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.


CONCLUSIONS
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.
Liu
Xiaoxia
X
The Key Laboratory for Chemical Biology of Fujian Province, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, PR China.
Zhang
Jingxian
J
Ni
Feng
F
Dong
Xu
X
Han
Bucong
B
Han
Daxiong
D
Ji
Zhiliang
Z
Zhao
Yufen
Y
D000596:Amino Acids / Q000235:genetics*; D001105:Archaea / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D056890:Eukaryota / Q000235:genetics; D019143:Evolution, Molecular; D005815:Genetic Code; D016678:Genome
D000596:Amino Acids