Wehbi, S. | bioRxiv Science

bioRxiv2024

Identifying the Last Universal Common Ancestor's protein domains resolves the order in which the amino acids were recruited into the genetic code

The current "consensus" order in which amino acids were added to the genetic code is based on potentially biased criteria, such as absence of sulfur-containing amino acids from the Urey-Miller experiment which lacked sulfur. More broadly, abiotic abundance might not reflect biotic abundance in the organisms in which the genetic code evolved. Here, we instead identify which protein domains date to the last universal common ancestor (LUCA), then infer the order of recruitment from deviations of their ancestrally reconstructed amino acid frequencies from the still-ancient post-LUCA controls. We find that smaller amino acids were added to the code earlier, with no additional predictive power in the previous "consensus" order. Metal-binding (cysteine and histidine) and sulfur-containing (cysteine and methionine) amino acids were added to the genetic code much earlier than previously thought. Methionine and histidine were added to the code earlier than expected from their molecular weights, and glutamine later. Early methionine availability is compatible with inferred early use of S-adenosylmethionine, and early histidine with its purine-like structure and the demand for metal-binding. Even more ancient protein sequences -- those that had already diversified into multiple distinct copies prior to LUCA -- have significantly higher frequencies of aromatic amino acids (tryptophan, tyrosine, phenylalanine and histidine), and lower frequencies of valine and glutamic acid than single copy LUCA sequences. If at least some of these sequences predate the current code, then their distinct enrichment patterns provide hints about earlier, alternative genetic codes. Significance StatementThe order in which the amino acids were added to the genetic code was previously inferred from consensus among forty metrics. Many of these reflect abiotic abundance on ancient Earth. However, the abundances that matter are those within primitive cells that already had sophisticated RNA and perhaps peptide metabolism. Here, we directly infer the order of recruitment from the relative ancestral amino acid frequencies of ancient protein sequences. Small size predicts ancient amino acid enrichment better than the previous consensus metric does. We place metal-binding and sulfur-containing amino acids earlier than previously thought, highlighting the importance of metal-dependent catalysis and sulfur metabolism to ancient life. Understanding early life has implications for our search for life elsewhere in the universe.

evolutionary biology↗

bioRxiv2023

The effectiveness of selection in a species affects the direction of amino acid frequency evolution

Nearly neutral theory predicts that species with higher effective population size (Ne) are better at purging slightly deleterious mutations. We compare evolution in high-Ne vs. low-Ne vertebrates to reveal subtle selective preferences among amino acids. We take three complementary approaches. First, we fit non-stationary substitution models using maximum likelihood, comparing the high-Ne clade of rodents and lagomorphs to its low-Ne sister clade of primates and colugos. Second, we compared evolutionary outcomes across a wider range of vertebrates, via correlations between amino acid frequencies and the codon adaptation index of species, a proxy for Ne. Third, we dissected which amino acids substitutions occurred in human, chimpanzee, mouse, and rat, as scored by parsimony - this also enabled comparison to a historical paper. All three methods agree on amino acid preference under more effective selection. Preferred amino acids are less costly to synthesize and use GC-rich codons, which are hard to maintain under AT-biased mutation. These factors explain 85% of the variance in amino acid preferences. Within highly exchangeable pairs of amino acids, arginine is strongly preferred over lysine, valine over isoleucine, and aspartate over glutamate, consistent with more effective selection preferring a marginally larger free energy of folding. The first two of these preferences, but not the third, match differences between thermophiles and mesophilic relatives. These results reveal the biophysical consequences of mutation-selection-drift balance, and demonstrate the utility of nearly neutral theory for understanding protein evolution. Significance statementAccording to the nearly neutral theory of molecular evolution, selection is less able to distinguish between similar alleles in species with lower population size. We identify which amino acids are subject to such weak preferences - these tend to be less costly to make, to use GC-rich codons easily destroyed by mutation, and to be enriched in thermophiles relative to mesophiles. The latter agrees with theories of marginal protein stability under mutation-selection-drift balance.

evolutionary biology↗