Distribution of Stable DnaA-Binding Sites on the Bacillus Subtilis Genome Detected using a Modified ChIP-chip Method

Ishikawa, Shu; Ogura, Yoshitoshi; Yoshimura, Mika; Okumura, Hajime; Cho, Eun-Ha; Kawai, Yoshikazu; Kurokawa, Ken; Oshima, Taku; Ogasawara, Nagahisa

doi:10.1093/dnares/dsm017

Cited by 63 publications

(143 citation statements)

References 47 publications

Supporting

Mentioning

139

Contrasting

Order By: Relevance

“…These data suggest that disruptants maintained a low level of metabolic activity during the stationary phase to preserve cellular energy and enhance viability. DnaA could also directly regulate expression of these genes, given its function as a transcription factor in many bacteria (Messer and Weigel, 1997;Ishikawa et al, 2007;McAdams and Shapiro, 2009). …”

Section: Increased Viability Of Dnaa Disruptants Under Long Culture Cmentioning

confidence: 99%

Diversification of DnaA dependency for DNA replication in cyanobacterial evolution

et al. 2015

View full text Add to dashboard Cite

Regulating DNA replication is essential for all living cells. The DNA replication initiation factor DnaA is highly conserved in prokaryotes and is required for accurate initiation of chromosomal replication at oriC. DnaA-independent free-living bacteria have not been identified. The dnaA gene is absent in plastids and some symbiotic bacteria, although it is not known when or how DnaA-independent mechanisms were acquired. Here, we show that the degree of dependency of DNA replication on DnaA varies among cyanobacterial species. Deletion of the dnaA gene in Synechococcus elongatus PCC 7942 shifted DNA replication from oriC to a different site as a result of the integration of an episomal plasmid. Moreover, viability during the stationary phase was higher in dnaA disruptants than in wild-type cells. Deletion of dnaA did not affect DNA replication or cell growth in Synechocystis sp. PCC 6803 or Anabaena sp. PCC 7120, indicating that functional dependency on DnaA was already lost in some nonsymbiotic cyanobacterial lineages during diversification. Therefore, we proposed that cyanobacteria acquired DnaA-independent replication mechanisms before symbiosis and such an ancestral cyanobacterium was the sole primary endosymbiont to form a plastid precursor.

show abstract

Section: Increased Viability Of Dnaa Disruptants Under Long Culture Cmentioning

confidence: 99%

Diversification of DnaA dependency for DNA replication in cyanobacterial evolution

et al. 2015

View full text Add to dashboard Cite

show abstract

“…The factors to promote the exchange of bound ADP for ATP on DnaA include fluid membranes with acidic phospholipids as well as a specific DNA sequence containing DnaA boxes (19 -22). DnaA acts as a transcription factor and autoregulates its expression (23)(24)(25)(26), and its activity is affected by nucleotide binding (27,28 Comparison of replication-related gene sequences suggests that there are different mechanisms for controlling initiation in Gram-positive bacteria with low GC content such as Staphylococcus aureus and Bacillus subtilis than in Gram-negative bacteria such as E. coli. Specifically, Gram-negative bacteria related to E. coli contain Dam methylase and SeqA (29 -31), which inactivate oriC and the dnaA promoter immediately after the initiation of DNA replication, whereas these proteins are absent in Gram-positive bacteria.…”

mentioning

confidence: 99%

Rapid Exchange of Bound ADP on the Staphylococcus aureus Replication Initiation Protein DnaA

Kurokawa

Mizumura

Takaki

et al. 2009

Journal of Biological Chemistry

View full text Add to dashboard Cite

In Escherichia coli, regulatory inactivation of the replication initiator DnaA occurs after initiation as a result of hydrolysis of bound ATP to ADP, but it has been unknown how DnaA is controlled to coordinate cell growth and chromosomal replication in Gram-positive bacteria such as Staphylococcus aureus. This study examined the roles of ATP binding and its hydrolysis in the regulation of the S. aureus DnaA activity. In vitro, S. aureus DnaA melted S. aureus oriC in the presence of ATP but not ADP by a mechanism independent of ATP hydrolysis. Unlike E. coli DnaA, binding of ADP to S. aureus DnaA was unstable. As a result, at physiological concentrations of ATP, ADP bound to S. aureus DnaA was rapidly exchanged for ATP, thereby regenerating the ability of DnaA to form the open complex in vitro. Therefore, we examined whether formation of ADP-DnaA participates in suppression of replication initiation in vivo. Induction of the R318H mutant of the AAA؉ sensor 2 protein, which has decreased intrinsic ATPase activity, caused over-initiation of chromosome replication in S. aureus, suggesting that formation of ADP-DnaA suppresses the initiation step in S. aureus. Together with the biochemical features of S. aureus DnaA, the weak ability to convert ATP-DnaA into ADP-DnaA and the instability of ADP-DnaA, these results suggest that there may be unidentified system(s) for reducing the cellular ratio of ATPDnaA to ADP-DnaA in S. aureus and thereby delaying the reinitiation of DNA replication.The initiation step of chromosome replication is an important set point for coordinating cell growth and chromosomal replication, and it is tightly regulated so that it takes place only once per cell cycle. DNA replication in bacteria starts when the cell mass reaches an appropriate size and at the appropriate time, which is controlled in part by the quantity and activity of initiator DnaA protein (1-3). In Escherichia coli, DnaA binds to 9-mer DnaA boxes in oriC, the origin of chromosome replication, and melts the duplex at AT-rich 13-mers adjacent to oriC. DnaA then directs loading of the DnaB replicative helicase, which depends on the DnaC helicase loader and priming by the DnaG primase. This is followed by the synthesis of DNA by the DNA polymerase III holoenzyme (4).DnaA is composed of four domains: N-terminal domains I and II are involved in DnaA oligomerization and DnaADnaB interaction, and they show a diversity of sequence among bacteria. Domain III contains AAAϩ motifs, and the C-terminal domain IV mediates DNA binding (3, 5). Biochemical and genetic studies in E. coli have revealed adenine nucleotide binding-mediated control of the DnaA activity (6 -11). Specifically, ATP-bound DnaA actively promotes replication initiation, whereas the ADP-bound form is inert (6, 7). ATP promotes the self-assembly of DnaA at replication origins via a conformational change to form a righthanded helical filament (8, 9). In E. coli, 70% to 80% of DnaA exists as the inactive ADP-bound form, and active ATPDnaA levels increase during the initiation ...

show abstract

“…The activity of KinA is inhibited not only by Sda, which is induced when DNA replication is perturbed (Burkholder et al, 2001;Goranov et al, 2005;Ruvolo et al, 2006;Ishikawa et al, 2007), but also by KipI, which is expressed under specific nutrient conditions (Wang et al, 1997). KipI appears to be poised to inhibit KinA in response to an additional unknown signal, because it is coexpressed with a protein that binds and inhibits KipI, KipA (Wang et al, 1997).…”

Section: Discussionmentioning

confidence: 99%

“…Sda expression is induced in response to perturbations in DNA replication or DNA damage, preventing cells from sporulating until chromosome replication has been resumed or completed (Burkholder et al, 2001;Goranov et al, 2005;Ruvolo et al, 2006;Ishikawa et al, 2007). KipI expression is induced when cells are required to use a non-preferred nitrogen source but still have a preferred carbon source (Wang et al, 1997).…”

Section: Introductionmentioning

confidence: 99%

The histidine kinase inhibitor Sda binds near the site of autophosphorylation and may sterically hinder autophosphorylation and phosphotransfer to Spo0F

Cunningham

Burkholder²

2009

Molecular Microbiology

View full text Add to dashboard Cite

SummaryHistidine kinases are widely used by bacteria, fungi and plants to sense and respond to changing environmental conditions. Signals in addition to those directly sensed by the kinase are often integrated by proteins that fine-tune the biological response by modulating the activity of the kinase or its targets. The Bacillus subtilis histidine kinase KinA promotes the initiation of sporulation when nutrients are limiting, but sporulation can be delayed by two inhibitors of KinA, Sda (when DNA replication is perturbed) or KipI (under unknown conditions). We have identified residues in the dimerization/histidinephosphotransfer (DHp) domain of KinA that are functionally important for inhibition by Sda and KipI and overlapping surface-exposed residues that lie close to or comprise the Sda binding site. Sda inhibits the intermolecular transfer of phosphate from the catalytic ATP-binding (CA) domain of KinA to the autophosphorylation site in the DHp domain when the domains are split into separate polypeptides, either by steric hindrance or by altering the conformation of the DHp domain. Sda also slows the rate of phosphotransfer from KinA~P to its target, Spo0F, consistent with our finding that a KinA residue important for Sda function overlaps with the predicted Spo0F binding site on KinA.

show abstract

Distribution of Stable DnaA-Binding Sites on the Bacillus Subtilis Genome Detected using a Modified ChIP-chip Method

Cited by 63 publications

References 47 publications

Diversification of DnaA dependency for DNA replication in cyanobacterial evolution

Diversification of DnaA dependency for DNA replication in cyanobacterial evolution

Rapid Exchange of Bound ADP on the Staphylococcus aureus Replication Initiation Protein DnaA

The histidine kinase inhibitor Sda binds near the site of autophosphorylation and may sterically hinder autophosphorylation and phosphotransfer to Spo0F

Contact Info

Product

Resources

About