Structural Phylogenomics Retrodicts the Origin of the Genetic Code and Uncovers the Evolutionary Impact of Protein Flexibility
Figure 4
Origin and evolution of the genetic code.
A. Inception of the ‘operational’ code. Mapping of amino acid charging functions onto a binary decision-tree and a condensed vis-á-vis complementarity representation of the genetic code. Cells are indexed with Group 1, 2 and 3 domain inception, discriminator base identity, and nucleotide composition (pie charts) of the N2 position of the acceptor stem of tRNA. In the right, structural models of TyrRS (1H3R) interacting with tRNATyr and an acceptor-minihelix illustrate a possible evolutionary route of domain growth and accretion as the binary tree unfolds in evolution (domains are colored with corresponding geological age). B. Evolution of the ‘standard’ code. Ancestries define a timeline of early genetic code expansion in the condensed vis-á-vis code representation with major and minor groove modes of tRNA recognition. The mappings take into consideration the alphabet and number of anticodon positions that are most parsimonious and anticodon loop identity elements. Note that Pro, the founder, already uses 2nd and 1st code positions (identity elements G35 and G36) and that the first use of 3rd codon position (G34) occurs first with Thr and then His (the last two initial recruitments of c.51.1.1) when the alphabet expands to the triplex code. Also, the Yin-Yang complementarity pattern is fulfilled with the last recruitment of a.27.1.1 once the modern tetraplex code is in place.