Rapid evolutionary repair by secondary perturbation of a primary disrupted transcriptional network.

The discrete steps of transcriptional rewiring have been proposed to occur neutrally to ensure steady gene expression under stabilizing selection. A conflict‐free switch of a regulon between regulators may require an immediate compensatory evolution to minimize deleterious effects. Here, we perform an evolutionary repair experiment on the Lachancea kluyveri yeast sef1Δ mutant using a suppressor development strategy. Complete loss of SEF1 forces cells to initiate a compensatory process for the pleiotropic defects arising from misexpression of TCA cycle genes. Using different selective conditions, we identify two adaptive loss‐of‐function mutations of IRA1 and AZF1. Subsequent analyses show that Azf1 is a weak transcriptional activator regulated by the Ras1‐PKA pathway. Azf1 loss‐of‐function triggers extensive gene expression changes responsible for compensatory, beneficial, and trade‐off phenotypes. The trade‐offs can be alleviated by higher cell density. Our results not only indicate that secondary transcriptional perturbation provides rapid and adaptive mechanisms potentially stabilizing the initial stage of transcriptional rewiring but also suggest how genetic polymorphisms of pleiotropic mutations could be maintained in the population. Synopsis: Evolutionary repair in sef1Δ mutant cells of the yeast Lachancea kluyveri highlights the rapid adaptive strategies to handle growth defects and to compensate for gene misexpression. Adaptive clones evolve rapidly in populations of sef1Δ cells under different selective conditions.Loss‐of‐function or hypomorphic mutations pervasively hit two genes, IRA1 and AZF1, which are responsible for the adaptive phenotypes.The pleiotropy of loss‐of‐function azf1 mutations has beneficial fitness and compensatory effects under favorable conditions but results in growth trade‐offs when encountering unfavorable conditions.The growth trade‐offs of azf1 genotypes can be alleviated by increasing the cell density in unfavorable conditions. [ABSTRACT FROM AUTHOR]