Damage-induced localized hypermutability

National Institute of Environmental Health Sciences, Research Triangle Park, NC USA.
Cell cycle (Georgetown, Tex.) (Impact Factor: 4.57). 04/2011; 10(7):1073-85. DOI: 10.4161/cc.10.7.15319
Source: PubMed


Genome instability continuously presents perils of cancer, genetic disease and death of a cell or an organism. At the same time, it provides for genome plasticity that is essential for development and evolution. We address here the genome instability confined to a small fraction of DNA adjacent to free DNA ends at uncapped telomeres and double-strand breaks. We found that budding yeast cells can tolerate nearly 20 kilobase regions of subtelomeric single-strand DNA that contain multiple UV-damaged nucleotides. During restoration to the double-strand state, multiple mutations are generated by error-prone translesion synthesis. Genome-wide sequencing demonstrated that multiple regions of damage-induced localized hypermutability can be tolerated, which leads to the simultaneous appearance of multiple mutation clusters in the genomes of UV- irradiated cells. High multiplicity and density of mutations suggest that this novel form of genome instability may play significant roles in generating new alleles for evolutionary selection as well as in the incidence of cancer and genetic disease.

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Available from: Lauranell Burch, Nov 17, 2014
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    • "None of the CanR Ura− clones contained four or more mutations. Such low multiplicity of mutations differed greatly from the density of the mutations reported for UV-induced damage in the lys2 reporter system (1,6), which is comparable in size to the CAN1-URA3 reporter employed in our study. Up to six independent mutations were found in the LYS2 locus and more than 30% of the Lys- clones contained more than two lesions. "
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    ABSTRACT: Localized hyper-mutability caused by accumulation of lesions in persistent single-stranded (ss) DNA has been recently found in several types of cancers. An increase in endogenous levels of reactive oxygen species (ROS) is considered to be one of the hallmarks of cancers. Employing a yeast model system, we addressed the role of oxidative stress as a potential source of hyper-mutability in ssDNA by modulation of the endogenous ROS levels and by exposing cells to oxidative DNA-damaging agents. We report here that under oxidative stress conditions the majority of base substitution mutations in ssDNA are caused by erroneous, DNA polymerase (Pol) zeta-independent bypass of cytosines, resulting in C to T transitions. For all other DNA bases Pol zeta is essential for ROS-induced mutagenesis. The density of ROS-induced mutations in ssDNA is lower, compared to that caused by UV and MMS, which suggests that ssDNA could be actively protected from oxidative damage. These findings have important implications for understanding mechanisms of oxidative mutagenesis, and could be applied to development of anticancer therapies and cancer prevention.
    Nucleic Acids Research 08/2013; 41(19). DOI:10.1093/nar/gkt671 · 9.11 Impact Factor
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    • "In the early RT regions, which are also enriched in protein-coding genes (3), LOH-mediated gene conversion can potentially replace wild-type alleles with recessive deleterious alleles, leading to increased risk of manifestation of recessive deleterious traits, complicating the resulting phenotype in the affected individuals. Damage-induced hypermutability and error-prone repair of such regions could lead to further genetic changes (42,43). Furthermore, the difference in RT preference between different classes of genomic alterations also provokes a testable hypothesis whether replicating cells show any changing preference between various DNA repair pathways, which have different levels of efficiency and fidelity (1), as the replication progresses. "
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    ABSTRACT: Erroneous repair of DNA double-strand breaks by homologous recombination (HR) leads to loss of heterozygosity (LOH). Analysing 22 392 and 74 415 LOH events in 363 glioblastoma and 513 ovarian cancer samples, respectively, and using three different metrics, we report that LOH selectively occurs in early replicating regions; this pattern differs from the trends for point mutations and somatic deletions, which are biased toward late replicating regions. Our results are independent of BRCA1 and BRCA2 mutation status. The LOH events are significantly clustered near RNA polII-bound transcription start sites, consistent with the reports that slow replication near paused RNA polII might initiate HR-mediated repair. The frequency of LOH events is higher in the chromosomes with shorter inter-homolog distance inside the nucleus. We propose that during early replication, HR-mediated rescue of replication near paused RNA polII using homologous chromosomes as template leads to LOH. The difference in the preference for replication timing between different classes of genomic alterations in cancer genomes also provokes a testable hypothesis that replicating cells show changing preference between various DNA repair pathways, which have different levels of efficiency and fidelity, as the replication progresses.
    Nucleic Acids Research 06/2013; 41(16). DOI:10.1093/nar/gkt552 · 9.11 Impact Factor
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    • "Indeed, the genetic system developed by Cairns that suggested genomic adaptation by directed mutagenesis can be fully explained by spontaneous mutation and growth under selection [41]. However, non-spontaneous but stress-induced adaptive mutagenesis is exceedingly well-documented in both bacterial and human cells and many factors that are involved in stress-induced adaptive mutagenesis have been identified in the meantime [42]–[45]. Recently, a large network comprising more than 90 genes was shown to be involved in stress-induced mutagenesis as a result of DNA double-strand breaks in E. coli [46]. This observation illustrates the complexity of how environmental or endogenous “stress” exerted on maladapted cells may stimulate factors, which in turn enable the cells to accelerate their own evolution. "
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    ABSTRACT: Soil bacteria like Bacillus subtilis can cope with many growth conditions by adjusting gene expression and metabolic pathways. Alternatively, bacteria can spontaneously accumulate beneficial mutations or shape their genomes in response to stress. Recently, it has been observed that a B. subtilis mutant lacking the catabolically active glutamate dehydrogenase (GDH), RocG, mutates the cryptic gudB(CR) gene at a high frequency. The suppressor mutants express the active GDH GudB, which can fully replace the function of RocG. Interestingly, the cryptic gudB(CR) allele is stably inherited as long as the bacteria synthesize the functional GDH RocG. Competition experiments revealed that the presence of the cryptic gudB(CR) allele provides the bacteria with a selective growth advantage when glutamate is scarce. Moreover, the lack of exogenous glutamate is the driving force for the selection of mutants that have inactivated the active gudB gene. In contrast, two functional GDHs are beneficial for the cells when glutamate was available. Thus, the amount of GDH activity strongly affects fitness of the bacteria depending on the availability of exogenous glutamate. At a first glance the high mutation frequency of the cryptic gudB(CR) allele might be attributed to stress-induced adaptive mutagenesis. However, other loci on the chromosome that could be potentially mutated during growth under the selective pressure that is exerted on a GDH-deficient mutant remained unaffected. Moreover, we show that a GDH-proficient B. subtilis strain has a strong selective growth advantage in a glutamate-dependent manner. Thus, the emergence and rapid clonal expansion of the active gudB allele can be in fact explained by spontaneous mutation and growth under selection without an increase of the mutation rate. Moreover, this study shows that the selective pressure that is exerted on a maladapted bacterium strongly affects the apparent mutation frequency of mutational hot spots.
    PLoS ONE 06/2013; 8(6):e66120. DOI:10.1371/journal.pone.0066120 · 3.23 Impact Factor
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