Two Mechanisms Produce Mutation Hotspots at DNA Breaks in Escherichia coli

Shee, Chandan; Gibson, James W.; Rosenberg, Susan M.

doi:10.1016/j.celrep.2012.08.033

Cited by 64 publications

(82 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…4) is readily attributed to DNA polymerase activity, further supporting the replication-dependent FoSTeS/MMBIR model, rather than replication-independent end-joining models, as a comprehensive interpretation of the rearrangement mechanism in the Blm-deficient situation. FoSTeS/MMBIR is thought to involve the repair mechanism of one-ended DSBs arising from collapsed replication forks (Liu et al 2012), whereas, in the present experimental study, the rearrangement mechanism should involve two-ended DSBs generated by I-SceI cleavage, which has not been implicated in previously proposed break-induced replication (BIR) models, with the exception of one-ended DSBs induced by I-SceI cleavage of prokaryotic circular genomes (Shee et al 2012). So far, the limited scale of the current experiment has hampered the complete tracing of the two DNA ends generated by a single I-SceI cleavage and has resulted in fate tracing of either end of the break (Fig.…”

Section: Possible Molecular Mechanisms For Genomic Rearrangements Indmentioning

confidence: 63%

Enhancement of microhomology-mediated genomic rearrangements by transient loss of mouse Bloom syndrome helicase

Yamanishi¹,

Yusa²,

Horie³

et al. 2013

Genome Res.

View full text Add to dashboard Cite

Bloom syndrome, an autosomal recessive disorder of the BLM gene, confers predisposition to a broad spectrum of earlyonset cancers in multiple tissue types. Loss of genomic integrity is a primary hallmark of such human malignancies, but many studies using disease-affected specimens are limited in that they are retrospective and devoid of an appropriate experimental control. To overcome this, we devised an experimental system to recapitulate the early molecular events in genetically engineered mouse embryonic stem cells, in which cells undergoing loss of heterozygosity (LOH) can be enriched after inducible down-regulation of Blm expression, with or without site-directed DNA double-strand break (DSB) induction. Transient loss of BLM increased the rate of LOH, whose breakpoints were distributed along the chromosome. Combined with site-directed DSB induction, loss of BLM synergistically increased the rate of LOH and concentrated the breakpoints around the targeted chromosomal region. We characterized the LOH events using specifically tailored genomic tools, such as high-resolution array comparative genomic hybridization and high-density single nucleotide polymorphism genotyping, revealing that the combination of BLM suppression and DSB induction enhanced genomic rearrangements, including deletions and insertions, whose breakpoints were clustered in genomic inverted repeats and associated with junctional microhomologies. Our experimental approach successfully uncovered the detailed molecular mechanisms of as-yet-uncharacterized loss of heterozygosities and reveals the significant contribution of microhomologymediated genomic rearrangements, which could be widely applicable to the early steps of cancer formation in general.

show abstract

Section: Possible Molecular Mechanisms For Genomic Rearrangements Indmentioning

confidence: 63%

Enhancement of microhomology-mediated genomic rearrangements by transient loss of mouse Bloom syndrome helicase

Yamanishi¹,

Yusa²,

Horie³

et al. 2013

Genome Res.

View full text Add to dashboard Cite

show abstract

“…Reciprocally, for the same value of b, species with larger a have relatively greater selective forces against larger deviations from neutral alleles, lowering possibilities for drift and adaptation. Since the mutation rate is subject to molecular and selection factors (Shee et al 2012), one may speculate whether similar factors might modulate a and b, and underlie shifts between evolutionary quiescence and bursts.…”

Section: Org Downloaded Frommentioning

confidence: 99%

A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness

Katsonis¹,

2014

View full text Add to dashboard Cite

The relationship between genotype mutations and phenotype variations determines health in the short term and evolution over the long term, and it hinges on the action of mutations on fitness. A fundamental difficulty in determining this action, however, is that it depends on the unique context of each mutation, which is complex and often cryptic. As a result, the effect of most genome variations on molecular function and overall fitness remains unknown and stands apart from population genetics theories linking fitness effect to polymorphism frequency. Here, we hypothesize that evolution is a continuous and differentiable physical process coupling genotype to phenotype. This leads to a formal equation for the action of coding mutations on fitness that can be interpreted as a product of the evolutionary importance of the mutated site with the difference in amino acid similarity. Approximations for these terms are readily computable from phylogenetic sequence analysis, and we show mutational, clinical, and population genetic evidence that this action equation predicts the effect of point mutations in vivo and in vitro in diverse proteins, correlates disease-causing gene mutations with morbidity, and determines the frequency of human coding polymorphisms, respectively. Thus, elementary calculus and phylogenetics can be integrated into a perturbation analysis of the evolutionary relationship between genotype and phenotype that quantitatively links point mutations to function and fitness and that opens a new analytic framework for equations of biology. In practice, this work explicitly bridges molecular evolution with population genetics with applications from protein redesign to the clinical assessment of human genetic variations.

show abstract

“…Indeed, thymine limitation/starvation was shown to be mutagenic in thymineless bacteria (50). Another example of stress-induced mutagenesis is adaptive mutagenesis (51) mediated by starvation for a carbon source, a form of DNA break-induced mutagenesis (52,53). In the present case, a number of factors conspired to create a potentially mutagenic condition.…”

Section: Figmentioning

confidence: 96%

“…Second, the induction of the SOS response (14,17) and the associated induction of error-prone DNA polymerases are expected to contribute to decreased replication fidelity. Third, the observed replication stress is accompanied by DNA breaks, as evidenced by the strong requirement for RecA function for promoting survival (14), and these breaks may promote mutagenesis as well, producing both point mutations and deletion/duplications (52,54).…”

Section: Figmentioning

confidence: 99%

Suppressors of dGTP Starvation in Escherichia coli

Itsko

Schaaper

2017

J Bacteriol

View full text Add to dashboard Cite

dGTP starvation, a newly discovered phenomenon in which Escherichia coli cells are starved specifically for the DNA precursor dGTP, leads to impaired growth and, ultimately, cell death. Phenomenologically, it represents an example of nutritionally induced unbalanced growth: cell mass amplifies normally as dictated by the nutritional status of the medium, but DNA content growth is specifically impaired. The other known example of such a condition, thymineless death (TLD), involves starvation for the DNA precursor dTTP, which has been found to have important chemotherapeutic applications. Experimentally, dGTP starvation is induced by depriving an E. coli gpt optA1 strain of its required purine source, hypoxanthine. In our studies of this phenomenon, we noted the emergence of a relatively high frequency of suppressor mutants that proved resistant to the treatment. To study such suppressors, we used next-generation sequencing on a collection of independently obtained mutants. A significant fraction was found to carry a defect in the PurR transcriptional repressor, controlling de novo purine biosynthesis, or in its downstream purEK operon. Thus, upregulation of de novo purine biosynthesis appears to be a major mode of overcoming the lethal effects of dGTP starvation. In addition, another large fraction of the suppressors contained a large tandem duplication of a 250-to 300-kb genomic region that included the purEK operon as well as the acrABencoded multidrug efflux system. Thus, the suppressive effects of the duplications could potentially involve beneficial effects of a number of genes/operons within the amplified regions.IMPORTANCE Concentrations of the four precursors for DNA synthesis (2=-deoxynucleoside-5=-triphosphates [dNTPs]) are critical for both the speed of DNA replication and its accuracy. Previously, we investigated consequences of dGTP starvation, where the DNA precursor dGTP was specifically reduced to a low level. Under this condition, E. coli cells continued cell growth but eventually developed a DNA replication defect, leading to cell death due to formation of unresolvable DNA structures. Nevertheless, dGTP-starved cultures eventually resumed growth due to the appearance of resistant mutants. Here, we used whole-genome DNA sequencing to identify the responsible suppressor mutations. We show that the majority of suppressors can circumvent death by upregulating purine de novo biosynthesis, leading to restoration of dGTP to acceptable levels.

show abstract

Two Mechanisms Produce Mutation Hotspots at DNA Breaks in Escherichia coli

Cited by 64 publications

References 58 publications

Enhancement of microhomology-mediated genomic rearrangements by transient loss of mouse Bloom syndrome helicase

Enhancement of microhomology-mediated genomic rearrangements by transient loss of mouse Bloom syndrome helicase

A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness

Suppressors of dGTP Starvation in Escherichia coli

Contact Info

Product

Resources

About