Genome-Wide Mutation Avalanches Induced in Diploid Yeast Cells by a Base Analog or an APOBEC Deaminase

Abstract

Genetic information should be accurately transmitted from cell to cell; conversely, the adaptation in evolution and disease is fueled by mutations. In the case of cancer development, multiple genetic changes happen in somatic diploid cells. Most classic studies of the molecular mechanisms of mutagenesis have been performed in haploids. We demonstrate that the parameters of the mutation process are different in diploid cell populations. The genomes of drug-resistant mutants induced in yeast diploids by base analog 6-hydroxylaminopurine (HAP) or AID/APOBEC cytosine deaminase PmCDA1 from lamprey carried a stunning load of thousands of unselected mutations. Haploid mutants contained almost an order of magnitude fewer mutations. To explain this, we propose that the distribution of induced mutation rates in the cell population is uneven. The mutants in diploids with coincidental mutations in the two copies of the reporter gene arise from a fraction of cells that are transiently hypersensitive to the mutagenic action of a given mutagen. The progeny of such cells were never recovered in haploids due to the lethality caused by the inactivation of single-copy essential genes in cells with too many induced mutations. In diploid cells, the progeny of hypersensitive cells survived, but their genomes were saturated by heterozygous mutations. The reason for the hypermutability of cells could be transient faults of the mutation prevention pathways, like sanitization of nucleotide pools for HAP or an elevated expression of the PmCDA1 gene or the temporary inability of the destruction of the deaminase. The hypothesis on spikes of mutability may explain the sudden acquisition of multiple mutational changes during evolution and carcinogenesis.

Functions and Malfunctions of Mammalian DNA-Cytosine Deaminases

“…287,288 Furthermore, more mutations were in the 5′-UTRs than in the bodies of the genes, and there were substantially more C to T mutations in the non-transcribed DNA strand than in the transcribed strand in all the parts of the genes. 287 This result is well-explained by the observation that the non-transcribed strand is more susceptible to damage than the transcribed strand 75,289 (Fig.…”

Clusters of Multiple Mutations: Incidence and Molecular Mechanisms

“…Alternatively, breaks could have arisen from replication fork collision with alkylated bases, or with AP-site intermediates of BER. Telling, mutation clusters were found when yeast were grown in the presence of other forms of DNA damage, including ssDNA-specific cytidine deaminases, PmCDA1 from lamprey (63; 64) or human AID/APOBEC (128; 129). Cytosine deamination in ssDNA creates uracils, which are substrates for the yeast uracil DNA glycosylase Ung1 (example on Figure 5a and (25)).…”

APOBEC3A damages the cellular genome during DNA replication

“…The role of APO-BEC3 enzymes in generating these mutational signatures in cancer genomes is further supported by the finding of clustered mutations in genomes of yeast that express ectopic APOBEC3 cytosine deaminases. [21][22][23][24][25] APOBEC3 enzymes function exclusively on ssDNA substrates, 8,26,27 and the mutation clusters may arise from highly processive deaminase activity on transiently exposed ssDNA. Within the cellular genome, ssDNA is exposed during several frequent cellular processes: transcription, recombination, and replication.…”