Abstract
Enzymes can evolve new catalytic activity when environmental changes present them with novel substrates. Despite this seemingly straightforward relationship, factors other than the direct catalytic target can also impact adaptation. Here, we characterize the catalytic activity of a recently evolved bacterial methyl-parathion hydrolase for all possible combinations of the five functionally relevant mutations under eight different laboratory conditions (in which an alternative divalent metal is supplemented). The resultant adaptive landscapes across this historical evolutionary transition vary in terms of both the number of “fitness peaks” as well as the genotype(s) at which they are found as a result of genotype-by-environment interactions and environment-dependent epistasis. This suggests that adaptive landscapes may be fluid and molecular adaptation is highly contingent not only on obvious factors (such as catalytic targets), but also on less obvious secondary environmental factors that can direct it towards distinct outcomes.
Highlights
Enzymes can evolve new catalytic activity when environmental changes present them with novel substrates
We selected eight different divalent metals that have been found in soil environments, in industrial and agricultural environments where methyl-parathion is used and where methyl-parathion hydrolase (MPH) enzymes were originally discovered in soil bacteria[33,39,40]
MPH is natively expressed in the periplasm of bacteria, where metal concentrations largely reflect metals present in the environment[41], and the metalation of MPH is likely to have been affected by environmental metal abundance
Summary
Enzymes can evolve new catalytic activity when environmental changes present them with novel substrates. While several enzyme studies have addressed the impact of “primary” environments (i.e., different substrates or ligands) on the topology of the adaptive landscapes[29,30], the degree to which the nonselective environmental factors can alter evolutionary outcomes even under the same primary selective pressure remains poorly understood[24,31]. We explore these questions and concepts in detail by characterizing the evolutionary transition between an ancestral dihydrocoumarin hydrolase (DHCH) and its methyl-parathion hydrolase (MPH) descendant within the metallo-β-lactamase superfamily[32,33]. This has general implications for the effect of nonselective, secondary environments on protein evolution
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