Shifting Fitness and Epistatic Landscapes Reflect Trade-offs along an Evolutionary Pathway

• Understanding evolutionary trade-offs is important for protein evolution.
• Quantified effect on ampicillin resistance of ~ 12,500 variants of TEM-1 β-lactamase.
• Provide a structural map of intragenic epistasis involving adaptive mutations.
• Increased frequency of negative epistasis is a cost of adaptation.
• Destabilizing effects of an adaptive mutation significantly contribute to this cost.

Nature repurposes proteins via evolutionary processes. Such adaptation can come at the expense of the original protein's function, which is a trade-off of adaptation. We sought to examine other potential adaptive trade-offs. We measured the effect on ampicillin resistance of ~ 12,500 unique single amino acid mutants of the TEM-1, TEM-17, TEM-19, and TEM-15 β-lactamase alleles, which constitute an adaptive path in the evolution of cefotaxime resistance. These protein fitness landscapes were compared and used to calculate epistatic interactions between these mutations and the two mutations in the pathway (E104K and G238S). This series of protein fitness landscapes provides a systematic, quantitative description of pairwise/tertiary intragenic epistasis involving adaptive mutations. We find that the frequency of mutations exhibiting epistasis increases along the evolutionary pathway. Adaptation moves the protein to a region in the fitness landscape characterized by decreased mutational robustness and increased ruggedness, as measured by fitness effects of mutations and epistatic interactions for TEM-1's original function. This movement to such a “fitness territory” has evolutionary consequences and is an important adaptive trade-off and cost of adaptation. Our systematic study provides detailed insight into the relationships between mutation, protein structure, protein stability, and epistasis and quantitatively depicts the different costs inherent in the evolution of new functions.

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