Functional interplay between the <i>Bacillus subtilis</i> DnaD and DnaB proteins essential for initiation and re‐initiation of DNA replication

Bruand, Claude; Velten, Marion; McGovern, Stephen; Marsin, Stéphanie; Sérèna, Céline; Ehrlich, S. Dusko; Polard, Patrice

doi:10.1111/j.1365-2958.2004.04451.x

Cited by 71 publications

(108 citation statements)

References 26 publications

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“…It requires a DnaA/ origin interaction as an initial step followed by a cascade of reactions involving DnaB, DnaC, DnaD and DnaI (for reviews, see Lemon et al, 2002;Yoshikawa & Wake, 1993). It is speculated that this cascade is similar to that occurring in the PriA-dependent pathway (Bruand et al, 2005;Velten et al, 2003). It is interesting to note here that DnaD interacts with DnaA and PriA (Bruand et al, 2005;Ishigo-Oka et al, 2001;Marsin et al, 2001).…”

Section: Discussionmentioning

confidence: 98%

“…It is speculated that this cascade is similar to that occurring in the PriA-dependent pathway (Bruand et al, 2005;Velten et al, 2003). It is interesting to note here that DnaD interacts with DnaA and PriA (Bruand et al, 2005;Ishigo-Oka et al, 2001;Marsin et al, 2001). This interaction might thus play a key role in bringing DnaB, DnaI and DnaC to the initiator/DNA complexes.…”

Section: Discussionmentioning

confidence: 98%

“…The complex then assists the binding of DnaB which recruits DnaI and DnaC. This cascade of reactions yields helicase DnaC loading on the appropriate single-stranded DNA by a ring-assembly mechanism (Bruand et al, , 2005Marsin et al, 2001;Polard et al, 2002;Velten et al, 2003). The second initiation pathway, the DnaA-dependent pathway, operates at the chromosomal origin of replication.…”

Section: Discussionmentioning

confidence: 99%

“…This suggests that the recruitment of the DnaD-driven cascade to the RepA/ origin complex might differ from that occurring at the DnaA/oriC and PriA/DNA complexes. A simple model would be that the single-stranded DNA generated by RepA at the plasmid origin is used as a landing pad for DnaD which has a single-stranded DNA-binding activity (Bruand et al, 2005;Marsin et al, 2001). In support of this hypothesis, it was previously shown that the DnaC helicase can be loaded on long stretches of single-stranded DNA via a weakly efficient DnaA-and PriA-independent pathway that requires DnaD, DnaB and DnaI (the DnaD pathway) (Bruand et al, 2005;Marsin et al, 2001).…”

Section: Discussionmentioning

confidence: 99%

“…A simple model would be that the single-stranded DNA generated by RepA at the plasmid origin is used as a landing pad for DnaD which has a single-stranded DNA-binding activity (Bruand et al, 2005;Marsin et al, 2001). In support of this hypothesis, it was previously shown that the DnaC helicase can be loaded on long stretches of single-stranded DNA via a weakly efficient DnaA-and PriA-independent pathway that requires DnaD, DnaB and DnaI (the DnaD pathway) (Bruand et al, 2005;Marsin et al, 2001). However, similar to all initiator/DNA complexes studied in detail so far [for reviews, see del Solar et al, 1998;Helinski et al, 1996), RepA must not generate a single-stranded region large enough to activate the DnaD pathway at the origin.…”

Section: Discussionmentioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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

et al. 2006

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Bacterial Primosome

Tanaka¹,

Masai²

2010

Encyclopedia of Life Sciences

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DNA ( deoxyribonucleic acid ) replication requires operation of a molecular machinery which efficiently synthesises of nucleotide chains on both strands. This process requires not only the enzymes synthesising DNA ( DNA polymerases ) but also those providing primer RNAs ( ribonucleic acid ) and continuously melting the duplex DNA. The primosome refers to a protein complex capable of processive unwinding of duplex DNA and primer RNA synthesis on the lagging strand at a replication fork. The prepriming proteins, DNA helicase and primase are sequentially assembled on the template DNA to generate primosome. Once assembled, it, in conjunction with DNA polymerases , facilitates DNA chain elongation. The assembly of bacterial primosome is triggered by an ‘initiator’ protein including DnaA and PriA , which recognise the site of assembly. Primosome is reassembled in replication restart process at stalled or processed replication forks, triggered by PriA . Thus, primosome constitutes an essential component for active replication fork machinery. Key concepts: Replication fork is the site of DNA replication where two replicating single‐stranded DNA separates. Primer RNA is a short stretch of RNA, the 3′‐terminus of which is utilised by DNA polymerases for DNA elongation. Primosome is a name given to the protein complex capable of duplex DNA unwinding and primer RNA synthesis at the replication fork. oriC is the replication ori gin of c hromosome. The initiation site of bacterial chromosomal DNA replication under a normal growth condition. DnaA is the initiator protein for bacterial chromosomal replication, which binds to oriC to assemble a primosome. PriA is a conserved replication factor which triggers assembly of the so‐called ϕX174‐type primosome, which is assembled at a stalled replication fork for replication restart. Stalled replication fork, the replication fork the movement of which is blocked by internal and external ‘replication stress’ including DNA damages and depletion of nucleotide precursors. Replication restart is a process of reassembly of primosome at a stalled replication fork to resume DNA chain elongation. Recombination intermediate is the intermediate structure (e.g. D‐loop structure) of homologous recombination reaction. DNA helicase is a protein capable of unwinding a duplex DNA at a replication fork by using the energy derived from the hydrolysis of nucleotides. Prepriming proteins are proteins required for the stage preceding the association of the primase (an enzyme synthesising primer RNAs) during the assembly of a primosome.

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Bacterial Primosome

Tanaka¹,

Masai²

2019

Encyclopedia of Life Sciences

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DNA (deoxyribonucleic acid) replication requires operation of molecular machinery which efficiently elongates nucleotide chains on both strands. This process requires not only the enzymes synthesising DNA (DNA polymerases) but also those providing primer RNAs (ribonucleic acid) and continuously melting the duplex DNA. The primosome refers to a protein complex capable of processive unwinding of duplex DNA and primer RNA synthesis on the lagging strand at a replication fork. The prepriming proteins, DNA helicase and primase are sequentially assembled on the template DNA to generate a primosome. Once assembled, it, in conjunction with DNA polymerases, facilitates DNA chain elongation. The assembly of bacterial primosome is triggered by an ‘initiator’ protein including DnaA or PriA, which recognises the site of assembly. Primosome is assembled also in replication restart process at stalled or processed replication forks, triggered by PriA. Primosome constitutes an essential component for active replication fork machinery. Recent advances in this field provide structural basis regarding how these factors function during the assembly of a primosome on viral origins as well as during the restart from the stalled DNA replication forks. These new knowledges provide important insight into how replication forks are protected from various genotoxic agents in eukaryotes. Key Concepts Replication fork is the site of DNA replication where DNA synthesis occurs, and primosome is its integral component. Primosome is capable of duplex DNA unwinding and primer RNA synthesis at the replication fork. In bacteria, replication is normally initiated at a single locus, oriC , on the genome. Bacterial DNA replication is initiated by an initiator, DnaA, which generates a oriC ‐primosome. The stalled DNA replication fork needs to be swiftly detected and rescued to prevent its collapse and to ensure the completion of genome replication. Another primosome mediated by PriA serves for reassembly of replication fork at a stalled fork in bacteria. Bacterial genomes can be replicated by an alternative mode that involves RNA‐DNA hybrids. Primosomes in eukaryotes may be more complex, but essential components would be conserved.

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Functional interplay between the Bacillus subtilis DnaD and DnaB proteins essential for initiation and re‐initiation of DNA replication

Cited by 71 publications

References 26 publications

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

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

Bacterial Primosome

Bacterial Primosome

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