Online citations, reference lists, and bibliographies.
← Back to Search

Replication Initiation At A Distance

Mukesh Saxena, M. Abhyankar, D. Bastia
Published 2009 · Biology, Medicine

Cite This
Download PDF
Analyze on Scholarcy
Share
Plasmid R6K, which contains 3 replication origins called α, γ, and β, is a favorable system to investigate the molecular mechanism(s) of action at a distance, i.e. replication initiation at a considerable distance from the primary initiator protein binding sites (iterons). The centrally located γ origin contains 7 iterons that bind to the plasmid-encoded initiator protein, π. Ori α, located at a distance of ∼4 kb from γ, contains a single iteron that does not directly bind to π but is believed to access the protein by π-mediated α-γ iteron-iteron interaction that loops out the intervening ∼3.7 kb of DNA. Although the cis-acting components and the trans-acting proteins required for ori γ function have been analyzed in detail, such information was lacking for ori α. Here, we have identified both the sequence elements located at α and those at γ, that together promoted α activity. The data support the conclusion that besides the single iteron, a neighboring DNA primase recognition element called G site is essential for α-directed plasmid maintenance. Sequences preceding the iteron and immediately following the G site, although not absolutely necessary, appear to play a role in efficient plasmid maintenance. In addition, while both dnaA1 and dnaA2 boxes that bind to DnaA protein and are located at γ were essential for α activity, only dnaA2 was required for initiation at γ. Mutations in the AT-rich region of γ also abolished α function. These results are consistent with the interpretation that a protein-DNA complex consisting of π and DnaA forms at γ and activates α at a distance by DNA looping.
This paper references
10.1016/0092-8674(80)90156-7
Supercoiled loops and eucaryotic DNA replication
B. Vogelstein (1980)
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/j.cell.2008.03.024
The 3D Structure of the Immunoglobulin Heavy-Chain Locus: Implications for Long-Range Genomic Interactions
S. Jhunjhunwala (2008)
10.1007/BF00330452
Identification and characterization of the functional α origin of DNA replication of the R6K plasmid and its relatedness to the R6K β and γ origins
A. Shafferman (2004)
Three origins of replication are active in vivo in the R plasmid RSF1040.
J. Crosa (1980)
10.1002/0471684228.egp05000
A Genetic Switch
M. Ptashne (1986)
Roles of phi X174 type primosome- and G4 type primase-dependent primings in initiation of lagging and leading strand syntheses of DNA replication.
H. Masai (1990)
10.1016/0092-8674(88)90030-X
Converting a eukaryotic transcriptional inhibitor into an activator
J. Ma (1988)
Total reconstitution of DNA polymerase III holoenzyme reveals dual accessory protein clamps.
M. O’Donnell (1990)
Molecular Cloning: A Laboratory Manual
J. Sambrook (1983)
10.1016/S1097-2765(02)00781-5
Looping and interaction between hypersensitive sites in the active beta-globin locus.
B. Tolhuis (2002)
Primase, the dnaG protein of Escherichia coli. An enzyme which starts DNA chains.
L. Rowen (1978)
10.1093/NAR/16.9.3829
The integration host factor of Escherichia coli binds to multiple sites at plasmid R6K gamma origin and is essential for replication.
M. Filutowicz (1988)
10.1038/nrg2555
Replication timing and epigenetic reprogramming of gene expression: a two-way relationship?
A. Göndör (2009)
10.1073/PNAS.96.1.73
Mechanism of recruitment of DnaB helicase to the replication origin of the plasmid pSC101.
H. J. Datta (1999)
10.1016/0092-8674(84)90539-7
Replication initiated at the origin (oriC) of the E. coli chromosome reconstituted with purified enzymes
J. Kaguni (1984)
10.1073/pnas.171065898
Mechanism of termination of DNA replication of Escherichia coli involves helicase–contrahelicase interaction
S. Mulugu (2001)
Activity in vitro of three replication origins of the antibiotic resistance plasmid RSF1040.
N. Inuzuka (1980)
10.1016/0022-2836(78)90181-X
Molecular cloning of replication and incompatibility regions from the R-plasmid R6K.
J. Crosa (1978)
10.1006/JMBI.2001.4741
DnaA boxes in the P1 plasmid origin: the effect of their position on the directionality of replication and plasmid copy number.
K. Park (2001)
10.1073/PNAS.87.23.9123
Alpha and beta replication origins of plasmid R6K show similar distortions of the DNA helix in vivo.
Y. Flashner (1990)
Complexes of Escherichia coli primase with the replication origin of G4 phage DNA.
M. Stayton (1983)
10.1073/PNAS.77.2.900
Initiation of DNA replication by the Escherichia coli dnaG protein: evidence that tertiary structure is involved.
J. Sims (1980)
10.1073/PNAS.72.8.2905
Bidirectional replication of plasmid R6K DNA in Escherichia coli; correspondence between origin of replication and position of single-strand break in relaxed complex.
M. Lovett (1975)
10.1046/j.1365-2958.1996.428960.x
Three novel plasmid R6K proteins act in concert to distort DNA within the α and β origins of DNA replication
Y. Flashner (1996)
Genetic Switch, 3rd Ed
M. Ptashne (2004)
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)
10.1016/0147-619X(78)90014-8
Construction of plasmid R6K derivatives in vitro: characterization of the R6K replication region.
R. Kolter (1978)
10.1093/emboj/17.17.5192
Mechanistic studies of initiator–initiator interaction and replication initiation
Y. Lu (1998)
10.1074/JBC.M312052200
Biochemical Investigations of Control of Replication Initiation of Plasmid R6K*
M. Abhyankar (2004)
Cloning: A LaboratoryManual, 2nd Ed
J. Sambrook (1989)
10.1016/0092-8674(87)90642-8
The localization of replication origins on ARS plasmids in S. cerevisiae
B. Brewer (1987)
10.1046/j.1365-2958.1997.4111778.x
Genes involved in conjugative DNA processing of plasmid R6K
B. Núñez (1997)
10.1128/JB.169.9.4124-4127.1987
Overproduction of Escherichia coli integration host factor, a protein with nonidentical subunits.
H. Nash (1987)
10.1074/JBC.271.17.10291
In Vivo Assembly of the -Complex of the DNA Polymerase III Holoenzyme Expressed from a Five-Gene Artificial Operon
A. Pritchard (1996)
10.1016/J.PEP.2003.10.001
Expression, purification, crystallization, and NMR studies of the helicase interaction domain of Escherichia coli DnaG primase.
Karin V. Loscha (2004)
10.1016/J.CEB.2007.04.004
Long-range DNA contacts: romance in the nucleus?
W. Laat (2007)
The RNA primer synthesized by primase to initiate phage G4 DNA replication.
J. Bouché (1978)
10.1074/JBC.M308516200
Reconstitution of R6K DNA Replication in Vitro Using 22 Purified Proteins*
M. Abhyankar (2003)
10.1128/JB.126.1.454-466.1976
Mode of replication of the conjugative R-plasmid RSF1040 in Escherichia coli.
J. Crosa (1976)
10.1038/nmeth1114
An evaluation of 3C-based methods to capture DNA interactions
M. Simonis (2007)
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)
Replication of plasmid R6K origin gamma in vitro. Dependence on dual initiator proteins and inhibition by transcription.
T. MacAllister (1991)
10.1073/PNAS.89.11.5078
Structural and functional analysis of a replication enhancer: separation of the enhancer activity from origin function by mutational dissection of the replication origin gamma of plasmid R6K.
W. Kelley (1992)
10.1016/0022-2836(91)90872-4
AraC-DNA looping: orientation and distance-dependent loop breaking by the cyclic AMP receptor protein.
R. Lobell (1991)
Conformational changes induced by integration host factor at origin gamma of R6K and copy number control.
W. Kelley (1991)
10.1074/JBC.M400021200
Reconstitution of F Factor DNA Replication in Vitro with Purified Proteins*
S. Zzaman (2004)
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)
10.1006/JMBI.1996.0447
Plasmid R6K contains two functional oriTs which can assemble simultaneously in relaxosomes in vivo.
P. Avila (1996)
10.1016/0378-1119(93)90584-P
Roles of the G site and φX174-type primosome assembly site in priming of leading-strand synthesis: initiation by a mobile primosome and replication-fork arrest by RepA protein bound to oriR
Kubota Yoshi-hisa (1993)



This paper is referenced by
Semantic Scholar Logo Some data provided by SemanticScholar