Long inverted repeat transiently stalls DNA replication by forming hairpin structures on both leading and lagging strands

Pey Jiun Lai; Chew Theng Lim; Hang Phuong Le; Tsutomu Katayama; David R. F. Leach; Asako Furukohri; Hisaji Maki

doi:10.1111/gtc.12326

Evidence for DNA Hairpin Recognition by Zta at the Epstein-Barr Virus Origin of Lytic Replication

Journal of Virology ◽

10.1128/jvi.02666-09 ◽

2010 ◽

Vol 84 (14) ◽

pp. 7073-7082 ◽

Cited By ~ 5

Author(s):

Andrew J. Rennekamp ◽

Pu Wang ◽

Paul M. Lieberman

Keyword(s):

Dna Replication ◽

Inverted Repeat ◽

Epstein Barr Virus ◽

Lytic Replication ◽

Lytic Cycle ◽

Productive Infection ◽

Dna Hairpin ◽

Barr Virus ◽

Early Protein ◽

Epstein Barr

ABSTRACT The Epstein-Barr virus immediate-early protein (Zta) plays an essential role in viral lytic activation and pathogenesis. Zta is a basic zipper (b-Zip) domain-containing protein that binds multiple sites in the viral origin of lytic replication (OriLyt) and is required for lytic-cycle DNA replication. We present evidence that Zta binds to a sequence-specific, imperfect DNA hairpin formed by an inverted repeat within the upstream essential element (UEE) of OriLyt. Mutations in the OriLyt sequence that are predicted to disrupt hairpin formation also disrupt Zta binding in vitro. Restoration of the hairpin rescues the defect. We also show that OriLyt DNA isolated from replicating cells contains a nuclease-sensitive region that overlaps with the inverted-repeat region of the UEE. Furthermore, point mutations in Zta that disrupt specific recognition of the UEE hairpin are defective for activation of lytic replication. These data suggest that Zta acts by inducing and/or stabilizing a DNA hairpin structure during productive infection. The DNA hairpin at OriLyt with which Zta interacts resembles DNA structures formed at other herpesvirus origins and may therefore represent a common secondary structure used by all herpesvirus family members during the initiation of DNA replication.

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Palindrome Regeneration by Template Strand-Switching Mechanism at the Origin of DNA Replication of Porcine Circovirus via the Rolling-Circle Melting-Pot Replication Model

Journal of Virology ◽

10.1128/jvi.78.17.9016-9029.2004 ◽

2004 ◽

Vol 78 (17) ◽

pp. 9016-9029 ◽

Cited By ~ 25

Author(s):

Andrew K. Cheung

Keyword(s):

Dna Replication ◽

Inverted Repeat ◽

Tertiary Structure ◽

Porcine Circovirus ◽

Stem Loop ◽

Melting Pot ◽

Rolling Circle ◽

Template Strand ◽

Origin Of Dna Replication ◽

Replication Model

ABSTRACT Palindromic sequences (inverted repeats) flanking the origin of DNA replication with the potential of forming single-stranded stem-loop cruciform structures have been reported to be essential for replication of the circular genomes of many prokaryotic and eukaryotic systems. In this study, mutant genomes of porcine circovirus with deletions in the origin-flanking palindrome and incapable of forming any cruciform structures invariably yielded progeny viruses containing longer and more stable palindromes. These results suggest that origin-flanking palindromes are essential for termination but not for initiation of DNA replication. Detection of template strand switching in the middle of an inverted repeat strand among the progeny viruses demonstrated that both the minus genome and a corresponding palindromic strand served as templates simultaneously during DNA biosynthesis and supports the recently proposed rolling-circle “melting-pot” replication model. The genome configuration presented by this model, a four-stranded tertiary structure, provides insights into the mechanisms of DNA replication, inverted repeat correction (or conversion), and illegitimate recombination of any circular DNA molecule with an origin-flanking palindrome.

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Functional organization of the simian virus 40 origin of DNA replication

Molecular and Cellular Biology ◽

10.1128/mcb.6.4.1117-1128.1986 ◽

1986 ◽

Vol 6 (4) ◽

pp. 1117-1128 ◽

Cited By ~ 1

Author(s):

J J Li ◽

K W Peden ◽

R A Dixon ◽

T Kelly

Keyword(s):

Dna Replication ◽

Inverted Repeat ◽

Functional Organization ◽

Simian Virus 40 ◽

Simian Virus ◽

T Antigen ◽

Origin Of Replication ◽

Antigen Binding Site

To define the sequence elements involved in initiation of DNA synthesis at the simian virus 40 origin of replication, we determined the relative replication efficiencies in vitro and in vivo of templates containing a variety of mutations within the origin region. Replication of the mutants in vitro was assayed by the cell-free DNA replication system that we recently described (J.J. Li and T.J. Kelly, Proc. Natl. Acad. Sci. USA 81:6973-6977, 1984; J.J. Li and T.J. Kelly, Mol. Cell. Biol. 5:1238-1246, 1985), and replication in vivo was assayed after transfection of the mutant templates into COS-1 cells. The minimal origin of replication defined by both assays included a 15-base-pair (bp) imperfect inverted repeat, a 27-bp perfect inverted repeat, and a 17-bp A/T-rich region. T-antigen binding site I was not required for DNA replication, but its presence increased replication efficiency severalfold both in vitro and in vivo. Although SP1 binding sites and enhancers had little or no effect on replication in vitro, the presence of either element markedly increased replication in vivo. Thus, the biological role of these elements is not restricted to stimulating transcription but may be more general.

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Functional organization of the simian virus 40 origin of DNA replication.

Molecular and Cellular Biology ◽

10.1128/mcb.6.4.1117 ◽

1986 ◽

Vol 6 (4) ◽

pp. 1117-1128 ◽

Cited By ~ 63

Author(s):

J J Li ◽

K W Peden ◽

R A Dixon ◽

T Kelly

Keyword(s):

Dna Replication ◽

Inverted Repeat ◽

Functional Organization ◽

Simian Virus 40 ◽

Simian Virus ◽

T Antigen ◽

Origin Of Replication ◽

Antigen Binding Site

To define the sequence elements involved in initiation of DNA synthesis at the simian virus 40 origin of replication, we determined the relative replication efficiencies in vitro and in vivo of templates containing a variety of mutations within the origin region. Replication of the mutants in vitro was assayed by the cell-free DNA replication system that we recently described (J.J. Li and T.J. Kelly, Proc. Natl. Acad. Sci. USA 81:6973-6977, 1984; J.J. Li and T.J. Kelly, Mol. Cell. Biol. 5:1238-1246, 1985), and replication in vivo was assayed after transfection of the mutant templates into COS-1 cells. The minimal origin of replication defined by both assays included a 15-base-pair (bp) imperfect inverted repeat, a 27-bp perfect inverted repeat, and a 17-bp A/T-rich region. T-antigen binding site I was not required for DNA replication, but its presence increased replication efficiency severalfold both in vitro and in vivo. Although SP1 binding sites and enhancers had little or no effect on replication in vitro, the presence of either element markedly increased replication in vivo. Thus, the biological role of these elements is not restricted to stimulating transcription but may be more general.

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Replication of Bacteriophage 186 DNA

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010009422x ◽

1972 ◽

Vol 30 ◽

pp. 194-195

Author(s):

Dhruba K. Chattoraj ◽

Ross B. Inman

Keyword(s):

Electron Microscopy ◽

Dna Replication ◽

Frame Of Reference ◽

Dna Molecules ◽

E Coli ◽

Phage Dna ◽

Partial Denaturation

Electron microscopy of replicating intermediates has been quite useful in understanding the mechanism of DNA replication in DNA molecules of bacteriophage, mitochondria and plasmids. The use of partial denaturation mapping has made the tool more powerful by providing a frame of reference by which the position of the replicating forks in bacteriophage DNA can be determined on the circular replicating molecules. This provided an easy means to find the origin and direction of replication in λ and P2 phage DNA molecules. DNA of temperate E. coli phage 186 was found to have an unique denaturation map and encouraged us to look into its mode of replication.

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