Abstract
Proteins change over the course of evolutionary time. New protein-coding genes and gene families emerge and diversify, ultimately affecting an organism’s phenotype and interactions with its environment. Here we survey the range of structural protein change observed in plants and review the role these changes have had in the evolution of plant form and function. Verified examples tying evolutionary change in protein structure to phenotypic change remain scarce. We will review the existing examples, as well as draw from investigations into domestication, and quantitative trait locus (QTL) cloning studies searching for the molecular underpinnings of natural variation. The evolutionary significance of many cloned QTL has not been assessed, but all the examples identified so far have begun to reveal the extent of protein structural diversity tolerated in natural systems. This molecular (and phenotypic) diversity could come to represent part of natural selection’s source material in the adaptive evolution of novel traits. Protein structure and function can change in many distinct ways, but the changes we identified in studies of natural diversity and protein evolution were predicted to fall primarily into one of six categories: altered active and binding sites; altered protein–protein interactions; altered domain content; altered activity as an activator or repressor; altered protein stability; and hypomorphic and hypermorphic alleles. There was also variability in the evolutionary scale at which particular changes were observed. Some changes were detected at both micro- and macroevolutionary timescales, while others were observed primarily at deep or shallow phylogenetic levels. This variation might be used to determine the trajectory of future investigations in structural molecular evolution.
Highlights
In the study of the molecular changes underlying adaptive evolution, there is debate as to whether regulatory or structural changes are of greater importance
In most cases there is no single quantitative trait nucleotide (QTN), but rather a collection of myriad small changes, both regulatory and structural, that have contributed to the evolution of a novel phenotype (Rockman, 2012)
In our review of the literature, we found that functional protein changes, the result of underlying structural mutations, fell into six broad, non-mutually exclusive categories
Summary
In the study of the molecular changes underlying adaptive evolution, there is debate as to whether regulatory or structural changes are of greater importance. They propose that mutations that occur in the coding sequences of genes are structural, and all other mutations, including those that occur in introns, are regulatory This definition includes nonsense null mutations, altered miRNA-binding sites, and silent mutations affecting transcription and translation dynamics as “structural” (Hoekstra and Coyne, 2007). We prefer a more narrow definition of “structural mutation,” and include only those examples where amino acid sequence is changed and protein function is not completely lost. This circumscription of structural mutations includes mostly missense mutations, and insertions and deletions, frameshifts, and premature stop codons that produce proteins with altered functions.
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