Evolution of the standard genetic code

Abstract

A 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. SGC-like coding tables emerge from traditional evolutionary mechanisms, and a superior route 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 are spacing/distance/delta Polar Requirement, detecting space between identical assignments /mutational distance to the SGC/chemical order, respectively. The coding system was based on selected RNAs performing aminoacyl-RNA synthetase reactions. Acceptor RNAs exhibit SGC-like wobble; alternatively, nonwobbling 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 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. In "late wobble", a majority of non-wobble assignments are made before wobble is adopted. In "continuous wobble", a uniquely advantageous early intermediate supplies the gateway to an ordered SGC. Revised coding table evolution (limited randomness, late wobble, concentration on amino acid encoding, chemically conservative coevolution with a simple elite) produces varied full codes with excellent joint progress values. A population of only 600 independent coding tables includes SGC-like members, and a Bayesian path to further refinement is available.A simplified model. To investigate SGC appearance, we desire the fewest, least specific assumptions, in order to maximally respect limited knowledge of the early code. These are: there was an era in which 22 meanings (20 amino acids and start and stop signals) became assigned to 64 possible triplets. This era begins with the first triplet assignment, and ends with a fully assigned coding table that resembles the SGC (Standard Genetic Code). Meaningful average rates of coding assignment, which includes both enabling mutation and ensuing events that fix the new meaning, are assumed to exist. Having said only this much, a great deal about code descent is implied.Relations between identical and similar functions. Examination of triplets occupied by similar or identical amino acids in the SGC suggests regular relations between multiple assignments for similar encoded functions.

Optimal Evolution of the Standard Genetic Code

“…These results are consistent with previous searches (Yarus 2020), in which codes with 1 or 2 misassignments were found among 600 coding tables, evolving under similar late wobble conditions. In those prior results, however, SGC-like code order was sought, rather than explicit assignment accuracy.…”

“…100,000 late wobble evolutions via Coevo_PR captures: coevolution (Wong 1981;Amirnovin 1997;Ronneberg et al 2000) with chemical similarity (Freeland and Hurst 1998;Massey 2019) to direct amino acid choice. Probabilities per passage are Pmut = 0.04 for mutational capture, Pdecay = 0.04 for assignment loss, Pinit = 0.6 for initial triplet assignment, Prand = 0.1 for random assignment (Yarus 2020). Figure 1B.…”

“…Fraction of coding tables with coding capacity (≥ 20 encoded functions: left ordinate) or with both coding capacity and accurate assignment, versus evolutionary time as passages (labeling, history and parameters as in Figure 1A). "order" indicates mean and sem for ≥ 20 functions with joint code order ≥ 0.9 of the SGC; "mean" indicates mean and sem for ≥ 20 encoded functions (Yarus 2020). Figure 1C.…”

“…More particularly, in order to fill a coding table, wobble must arise late; for example, appearing after 20 amino acids are assigned. This leaves modern initiation and termination for a later origin, consistent with their unconserved, and thus late-arising, molecular components (Yarus 2020). Below, late wobble not only provides access, but also an accessible, optimal route to SGC-like order with amino acid coding capacity.…”

“…This procedure yields normal dynamic phenomena, like first and second order rates, as well as standard near-steady states. It is mathematically equivalent to defining typical first and second order kinetic constants for initiation, decay and capture of codon assignments (Yarus 2020). SGC-like coding tables arise by combining stereochemical initial codon assignment (Yarus 2017, 10% randomness allowed) with coevolutionary capture (Wong 1981) that prefers amino acids with similar polar requirements (Woese et al 1966;Mathew and Luthey-Schulten 2008).…”