Asymmetrical dose-responses shape the evolutionary trade-off between antifungal resistance and nutrient use

Abstract

Antimicrobial resistance is an emerging threat for public health. The success of resistance mutations depends on the trade-off between the benefits and costs they incur. This trade-off is largely unknown and uncharacterized for antifungals. Here, we systematically catalog the effect of all amino acid substitutions in the yeast cytosine deaminase FCY1, the target of the antifungal 5-FC. We identify over 900 missense mutations granting resistance to 5-FC, a large fraction of which appear to act through destabilisation of the protein. The relationship between 5-FC resistance and growth sustained by cytosine deamination is characterized by a sharp trade-off, such that small gains in resistance universally lead to large losses in canonical enzyme function. We show that this steep relationship can be explained by differences in the dose-response function of 5-FC and cytosine. Our results provide a powerful resource and platform for interpreting drug target variants in fungal pathogens as well as unprecedented insights into resistance-function trade-offs.

Epistasis between promoter activity and coding mutations shapes gene evolvability

“…For instance, many combinations of transcription and translation rates can lead to the same amount of protein (33). Coding mutations that increase protein abundance, for instance, through codon usage (23), can therefore be beneficial at low promoter activity, as we observed here. Even if they produce similar steady-state amounts of proteins, combination of transcription and translation rates and protein stability are not evolutionarily equivalent because of selection on other features such as expression noise (33).…”

“…We next examined whether the higher observed activity of the E2R and E2V mutants could be caused by higher protein abundance. Nucleotide content and their corresponding amino acids in the first few codons of a gene are known to modulate protein expression in E. coli ( 23 ), which makes this region a target for beneficial mutations when transcription levels are low. To test the effect of amino acid changes on protein abundance, we generated GFP fusions with (i) the entire DfrB1 WT sequence with and without (ii) the most beneficial mutation (E2R), (iii) the WT disordered N-terminal region (amino acids 1 to 25), and (iv) the disordered region with the E2R mutation (fig.…”

Mutational landscape and molecular bases of echinocandin resistance

“…This approach has successfully been applied to the etiologic agents of malaria or tuberculosis (23,24), but has yet to be implemented in fungi. Our data and recent work on other antifungal drug targets (25,26) contribute to this collective effort.…”

Epistasis between promoter activity and coding mutations shapes gene evolvability

“…Promoter activity could therefore potentially evolve to increase the abundance of slightly underperforming enzymes. Similarly, a recent study showed that the effects on fitness of slightly destabilizing mutations in a metabolic enzyme can be compensated by a higher availability of the substrate ( 29 ). As for the highly destabilizing mutations and those affecting the catalytic sites of the enzyme, they have selection coefficients that are less likely to be buffered by increasing promoter activity within the range examined.…”