The<i>Bacillus subtilis</i>Primosomal Protein DnaD Untwists Supercoiled DNA

Zhang, Wenke; Allen, Stephanie; Roberts, Clive J.; Soultanas, Panos

doi:10.1128/jb.00339-06

Cited by 37 publications

(61 citation statements)

References 40 publications

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“…In vitro, DnaA, but not DnaD, is needed for open complex formation (2,35). The association of DnaD (and DnaB) with oriC requires DnaA function (58), and DnaD and DnaB can bind both single-and double-stranded DNA (40,61,66,67). These findings are compatible with the possibility that the stable association of DnaD with oriC occurs after, and may even depend on, DnaA-mediated open complex formation.…”

Section: Discussionsupporting

confidence: 77%

“…These events are necessary for the loading of the replicative helicase by the AAAϩ loader protein DnaI. There might be additional roles for DnaD and DnaB in chromosome architecture and DNA remodeling (66,67).…”

Section: Discussionmentioning

confidence: 99%

“…We considered several possible functions of DnaA, DnaD, and DnaB away from oriC. The function of DnaD and DnaB at the DnaA binding regions might be related to their DNA remodeling activities (10,57,61,(66)(67)(68). For example, DnaA could recruit DnaD and DnaB to the DnaA binding regions around the chromosome, and these regions could serve as hubs for an aspect of chromosome organization.…”

Section: Discussionmentioning

confidence: 99%

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Primosomal Proteins DnaD and DnaB Are Recruited to Chromosomal Regions Bound by DnaA inBacillus subtilis

et al. 2011

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The initiation of DNA replication requires the binding of the initiator protein, DnaA, to specific binding sites in the chromosomal origin of replication, oriC. DnaA also binds to many sites around the chromosome, outside oriC, and acts as a transcription factor at several of these. In low-G؉C Gram-positive bacteria, the primosomal proteins DnaD and DnaB, in conjunction with loader ATPase DnaI, load the replicative helicase at oriC, and this depends on DnaA. DnaD and DnaB also are required to load the replicative helicase outside oriC during replication restart, independently of DnaA. Using chromatin immunoprecipitation, we found that DnaD and DnaB, but not the replicative helicase, are associated with many of the chromosomal regions bound by DnaA in Bacillus subtilis. This association was dependent on DnaA, and the order of recruitment was the same as that at oriC, but it was independent of a functional oriC and suggests that DnaD and DnaB do not require open complex formation for the stable association with DNA. These secondary binding regions for DnaA could be serving as a reservoir for excess DnaA, DnaD, and DnaB to help properly regulate replication initiation and perhaps are analogous to the proposed function of the datA locus in Escherichia coli. Alternatively, DnaD and DnaB might modulate the activity of DnaA at the secondary binding regions. All three of these proteins are widely conserved and likely have similar functions in a range of organisms. The replication initiation protein and transcription factorDnaA is an AAAϩ ATPase that binds to many regions on the chromosome. The primary binding region is at the origin of chromosomal replication, oriC (at 0°on the B. subtilis chromosome), where there are many individual DnaA binding sites (Fig. 1). DnaA binds to oriC and causes local unwinding (melting) of the AϩT-rich DNA unwinding element (DUE) (Fig. 1) and the subsequent assembly of the replicative helicase, followed by the assembly of the rest of the replication machinery (reviewed in references 27, 29, 49, and 56).The assembly of the replicative helicase is mediated by helicase loader proteins. In Escherichia coli, a single protein, the AAAϩ ATPase DnaC, functions to load the helicase (reviewed in references 13 and 34). In contrast, in B. subtilis and other low-GϩC Gram-positive bacteria, three different proteins, DnaD, DnaB, and the AAAϩ ATPase DnaI, are needed to load the replicative helicase (DnaC in B. subtilis) during replication initiation at oriC and replication restart at stalled replication forks (5-7, 13, 24, 40, 54, 55, 63). There is a defined order of stable association of the replication initiation proteins with oriC. DnaA binds first, followed by DnaD and then DnaB, and finally the DnaI-mediated loading of helicase occurs (58). It is not known, however, if the association of DnaD and DnaB with oriC requires the melting of the DUE.In addition to its primary role in replication initiation and binding to sites in the oriC region, DnaA also binds to many secondary sites around the chromosome...

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Section: Discussionsupporting

confidence: 77%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Primosomal Proteins DnaD and DnaB Are Recruited to Chromosomal Regions Bound by DnaA inBacillus subtilis

et al. 2011

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“…DnaB laterally compacts DNA (81), while DnaD bends DNA, eliminates writhe, and converts it to negative twist, i.e., duplex unwinding (71,80,81,82). Binding of the DnaD DDBH2 to DNA untwists the double helix, whereas the scaffolds formed via the DDBH1 interactions appear to reinforce the helix-untwisting activity by forming anchorage points for the DDBH2-DNA complexes (80,82). As DnaD interacts directly with DnaA (26), it is attractive to speculate that the duplex untwisting activity of DnaD may enhance or stabilize the melting of the chromosomal origin, oriC, through an oriC-DnaA-DnaD complex during initiation of DNA replication.…”

Section: Interactions With Dna During Replication Initiation/reinitiamentioning

confidence: 99%

Chromosomal Replication Initiation Machinery of Low-G+C-Content Firmicutes

2012

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bMuch of our knowledge of the initiation of DNA replication comes from studies in the Gram-negative model organism Escherichia coli. However, the location and structure of the origin of replication within the E. coli genome and the identification and study of the proteins which constitute the E. coli initiation complex suggest that it might not be as universal as once thought. The archetypal low-G؉C-content Gram-positive Firmicutes initiate DNA replication via a unique primosomal machinery, quite distinct from that seen in E. coli, and an examination of oriC in the Firmicutes species Bacillus subtilis indicates that it might provide a better model for the ancestral bacterial origin of replication. Therefore, the study of replication initiation in organisms other than E. coli, such as B. subtilis, will greatly advance our knowledge and understanding of these processes as a whole. In this minireview, we highlight the structure-function relationships of the Firmicutes primosomal proteins, discuss the significance of their oriC architecture, and present a model for replication initiation at oriC. The Firmicutes are Gram-positive bacteria encompassing three major classes, Bacilli, Clostridia, and Mollicutes. They have a relatively low GϩC content in their genomes and are morphologically and physiologically diverse. Rod-shaped bacilli, spherical cocci, and aerobic, anaerobic spore-forming, and non-sporeforming bacteria are found in this group. They likely represent the most ancestral phylum of prokaryotes, with high-GϩC-content Gram-positive and Gram-negative bacteria having diverged from the Firmicutes at a later stage in evolution (13,70). Bacillus subtilis is the best studied of the Firmicutes and is widely considered the Gram-positive model bacterium, but other bacilli, streptococci, staphylococci, and clostridia have been extensively studied because of their medical and industrial importance.In addition to the universally conserved replication initiation protein DnaA (32, 65) and the replication restart protein PriA (17, 39), the low-GϩC-content Firmicutes generally have two unique essential genes, dnaD and dnaB, coding for the replication initiation proteins DnaD and DnaB, respectively ( Table 1) (note that DnaB in B. subtilis is unrelated to DnaB in Escherichia coli). In some cases-for example, in several Mollicutes-there are no distinct dnaD and dnaB genes, but there is, instead, a single gene annotated as dnaD-like which may combine both functions. No homologous proteins are found outside the Firmicutes, suggesting a replication initiation machinery distinctly different from those of other bacteria (31). In addition, there are a number of regulatory proteins which are not found in the Gram-negative model organism Escherichia coli, including YabA, Soj, SirA, and Spo0A, while other regulatory proteins are found in E. coli but not B. subtilis (these regulatory proteins have been subject to a recent review [29]). DnaA, DnaD, and DnaB, together with the helicase loader DnaI (called DnaC in E. coli), the replicativ...

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“…Association of DnaB with oriC depends on DnaD, and finally, DnaImediated assembly of the helicase at oriC depends on DnaB. DnaD and DnaB bind both double-and single-stranded DNA, which may help stabilize the opening up of the origin of replication (7,38,68).…”

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confidence: 99%

The Primosomal Protein DnaD Inhibits Cooperative DNA Binding by the Replication Initiator DnaA in Bacillus subtilis

Bonilla¹,

Grossman²

2012

J. Bacteriol.

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DnaA is an AAA؉ ATPase and the conserved replication initiator in bacteria. Bacteria control the timing of replication initiation by regulating the activity of DnaA. DnaA binds to multiple sites in the origin of replication (oriC) and is required for recruitment of proteins needed to load the replicative helicase. DnaA also binds to other chromosomal regions and functions as a transcription factor at some of these sites. Bacillus subtilis DnaD is needed during replication initiation for assembly of the replicative helicase at oriC and during replication restart at stalled replication forks. DnaD associates with DnaA at oriC and at other chromosomal regions bound by DnaA. Using purified proteins, we found that DnaD inhibited the ability of DnaA to bind cooperatively to DNA and caused a decrease in the apparent dissociation constant. These effects of DnaD were independent of the ability of DnaA to bind or hydrolyze ATP. Other proteins known to regulate B. subtilis DnaA also affect DNA binding, whereas much of the regulation of Escherichia coli DnaA affects nucleotide hydrolysis or exchange. We found that the rate of nucleotide exchange for B. subtilis DnaA was high and not affected by DnaD. The rapid exchange is similar to that of Staphylococcus aureus DnaA and in contrast to the low exchange rate of Escherichia coli DnaA. We suggest that organisms in which DnaA has a high rate of nucleotide exchange predominantly regulate the DNA binding activity of DnaA and that those with low rates of exchange regulate hydrolysis and exchange.

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TheBacillus subtilisPrimosomal Protein DnaD Untwists Supercoiled DNA

Cited by 37 publications

References 40 publications

Primosomal Proteins DnaD and DnaB Are Recruited to Chromosomal Regions Bound by DnaA inBacillus subtilis

Primosomal Proteins DnaD and DnaB Are Recruited to Chromosomal Regions Bound by DnaA inBacillus subtilis

Chromosomal Replication Initiation Machinery of Low-G+C-Content Firmicutes

The Primosomal Protein DnaD Inhibits Cooperative DNA Binding by the Replication Initiator DnaA in Bacillus subtilis

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