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

Area of Science:

• Evolutionary Biology
• Molecular Evolution
• Genomics

Background:

• Protein evolution is influenced by amino acid composition and codon recruitment order.
• The Last Universal Common Ancestor (LUCA) provides insights into early protein evolution.
• GC content, a measure of guanine and cytosine in DNA, is a key genomic feature.

Purpose of the Study:

• To investigate the factors shaping amino acid composition during protein evolution.
• To determine the role of GC content in the evolutionary rates and composition of proteins.
• To analyze LUCA genes/proteins for insights into early evolutionary pressures.

Main Methods:

• Analysis of LUCA genes/proteins from *Methanococcus maripaludis* S2.
• Correlation analysis between evolutionary rates and GC content.
• Linear regression to assess the contribution of GC-rich and AT-rich codons to evolutionary rates.
• Principal component analysis to identify major factors influencing amino acid composition.

Main Results:

• Evolutionary rates of LUCA genes positively correlate with GC content (P < 0.05 for 94% of genes).
• Amino acids coded by GC-rich codons contribute to higher evolutionary rates and are prevalent in GC-rich organisms.
• GC content strongly correlates with the first principal component of amino acid composition.
• Ratios of amino acids coded by GC-rich codons positively correlate with bacterial genome GC content.

Conclusions:

• GC content is a primary determinant of protein amino acid composition.
• The observed patterns suggest an evolutionary trade-off related to the cost and energy efficiency of amino acids and bases.
• Codon recruitment order influences composition, but GC content appears to be the dominant selective pressure.