AT-rich region and repeated sequences – the essential elements of replication origins of bacterial replicons

Rajewska, Magdalena; Wegrzyn, Katarzyna; Konieczny, Igor

doi:10.1111/j.1574-6976.2011.00300.x

Cited by 104 publications

(96 citation statements)

References 259 publications

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“…DnaA forms a nucleoprotein complex with Ori that results in the loading of different components of the replisome, leading to DNA replication. 3 The archaeal DNA replication machinery has many similarities and is a simplified form of the one in eukaryotes. 4 The archaeal chromosome generally contains one Ori that has autonomously replicating sequence activity, although some Achaea contain multiple Oris.…”

Section: New Insights Into Replication Origin Characteristics In Metamentioning

confidence: 99%

New insights into replication origin characteristics in metazoans

Cayrou¹,

Coulombe²,

Puy³

et al. 2012

Cell Cycle

167

143

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We recently reported the identification and characterization of DNA replication origins (Oris) in metazoan cell lines. Here, we describe additional bioinformatic analyses showing that the previously identified GC-rich sequence elements form origin G-rich repeated elements (OGREs) that are present in 67% to 90% of the DNA replication origins from Drosophila to human cells, respectively. Our analyses also show that initiation of DNA synthesis takes place precisely at 160 bp (Drosophila) and 280 bp (mouse) from the OGRE. We also found that in most CpG islands, an OGRE is positioned in opposite orientation on each of the two DNA strands and detected two sites of initiation of DNA synthesis upstream or downstream of each OGRE. Conversely, Oris not associated with CpG islands have a single initiation site. OGRE density along chromosomes correlated with previously published replication timing data. Ori sequences centered on the OGRE are also predicted to have high intrinsic nucleosome occupancy. Finally, OGREs predict G-quadruplex structures at Oris that might be structural elements controlling the choice or activation of replication origins.

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Section: New Insights Into Replication Origin Characteristics In Metamentioning

confidence: 99%

New insights into replication origin characteristics in metazoans

Cayrou¹,

Coulombe²,

Puy³

et al. 2012

Cell Cycle

167

143

View full text Add to dashboard Cite

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“…m 6 A was found to mark replication origins of genomic and plasmid replicons, and regulate replication and chromosome segregation 27, 28, 29, 30. Similarly, m 6 A marks also help distinguishing the DNA strands during mismatch repair 31.…”

Section: Introductionmentioning

confidence: 99%

Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification

2015

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While N6‐methyladenosine (m6A) is a well‐known epigenetic modification in bacterial DNA, it remained largely unstudied in eukaryotes. Recent studies have brought to fore its potential epigenetic role across diverse eukaryotes with biological consequences, which are distinct and possibly even opposite to the well‐studied 5‐methylcytosine mark. Adenine methyltransferases appear to have been independently acquired by eukaryotes on at least 13 occasions from prokaryotic restriction‐modification and counter‐restriction systems. On at least four to five instances, these methyltransferases were recruited as RNA methylases. Thus, m6A marks in eukaryotic DNA and RNA might be more widespread and diversified than previously believed. Several m6A‐binding protein domains from prokaryotes were also acquired by eukaryotes, facilitating prediction of potential readers for these marks. Further, multiple lineages of the AlkB family of dioxygenases have been recruited as m6A demethylases. Although members of the TET/JBP family of dioxygenases have also been suggested to be m6A demethylases, this proposal needs more careful evaluation.Also watch the Video Abstract.

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“…In case of bacterial plasmids, involvement of both the plasmidencoded Rep and the host-encoded replication initiator DnaA was reported as essential for origin opening and helicase complex recruitment (19)(20)(21). DNA replication of the broad-hostrange plasmid RK2 (reviewed in ref.…”

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confidence: 99%

Plasmid replication initiator interactions with origin 13-mers and polymerase subunits contribute to strand-specific replisome assembly

Wawrzycka

Gross

Wasaznik

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Although the molecular basis for replisome activity has been extensively investigated, it is not clear what the exact mechanism for de novo assembly of the replication complex at the replication origin is, or how the directionality of replication is determined. Here, using the plasmid RK2 replicon, we analyze the protein interactions required for Escherichia coli polymerase III (Pol III) holoenzyme association at the replication origin. Our investigations revealed that in E. coli, replisome formation at the plasmid origin involves interactions of the RK2 plasmid replication initiation protein (TrfA) with both the polymerase β-and α-subunits. In the presence of other replication proteins, including DnaA, helicase, primase and the clamp loader, TrfA interaction with the β-clamp contributes to the formation of the β-clamp nucleoprotein complex on origin DNA. By reconstituting in vitro the replication reaction on ssDNA templates, we demonstrate that TrfA interaction with the β-clamp and sequence-specific TrfA interaction with one strand of the plasmid origin DNA unwinding element (DUE) contribute to strand-specific replisome assembly. Wild-type TrfA, but not the TrfA QLSLF mutant (which does not interact with the β-clamp), in the presence of primase, helicase, Pol III core, clamp loader, and β-clamp initiates DNA synthesis on ssDNA template containing 13-mers of the bottom strand, but not the top strand, of DUE. Results presented in this work uncovered requirements for anchoring polymerase at the plasmid replication origin and bring insights of how the directionality of DNA replication is determined.DNA replication initiation | polymerase III | β-clamp | Rep | plasmid RK2

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AT-rich region and repeated sequences – the essential elements of replication origins of bacterial replicons

Cited by 104 publications

References 259 publications

New insights into replication origin characteristics in metazoans

New insights into replication origin characteristics in metazoans

Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification

Plasmid replication initiator interactions with origin 13-mers and polymerase subunits contribute to strand-specific replisome assembly

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