Sequence Recognition, Cooperative Interaction, and Dimerization of the Initiator Protein DnaA of Streptomyces

Majka, Jerzy; Zakrzewska‐Czerwińska, Jolanta; Messer, Walter

doi:10.1074/jbc.m007876200

Cited by 26 publications

(45 citation statements)

References 23 publications

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“…The gels were dried and analyzed with a Typhoon 8600 variable-mode imager. The apparent equilibrium dissociation constant [K D (app)] was determined as described previously (3,35,36). The reaction mixtures contained a fixed amount of DNA and various concentrations of DnaA protein.…”

Section: Methodsmentioning

confidence: 99%

“…In Escherichia coli and S. coelicolor the replication origins are different sizes (250 bp and 1,000 bp, respectively) and have different numbers of DnaA boxes (5 and 19, respectively) (58). The S. coelicolor DnaA protein exhibits the highest affinity for the consensus sequence TT(A/G)TCCACA, which is designated the "strong" DnaA box (36). Like all other DnaA proteins, the Streptomyces DnaA protein consists of four domains; domain III and the carboxy-terminal part (domain IV) are responsible for binding of ATP and DNA, respectively, and the N-terminal part (domain I) and domain III contain oligomerization sites.…”

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confidence: 99%

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Cluster of DnaA Boxes Involved in Regulation of Streptomyces Chromosome Replication: from In Silico to In Vivo Studies

et al. 2006

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In Streptomyces coelicolor, replication is initiated by the DnaA protein in the centrally located oriC region and proceeds bidirectionally until the replication forks reach the ends of the linear chromosome. We identified three clusters of DnaA boxes (H69, H24, and D78) which are in a relatively short segment of the chromosome centered on the oriC region. Of the clusters analyzed, D78 exhibited the highest affinity for the DnaA protein; the affinity of DnaA for the D78 cluster was about eightfold higher than the affinity for oriC. The high-affinity DnaA boxes appear to be involved in the control of chromosome replication. Deletion of D78 resulted in more frequent chromosome replication (an elevated ratio of origins to chromosome ends was observed) and activated aerial mycelium formation, leading to earlier colony maturation. In contrast, extra copies of D78 (delivered on a plasmid) caused slow colony growth, presumably because of a reduction in the frequency of initiation of chromosome replication. This suggests that the number of high-affinity DnaA boxes is relatively constant in hyphal compartments and that deletion of D78 therefore permits an increased copy number of either the chromosomal origin region or a plasmid harboring the D78 cluster. This system conceivably influences the timing of decisions to initiate aerial mycelial formation and sporulation.

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Section: Methodsmentioning

confidence: 99%

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Cluster of DnaA Boxes Involved in Regulation of Streptomyces Chromosome Replication: from In Silico to In Vivo Studies

et al. 2006

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“…This then promotes the binding of additional DnaA monomers that not only stabilizes the binding of DnaB, but also blocks the subsequent binding of more DnaB hexamers. Because of the 2-fold increase in stoichiometry of DnaA at this step, and the report that Streptomyces DnaA binds to a single DnaA box as a dimer (33), it is attractive to think that each DnaA box is bound by a dimer of DnaA. Once DnaB is bound to the template, DnaC is released.…”

Section: Conditions For Formation Of the Prepriming Complex-atp And Mgmentioning

confidence: 99%

Stoichiometry of DnaA and DnaB Protein in Initiation at the Escherichia coli Chromosomal Origin

Carr

Kaguni

2001

Journal of Biological Chemistry

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Initiation of DNA replication at the Escherichia coli chromosomal origin, oriC, occurs through an ordered series of events that depend first on the binding of DnaA protein, the replication initiator, to DnaA box sequences within oriC followed by unwinding of an AT-rich region near the left border. The prepriming complex then forms, involving the binding of DnaB helicase at oriC so that it is properly positioned at each replication fork. We assembled and isolated the prepriming complexes on an oriC plasmid, then determined the stoichiometries of proteins in these complexes by quantitative immunoblot analysis. DnaA protein alone binds to oriC with a stoichiometry of 4 -5 monomers per oriC DNA. In the prepriming complex, the stoichiometries are 10 DnaA monomers and 2 DnaB hexamers per oriC plasmid. That only two DnaB hexamers are bound, one for each replication fork, suggests that the binding of additional molecules of DnaA in forming the prepriming complex restricts the loading of additional DnaB hexamers that can bind at oriC.Initiation of Escherichia coli chromosomal DNA replication involves the stepwise assembly of proteins at the chromosomal origin, oriC 1 (reviewed in Refs. 1 and 2). This DNA locus is first recognized by the binding of DnaA protein to individual DnaA boxes in oriC in an ordered manner (3). Unwinding of an AT-rich region near the left border of oriC then occurs and requires the ATP-bound form of DnaA protein (4, 5). HU or IHF assist at this step to form an intermediate termed the open complex (6). The binding of ATP to DnaC, a prerequisite, forms the DnaB-DnaC complex (7,8), which is then recruited to oriC to form the prepriming complex (9). At this step, DnaB interacts with two functional domains of DnaA protein; the stabilization of the prepriming complex also may involve a cryptic single-stranded DNA binding activity of . Upon the release of DnaC from the prepriming complex, DnaB is then free to act as a helicase to unwind further the parental DNA template. Its distributive interaction with primase leads to the priming of both leading and lagging strands that are then concurrently extended by each catalytic unit of the dimeric DNA polymerase III holoenzyme in the enzymatic machinery at each replication fork (Ref . 13 and references therein).The E. coli replication origin is a locus at which DNA replication is controlled. This site also serves as the assembly site for the enzymatic machinery destined to function at each of the two replication forks that move in opposite directions on the bacterial chromosome. The work described below addresses two questions. First, what is the molecular composition of complexes formed at oriC in assembling the replication fork machinery? Second, because DnaB is the replicative helicase that drives replication fork movement, is the entry of DnaB at oriC somehow modulated so that one and only one helicase molecule is bound per replication fork, or can multiple DnaB molecules bind? The stoichiometries of DnaA and DnaB protein in the prepriming complex assembled...

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“…DnaA box 3 (also an 8/9 bp match to the consensus) is identical to the sequences of DnaA boxes found in chromosome origins from Streptomyces spp. (Majka et al, 2001) and Micrococcus luteus (Fujita et al, 1990).…”

Section: Oligonucleotide Namementioning

confidence: 99%

The Sinorhizobium meliloti chromosomal origin of replication

2006

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The predicted chromosomal origin of replication (oriC) from the alfalfa symbiont Sinorhizobium meliloti is shown to allow autonomous replication of a normally non-replicating plasmid within S. meliloti cells. This is the first chromosomal replication origin to be experimentally localized in the Rhizobiaceae and its location, adjacent to hemE, is the same as for oriC in Caulobacter crescentus, the only experimentally characterized alphaproteobacterial oriC. Using an electrophoretic mobility shift assay and purified S. meliloti DnaA replication initiation protein, binding sites for DnaA were mapped in the S. meliloti oriC region. Mutations in these sites eliminated autonomous replication. S. meliloti that expressed DnaA from a plasmid lac promoter was observed to form pleomorphic filamentous cells, suggesting that cell division was perturbed. Interestingly, this cell phenotype is reminiscent of differentiated bacteroids found inside plant cells in alfalfa root nodules.

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Sequence Recognition, Cooperative Interaction, and Dimerization of the Initiator Protein DnaA of Streptomyces

Cited by 26 publications

References 23 publications

Cluster of DnaA Boxes Involved in Regulation of Streptomyces Chromosome Replication: from In Silico to In Vivo Studies

Cluster of DnaA Boxes Involved in Regulation of Streptomyces Chromosome Replication: from In Silico to In Vivo Studies

Stoichiometry of DnaA and DnaB Protein in Initiation at the Escherichia coli Chromosomal Origin

The Sinorhizobium meliloti chromosomal origin of replication

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