“Superwobbling” and tRNA-34 Wobble and tRNA-37 Anticodon Loop Modifications in Evolution and Devolution of the Genetic Code

Abstract

The genetic code evolved around the reading of the tRNA anticodon on the primitive ribosome, and tRNA-34 wobble and tRNA-37 modifications coevolved with the code. We posit that EF-Tu, the closing mechanism of the 30S ribosomal subunit, methylation of wobble U34 at the 5-carbon and suppression of wobbling at the tRNA-36 position were partly redundant and overlapping functions that coevolved to establish the code. The genetic code devolved in evolution of mitochondria to reduce the size of the tRNAome (all of the tRNAs of an organism or organelle). “Superwobbling” or four-way wobbling describes a major mechanism for shrinking the mitochondrial tRNAome. In superwobbling, unmodified wobble tRNA-U34 can recognize all four codon wobble bases (A, G, C and U), allowing a single unmodified tRNA-U34 to read a 4-codon box. During code evolution, to suppress superwobbling in 2-codon sectors, U34 modification by methylation at the 5-carbon position appears essential. As expected, at the base of code evolution, tRNA-37 modifications mostly related to the identity of the adjacent tRNA-36 base. TRNA-37 modifications help maintain the translation frame during elongation.

From initial RNA encoding to the Standard Genetic Code

“…4B). After the resulting ribonucleopeptide (RNP) transition, evolution to modern translation and the full SGC is enabled, requiring exquisite adaptation between proteins and RNAs (55) and wide-ranging ribonucleotide refinement for coding (56, 57), but not radical evolutionary innovation.…”

“…Accordingly, the Initial Darwinian Ancestor emerges (95). These events are accompanied by nucleotide modifying enzymes that refine the codon-anticodon complex (56, 57). One complete code becomes the universal SGC (96) and diverges from LUCA to produce a modern multi-domain biota employing the Standard Genetic Code (97).…”

“…These data therefore suggest that an initial code relying on RNA chemistry encoded and used polypeptides with major structural and enzymatic capabilities. After this ribonucleopeptide (RNP) transition, evolution to modern translation and the full SGC is accessible, requiring extensive refinement (Grosjean and Westhof 2016; Lei and Burton 2022), but not radical evolutionary innovation.…”

“…Translation initiation (Schmitt et al 2019) and termination (Burroughs and Aravind 2019) evolve over a prolonged period, and become late coding events, their evolution continuing after the separation of major biological domains. Near-modern coding capabilities produce the protein aaRS (Ribas de Pouplana 2020), and deoxyribonucleotides (Poole et al 2014), as well as nucleotide modifying enzymes that refine the codon-anticodon complex (Grosjean and Westhof 2016; Lei and Burton 2022). One complete code becomes universal (Vetsigian et al 2006) and diverges from LUCA to produce multi-domain modern biota (Crapitto et al 2022)…”

GNN codon adjacency regulates protein translation

“…The anticodons of these tRNAs have either a G34 or I34 (inosine 34) nucleotide, both of which can base pair with the wobble U or C nucleotides of the mRNA A-site codon. I34 (adenine 34 converted to inosine 34) is a eukaryote innovation that is used by NNU/C codon pairs in cases where the corresponding NNA codon also codes for the same amino acid (because inosine can also base pair with wobble A [10]). NNU codons are significantly more abundant than NNC in yeast ORFs (Fig S1A ), although for NNU codons that utilize tRNA G34 this trend is less strong in ORFs of genes with high protein expression (Fig S1B , C).…”