Determination of the Amino Acid Recruitment Order in Early Life by Genome-Wide Analysis of Amino Acid Usage Bias

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.

Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis

“…For instance, considering microorganisms from several extreme habitats, it was suggested that microbes that could survive in a wide range of habitats exhibit high CUB 2 . An environment-specific trend has also been noticed in the relative usage of different AAs 5 – 7 , 23 , 24 . However, most of these studies were conducted at the species level considering genomes of cultured microorganisms precluding the community effect.…”

“…The environment where the microbes populate was suggested to influence every aspect of the microbial genome, including their codon and AA choice. Following this, previous studies speculated that codon or AA usage might be associated with the lifestyle of the organism 1 – 10 , 23 , 24 . For instance, considering microorganisms from several extreme habitats, it was suggested that microbes that could survive in a wide range of habitats exhibit high CUB 2 .…”

The sphingolipid anteome: implications for evolution of the sphingolipid metabolic pathway

“…Some of the components of the anteome of the SL biosynthetic pathway (Fig. 2) have been proposed as components of metabolic pathways that may have existed in the last universal common ancestor (LUCA) (the most recent organism from which all existing organisms appear to share common descent), including PLP-dependent enzymes, L-serine, L-alanine, NADPH and CoA [114,[122][123][124]. However, as suggestive as the appearance of these anteome components is, genes encoding enzymes of the SL pathway have not been proposed to exist in LUCA, indicating that the evolution of the pathway must have happened later.…”