Big on Change, Small on Innovation: Evolutionary Consequences of RNA Sequence Duplication

The potential for biopolymers to evolve new structures has important consequences for their ability to optimize function and our attempts to reconstruct their evolutionary histories. Prior work with in vitro systems suggests that structural remodeling of RNA is difficult to achieve through the accumulation of point mutations or through recombination events. Sequence duplication may represent an alternative mechanism that can more readily lead to the evolution of new structures. Structural and sequence elements in many RNAs and proteins appear to be the products of duplication events, indicating that this mechanism plays a major role in molecular evolution. Despite the potential significance of this mechanism, little experimental data is available concerning the structural and evolutionary consequences of duplicating biopolymer sequences. To assess the structural consequences of sequence duplication on the evolution of RNA, we mutagenized an RNA sequence containing two copies of an ATP aptamer and subjected the resulting population to multiple in vitro evolution experiments. We identified multiple routes by which duplication, followed by the accumulation of functional point mutations, allowed our populations to sample two entirely different secondary structures. The two structures have no base pairs in common, but both structures contain two copies of the same ATP-binding motif. We do not observe the emergence of any other functional secondary structures beyond these two. Although this result suggests a limited capacity for duplication to support short-term functional innovation, major changes in secondary structure, like the one observed here, should be given careful consideration as they are likely to frustrate attempts to infer deep evolutionary histories of functional RNAs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00239-019-09906-3) contains supplementary material, which is available to authorized users.