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

Cho, Eun-Ha; Ogasawara, Nagahisa; Ishikawa, Shu

doi:10.1266/ggs.83.111

Cited by 41 publications

(86 citation statements)

References 38 publications

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“…2A and 3 and Table 2). In addition to oriC, there were four predominant regions, along with yqeG-sda, detected in the ChIPchip experiments, which is consistent with previous results (3,11,25). There was an approximately 2-to 4-fold increase in the association of DnaA with the secondary chromosomal regions, and a greater increase in association near oriC, during replication stress compared to that during exponential growth (Table 2).…”

Section: Resultssupporting

confidence: 90%

“…DnaA binds to specific sites located in many chromosomal regions, some of which are in transcriptional regulatory regions and affect gene expression (3,9,18,22,25,62). Several of the regions bound by DnaA are readily detected by ChIP-chip (3) and the analogous ChAP-chip (11,25). Virtually all of these regions were associated with DnaD and DnaB (Fig.…”

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: Resultssupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

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

et al. 2011

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“…YabA negatively regulates replication initiation through its interactions with the ␤ clamp and DnaA (12,29,52). Mutations in YabA have been constructed that alter both interaction with DnaA and the ␤ clamp (12,29,52); however, the site on the ␤ clamp that YabA binds is unknown. In this work, we found that overexpression of YabA led to an increase in mutagenesis, which is MMR dependent (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…The ␤ clamp is responsible for coordinating many activities at the replication fork. Also, the ␤ clamp interacts with YabA, a negative regulator of replication initiation in B. subtilis (12,27,29,52). Overexpression of the YabA protein causes a decrease in replication initiation, and deletion of yabA increases replication initiation (12,29,52) (Fig.…”

Section: Dnan5(g73r)mentioning

confidence: 99%

“…This allows the ␤ clamp to regulate replication initiation through the amount of available DnaA-ATP. In Bacillus subtilis, the ␤ clamp binds YabA, a negative regulator of DNA replication initiation (12,29,52). It has also been suggested that the B. subtilis ␤ clamp sequesters DnaA from the replication origin during the cell cycle through the binding of DnaA to YabA and the binding of YabA to the ␤ clamp (70).…”

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Mutations in the Bacillus subtilis β Clamp That Separate Its Roles in DNA Replication from Mismatch Repair

et al. 2010

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The ␤ clamp is an essential replication sliding clamp required for processive DNA synthesis. The ␤ clamp is also critical for several additional aspects of DNA metabolism, including DNA mismatch repair (MMR). The dnaN5 allele of Bacillus subtilis encodes a mutant form of ␤ clamp containing the G73R substitution. Cells with the dnaN5 allele are temperature sensitive for growth due to a defect in DNA replication at 49°C, and they show an increase in mutation frequency caused by a partial defect in MMR at permissive temperatures. We selected for intragenic suppressors of dnaN5 that rescued viability at 49°C to determine if the DNA replication defect could be separated from the MMR defect. We isolated three intragenic suppressors of dnaN5 that restored growth at the nonpermissive temperature while maintaining an increase in mutation frequency. All three dnaN alleles encoded the G73R substitution along with one of three novel missense mutations. The missense mutations isolated were S22P, S181G, and E346K. Of these, S181G and E346K are located near the hydrophobic cleft of the ␤ clamp, a common site occupied by proteins that bind the ␤ clamp. Using several methods, we show that the increase in mutation frequency resulting from each dnaN allele is linked to a defect in MMR. Moreover, we found that S181G and E346K allowed growth at elevated temperatures and did not have an appreciable effect on mutation frequency when separated from G73R. Thus, we found that specific residue changes in the B. subtilis ␤ clamp separate the role of the ␤ clamp in DNA replication from its role in MMR.Replication sliding clamps are essential cellular proteins imparting a spectacular degree of processivity to DNA polymerases during genome replication (24,(39)(40)(41). Encoded by the dnaN gene, the ␤ clamp is a highly conserved bacterial sliding clamp found in virtually all eubacterial species (reviewed in reference 7). The ␤ clamp is a head-to-tail, ringshaped homodimer that encircles double-stranded DNA (1, 39). In eukaryotes and archaea, the analog of the ␤ clamp is proliferating cell nuclear antigen (PCNA) (15,28,40,41). Eukaryotic PCNA is a ring-shaped homotrimer that also acts to encircle DNA, increasing the processivity of the replicative DNA polymerases (40,41). Although the primary structures of the ␤ clamp and PCNA are not conserved, the tertiary structures of these proteins are very similar, demonstrating structural conservation among bacterial, archaeal, and eukaryotic replication sliding clamps (28, 39-41; reviewed in reference 6).The function of the ␤ clamp is not limited to its well-defined role in genome replication. The Escherichia coli ␤ clamp binds Hda, which also binds the replication initiation protein DnaA, regulating the active form of DnaA complexed with ATP (19,37,43). This allows the ␤ clamp to regulate replication initiation through the amount of available DnaA-ATP. In Bacillus subtilis, the ␤ clamp binds YabA, a negative regulator of DNA replication initiation (12,29,52). It has also been suggested that the B. subt...

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Bacterial chromosomes and their replication

Frimodt-Møller,

Boesen,

Charbon

et al. 2024

Molecular Medical Microbiology

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

Cited by 41 publications

References 38 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

Mutations in the Bacillus subtilis β Clamp That Separate Its Roles in DNA Replication from Mismatch Repair

Bacterial chromosomes and their replication

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