Regulation of Initiation ofBacillus subtilisChromosome Replication

Moriya, Shigeki; Imai, Yukiho; Hassan, Anwarul K. M.; Ogasawara, Nagahisa

doi:10.1006/plas.1998.1381

Cited by 62 publications

(71 citation statements)

References 68 publications

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“…The same conditions were applied for all DnaA proteins form S. aureus, B. subtilis, S. pyogenes, and E. coli. Typical reactions were performed on ice in a 50-l solution of 40 mM HEPES-KOH, pH 7.6, 100 mM potassium glutamate, 10 mM magnesium acetate, 0.5 mM EDTA, 1 mM DTT, 50 g/ml BSA, 10% sucrose, 1 M [␣- 32 values were determined by incubating 5 pmol of purified S. aureus DnaA proteins for 3 h on ice with ATP or ADP and in a volume of 0.5 ml or 5 ml, respectively. ATP and ADP binding in dissociation and exchange reactions were also detected by the filter binding assay.…”

Section: Methodsmentioning

confidence: 99%

“…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. Conversely, Gram-positive bacteria contain DnaB and DnaD proteins, which are involved in the initiation step of DNA replication (32)(33)(34)(35)(36)(37). Gram-positive bacteria also express an additionally essential catalytic subunit of DNA polymerase III (38,39).…”

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confidence: 99%

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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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Section: Methodsmentioning

confidence: 99%

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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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“…The autorepressed dnaA gene of Bacillus subtilis behaves similarly to the P1repA: the gene is not induced by titration but by replication (26). The concentration of the active form of DnaA also is believed to trigger initiation in Escherichia coli (27).…”

Section: Discussionmentioning

confidence: 99%

Replication-induced transcription of an autorepressed gene: The replication initiator gene of plasmid P1

Mukhopadhyay¹,

Chattoraj²

2000

Proc. Natl. Acad. Sci. U.S.A.

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The replication origin of plasmid P1 contains an array of five repeats (iterons) that bind the plasmid-encoded initiator RepA. Within the array lies the repA promoter, which becomes largely repressed on RepA binding (autorepression). One might expect that extra iterons produced on plasmid replication would titrate RepA and release the repression. The promoter, however, is induced poorly by extra iterons. The P1 copy number is reduced by extra iterons in the presence of the autorepressed repA gene but not when additional RepA is provided from constitutive sources. It has been proposed that the iteron-bound RepA couples with the promoter-bound RepA and thereby maintains repression. Although not the product of replication, we find that the act of replication itself can renew RepA synthesis. Replication apparently cleans the promoter of bound RepA and provides a window of opportunity for repA transcription. We propose that replicationinduced transcription is required to ensure initiator availability in a system that is induced poorly when challenged with additional initiator binding sites.

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“…To search for host-encoded proteins required for plasmid replication, pMTLBS72 was introduced into wild-type and isogenic mutants affected in DNA polymerases PolC (dnaF69), DnaE (dnaETs2.6 and 2.10) or Pol I (polA5), the processivity factor DnaN (dnaG5), the replication machinery organizer DnaX (dnaX8132), the initiator proteins DnaA (DdnaA) and PriA (DpriA), the replicative helicase DnaC (dnaC14), the DnaC loaders DnaB, DnaD and DnaI (dnaB19, dnaD23 and dnaI2), the primase DnaG (dnaE20) and the PcrA helicase required for rolling-circle replication and involved in Cairns replication (pcrA3) (for reviews, see Khan, 2005;Lemon et al, 2002;Moriya et al, 1999;Winston, 1982;Yoshikawa & Wake, 1993). Transformants were readily obtained at 30 uC with the complete set of strains.…”

Section: Host-encoded Replication Functionsmentioning

confidence: 99%

The replicative polymerases PolC and DnaE are required for theta replication of the Bacillus subtilis plasmid pBS72

et al. 2006

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Plasmids are the tools of choice for studying bacterial functions involved in DNA maintenance. Here a genetic study on the replication of a novel, low-copy-number, Bacillus subtilis plasmid, pBS72, is reported. The results show that two plasmid elements, the initiator protein RepA and an iteron-containing origin, and at least nine host-encoded replication proteins, the primosomal proteins DnaB, DnaC, DnaD, DnaG and DnaI, the DNA polymerases DnaE and PolC, and the polymerase cofactors DnaN and DnaX, are required for pBS72 replication. On the contrary, the cellular initiators DnaA and PriA, the helicase PcrA and DNA polymerase I are dispensable. From this, it is inferred that pBS72 replication is of the theta type and is initiated by an original mechanism. Indirect evidence suggests that during this process the DnaC helicase might be delivered to the plasmid origin by the weakly active DnaD pathway stimulated by a predicted interaction between DnaC and a domain of RepA homologous to the major DnaC-binding domain of the cellular initiator DnaA. The plasmid pBS72 replication fork appears to require the same functions as the bacterial chromosome and the unrelated plasmid pAMb1. Most importantly, this replication machinery contains the two type C polymerases, PolC and DnaE. As the mechanism of initiation of the three genomes is substantially different, this suggests that both type C polymerases might be required in any Cairns replication in B. subtilis and presumably in other bacteria encoding PolC and DnaE. INTRODUCTIONDNA replication is a ubiquitous biological process carried out by proteins that have evolved profoundly since the last common ancestor. For key elements like initiators, helicases, primases, catalytic DNA polymerases and processivity factors, their evolution has been so extensive that they are postulated to originate from peptides that diverged beyond recognition or from different proteins (Edgell & Doolittle, 1997;Giraldo, 2003;Leipe et al., 1999). Surprisingly, this diversity, obvious when comparing Eubacteria to Archaea and Eukarya, is also manifest among bacterial species. For instance, in the well characterized eubacteria Escherichia coli and Bacillus subtilis, the primosomes required for initiating replication at origins or collapsed replication forks have been shown to greatly differ in their constitution and mechanism of helicase loading (Bruand et al., 1995;Cox et al., 2000;Davey & O'Donnell, 2003;Lemon et al., 2002;Marsin et al., 2001;Polard et al., 2002; Velten et al., 2003). Differences have also been documented in the DNA polymerase III (Pol III) holoenzyme, a subassembly of the replication machinery where DNA synthesis is catalysed. In E. coli this element contains 10 different subunits of which four (h, c, x and y) are missing in B. subtilis (Bruck & O'Donnell, 2000;Bruck et al., 2002;Lemon et al., 2002; MartinezJimenez et al., 2002;McHenry, 2003).Based on systems for which a Pol III holoenzyme has been isolated and/or reconstructed in vitro, it is generally thought that both DNA strands...

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Regulation of Initiation ofBacillus subtilisChromosome Replication

Cited by 62 publications

References 68 publications

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

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

Replication-induced transcription of an autorepressed gene: The replication initiator gene of plasmid P1

The replicative polymerases PolC and DnaE are required for theta replication of the Bacillus subtilis plasmid pBS72

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