title: Distribution of stable DnaA-binding sites on the Bacillus subtilis genome detected using a modified ChIP-chip method.
abstract: We developed a modified ChIP-chip method, designated ChAP-chip (Chromatin Affinity Precipitation coupled with tiling chip). The binding sites of Bacillus subtilis Spo0J determined using this technique were consistent with previous findings. A DNA replication initiator protein, DnaA, formed stable complexes at eight intergenic regions on the B. subtilis genome. Characterization of the binding sequences suggested that two factors -- the local density of DnaA boxes and their affinities for DnaA -- are critical for stable binding. We further showed that in addition to autoregulation, DnaA directly modulate the expression of sda in a positive, and ywlC and yydA in a negative manner. Examination of possible stable DnaA-binding sequences in other Bacillus species suggested that DnaA-dependent regulation of those genes is maintained in most bacteria examined, supporting their biological significance. In addition, a possible stable DnaA-binding site downstream of gcp is also suggested to be conserved. Furthermore, potential DnaA-binding sequences specific for each bacterium have been identified, generally in close proximity to oriC. These findings suggest that DnaA plays several additional roles, such as control of the level of effective initiator, ATP-DnaA, and/or stabilization of the domain structure of the genome around oriC for the proper initiation of chromosome replication.
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, Japan.
authors.forename: Shu
authors.initials: S
authors.lastname: Ishikawa
authors.forename: Yoshitoshi
authors.initials: Y
authors.lastname: Ogura
authors.forename: Mika
authors.initials: M
authors.lastname: Yoshimura
authors.forename: Hajime
authors.initials: H
authors.lastname: Okumura
authors.forename: Eunha
authors.initials: E
authors.lastname: Cho
authors.forename: Yoshikazu
authors.initials: Y
authors.lastname: Kawai
authors.forename: Ken
authors.initials: K
authors.lastname: Kurokawa
authors.forename: Taku
authors.initials: T
authors.lastname: Oshima
authors.forename: Naotake
authors.initials: N
authors.lastname: Ogasawara
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D017124:Conserved Sequence; D004268:DNA-Binding Proteins / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D016680:Genome, Bacterial / Q000235:genetics*; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; C066312:DnaA protein, Bacteria