The GC Content as a Main Factor Shaping the Amino Acid Usage During Bacterial Evolution Process.

Meng-Ze Du,Changjiang Zhang,Huan Wang,Feng-Biao Guo,Wen Wei,Shuo Liu

doi:10.3389/fmicb.2018.02948

Abstract

Understanding how proteins evolve is important, and the order of amino acids being recruited into the genetic codons was found to be an important factor shaping the amino acid composition of proteins. The latest work about the last universal common ancestor (LUCA) makes it possible to determine the potential factors shaping amino acid compositions during evolution. Those LUCA genes/proteins from Methanococcus maripaludis S2, which is one of the possible LUCA, were investigated. The evolutionary rates of these genes positively correlate with GC contents with P-value significantly lower than 0.05 for 94% homologous genes. Linear regression results showed that compositions of amino acids coded by GC-rich codons positively contribute to the evolutionary rates, while these amino acids tend to be gained in GC-rich organisms according to our results. The first principal component correlates with the GC content very well. The ratios of amino acids of the LUCA proteins coded by GC rich codons positively correlate with the GC content of different bacteria genomes, while the ratios of amino acids coded by AT rich codons negatively correlate with the increase of GC content of genomes. Next, we found that the recruitment order does correlate with the amino acid compositions, but gain and loss in codons showed newly recruited amino acids are not significantly increased along with the evolution. Thus, we conclude that GC content is a primary factor shaping amino acid compositions. GC content shapes amino acid composition to trade off the cost of amino acids with bases, which could be caused by the energy efficiency.

Highlights

Amino acid composition reflects the usage of twenty standard amino acids in proteins
Cost-minimization could shape the amino acid composition (Seligmann, 2003; Raiford et al, 2008; Bivort et al, 2009). Another factor, which influences the amino acid gain and loss in protein evolution and causes the biased amino acid usage is the order of amino acids being recruited into the genetic codes (Jordan et al, 2005; Hurst et al, 2006; Mcdonald, 2006; Liu et al, 2015)
Published research explained the gain and loss of amino acid variation during evolution with a neutral hypothesis, claiming that the trend in protein evolution was not driven by any simple trend at the DNA level (Jordan et al, 2005)

Summary

Introduction

Amino acid composition reflects the usage of twenty standard amino acids in proteins. GC contents and amino acid composition of proteins, and the nucleotide bias causes the biased amino acid usage in bacterial and viral genomes was broadly reported (Rooney, 2003; Bohlin et al, 2013; Goswami et al, 2015). Cost-minimization could shape the amino acid composition (Seligmann, 2003; Raiford et al, 2008; Bivort et al, 2009) Another factor, which influences the amino acid gain and loss in protein evolution and causes the biased amino acid usage is the order of amino acids being recruited into the genetic codes (Jordan et al, 2005; Hurst et al, 2006; Mcdonald, 2006; Liu et al, 2015). We still do not know how the feature of amino acids contributes to shape their biased compositions in proteins

Methods

Results

Conclusion