A rapidly reversible mutation generates subclonal genetic diversity and unstable drug resistance

Abstract

Significance Mutations that confer drug resistance often confer a growth defect in the absence of drug. Mechanisms that enable temporary mutations—mutations that provide drug resistance but frequently revert back to the wild-type genomic DNA sequence—would therefore be advantageous for organisms forced to adapt in changing environments. Here, we show that rapidly reversible mutations are frequently generated by microhomology-mediated tandem duplications (MTDs) in the gene ssp1, causing rapamycin resistance and a growth defect, and reversal back to wild type restores fitness and drug sensitivity. We also found that genomes have evolved to minimize the number of potentially deleterious MTDs and used machine learning to determine the sequence-encoded rules that govern the formation and collapse of MTDs. Most genetic changes have negligible reversion rates. As most mutations that confer resistance to an adverse condition (e.g., drug treatment) also confer a growth defect in its absence, it is challenging for cells to genetically adapt to transient environmental changes. Here, we identify a set of rapidly reversible drug-resistance mutations in Schizosaccharomyces pombe that are caused by microhomology-mediated tandem duplication (MTD) and reversion back to the wild-type sequence. Using 10,000× coverage whole-genome sequencing, we identify nearly 6,000 subclonal MTDs in a single clonal population and determine, using machine learning, how MTD frequency is encoded in the genome. We find that sequences with the highest-predicted MTD rates tend to generate insertions that maintain the correct reading frame, suggesting that MTD formation has shaped the evolution of coding sequences. Our study reveals a common mechanism of reversible genetic variation that is beneficial for adaptation to environmental fluctuations and facilitates evolutionary divergence.