Unexpected amino acid composition of modern Reptilia and its implications in molecular mechanisms of dinosaur extinction

Genome wide exploration of the origin and evolution of amino acids

Background

Even after years of exploration, the terrestrial origin of bio-molecules remains unsolved and controversial. Today, observation of amino acid composition in proteins has become an alternative way for a global understanding of the mystery encoded in whole genomes and seeking clues for the origin of amino acids.

Results

In this study, we statistically monitored the frequencies of 20 alpha-amino acids in 549 taxa from three kingdoms of life: archaebacteria, eubacteria, and eukaryotes. We found that the amino acids evolved independently in these three kingdoms; but, conserved linkages were observed in two groups of amino acids, (A, G, H, L, P, Q, R, and W) and (F, I, K, N, S, and Y). Moreover, the amino acids encoded by GC-poor codons (F, Y, N, K, I, and M) were found to "lose" their usage in the development from single cell eukaryotic organisms like S. cerevisiae to H. sapiens, while the amino acids encoded by GC-rich codons (P, A, G, and W) were found to gain usage. These findings further support the co-evolution hypothesis of amino acids and genetic codes.

Conclusion

We proposed a new chronological order of the appearance of amino acids (L, A, V/E/G, S, I, K, T, R/D, P, N, F, Q, Y, M, H, W, C). Two conserved evolutionary paths of amino acids were also suggested: A→G→R→P and K→Y.

CvP-bias as an index to predict the life style of last common ancestor

CvP-bias (difference between proportions of charged and polar non-charged amino acids) has been recognized as an efficient criterion to distinguish hyperthermophiles from mesothermophiles. By analyzing the CvP-biases of seven barophiles's proteomes, we reveal that this criterion still works for barophiles. As a result, CvP-bias criterion is applicable to disclosing some secrets in the lifestyles of the last common ancestor (LCA), no matter the LCA lived in deep sea or not, which is helpful to building a self-consistent model for the LCA.