FEATURE ARTICLE
The Molecular Anatomy of an Ancient Adaptive Event
Protein engineering identifies the structural basis of a 3.5 billion-year-old adaptation
Antony Dean
Implications
If it is difficult for many evolutionary biologists to contend with the idea that only six of approximately 250 amino acid replacements determine coenzyme usage, then their shock borders on disbelief when they learn that Steve Holbrook and his colleagues at University of Bristol changed a lactate dehydrogenase into a malate dehydrogenase by replacing just one amino acid, chosen from approximately 230 differences. This provides additional evidence that the traditional notion of gradual phenotypic change is quite clearly wrong. Major shifts in enzyme function may often require no more than a few changes.
The discovery that functional differences between members of a protein family are determined by only a few amino acid replacements is liberating. Freed from the assumption that such differences are determined by many replacements, each of small effect and all engaged in an orgy of horrendously nonlinear interactions, we come to the realization that the problem is far simpler than most of us ever imagined. We can study the history of natural selection. We can reconstruct the molecular basis of adaptations that first appeared in organisms long since extinct.
The realization that so few amino acid replacements determine function also helps explain a striking pattern of molecular evolution. Phylogenetic analyses reveal that major shifts in enzyme function are relatively infrequent, so that the evolution of enzyme function is characterized by (and with apologies to all paleontologists) a sort of punctuated equilibrium—long periods of stasis interspersed by brief periods of rapid phenotypic change. The shifts are infrequent because the interim periods are presumably characterized by strong stabilizing selection.
For example, cellular demand for NADH remains an unlikely explanation for the NAD dependence of IPMDH, particularly since its gene expression is regulated by the availability of leucine. Rather, NAD dependence has been retained because selection eliminates mutants of intermediate specificity—these, as protein engineering has shown, have lower overall catalytic efficiencies. The adaptive shifts are rapid because so few amino acid replacements are necessary to change function. Hence, an understanding of metabolism, and the relations between form and function in enzymes, combine to provide a ready explanation for a commonly observed pattern in molecular evolution.
Having found an adaptive explanation for half a dozen amino acid replacements, we might reasonably ask what the remaining 244 are doing. Some are undoubtedly involved with other major phenotypic adaptations, such as specificity toward isocitrate and isopropylmalate, thermostability, quaternary structure and regulation. For instance, the eukaryotic mitochondrial ICDHs consist of four subunits, two of which contain active sites and two of which carry out regulatory functions. Being overly generous we might ascribe 20 amino acid replacements for each major phenotypic change and still be left with a vast number of replacements of no apparent phenotypic consequence. What of these?
Many may be of no functional consequence, and hence selectively neutral. Many others may be involved with modulating enzyme function and hence be of adaptive value from time to time or from place to place. For example, one of the amino acid replacements remote from the active site in engineered NAD-dependent ICDH improved activity twofold and might reasonably be considered to fall into this category. Such treadmill replacements, selected at one time or another as evolving populations track environmental changes, do not alter the overall function of enzymes in any significant way.
Biologists will never be able to ascribe to each and every mutation accrued during the vast history of evolution a cause, be it adaptive or neutral. But as these studies show we can understand why, when and how certain mutations were adaptive, and thereby enrich our understanding of the molecular basis of evolution.
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