ArticlePLoS genetics2015
In Vitro Whole Genome DNA Binding Analysis of the Bacterial Replication Initiator and Transcription Factor DnaA.
Article in PLoS genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 0 citations in OpenAlex.
- A rapid test for protein-DNA interactions.Nucleic acids research · 2026Article
- PolyP inhibits CobB deacetylase triggering a regulatory coupling to prevent DNA replication initiation.Nucleic acids research · 2026Article
- Mechanisms of chromosomal DNA replication in Escherichia coli and Bacillus subtilis.FEMS microbiology reviews · 2026Review
- Article
- An antisense RNA regulates production of DnaA and affects sporulation in Bacillus subtilis.PLoS genetics · 2025Article
- Rok from B. subtilis: Bridging genome structure and transcription regulation.Molecular microbiology · 2025Review
- Bacterial single-cell RNA sequencing captures biofilm transcriptional heterogeneity and differential responses to immune pressure.Nature communications · 2024Article
- Borrelia burgdorferi DnaA and the Nucleoid-Associated Protein EbfC Coordinate Expression of theJournal of bacteriology · 2023Article
- Transcriptional Activity of the Bacterial Replication Initiator DnaA.Frontiers in microbiology · 2021Review
- Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.PLoS pathogens · 2020Article
- Genome-wide identification of Listeria monocytogenes CodY-binding sites.Molecular microbiology · 2020Article
- A progesterone biosensor derived from microbial screening.Nature communications · 2020Article
- The Lyme disease spirochete's BpuR DNA/RNA-binding protein is differentially expressed during the mammal-tick infectious cycle, which affects translation of the SodA superoxide dismutase.Molecular microbiology · 2019Article
- How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome.Nucleic acids research · 2018Article
- Genes and Proteins Involved inAntimicrobial agents and chemotherapy · 2018Article
- DNA gyrase activity regulates DnaA-dependent replication initiation in Bacillus subtilis.Molecular microbiology · 2018Article
- Phosphorylation of theFrontiers in microbiology · 2018Article
- Structure and Function of theFrontiers in microbiology · 2018Article
- Genetic networks controlled by the bacterial replication initiator and transcription factor DnaA in Bacillus subtilis.Molecular microbiology · 2017Article
- The nucleoid occlusion factor Noc controls DNA replication initiation in Staphylococcus aureus.PLoS genetics · 2017Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
DnaA, the replication initiation protein in bacteria, is an AAA+ ATPase that binds and hydrolyzes ATP and exists in a heterogeneous population of ATP-DnaA and ADP-DnaA. DnaA binds cooperatively to the origin of replication and several other chromosomal regions, and functions as a transcription factor at some of these regions. We determined the binding properties of Bacillus subtilis DnaA to genomic DNA in vitro at single nucleotide resolution using in vitro DNA affinity purification and deep sequencing (IDAP-Seq). We used these data to identify 269 binding regions, refine the consensus sequence of the DnaA binding site, and compare the relative affinity of binding regions for ATP-DnaA and ADP-DnaA. Most sites had a slightly higher affinity for ATP-DnaA than ADP-DnaA, but a few had a strong preference for binding ATP-DnaA. Of the 269 sites, only the eight strongest binding ones have been observed to bind DnaA in vivo, suggesting that other cellular factors or the amount of available DnaA in vivo restricts DnaA binding to these additional sites. Conversely, we found several chromosomal regions that were bound by DnaA in vivo but not in vitro, and that the nucleoid-associated protein Rok was required for binding in vivo. Our in vitro characterization of the inherent ability of DnaA to bind the genome at single nucleotide resolution provides a backdrop for interpreting data on in vivo binding and regulation of DnaA, and is an approach that should be adaptable to many other DNA binding proteins.
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