Abstract
The mechanisms shaping the amino acids recruitment pattern into the proteins in the early life history presently remains a huge mystery. In this study, we conducted genome-wide analyses of amino acids usage and genetic codons structure in 7270 species across three domains of life. The carried-out analyses evidenced ubiquitous usage bias of amino acids that were likely independent from codon usage bias. Taking advantage of codon usage bias, we performed pseudotime analysis to re-determine the chronological order of the species emergence, which inspired a new species relationship by tracing the imprint of codon usage evolution. Furthermore, the multidimensional data integration showed that the amino acids A, D, E, G, L, P, R, S, T and V might be the first recruited into the last universal common ancestry (LUCA) proteins. The data analysis also indicated that the remaining amino acids most probably were gradually incorporated into proteogenesis process in the course of two long-timescale parallel evolutionary routes: I→F→Y→C→M→W and K→N→Q→H. This study provides new insight into the origin of life, particularly in terms of the basic protein composition of early life. Our work provides crucial information that will help in a further understanding of protein structure and function in relation to their evolutionary history.
Highlights
Academic Editor: Lukasz KurganUniversal common ancestry (UCA) is a core pillar of modern evolutionary theory [1], which was first proposed by Darwin in On the Origin of Species
We provided a portrayal of the genome-wide landscape of amino acid usage across the three domains of life
coefficient of variation (CV) analysis indicated that the majority of amino acids in Eukaryota had low usage change (CV < 15), except alanine (A) and asparagine (N)
Summary
Academic Editor: Lukasz KurganUniversal common ancestry (UCA) is a core pillar of modern evolutionary theory [1], which was first proposed by Darwin in On the Origin of Species. UCA theory is grounded in the hypothesis that all organisms are the offspring of an ancient single life form socalled the last universal common ancestor (LUCA) [2,3]. Woese proposed that LUCA could have been a diverse cell community that survived and evolved as a biological unit based on the existing genetic annealing model of life [5]. Both studies suggested that the contemporary system of the genetic code in living organisms may be different from that existing in LUCA. LUCA may just have had a simpler genetic codon system than that in present-day life forms [6], which gained higher complexity along the process of life evolution [7,8]
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