Evolution of the standard genetic code

Abstract

AbstractA near-universal Standard Genetic Code (SGC) implies a single origin for Earthly life. To study this unique event, I compute paths to the SGC, comparing different plausible histories. Notably, SGC-like coding emerges from traditional evolutionary mechanisms, and a superior path can be identified.To objectively measure evolution, progress values from 0 (random coding) to 1 (SGC-like) are defined: these measure fractions of random-code-to-SGC distance. Progress types arespacing/distance/deltaPolarRequirement, detecting space between identical assignments /mutational distance to the SGC/chemical order, respectively. A coding system was based on known RNAs performing aminoacyl-RNA synthetase reactions. Acceptor RNAs exhibit SGC-like wobble; alternatively, non-wobbling triplets uniquely encode 20 amino acids/start/stop. Triplets acquire 22 functions by stereochemistry, selection, coevolution, or randomly. Assignments also propagate to an assigned triplet’s neighborhood via single mutations, but can also decay.Futile evolutionary paths are plentiful due to the vast code universe. Thus SGC evolution is critically sensitive to disorder from random assignments. Evolution also inevitably slows near coding completion. Coding likely avoided these difficulties, and two suitable paths are compared. Inlate wobble, a majority of non-wobble assignments are made before wobble is adopted. Incontinuous wobble, a uniquely advantageous early intermediate supplies the gateway to an ordered SGC. Revised coding evolution (limited randomness, late wobble, concentration on amino acid encoding, chemically conservative coevolution with a chemically-ordered elite) produces varied full codes with excellent joint progress values. A population of only 600 independent coding tables includes SGC-like members; a Bayesian path toward more accurate SGC evolution is available.