem. 1995;64:171-200DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machineKelman Z, O'Donnell M.
2 DNA polymerase molecules and 9 other accessory factors
E. coli DNA polymerase III holoenzyme
Principles of Biochemistry, 3rd EditionHorton HR, Moran LA, Ochs RS, Rawn DJ, Scrimgeour KGPrentice Hall 2002
replicationfork
replicationfork
Principles of Biochemistry, 3rd EditionHorton HR, Moran LA, Ochs RS, Rawn DJ, Scrimgeour KGPrentice Hall 2002
Replicating E. coli genome
Other E. coli DNA polymerases
DNA pol I remove RNA primers and join Okazaki fragments
DNA pol II aka: dinA (damage inducible), polBproofread terminal mismatchesextend terminal mismatches
DNA pol IV aka: dinB (damage inducible)extend terminal mismatches without proofreading
DNA pol V aka: umuD'2Ctranslesion synthesis
When Pol III goes wrong…mismatches
Mol Microbiol.2005 Oct;58(1):61-70DNA polymerase II as a fidelity factor in chromosomal DNA synthesis in Escherichia coliBanach-Orlowska M, Fijalkowska IJ, Schaaper RM, Jonczyk P
pol IV also used for template slippage
Trends Biochem Sci.2000 Apr;25(4):189-95Coping with replication 'train wrecks' in Escherichia coli using PolV, Pol II and RecA proteinsGoodman MF.
Bigger problems for DNA replication
abasicsite
UV 6-4 photoproduct UV cyclobutane dimer
SOS response
TTRecA
RecA *
RecA* LexA
Genetics, Vol. 158, 41-64, May 2001Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coliCourcells J, Khodursky A, Peter B, Borwn PO, Hanawalt PC
uvrA nucleotideuvrB excisionuvrD repair
dinA = polB = pol IIdinB = pol IV
sulA block cell division
lexArecA
ruvA resistanceruvB to UV
umuC UVumuD'umuD mutagenesis
RecA*
1 2
3
Proc Natl Acad Sci USA2001 Jul 17;98(15):8350-4Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coliPham P, Rangarajan S, Woodgate R, Goodman MF
Pol II helping out
Proc Natl Acad Sci USA2001 Jul 17;98(15):8350-4Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coliPham P, Rangarajan S, Woodgate R, Goodman MF
Translesion synthesis
polV: umuD'2C
E. coli genome
Microbiol Mol Biol Rev. 2005 Sep;69(3):501-26Replication termination in Escherichia coli: structure and antihelicase activity of the Tus-Ter complexNeylon C, Kralicek AV, Hill TM, Dixon NE
Mol Microbiol. 1999 Mar;31(6):1611-8Termination of DNA replication of bacterial and plasmid chromosomesBussiere DE, Bastia D
Replication termination
TerF TerB TerC TerA TerD TerE
Tus - Ter
Mol Microbiol. 1999 Mar;31(6):1611-8Termination of DNA replication of bacterial and plasmid chromosomesBussiere DE, Bastia D
5'-TTAGTTACAACATNCA-3'
Tus - Ter and DNA polymerase III
Microbiol Mol Biol Rev. 2005 Sep;69(3):501-26Replication termination in Escherichia coli: structure and antihelicase activity of the Tus-Ter complexNeylon C, Kralicek AV, Hill TM, Dixon NE
Replication fork disassembly
Microbiol Mol Biol Rev. 2005 Sep;69(3):501-26Replication termination in Escherichia coli: structure and antihelicase activity of the Tus-Ter complexNeylon C, Kralicek AV, Hill TM, Dixon NE