Abstract
Life uses a common set of 20 coded amino acids (CAAs) to construct proteins. This set was likely canonicalized during early evolution; before this, smaller amino acid sets were gradually expanded as new synthetic, proofreading and coding mechanisms became biologically available. Many possible subsets of the modern CAAs or other presently uncoded amino acids could have comprised the earlier sets. We explore the hypothesis that the CAAs were selectively fixed due to their unique adaptive chemical properties, which facilitate folding, catalysis, and solubility of proteins, and gave adaptive value to organisms able to encode them. Specifically, we studied in silico hypothetical CAA sets of 3–19 amino acids comprised of 1913 structurally diverse α-amino acids, exploring the adaptive value of their combined physicochemical properties relative to those of the modern CAA set. We find that even hypothetical sets containing modern CAA members are especially adaptive; it is difficult to find sets even among a large choice of alternatives that cover the chemical property space more amply. These results suggest that each time a CAA was discovered and embedded during evolution, it provided an adaptive value unusual among many alternatives, and each selective step may have helped bootstrap the developing set to include still more CAAs.
Highlights
It seems reasonable that several mechanisms led to the evolutionary selection of the coded amino acids (CAAs) as they were made available during the emergence of metabolism, and their incorporation into the genetic code was determined based on factors besides prebiotic availability[14,21,22,23]
In order to test the adaptive value of the CAAs at smaller set sizes, we first measured the number of better sets, as described in the methods section, for each set size
Our analysis suggests that stepwise expansion of the CAA repertoire proceeding through the present CAAs represents a trajectory that became increasingly adaptive relative to hypothetical sets that can be constructed from xeno amino acids (XAAs)
Summary
The 20 CAAs’ repertoire seems to reflect the requirements of providing enough structural diversity that proteins derived from these amino acids are able to define unique three-dimensional shapes[18], and able to produce more adaptive proteins (e.g., those whose catalytic properties improve the function of the cell which hosts them, whether it be by improving turnover number, tuning it to the flux of intracellular intermediates, or by other means) when the repertoire of amino acids is enlarged[19] These general ideas have been subsequently refined into mounting evidence for the detailed claim that a combination of size, pKa and hydrophobicity seem to combine as a good first approximation of the CAA’s value to natural selection[2,3,20]. Www.nature.com/scientificreports other factors, including biosynthetic availability, could have contributed to shaping the growth of the modern near-universal CAA alphabet, we sought to establish whether the CAAs can be distinguished as optimal using a minimal set of parameters, namely size, hydrophobicity and pKa3
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