E. coli SeqA protein binds oriC in two different methyl-modulated reactions appropriate to its roles in DNA replication initiation and origin sequestration

@article{Slater1995ECS,
  title={E. coli SeqA protein binds oriC in two different methyl-modulated reactions appropriate to its roles in DNA replication initiation and origin sequestration},
  author={Steven C. Slater and Sture Wold and Min Lu and Erik Boye and Kirsten Skarstad and Nancy Kleckner},
  journal={Cell},
  year={1995},
  volume={82},
  pages={927-936}
}
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SeqA, the Escherichia coli origin sequestration protein, is also a specific transcription factor
TLDR
It is demonstrated that SeqA stimulates transcription from the bacteriophage λpR promoter both in vivo and in vitro, and is concluded that, apart from its function in the control of DNA replication, SequA is also a specific transcription factor.
The Escherichia coli SeqA protein binds specifically and co‐operatively to two sites in hemimethylated and fully methylated oriC
TLDR
It is suggested that SeqA binds to two nucleation sites in oriC, and by the aid of protein–protein interaction spreads to adjacent regions in the same oriC as well as recruiting additional oriC molecules and/or complexes into larger aggregates.
The Escherichia coli SeqA protein binds specifically to two sites in fully and hemimethylated oriC and has the capacity to inhibit DNA replication and affect chromosome topology.
Escherichia coli SeqA protein affects DNA topology and inhibits open complex formation at oriC
TLDR
SeqA restrained the negative supercoils of unmethylated oriC plasmids, suggesting that the effect on topology is not dependent on binding of SeqA to a specific sequence in oriC, and seemed to act more cooperatively than the effect of HU on plasmid topology.
SeqA, the Escherichia coli origin sequestration protein, can regulate the replication of the pBR322 plasmid.
Effects of purified SeqA protein on oriC‐dependent DNA replication in vitro
TLDR
The data suggest that SeqA participates in the assembly of initiation‐competent complexes at oriC and, at a later stage, influences the behaviour of these complexes, and alters the dependence of the replication system on DnaA protein concentration, stimulating replication at low concentrations ofDnaA.
Dynamic Distribution of SeqA Protein across the Chromosome of Escherichia coli K-12
TLDR
A study of the binding of SeqA across the entire Escherichia coli K-12 chromosome, using chromatin immunoprecipitation in combination with DNA microarrays, suggests that sequential changes in SequA distribution orchestrate a program of gene expression that ensures coordinated DNA replication and cell division.
Stimulation of the lambda pR promoter by Escherichia coli SeqA protein requires downstream GATC sequences and involves late stages of transcription initiation.
TLDR
In vitro transcription analysis demonstrated that the most important regulatory effect of SeqA in p(R) transcription occurs after open complex formation, namely during promoter clearance, which is one of few known prokaryotic transcription factors which bind downstream of the regulated promoter.
Sequential binding of SeqA protein to nascent DNA segments at replication forks in synchronized cultures of Escherichia coli
TLDR
Results indicate that sequestration A binds hemimethylated nascent DNA segments according to the proceeding of replication forks in the chromosome, and SeqA releases from the DNA segments when fully methylated, which supports the translocating replication apparatuses model.
Interaction of SeqA and Dam Methylase on the Hemimethylated Origin of Escherichia coli Chromosomal DNA Replication*
TLDR
In vitro results suggest that the intrinsic binding instability of SeqA protein results in release of sequestrated hemimethylated oriC.
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References

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A protein that binds to the P1 origin core and the oriC 13mer region in a methylation‐specific fashion is the product of the host seqA gene.
TLDR
The role of the SeqA protein in sequestration is to recognize the methylation state of P1oriR and oriC by direct DNA binding and it is concluded that the protein can recognize sequences with multiple GATC sites, irrespective of the surrounding sequence.
E. coli oriC and the dnaA gene promoter are sequestered from dam methyltransferase following the passage of the chromosomal replication fork
SeqA: A negative modulator of replication initiation in E. coli
Strand separation required for initiation of replication at the chromosomal origin of E.coli is facilitated by a distant RNA–DNA hybrid.
TLDR
Activation of oriC by the distantly located R‐loop appears to require propagation of DNA melting through the intervening sequence.
Importance of state of methylation of oriC GATC sites in initiation of DNA replication in Escherichia coli.
TLDR
In vivo and in vitro evidence is presented implicating a function of GATC methylation in the Escherichia coli replication origin, oriC, during initiation of DNA synthesis, suggesting a new function for the Dam methylase.
The requirement of IHF protein for extrachromosomal replication of the Escherichia coli oriC in a mutant deficient in DNA polymerase I activity.
TLDR
It is shown here that plasmids containing the replication origin of Escherichia coli (oriC) cannot replicate in an extrachromosomal state in E. coli cells with the polA1hip3 double mutation and it is proposed that IHF-deficient cells utilize an alternative pathway of the DNA replication in which Pol I is required.
Parental strand recognition of the DNA replication origin by the outer membrane in Escherichia coli.
TLDR
A footprinting analysis with the outer membrane of Escherichia coli demonstrates that its interaction with oriC occurs mainly at the left moiety of the minimal oriC, where 10 out of 11 Dam methylation sites are concentrated.
Correlation of gene transcription with the time of initiation of chromosome replication in Escherichia coli
TLDR
It is proposed that mioC transcription prevents initiation of chromosome replication, and must terminate before replication can begin, and it is further proposed that the eclipse period between rounds of replication, i.e. the minimum interval between successive initiations, encompasses the time required to methylate GATC sequences in newly replicated oriC plus the time needed to terminate mIOC transcription.
Localized DNA melting and structural pertubations in the origin of replication, oriC, of Escherichia coli in vitro and in vivo.
TLDR
First in vivo evidence for a structural change at the 13mers during initiation complex formation is observed at oriC, the leftmost region of the Escherichia coli origin of DNA replication.
The dnaA initiator protein binds separate domains in the replication origin of Escherichia coli.
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