Hda-mediated inactivation of the DnaA protein and <i>dnaA</i> gene autoregulation act in concert to ensure homeostatic maintenance of the <i>Escherichia coli</i> chromosome

Riber, Leise; Olsson, Jan; Jensen, Rasmus Bugge; Skovgaard, Ove; Dasgupta, Santanu; Marinus, Martin; Løbner-Olesen, Anders

doi:10.1101/gad.379506

Cited by 78 publications

(143 citation statements)

References 54 publications

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Section: Yaba Level Does Not Affect Expression Level Of Dnaamentioning

confidence: 99%

“…Additionally, overexpression of YabA and Hda causes a delay in replication initiation (Hayashi et al, 2005;Riber et al, 2006). In the case of Hda, its absence and overexpression decrease and increase, respectively, the expression level of DnaA, probably as a result of Hda-dependent RIDA changing the amount of ATP-DnaA and thus its binding affinity to the promoter region of dnaA (Riber et al, 2006). Since expression of the dnaA gene is autoregulated in both E. coli and B. subtilis (Ogura et al, 2001;Messer, 2002), we speculated that depletion and overproduction of YabA might likewise affect the expression level of the dnaA gene, if YabA also stimulates the hydrolysis of DnaAbound ATP.…”

Section: Yaba Level Does Not Affect Expression Level Of Dnaamentioning

confidence: 99%

“…In this latter system, hydrolysis of ATP-DnaA is promoted when ATPDnaA interacts in the presence of DNA-loaded DnaN with Hda, which can form a stable complex in vitro, ensuring the timely inactivation of DnaA during the replication cycle (Katayama et al, 1998;Kurokawa et al, 1999;Katayama, 2001;Kato and Katayama, 2001;Su'etsugu et al, 2004Su'etsugu et al, , 2005Gon et al, 2006;Kawakami et al, 2006). It has also been suggested recently that RIDA and dnaA gene autoregulation act in concert to secure once-per-cell-cycle initiation, based on the observations that Hda deficiency leads to reduced dnaA gene expression and that overproduction of Hda leads to DnaA overproduction (Riber et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

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The functional analysis of YabA, which interacts with DnaA and regulates initiation of chromosome replication in Bacillus subtils

2008

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The initiation of bacterial chromosome DNA replication and its regulation are critical events. DnaA is essential for initiation of DNA replication and is conserved throughout bacteria. In Escherichia coli, hydrolysis of ATP-DnaA is promoted by Hda through formation of a ternary complex with DnaA and DnaN, ensuring the timely inactivation of DnaA during the replication cycle. In Bacillus subtilis, YabA also forms a ternary complex with DnaA and DnaN, and negatively regulates the initiation step of DNA replication. However, YabA shares no structural homology with Hda and the regulatory mechanism itself has not been clarified. Here, in contrast to Hda, we observed that dnaA transcription was stable during under-and overexpression of YabA. ChAP-chip assays showed that the depletion of YabA did not affect DNA binding by DnaA. On the other hand, yeast two-hybrid analysis indicated that the DnaA ATP-binding domain interacts with YabA. Moreover, mutations in YabA interaction-deficient mutants, isolated by yeast two-hybrid analysis, are located at the back of the ATP-binding domain, whereas Hda is thought to interact with the ATP-binding pocket itself. The introduction into B. subtilis of a dnaA Y144C mutation, which disabled the interaction with YabA but did not affect interactions either with DnaA itself or with DnaD, resulted in over-initiation and asynchronous initiation of replication and disabled the formation of YabA foci, further demonstrating that the amino acid on the opposite side to the ATP-binding pocket is important for YabA binding. These results indicate that YabA indeed regulates the initiation of DNA replication by a different mechanism from that used by Hda in the E. coli RIDA system. Interestingly, all DnaA mutants deficient in YabA binding also displayed reduced DnaD binding in yeast two-hybrid assays, suggesting that YabA can inhibit replication initiation through competitive inhibition of DnaD binding to DnaA.

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Section: Yaba Level Does Not Affect Expression Level Of Dnaamentioning

confidence: 99%

Section: Yaba Level Does Not Affect Expression Level Of Dnaamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The functional analysis of YabA, which interacts with DnaA and regulates initiation of chromosome replication in Bacillus subtils

2008

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“…The ratio of ATP-DnaA to ADP-DnaA is regulated by de novo synthesis of the ATP-bound DnaA, hydrolysis of bound ATP to ADP by the intrinsic ATPase activity of DnaA, the stimulatory factor RIDA (regulatory inactivation of DnaA), 6 and the exchange of bound ADP for ATP (10,12). RIDA requires a ␤ clamp of DNA polymerase III and Hda protein and negatively regulates the initiation step of DNA replication by promoting hydrolysis of bound ATP on DnaA, which is coupled to the progression of chromosome replication (13)(14)(15)(16)(17)(18). 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).…”

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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

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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 ...

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“…A protein homologous to DnaA (Hda, for homolog of DnaA) binds the processivity clamp, b, and DnaA, promoting hydrolysis of ATP (Kato and Katayama 2001). Mutants in hda are somewhat inviable and show over-replication, particularly when DnaA levels are elevated (Kato and Katayama 2001;Camara et al 2005;Riber et al 2006;Fujimitsu et al 2008).…”

Section: R Eplication Initiation In Bacteria Is Controlled Bymentioning

confidence: 99%

A Role for Nonessential Domain II of Initiator Protein, DnaA, in Replication Control

Molt

Sutera

Moore³

et al. 2009

Genetics

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The initiation of replication in bacteria is regulated via the initiator protein DnaA. ATP-bound DnaA binds to multiple sequences at the origin of replication, oriC, unwinding the DNA and promoting the binding of DnaB helicase. From an Escherichia coli mutant highly perturbed for replication control, obgETTn5-EZ seqAD, we isolated multiple spontaneous suppressor mutants with enhanced growth and viability. These suppressors suppressed the replication control defects of mutants in seqA alone and genetically mapped to the essential dnaA replication initiator gene. DNA sequence analysis of four independent isolates revealed an identical deletion of the DnaA-coding region at a repeated hexanucleotide sequence, causing a loss of 25 amino acids in domain II of the DnaA protein. Previous work has established no function for this region of protein, and deletions in the region, unlike other domains of the DnaA protein, do not produce lethality. Flow cytometric analysis established that this allele, dnaAD 96-120 , ameliorated the over-replication phenotype of seqA mutants and reduced the DNA content of wild-type strains; virtually identical effects were produced by loss of the DnaA-positive regulatory protein DiaA. DiaA binds to multiple DnaA subunits and is thought to promote cooperative DnaA binding to weak affinity DNA sites through interactions with DnaA in domains I and/or II. The dnaAD 96-120 mutation did not affect DiaA binding in pull-down assays, and we propose that domain II, like DiaA, is required to promote optimal DnaB recruitment to oriC.

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Hda-mediated inactivation of the DnaA protein and dnaA gene autoregulation act in concert to ensure homeostatic maintenance of the Escherichia coli chromosome

Abstract: Initiation of DNA replication in

Cited by 78 publications

References 54 publications

The functional analysis of YabA, which interacts with DnaA and regulates initiation of chromosome replication in Bacillus subtils

The functional analysis of YabA, which interacts with DnaA and regulates initiation of chromosome replication in Bacillus subtils

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

A Role for Nonessential Domain II of Initiator Protein, DnaA, in Replication Control

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