The team built a diploid yeast strain in which both copies of the SOD1 gene had been deleted, creating a hybrid background containing roughly 50,000 sequence differences between its two parental genomes. This design allowed the researchers to map, with extraordinary resolution, every loss of heterozygosity event that accumulated as cells divided. After subculturing 32 independent isolates for hundreds of generations, whole-genome sequencing revealed a staggering catalogue of damage. Single nucleotide variations accumulated at 13 times the wild-type rate, loss of heterozygosity rose 12-fold, large chromosomal rearrangements increased 4-fold, and aneuploidy—the gain or loss of entire chromosomes—surged an astonishing 48-fold above normal levels.

The scale and diversity of these lesions underscored that Sod1 deficiency does not merely nudge the genome toward instability; it fundamentally rewrites the rules of genome maintenance. The researchers detected 322 interstitial and 134 terminal loss-of-heterozygosity events across their isolates, occurring at rates 15- and 16-fold higher than in wild-type cells, respectively. Gene conversion tracts—the stretches of DNA copied from one homologous chromosome to repair damage on the other—were also markedly longer in the mutant, averaging 10.8 kilobases compared with 5.9 kilobases in healthy cells. Most structural rearrangements were flanked by Ty retrotransposon sequences, pointing to unequal recombination between repetitive elements as a major driver of large-scale chromosome changes.

Perhaps the most striking result came when the researchers repeated the experiment under anaerobic conditions. Deprived of oxygen, the sod1 mutant’s genomic chaos vanished almost entirely: mutation rates fell to wild-type levels and recombination rates dropped dramatically. Supplementing the growth medium with glutathione, a potent cellular antioxidant, similarly cut mutation and recombination frequencies by more than half. Together, these experiments identified reactive oxygen species as the sole executioner behind the genomic storm, confirming that the instability arises from direct chemical attack on DNA rather than from indirect disruption of repair machinery or metabolic collapse.

The mutational fingerprint left by Sod1 loss proved highly distinctive. All six classes of base substitutions increased, but transversions dominated, particularly C:G to A:T changes concentrated within 5′-CCA-3′ sequence motifs. This pattern is the classic signature of 8-oxoguanine, an oxidized form of guanine that mispairs with adenine during replication, producing the characteristic transversion after a second round of DNA copying. The finding directly implicates 8-oxoguanine overproduction as the molecular engine of Sod1-deficient mutagenesis, and it links the enzyme’s antioxidant function to a specific, measurable chemical lesion on DNA.

Dissecting how cells cope with these lesions revealed a sophisticated hierarchy of repair and bypass. The base excision repair glycosylase Ogg1 emerged as the frontline defense: deleting OGG1 alone caused a 19-fold rise in C:G to A:T transversions, and combining OGG1 deletion with SOD1 deletion produced a synergistic 7.5-fold increase over the ogg1 mutant alone. By these calculations, Ogg1-mediated excision corrects roughly 90 percent of the 8-oxoguanine lesions generated in the absence of Sod1. When repair is overwhelmed, translesion synthesis polymerases take over, and here the outcomes diverge sharply. DNA polymerase eta, encoded by RAD30, performs relatively accurate bypass by inserting cytosine opposite the oxidized base, preventing about a third of the characteristic transversions. In contrast, the error-prone polymerase zeta and its partner Rev1 account for approximately two-thirds of all Sod1-induced point mutations, illustrating the costly trade-off between completing replication and preserving sequence fidelity.

Timing analysis of recombination events added another layer of mechanistic insight. Using a colony-sectoring assay on chromosome IV, the team showed that about 65 percent of mitotic crossovers in sod1 mutants were initiated by double-strand breaks arising during the G1 phase of the cell cycle, closely mirroring the pattern in wild-type cells. Fluorescence microscopy of Rad52 repair foci confirmed a four-fold increase in spontaneous DNA breaks. Intriguingly, the distribution of crossover breakpoints was not random: 33 of 35 events on chromosome IV clustered distal to the SSD1 locus, a bias the researchers traced to post-mutational selection rather than intrinsic recombination hotspots. Restoring a functional SSD1 allele, which improved fitness in the sod1 background, redistributed breakpoints uniformly, demonstrating that observed genomic landscapes reflect both where damage occurs and which recombinant cells survive to form colonies.

The study then turned to human disease, testing eight ALS-associated SOD1 variants in the yeast system. Wild-type human SOD1 fully rescued the growth defects and genomic instability of yeast lacking endogenous Sod1, confirming deep functional conservation. But the clinical variants were not created equal. The H48Q mutation, which disrupts a copper-binding residue essential for catalytic activity, shattered genome stability, producing 8- and 10-fold increases in mutation and recombination rates alongside severe growth impairment. The G85R and S133N variants showed moderate effects, while the well-known A4V, G36R, D90A, and G93A variants remained essentially benign in this context. These results suggest that for a subset of ALS patients, loss of genomic protection—driven by failure to quench nuclear reactive oxygen species—may constitute an additional, mutation-specific pathogenic mechanism beyond the prevailing toxic gain-of-function model of protein aggregation.

Notably, the researchers found that human Sod1 is far more tolerant of amino acid substitutions than its yeast counterpart, a difference they attribute to the extraordinary structural robustness of the human enzyme, which remains stable even in metal-deficient states. This resilience likely reflects evolutionary pressure in long-lived organisms to protect the proteome against decades of somatic mutation. The work also carries a cautionary message for cancer therapy: because tumor cells often depend on elevated Sod1 to manage their oxidative burden, pharmacological inhibition of the enzyme, while potentially cytotoxic, risks triggering a mutational burst that could accelerate the emergence of drug-resistant clones. By mapping the full genomic consequences of antioxidant failure—from single nucleotides to whole chromosomes—this study establishes a mechanistic framework for understanding how metabolic defense and genome integrity are inseparably coupled in eukaryotic life.

Subject of Research: The role of superoxide dismutase 1 in protecting eukaryotic genome stability against oxidative DNA damage

Article Title: Decoupling metabolic defense: Mutational and recombinational chaos in Sod1-deficient cells

Article References: Sui, Y., Zheng, D.-Q., Wang, Y., Zhao, S.-S., Li, K.-J., Ye, C., & Zhang, K. (2026). Decoupling metabolic defense: Mutational and recombinational chaos in Sod1-deficient cells. PLOS Genetics, 22(10), e1012326. https://doi.org/10.1371/journal.pgen.1012326

Image Credits: AI Generated

DOI: 10.1371/journal.pgen.1012326

Keywords: Sod1, genome instability, reactive oxygen species, 8-oxoguanine, yeast, loss of heterozygosity, aneuploidy, base excision repair, translesion synthesis, ALS, SOD1 mutations, oxidative stress

Loss of heterozygosity, or LOH, is a familiar concept in genetics. In a diploid organism, each gene normally exists in two copies, one inherited from each parent. Errors during mitosis, the process by which a cell duplicates and divides, can eliminate one of those copies, either through recombination, chromosome loss or segmental deletion. Previous work had established that mitotic errors alter the allelic composition of a gene roughly a thousand times more often than replication errors produce point mutations. This means that when selection favors the loss of a gene’s function, it will frequently be achieved by discarding the chromosome or chromosomal segment that carries it, rather than by mutating the gene itself. Aneuploidy, the state of having an abnormal number of chromosomes, is found in up to a quarter of newly isolated wild strains of Saccharomyces cerevisiae, a striking testament to how common these events are.

What remained unclear was whether complex rearrangements, those affecting multiple chromosomes at once, accumulate gradually through a series of independent steps or emerge suddenly in coordinated bursts. To find out, the team built an experimental system in which genome rearrangements could be generated de novo and their frequency, triggers, architecture and stability all measured. They compiled a list of 454 yeast genes whose deletion had been shown, in earlier screens using two well-established but distinct methods, one detecting gross chromosomal rearrangements and one detecting chromosome instability, to increase LOH. After accounting for strains that could not be manipulated successfully, 392 diploid deletion strains remained, each carrying a homozygous deletion of a different gene together with two heterozygous marker loci: CAN1 on the left arm of chromosome V and ade2::URA3 in the middle of the right arm of chromosome XV.

The researchers propagated 20 replicate mutation-accumulation cultures of each strain and plated cells onto selective media containing canavanine or 5-fluoroorotic acid, which only cells that had lost the functional allele at the corresponding marker could colonize. These assays yielded robust, strain-specific estimates of the single LOH rate per cell division, with 95 percent confidence limits typically spanning only a narrow range around the central value. A substantial majority of the deletion strains, 68 percent at the CAN1 locus and 82 percent at the URA3 locus, showed higher single LOH rates than the wild-type control, confirming that the mutations compiled from earlier qualitative screens indeed destabilize the genome in quantitative assays. The team then scored how frequently double mutants, resistant to both drugs simultaneously, appeared. Deletion strains varied enormously, and the most unstable strains under double selection were also among the most unstable under single selection, with a Spearman rank correlation of 0.61.

The critical question was whether these double events could be explained as two independent single events occurring in sequence. Because the experimental data alone could not distinguish one-step from two-step origins, the team turned to computer simulations. Using the empirically measured single LOH rates, they modeled mutation accumulation across colony growth, allowing cells to become single mutants at their measured rates and double mutants either sequentially or coincidentally at a rate equal to the product of the two single rates. Even under the deliberately conservative assumption that neither single nor double mutants paid any fitness penalty, an assumption that would maximize the survival and spread of sequentially derived double mutants, the simulated frequencies fell far short of what was observed. When fitness costs of 10 and 20 percent were applied, as is more realistic, the gap widened further. The observed double LOH frequencies exceeded the coincidental predictions by tens or even hundreds of times in the most unstable strains, and after subtracting the predicted sequential component, the residual coincidental events remained 26 times more frequent than expected.

What kinds of cellular defects produce such explosive instability? The answer emerged from Gene Ontology analysis of the deleted genes in the most unstable strains. Nearly half of the genes carry annotations related to cell cycle checkpoints, the surveillance mechanisms that halt progression through the division cycle when DNA is damaged or the mitotic spindle is improperly assembled. The checkpoint category as a whole is assigned to only 1.3 percent of all yeast genes, so its dominance among the strongest mutators is statistically striking. The remaining genes in the set are involved in DNA maintenance and repair, sister chromatid cohesion, and spindle formation, processes whose failure can generate damage so extensive that even intact checkpoints cannot contain it. The message is clear: genomes are most vulnerable to complex, multi-chromosome rearrangements when the checkpoints that police DNA integrity and spindle function fail to stop the cell cycle.

Direct examination of the double mutants themselves confirmed the picture. Flow cytometry of roughly 80 independent mutants from each of 43 highly unstable deletion strains revealed that DNA content was often substantially increased or decreased relative to the diploid ancestors, with the variance in DNA content among mutants significantly exceeding that among ancestral replicates. Whole-genome sequencing of mutants from 20 deletion strains went further. The dominant alteration was whole-chromosome aneuploidy, frequently affecting multiple chromosomes beyond the two targeted by selection, with many chromosomes showing non-integer coverage values that indicated mixed populations of cells carrying different chromosome counts. Averaged across all strains and chromosomes, deviations from diploidy appeared in nearly every mutant examined. Crucially, the chromosomes under direct selection, V and XV, showed no more than the average number of changes, evidence that selection at two sites was merely revealing systemic destabilization rather than focused local mutation. Heterozygous point mutations were rare, and the team found essentially no segmental copy number variants, no non-homologous recombination products and no convincing translocations or inversions in non-telomeric regions, despite deliberately validating that their pipelines could detect all such events.

Genetic tests of four particularly unstable strains, deleted for sem1, chl1, mre11 or rad27, provided independent confirmation. When double mutants from these strains were screened for retention of heterozygosity at two additional marker loci on chromosomes II and XII, the frequencies of additional losses were extraordinarily high. In the sem1 background, for example, 16 of 61 double mutants had also lost heterozygosity on chromosome II and 14 on chromosome XII, with 7 losing both, even though such losses normally occur at a rate of only one to a few per ten thousand cell divisions. Triple and quadruple LOH events appeared at frequencies far beyond anything a sequential model could accommodate, reinforcing the conclusion that short periods of hyper-instability, rather than a string of independent accidents, generate these genomes.

The final experiments addressed what happens to these dramatically rearranged genomes over evolutionary time. The team propagated 63 mutant cultures derived from 21 deletion strains for 200 generations in batch culture and re-measured their DNA content. The result was a nearly uniform contraction toward diploidy: strains that started far from two chromosome sets moved markedly closer, and the most divergent isolates showed the greatest fitness gains, growing faster after evolution than before. Aneuploidy, in other words, is typically a transient state, imposed as a cost of rapid adaptation and then pruned by natural selection as faster-growing re-diploidized variants outcompete their unstable relatives. The authors suggest that this ephemerality is exactly why such bursts are so hard to catch in nature, since selection rapidly erases the evidence of a genomic episode.

The findings carry implications well beyond yeast. In free-living microbes, aneuploidy usually slows growth and is quickly eliminated, but it may pay off under multiple stresses, such as exposure to several toxins at once. In the somatic cells of multicellular organisms, the calculus is different. These cells are programmed not to divide, so there is no immediate growth cost to genome restructuring, and a loosening of the brakes on cell division can incidentally expose recessive alleles, a mechanism central to cancer, where the loss of the remaining wild-type copy of a tumor suppressor gene is the classic second hit. The study suggests that failures of cell cycle control may be a common source of the large-scale chromosomal changes that dismantle multiple adaptation barriers during tumor evolution. Complex genome change, on this view, rarely arrives as a leisurely accumulation of small steps; it tends to arrive as a burst, born of a momentarily failing control system, and natural selection then decides what, if anything, survives.

Subject of Research: Loss of heterozygosity and aneuploidy driven by cell cycle control defects in diploid budding yeast

Article Title: Burst of aneuploidy: a cost of adaptation driven by breakdown of cell cycle control

Article References: Pirog, A., Tutaj, H., Tomala, K., & Korona, R. (2026). Burst of aneuploidy: a cost of adaptation driven by breakdown of cell cycle control. Molecular Systems Biology, 22(8), 1292-1311. https://doi.org/10.1038/s44320-026-00217-6

Image Credits: AI Generated

DOI: 10.1038/s44320-026-00217-6

Keywords: aneuploidy, loss of heterozygosity, cell cycle checkpoints, Saccharomyces cerevisiae, genome instability, mitosis, chromosome segregation, DNA repair, mutation rate, experimental evolution, cancer, genome rearrangements