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Oligomeric Initiator Protein-mediated DNA Looping Negatively Regulates Plasmid Replication In Vitro By Preventing Origin Melting.

S. Zzaman, D. Bastia
Published 2005 · Biology, Medicine

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Although DNA looping between the initiator binding sites (iterons) of the replication origin (ori) of a plasmid and the iterons located in a cis-acting control sequence called inc has been postulated to promote negative control of plasmid DNA replication, not only was definitive evidence for such looping lacking, but also the detailed molecular mechanism of this control had not been elucidated. Here, we present direct evidence showing that both the monomeric and the dimeric forms of the RepE initiator protein of F factor together promote pairing of incC-oriF sites by DNA looping. By using a reconstituted replication system consisting of 26 purified proteins, we show further that the DNA loop formation negatively regulates plasmid replication by inhibiting the formation of an open complex at the replication origin, thus elucidating a key step of replication control.
This paper references
10.1101/SQB.1963.028.01.048
On the Regulation of DNA Replication in Bacteria
F. Jacob (1963)
10.1111/j.1365-2958.2004.04322.x
Origin pairing (‘handcuffing’) and unpairing in the control of P1 plasmid replication
N. Das (2004)
10.1073/PNAS.94.26.14378
The replication initiation protein of the broad-host-range plasmid RK2 is activated by the ClpX chaperone.
I. Konieczny (1997)
10.1073/PNAS.93.23.12902
Direct physical interaction between DnaG primase and DnaB helicase of Escherichia coli is necessary for optimal synthesis of primer RNA.
Y. Lu (1996)
10.1016/S1097-2765(00)80205-1
Replisome assembly at oriC, the replication origin of E. coli, reveals an explanation for initiation sites outside an origin.
L. Fang (1999)
10.1073/PNAS.77.5.2450
Formation of an RNA primer for initiation of replication of ColE1 DNA by ribonuclease H.
T. Itoh (1980)
10.1073/PNAS.94.10.4901
Mechanism of protein remodeling by ClpA chaperone.
M. Pak (1997)
10.1128/JB.155.1.337-344.1983
Role of nine repeating sequences of the mini-F genome for expression of F-specific incompatibility phenotype and copy number control.
H. Tsutsui (1983)
10.1074/JBC.M312052200
Biochemical Investigations of Control of Replication Initiation of Plasmid R6K*
M. Abhyankar (2004)
10.1016/0147-619X(78)90007-0
F plasmid incompatibility and copy number genes: their map locations and interactions.
J. Manis (1978)
10.1093/emboj/18.17.4597
Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6 Å resolution
H. Komori (1999)
10.1002/j.1460-2075.1992.tb05161.x
Activation of distant replication origins in vivo by DNA looping as revealed by a novel mutant form of an initiator protein defective in cooperativity at a distance.
A. Miron (1992)
10.1016/0092-8674(83)90142-3
Interaction of the plasmid R6K-encoded replication initiator protein with its binding sites on DNA
J. Germino (1983)
10.1073/PNAS.85.17.6287
Detection of DNA looping due to simultaneous interaction of a DNA-binding protein with two spatially separated binding sites on DNA.
S. Mukherjee (1988)
10.1073/PNAS.86.20.7942
Negative control of plasmid R6K replication: possible role of intermolecular coupling of replication origins.
M. Mceachern (1989)
10.1007/BF00338996
Replication and incompatibility properties of segments of the origin region of replication of the broad host range plasmid RK2
Christopher M Thomas (2004)
10.1016/0378-1119(81)90135-9
Nine unique repeating sequences in a region essential for replication and incompatibility of the mini-F plasmid.
T. Murotsu (1981)
10.1007/s004380050294
The localized melting of mini-F origin by the combined action of the mini-F initiator protein (RepE) and HU and DnaA of Escherichia coli
Y. Kawasaki (1996)
DnaA protein directs the binding of DnaB protein in initiation of DNA replication in Escherichia coli.
J. Marszalek (1994)
10.1074/JBC.M400021200
Reconstitution of F Factor DNA Replication in Vitro with Purified Proteins*
S. Zzaman (2004)
10.1016/0092-8674(81)90095-7
Direct repeats of the F plasmid incC region express F incompatibility
A. Tolun (1981)
10.1046/j.1365-2958.2000.02096.x
The interaction domains of the DnaA and DnaB replication proteins of Escherichia coli
H. Seitz (2000)
10.1016/S0300-9084(00)01151-2
Overproduction and improved strategies to purify the threenative forms of nuclease-free HU protein.
O. Pellegrini (2000)
10.1007/BF00260494
Roles of Escherichia coli heat shock proteins DnaK, DnaJ and GrpE in mini-F plasmid replication
Y. Kawasaki (2004)
10.1128/JB.170.8.3554-3560.1988
P1 plasmid replication: initiator sequestration is inadequate to explain control by initiator-binding sites.
S. K. Pal (1988)
10.1007/978-1-4613-2447-8
Plasmids in Bacteria
D. Helinski (1985)
10.1073/PNAS.96.1.73
Mechanism of recruitment of DnaB helicase to the replication origin of the plasmid pSC101.
H. J. Datta (1999)
10.1016/0022-2836(82)90276-5
Plasmid R6K DNA replication. I. Complete nucleotide sequence of an autonomously replicating segment.
D. Stalker (1982)
10.1007/978-1-4613-2447-8_13
Role of the pi initiation protein and direct nucleotide sequence repeats in the regulation of plasmid R6K replication.
M. Filutowicz (1985)
10.1016/S0092-8674(88)80030-8
Enhancer-origin interaction in plasmid R6K involves a DNA loop mediated by initiator protein
S. Mukherjee (1988)
10.1016/0022-2836(90)90230-J
Control of ColE1 plasmid replication. Intermediates in the binding of RNA I and RNA II.
J. Tomizawa (1990)
10.1093/emboj/17.17.5192
Mechanistic studies of initiator–initiator interaction and replication initiation
Y. Lu (1998)
10.1016/0092-8674(83)90183-6
DNA-protein interaction at the origin of DNA replication of the plasmid pSC101
C. Vocke (1983)
10.1016/S0378-1119(98)00370-9
TrfA dimers play a role in copy-number control of RK2 replication.
A. Toukdarian (1998)
10.1016/0022-2836(90)90231-A
Control of ColE1 plasmid replication. Interaction of Rom protein with an unstable complex formed by RNA I and RNA II.
J. Tomizawa (1990)
10.1016/0092-8674(84)90539-7
Replication initiated at the origin (oriC) of the E. coli chromosome reconstituted with purified enzymes
J. Kaguni (1984)
10.1074/jbc.273.38.24906
Requirements for and Regulation of Origin Opening of Plasmid P1*
K. Park (1998)
10.1021/BI00266A042
Specific stimulation of the T7 gene 6 exonuclease by the phage T7 coded deoxyribonucleic acid binding protein.
L. Roberts (1982)
10.1073/PNAS.79.18.5475
Primary structure of the replication initiation protein of plasmid R6K.
J. Germino (1982)
10.1006/JMBI.2000.4426
Monomer/dimer ratios of replication protein modulate the DNA strand-opening in a replication origin.
R. Krueger (2001)
10.1093/emboj/18.13.3856
Regulation of DNA replication by iterons: an interaction between the ori2 and incC regions mediated by RepE‐bound iterons inhibits DNA replication of mini‐F plasmid in Escherichia coli
H. Uga (1999)
10.1074/jbc.M407531200
The DnaK-DnaJ-GrpE Chaperone System Activates Inert Wild Type π Initiator Protein of R6K into a Form Active in Replication Initiation*
S. Zzaman (2004)
10.1093/emboj/20.16.4577
Mechanistic aspects of DnaA–RepA interaction as revealed by yeast forward and reverse two‐hybrid analysis
R. Sharma (2001)
10.1016/0092-8674(83)90503-2
The replication initiator protein of plasmid R6K tagged with β-galactosidase shows sequence-specific DNA-binding
J. Germino (1983)
10.1073/PNAS.89.21.10345
DnaJ, DnaK, and GrpE heat shock proteins are required in oriP1 DNA replication solely at the RepA monomerization step.
S. Wickner (1992)
10.1016/0092-8674(88)90235-8
ColE1 replication control circuitry: Sense from antisense
B. Polisky (1988)



This paper is referenced by
10.1111/j.1365-2958.2006.05479.x
IHF‐dependent activation of P1 plasmid origin by DnaA
R. A. Fekete (2006)
10.1016/j.plasmid.2009.05.001
Replication and conjugative mobilization of broad host-range IncQ plasmids.
R. Meyer (2009)
10.1111/j.1365-2958.2006.05229.x
Origin inactivation in bacterial DNA replication control
J. Paulsson (2006)
10.1128/microbiolspec.PLAS-0026-2014
Iteron Plasmids.
I. Konieczny (2014)
10.3389/fmolb.2016.00062
Opening the Strands of Replication Origins—Still an Open Question
Jyoti K. Jha (2016)
concept co cept Gene and cell survival : lessons from prokaryotic plasmid R 1
G. D. L. Cueva-Méndez (2013)
10.1073/pnas.0609046103
Crystal structure of π initiator protein–iteron complex of plasmid R6K: Implications for initiation of plasmid DNA replication
M. Swan (2006)
10.1128/JB.00814-06
Initiation of heat-induced replication requires DnaA and the L-13-mer of oriC.
Rocío González-Soltero (2006)
10.1074/jbc.M109.067439
Investigations of π Initiator Protein-mediated Interaction between Replication Origins α and γ of the Plasmid R6K*
Mukesh Saxena (2009)
10.1128/MICROBIOLSPEC.PLAS-0029-2014
Mechanisms of Theta Plasmid Replication.
Joshua Lilly (2015)
10.1111/j.1365-2958.2008.06166.x
Negative regulation of pPS10 plasmid replication: origin pairing by zipping‐up DNA‐bound RepA monomers
F. Gasset-Rosa (2008)
10.1016/B978-0-12-374984-0.01099-8
Replication Origin Sequences
D. Bastia (2013)
10.1007/s12033-013-9680-6
The Rep20 Replication Initiator From the pAG20 Plasmid of Acetobacter aceti
M. Babič (2013)
10.1111/j.1365-2958.2011.07789.x
RepC protein of the octopine‐type Ti plasmid binds to the probable origin of replication within repC and functions only in cis
U. M. Pinto (2011)
10.1038/sj.embor.7400957
Gene and cell survival: lessons from prokaryotic plasmid R1
Guillermo de la Cueva-Méndez (2007)
10.1073/pnas.0705623104
Structural basis for regulation of bifunctional roles in replication initiator protein
A. Nakamura (2007)
10.1073/pnas.0605120103
Transcriptional inactivation of a regulatory site for replication of Vibrio cholerae chromosome II
Tatiana Venkova-Canova (2006)
10.1038/srep25425
Functional amyloids as inhibitors of plasmid DNA replication
Laura Molina-García (2016)
10.1016/j.plasmid.2012.01.006
Structure-function analysis of the SaPIbov1 replication origin in Staphylococcus aureus.
C. Úbeda (2012)
10.1128/MMBR.00033-16
Random versus Cell Cycle-Regulated Replication Initiation in Bacteria: Insights from Studying Vibrio cholerae Chromosome 2
R. Ramachandran (2016)
10.1074/jbc.M112.430595
Structural Insights into the Chaperone Activity of the 40-kDa Heat Shock Protein DnaJ
J. Cuéllar (2013)
10.1016/j.cell.2010.08.013
Regulation of Replication Termination by Reb1 Protein-Mediated Action at a Distance
S. K. Singh (2010)
10.1016/J.JMB.2006.09.013
Early events in the binding of the pPS10 replication protein RepA to single iteron and operator DNA sequences.
Teresa Díaz-López (2006)
10.1093/nar/gku771
Initiator protein dimerization plays a key role in replication control of Vibrio cholerae chromosome 2
Jyoti K. Jha (2014)
10.1128/JB.06395-11
Roles of long and short replication initiation proteins in the fate of IncP-1 plasmids.
H. Yano (2012)
Quorum Sensing, Entry Exclusion And Replication Of The Ti Plasmid Of Agrobacterium Tumefaciens
Uelinton Manoel Pinto (2011)
10.1093/nar/gkx166
Handcuffing reversal is facilitated by proteases and replication initiator monomers
Katarzyna Bury (2017)
10.1016/j.plasmid.2013.02.003
Plasmid R6K replication control.
Sheryl A. Rakowski (2013)
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