Role of the Y-Family DNA Polymerases YqjH and YqjW in Protecting Sporulating Bacillus subtilis Cells from DNA Damage

Rivas-Castillo, Andrea M.; Yasbin, Ronald E.; Robleto, Eduardo A.; Nicholson, Wayne L.; Pedraza-Reyes, Mario

doi:10.1007/s00284-009-9535-3

Cited by 25 publications

(34 citation statements)

References 14 publications

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“…Therefore, we tested the idea that the mutagenesis observed in the ⌬recD2 strain is caused by increased usage of lesion bypass DNA polymerases in the absence of RecD2. In B. subtilis, polymerases PolY1 (YqjH) and PolY2 (YqjW) and essential replicative polymerase DnaE have been shown to be involved in lesion bypass in vitro or in vivo (46)(47)(48)(49)(50) …”

Section: Resultsmentioning

confidence: 99%

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RecD2 Helicase Limits Replication Fork Stress in Bacillus subtilis

et al. 2014

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bDNA helicases have important roles in genome maintenance. The RecD helicase has been well studied as a component of the heterotrimeric RecBCD helicase-nuclease enzyme important for double-strand break repair in Escherichia coli. Interestingly, many bacteria lack RecBC and instead contain a RecD2 helicase, which is not known to function as part of a larger complex. Depending on the organism studied, RecD2 has been shown to provide resistance to a broad range of DNA-damaging agents while also contributing to mismatch repair (MMR). Here we investigated the importance of Bacillus subtilis RecD2 helicase to genome integrity. We show that deletion of recD2 confers a modest increase in the spontaneous mutation rate and that the mutational signature in ⌬recD2 cells is not consistent with an MMR defect, indicating a new function for RecD2 in B. subtilis. To further characterize the role of RecD2, we tested the deletion strain for sensitivity to DNA-damaging agents. We found that loss of RecD2 in B. subtilis sensitized cells to several DNA-damaging agents that can block or impair replication fork movement. Measurement of replication fork progression in vivo showed that forks collapse more frequently in ⌬recD2 cells, supporting the hypothesis that RecD2 is important for normal replication fork progression. Biochemical characterization of B. subtilis RecD2 showed that it is a 5=-3= helicase and that it directly binds single-stranded DNA binding protein. Together, our results highlight novel roles for RecD2 in DNA replication which help to maintain replication fork integrity during normal growth and when forks encounter DNA damage.

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Section: Resultsmentioning

confidence: 99%

“…The data shown here are also presented in more detail in Table S2 in the supplemental material. 50 defined minimal medium to an OD 600 of 0.4 to 0.6 with 1% arabinose and 0.125% xylose prior to treatment. Cultures were left untreated prior to imaging.…”

Section: Fig 2 Deletion Of Recd2 Increases Spontaneous Mutagenesis Inmentioning

confidence: 99%

RecD2 Helicase Limits Replication Fork Stress in Bacillus subtilis

et al. 2014

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“…This endospore can remain dormant for long periods of time, until it encounters the appropriate conditions to germinate and resume growth (42). It has been proposed that the formation of the spore may potentially be compromised by damaging the chromosomes of either cell compartment and that the sporulating cell presumably relies on mechanisms to sense, repair, or even tolerate DNA damage in order to generate the two cell types (31). In support of these notions, results have revealed that defects in chromosome partitioning or DNA damage can delay sporulation at the level of Spo0A activation (4,18) and that DisA, a scanning checkpoint protein, temporarily blocks the initiation of sporulation when DNA damage is encountered (2).…”

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confidence: 99%

“…B. subtilis possesses an arsenal of preventive and repair mechanisms to counteract the mutagenic and deleterious effects of these insults (5,10,28,29,30,31,33,38,53,55). The expression of genes that prevent and repair genetic insults in this bacterium is regulated in time and space by gene circuitries that respond to developmental and environmental conditions during growth and cell differentiation (6,23,24,28,34,38,49,54,55).…”

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Alternative Excision Repair of Ultraviolet B- and C-Induced DNA Damage in Dormant and Developing Spores of Bacillus subtilis

et al. 2012

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The nucleotide excision repair (NER) and spore photoproduct lyase DNA repair pathways are major determinants of Bacillus subtilis spore resistance to UV radiation. We report here that a putative ultraviolet (UV) damage endonuclease encoded by ywjD confers protection to developing and dormant spores of B. subtilis against UV DNA damage. In agreement with its predicted function, a His 6 -YwjD recombinant protein catalyzed the specific incision of UV-irradiated DNA in vitro. The maximum expression of a reporter gene fusion to the ywjD opening reading frame occurred late in sporulation, and this maximal expression was dependent on the forespore-specific RNA polymerase sigma factor, G . Although the absence of YwjD and/or UvrA, an essential protein of the NER pathway, sensitized developing spores to UV-C, this effect was lower when these cells were treated with UV-B. In contrast, UV-B but not UV-C radiation dramatically decreased the survival of dormant spores deficient in both YwjD and UvrA. The distinct range of lesions generated by UV-C and UV-B and the different DNA photochemistry in developing and dormant spores may cause these differences. We postulate that in addition to the UvrABC repair system, developing and dormant spores of B. subtilis also rely on an alternative excision repair pathway involving YwjD to deal with the deleterious effects of various UV photoproducts.T he constant exposure of cells and spores of Bacillus subtilis to a number of environmental factors of chemical and physical origin may result in the production of number of types of DNA lesions, including strand breaks, apurinic/apyrimidinic (AP) sites, UV-induced pyrimidine dimers (PD) of various types and chemically altered bases (21,25,43). B. subtilis possesses an arsenal of preventive and repair mechanisms to counteract the mutagenic and deleterious effects of these insults (5,10,28,29,30,31,33,38,53,55). The expression of genes that prevent and repair genetic insults in this bacterium is regulated in time and space by gene circuitries that respond to developmental and environmental conditions during growth and cell differentiation (6,23,24,28,34,38,49,54,55).When nutritional and/or environmental conditions trigger sporulation, B. subtilis undergoes a final round of DNA replication, followed by polar septation and segregation of the chromosomal copies between two unequal cell-sized compartments that follow dissimilar programs of gene expression (reviewed in references 9 and 27). The end product of sporulation is a highly resistant endospore with no detectable metabolism that lacks most common high-energy compounds (39). This endospore can remain dormant for long periods of time, until it encounters the appropriate conditions to germinate and resume growth (42). It has been proposed that the formation of the spore may potentially be compromised by damaging the chromosomes of either cell compartment and that the sporulating cell presumably relies on mechanisms to sense, repair, or even tolerate DNA damage in order to generate the two cell ...

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“…subtilis relies on several repair mechanisms to counteract the adverse effects of intra-and extracellular factors that generate a myriad of insults to DNA (3,7,11,24,49,64). DNA repair genes are differentially expressed during growth and/or sporulation, and the physiological roles played by their encoded products have been demonstrated in several cases (45,47,50,62). Analysis of the genome of B. subtilis reveals the presence of a uracil-DNAglycosylase-encoding gene (ung) that can be classified into family 1 of the UDGs.…”

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Roles of Endonuclease V, Uracil-DNA Glycosylase, and Mismatch Repair in Bacillus subtilis DNA Base-Deamination-Induced Mutagenesis

et al. 2012

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The disruption of ung, the unique uracil-DNA-glycosylase-encoding gene in Bacillus subtilis, slightly increased the spontaneous mutation frequency to rifampin resistance (Rif r ), suggesting that additional repair pathways counteract the mutagenic effects of uracil in this microorganism. An alternative excision repair pathway is involved in this process, as the loss of YwqL, a putative endonuclease V homolog, significantly increased the mutation frequency of the ung null mutant, suggesting that Ung and YwqL both reduce the mutagenic effects of base deamination. Consistent with this notion, sodium bisulfite (SB) increased the Rif r mutation frequency of the single ung and double ung ywqL strains, and the absence of Ung and/or YwqL decreased the ability of B. subtilis to eliminate uracil from DNA. Interestingly, the Rif r mutation frequency of single ung and mutSL (mismatch repair [MMR] system) mutants was dramatically increased in a ung knockout strain that was also deficient in MutSL, suggesting that the MMR pathway also counteracts the mutagenic effects of uracil. Since the mutation frequency of the ung mutSL strain was significantly increased by SB, in addition to Ung, the mutagenic effects promoted by base deamination in growing B. subtilis cells are prevented not only by YwqL but also by MMR. Importantly, in nondividing cells of B. subtilis, the accumulations of mutations in three chromosomal alleles were significantly diminished following the disruption of ung and ywqL. Thus, under conditions of nutritional stress, the processing of deaminated bases in B. subtilis may normally occur in an error-prone manner to promote adaptive mutagenesis.

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Role of the Y-Family DNA Polymerases YqjH and YqjW in Protecting Sporulating Bacillus subtilis Cells from DNA Damage

Cited by 25 publications

References 14 publications

RecD2 Helicase Limits Replication Fork Stress in Bacillus subtilis

RecD2 Helicase Limits Replication Fork Stress in Bacillus subtilis

Alternative Excision Repair of Ultraviolet B- and C-Induced DNA Damage in Dormant and Developing Spores of Bacillus subtilis

Roles of Endonuclease V, Uracil-DNA Glycosylase, and Mismatch Repair in Bacillus subtilis DNA Base-Deamination-Induced Mutagenesis

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