Anomalous DnaA protein binding to the regulatory region of the Escherichia coli aldA gene

Ozaki, T.; Kumaki, Yuichi; Kitagawa, Risa; Ogawa, Tohru

doi:10.1099/00221287-147-1-153

Cited by 4 publications

(4 citation statements)

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“…One of them is the datA site, which acts to prevent asynchronous and extra initiations of replication at oriC by titrating a large number of DnaA molecules (Kitagawa et al , 1998). To test the possible involvement of other major DnaA‐binding sites in such regulation, four regions ( appY , mutH , yddJK and yfdI ) reported by Roth and Messer (Roth and Messer 1998), as well as the DnaA‐binding sequences at the promoter regions of the uvrB (van den Berg et al , 1985), rpoH (Wang and Kaguni, 1989) and aldA (Ozaki et al , 2001) genes were examined for their role in the timing of replication initiation. The latter three sites were identified in our independent survey for relatively strong DnaA‐binding sites by fragment retention assays.…”

Section: Resultsmentioning

confidence: 99%

“…These regions of appY , yddJK and yfdI had each contained one or two potential DnaA boxes, which could represent high affinity binding sites for DnaA protein. The promoter region of aldA gene has no apparent DnaA box but has significant affinity for DnaA protein (Ozaki et al , 2001).…”

Section: Resultsmentioning

confidence: 99%

“…DnaA‐binding sites at the aldA region (Ozaki et al , 2001), the appY region (Roth and Messer, 1998), the yddJK region ( narU upstream) (Roth and Messer, 1998) and the yfdI region (Fragment H) (Roth and Messer, 1998) were deleted by replacing with fragments that confer drug resistance as shown in Fig. 1.…”

Section: Methodsmentioning

confidence: 99%

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The datA locus predominantly contributes to the initiator titration mechanism in the control of replication initiation in Escherichia coli

Ogawa

Yamada

Kuroda

et al. 2002

Molecular Microbiology

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Summary Replication of the Escherichia coli chromosome is initiated synchronously from all origins (oriC) present in a cell at a fixed time in the cell cycle under given steady state culture conditions. A mechanism to ensure the cyclic initiation events operates through the chromosomal site, datA, which titrates exceptionally large amounts of the bacterial initiator protein, DnaA, to prevent overinitiation. Deletion of the datA locus results in extra initiations and altered temporal control of replication. There are many other sites on the E. coli chromosome that can bind DnaA protein, but the contribution of these sites to the control of replication initiation has not been investigated. In the present study, seven major DnaA binding sites other than datA have been examined for their influence on the timing of replication initiation. Disruption of these seven major binding sites, either individually or together, had no effect on the timing of initiation of replication. Thus, datA seems to be a unique site that adjusts the balance between free and bound DnaA to ensure that there is only a single initiation event in each bacterial cell cycle. Mutation either in the second or the third DnaA box (a 9 basepair DnaA‐binding sequence) in datA was enough to induce asynchronous and extra initiations of replication to a similar extent as that observed with the datA‐deleted strain. These DnaA boxes may act as cores for the cooperative binding of DnaA to the entire datA region.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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The datA locus predominantly contributes to the initiator titration mechanism in the control of replication initiation in Escherichia coli

Ogawa

Yamada

Kuroda

et al. 2002

Molecular Microbiology

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“…In addition to its role in DNA replication initiation, DnaA regulates the transcription initiation of several genes by binding to sites in promoter regions [14,15]. nrdA, glpD, polA and fliC have been described as positively regulated DnaA targets [14,[16][17][18]; mioC, uvrB, aldA, guaB, proS, rpoH, iraD and dnaA itself have been described as negatively regulated DnaA targets [14,[19][20][21][22][23][24][25][26]. The mechanism of regulation by DnaA, especially that of transcription activation, is poorly understood.…”

Section: Introductionmentioning

confidence: 99%

Mapping the Escherichia coli DnaA-binding landscape reveals a preference for binding pairs of closely spaced DNA sites

Stringer,

Fitzgerald,

Wade

2024

Microbiology

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DnaA is a widely conserved DNA-binding protein that is essential for the initiation of DNA replication in many bacterial species, including Escherichia coli. Cooperative binding of ATP-bound DnaA to multiple 9mer sites (‘DnaA boxes’) at the origin of replication results in local unwinding of the DNA and recruitment of the replication machinery. DnaA also functions as a transcription regulator by binding to DNA sites upstream of target genes. Previous studies have identified many sites of direct positive and negative regulation by E. coli DnaA. Here, we use a ChIP-seq to map the E. coli DnaA-binding landscape. Our data reveal a compact regulon for DnaA that coordinates the initiation of DNA replication with expression of genes associated with nucleotide synthesis, replication, DNA repair and RNA metabolism. We also show that DnaA binds preferentially to pairs of DnaA boxes spaced 2 or 3 bp apart. Mutation of either the upstream or downstream site in a pair disrupts DnaA binding, as does altering the spacing between sites. We conclude that binding of DnaA at almost all target sites requires a dimer of DnaA, with each subunit making critical contacts with a DnaA box.

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Insights into the Quality of DnaA Boxes and Their Cooperativity

Hansen

Christensen

Nielsen

et al. 2006

Journal of Molecular Biology

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Anomalous DnaA protein binding to the regulatory region of the Escherichia coli aldA gene

Cited by 4 publications

References 18 publications

The datA locus predominantly contributes to the initiator titration mechanism in the control of replication initiation in Escherichia coli

The datA locus predominantly contributes to the initiator titration mechanism in the control of replication initiation in Escherichia coli

Mapping the Escherichia coli DnaA-binding landscape reveals a preference for binding pairs of closely spaced DNA sites

Insights into the Quality of DnaA Boxes and Their Cooperativity

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