Abstract
Analysis of extant proteomes has the potential of revealing how amino acid frequencies within proteins have evolved over biological time. Evidence is presented here that cysteine, tyrosine, and phenylalanine residues have substantially increased in frequency since the three primary lineages diverged more than three billion years ago. This inference was derived from a comparison of amino acid frequencies within conserved and non-conserved residues of a set of proteins dating to the last universal ancestor in the face of empirical knowledge of the relative mutability of these amino acids. The under-representation of these amino acids within last universal ancestor proteins relative to their modern descendants suggests their late introduction into the genetic code. Thus, it appears that extant ancient proteins contain evidence pertaining to early events in the formation of biological systems.
Highlights
Analysis of extant proteomes has the potential of revealing how amino acid frequencies within proteins have evolved over biological time
We sought to determine whether amino acid frequencies within conserved positions of proteins dating to the last universal ancestor (LUA)1 of all life indicate that any of the 20 amino acids occurred more or less frequently within early proteins than within their modern descendants
We were motivated by the idea that the amino acid composition of proteins within the LUA might have reflected the order of addition of amino acids to the genetic code, i.e. that compared to modern proteins, the composition was relatively richer in amino acids added to the code early and poorer in those added late
Summary
Pletely independent of substitution events occurring within non-conserved sequence positions. It is worth remarking that, based on this approach, no inferences regarding changing amino acid frequencies may be made in cases in which an amino acid with low mutability occurs more frequently, or an amino acid with high mutability occurs less frequently, within conserved than non-conserved residues This approach may identify some amino acids that have changed in frequency over deep evolutionary time and thereby provide novel insights regarding early proteins. Guided by this rationale, we determined the frequency of each amino acid in conserved and non-conserved sequence elements of a set of extant proteins dating to the LUA in 26 species spanning the three primary lineages
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