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Open Access Highly Accessed Research article

Genome wide exploration of the origin and evolution of amino acids

Xiaoxia Liu1, Jingxian Zhang2, Feng Ni1, Xu Dong2, Bucong Han2, Daxiong Han1, Zhiliang Ji12* and Yufen Zhao13*

Author Affiliations

1 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

2 School of Life Science, Xiamen University, Xiamen 361005, Fujian, PR China

3 The Key Laboratory for Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, School of Life Sciences and Engineering, Tsinghua University, Beijing 100084, PR China

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BMC Evolutionary Biology 2010, 10:77  doi:10.1186/1471-2148-10-77

Published: 15 March 2010

Abstract

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.