Role of architectural elements in combinatorial regulation of initiation of DNA replication in <i>Escherichia coli</i>

Polaczek, Piotr; Kwan, Kelvin Y.; Liberles, David A.; Campbell, Judith L.

doi:10.1046/j.1365-2958.1997.5701931.x

Cited by 45 publications

(38 citation statements)

References 48 publications

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“…Adenine methylation can alter the interactions of regulatory proteins with DNA, either by a direct steric effect or by an indirect effect on DNA structure (18,61,62). Initial studies with dam mutants showed that Dam regulates the expression of certain genes in E. coli including trpR (60), Tn10 transposase (68), and dnaA (13) as well as phage genes including mom of Mu (24).…”

Section: Dam Familymentioning

confidence: 99%

Roles of DNA Adenine Methylation in Regulating Bacterial Gene Expression and Virulence

2001

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Section: Dam Familymentioning

confidence: 99%

Roles of DNA Adenine Methylation in Regulating Bacterial Gene Expression and Virulence

2001

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“…A DNA methylation pattern is formed by binding of a regulatory protein(s) to a site that overlaps a methylation target, blocking methylation. This pattern can control gene expression if methylation, in turn, affects binding of the regulatory protein(s) to its DNA target site, which could occur by steric hindrance or alteration of DNA structure due to methylation (206,207). Notably, most adhesin genes in E. coli are regulated by epigenetic mechanisms involving DNA methylation patterns (32,115,116,262).…”

Section: Introductionmentioning

confidence: 99%

Epigenetic Gene Regulation in the Bacterial World

Casadesús

Low

2006

Microbiol Mol Biol Rev

558

562

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SUMMARY Like many eukaryotes, bacteria make widespread use of postreplicative DNA methylation for the epigenetic control of DNA-protein interactions. Unlike eukaryotes, however, bacteria use DNA adenine methylation (rather than DNA cytosine methylation) as an epigenetic signal. DNA adenine methylation plays roles in the virulence of diverse pathogens of humans and livestock animals, including pathogenic Escherichia coli, Salmonella, Vibrio, Yersinia, Haemophilus, and Brucella. In Alphaproteobacteria, methylation of adenine at GANTC sites by the CcrM methylase regulates the cell cycle and couples gene transcription to DNA replication. In Gammaproteobacteria, adenine methylation at GATC sites by the Dam methylase provides signals for DNA replication, chromosome segregation, mismatch repair, packaging of bacteriophage genomes, transposase activity, and regulation of gene expression. Transcriptional repression by Dam methylation appears to be more common than transcriptional activation. Certain promoters are active only during the hemimethylation interval that follows DNA replication; repression is restored when the newly synthesized DNA strand is methylated. In the E. coli genome, however, methylation of specific GATC sites can be blocked by cognate DNA binding proteins. Blockage of GATC methylation beyond cell division permits transmission of DNA methylation patterns to daughter cells and can give rise to distinct epigenetic states, each propagated by a positive feedback loop. Switching between alternative DNA methylation patterns can split clonal bacterial populations into epigenetic lineages in a manner reminiscent of eukaryotic cell differentiation. Inheritance of self-propagating DNA methylation patterns governs phase variation in the E. coli pap operon, the agn43 gene, and other loci encoding virulence-related cell surface functions.

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“…IHF is a multipurpose architectural protein, which plays an essential role in several cellular processes including sitespecific recombination, transcription, DNA replication, and phage packaging (16)(17)(18)(19). The crystal structure of IHF bound to the HЈ site indicates that the DNA is kinked at two sites separated by Ϸ9 bp and that the overall bend in the DNA is Ϸ160° (Fig.…”

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confidence: 99%

Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF

Kuznetsov¹,

Sugimura

Vivas³

et al. 2006

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

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Regulation of gene expression involves formation of specific protein-DNA complexes in which the DNA is often bent or sharply kinked. Kinetics measurements of DNA bending when in complex with the protein are essential for understanding the molecular mechanism that leads to precise recognition of specific DNAbinding sites. Previous kinetics measurements on several DNAbending proteins used stopped-flow techniques that have limited time resolution of few milliseconds. Here we use a nanosecond laser temperature-jump apparatus to probe, with submillisecond time resolution, the kinetics of bending͞unbending of a DNA substrate bound to integration host factor (IHF), an architectural protein from Escherichia coli. The kinetics are monitored with time-resolved FRET, with the DNA substrates end-labeled with a FRET pair. The temperature-jump measurements, in combination with stopped-flow measurements, demonstrate that the binding of IHF to its cognate DNA site involves an intermediate state with straight or, possibly, partially bent DNA. The DNA bending rates range from Ϸ2 ms ؊1 at Ϸ37°C to Ϸ40 ms ؊1 at Ϸ10°C and correspond to an activation energy of Ϸ14 ؎ 3 kcal͞mol. These rates and activation energy are similar to those of a single A:T base pair opening inside duplex DNA. Thus, our results suggest that spontaneous thermal disruption in base-paring, nucleated at an A:T site, may be sufficient to overcome the free energy barrier needed to partially bend͞kink DNA before forming a tight complex with IHF.DNA bending kinetics ͉ laser temperature jump ͉ protein-DNA interactions ͉ time-resolved FRET measurements

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Role of architectural elements in combinatorial regulation of initiation of DNA replication in Escherichia coli

Cited by 45 publications

References 48 publications

Roles of DNA Adenine Methylation in Regulating Bacterial Gene Expression and Virulence

Roles of DNA Adenine Methylation in Regulating Bacterial Gene Expression and Virulence

Epigenetic Gene Regulation in the Bacterial World

Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF

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