Intense neutral drifts yield robust and evolvable consensus proteins

Abstract

What changes occur when a natural protein that had been under low mutation rates is subjected to a neutral drift at high mutational loads, thus generating genetically diverse (polymorphic) gene ensembles that all maintain the protein's original function and structure? To address this question we subjected large populations of TEM-1 beta-lactamase to a prolonged neutral drift, applying high mutation rates and purifying selection to maintain TEM-1's existing penicillinase activity. Purging of deleterious mutations and enrichment of beneficial ones maintained the sequence of these ensembles closer to TEM-1's family consensus and inferred ancestor. In particular, back-to-consensus/ancestor mutations that increase TEM-1's kinetic and thermodynamic stability were enriched. These acted as global suppressors and enabled the tolerance of a broad range of deleterious mutations, thus further increasing the genetic diversity of the drifting populations. The probability of a new function emerging (cefotaxime degradation) was also substantially increased in these ensembles owing to the presence of many gene variants carrying the global suppressors. Our findings indicate the unique features of large, polymorphic neutral ensembles generated under high mutational loads and prompt the speculation that the progenitors of today's proteins may have evolved under high mutational loads. The results also suggest that predictable back-to-consensus/ancestor changes can be used in the laboratory to generate highly diverse and evolvable gene libraries.