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Andrew J. Pierce. Department of Microbiology, Immunology and Molecular Genetics. University of Kentucky. Microbial Structure and Function. MI720. Fall 2007. DNA Replication. E. coli origin structure. FEMS Microbiol Rev. 2002 Nov;26(4):355-74.

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Microbial Structure and Function

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Andrew J. Pierce

Department of Microbiology, Immunology and Molecular Genetics

University of Kentucky

Microbial Structure and Function

MI720

Fall 2007

DNA Replication


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E. coli origin structure

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.


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Replication origins of different bacteria

DnaA boxes are shown as red arrows

AT-rich regions are shown in yellow

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.


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A-box: KD ~25 nM

initial unwinding:

DnaA: 28 bp

DnaA+SSB: 44-52 bp

5'-TTA/TTNCACA-3'

Initial origin melting

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.


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dnaA

melt duplex

dnaB

main replicative helicase

commitment step for replication fork formation

dnaC

load dnaB

dnaG

primase

Origin proteins


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Initiating DNA replication

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.


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E. coli DNA polymerase III holoenzyme

2 DNA polymerase molecules and 9 other accessory factors

Annu Rev Biochem. 1995;64:171-200

DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine

Kelman Z, O'Donnell M.


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Principles of Biochemistry, 3rd Edition

Horton HR, Moran LA, Ochs RS, Rawn DJ, Scrimgeour KG

Prentice Hall 2002


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replication

fork

replication

fork

Replicating E. coli genome

Principles of Biochemistry, 3rd Edition

Horton HR, Moran LA, Ochs RS, Rawn DJ, Scrimgeour KG

Prentice Hall 2002


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Other E. coli DNA polymerases

DNA pol I

remove RNA primers and join Okazaki fragments

DNA pol II

aka: dinA (damage inducible), polB

proofread terminal mismatches

extend terminal mismatches

DNA pol IV

aka: dinB (damage inducible)

extend terminal mismatches without proofreading

DNA pol V

aka: umuD'2C

translesion synthesis


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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


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Bigger problems for DNA replication

abasic

site

UV 6-4 photoproduct

UV cyclobutane dimer

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.


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1

2

RecA

TT

RecA*

3

uvrA nucleotide

uvrB excision

uvrD repair

lexA

recA

ruvA resistance

ruvB to UV

dinA = polB = pol II

dinB = pol IV

LexA

sulA block cell division

umuC UV

RecA*

umuD mutagenesis

umuD'

SOS response

RecA*

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


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Pol II helping out

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


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Translesion synthesis

polV: umuD'2C

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


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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


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Replication termination

TerF

TerB

TerC

TerA

TerD

TerE

Mol Microbiol. 1999 Mar;31(6):1611-8

Termination of DNA replication of bacterial and plasmid chromosomes

Bussiere DE, Bastia D


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Tus - Ter

5'-TTAGTTACAACATNCA-3'

Mol Microbiol. 1999 Mar;31(6):1611-8

Termination of DNA replication of bacterial and plasmid chromosomes

Bussiere DE, Bastia D


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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


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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


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