Crick Wobble and Superwobble in Standard Genetic Code Evolution

Abstract

Wobble coding is inevitable during evolution of the Standard Genetic Code (SGC). It ultimately splits half of NN U/C/A/G coding boxes with different assignments. Further, it contributes to pervasive SGC order by reinforcing close spacing for identical SGC assignments. But wobble cannot appear too soon, or it will inhibit encoding and more decisively, obstruct evolution of full coding tables. However, these prior results assumed Crick wobble, NN U/C and NN A/G, read by a single adaptor RNA. Superwobble translates NN U/C/A/G codons, using one adaptor RNA with an unmodified 5′ anticodon U (appropriate to earliest coding) in modern mitochondria, plastids, and mycoplasma. Assuming the SGC was selected when evolving codes most resembled it, characteristics of the critical selection events can be calculated. For example, continuous superwobble infrequently evolves SGC-like coding tables. So, continuous superwobble is a very improbable origin hypothesis. In contrast, late-arising superwobble shares late Crick wobble’s frequent resemblance to SGC order. Thus late superwobble is possible, but yields SGC-like assignments less frequently than late Crick wobble. Ancient coding ambiguity, most simply, arose from Crick wobble alone. This is consistent with SGC assignments to NAN codons.

Packing the Standard Genetic Code in its box: 3-dimensional late Crick wobble

“…Assignment of these latter triplet meanings would be tortuous, each decaying many times before 22 functions are attained. These results reproduce and extend previous comparisons in which early wobble, and early wobble to an extended range of triplets, resulted in delay and inefficient evolution (Yarus 2021b, 2021a). Increased effort for completion - from near-random filling (Fig.…”

“…Previously, among populations of evolving late Crick wobble codes, the minority of codes that most resembled the SGC had also made fewer mutational captures (Yarus 2021b). Specific comparisons of unique and Crick wobble (Yarus 2021b) and Crick and superwobble (Yarus 2021a) previously favored the smaller, simpler forms. Moreover, these results (Fig.…”

“…The existing result is late Crick wobble (Yarus 2021a). “Late” implies that wobble was deferred, being preceded by unique triplet pairing assignments.…”

“…Accurate Crick wobble (Crick 1966) would therefore likely be a later, more modern code refinement. Such late wobble also shows superior ability to fill an SGC-like coding table, and offers more probable SGC access to evolving codes (Yarus 2021b, 2021a). Moreover, the first wobble (the SGC necessarily uses ambiguous coding) probably resembled simplified Crick wobble, defined here as translation of NNY (Y = pyrimidine) and NNR (R = purine) codons, each with one adaptor RNA (Crick 1966).…”

“…Moreover, the first wobble (the SGC necessarily uses ambiguous coding) probably resembled simplified Crick wobble, defined here as translation of NNY (Y = pyrimidine) and NNR (R = purine) codons, each with one adaptor RNA (Crick 1966). For comparison, superwobble, translation of four NNY/R codons with one unmodified adaptor (Alkatib et al 2012), less frequently yields the SGC (Yarus 2021a). Other evolutionary obstacles to SGC-like coding can be defined similarly, within this simulated framework.…”