Selection on GGU and CGU codons in the high expression genes in bacteria

Area of Science:

• Genomics
• Molecular Biology
• Evolutionary Biology

Background:

• The fourfold degenerate site (FDS) is crucial for studying selection pressure on codon usage bias (CUB) as mutations here do not alter amino acid sequences.
• Codon usage bias (CUB) reflects evolutionary forces acting on genome sequences.

Purpose of the Study:

• To investigate nucleotide frequency variations at FDS across bacterial genomes.
• To determine the relationship between FDS nucleotide variation and CUB measures.
• To identify indicators of selection pressure on CUB in bacteria.

Main Methods:

• Analysis of nucleotide frequencies at FDS across eight defined bacterial family boxes (FBs).
• Estimation of the unevenness measure (Um(g)) for genes.
• Correlation analysis between Um(g) and the effective number of codons (Nc') across 545 bacterial species.

Main Results:

• A strong correlation was observed between Um(g) and Nc' in many bacterial species.
• In bacteria with strong correlations, U-ending codons (GGU, CGU) were preferentially used over G-ending codons (GGG, CGG) for Gly and Arg.
• This preference persisted even in genomes with G+C content exceeding 65.0%.

Conclusions:

• Nucleotide frequencies at FDS are influenced by selection pressures affecting CUB.
• The preference for U-ending codons over G-ending codons in Gly and Arg FBs serves as a reliable indicator of selection pressure on CUB.
• This indicator is particularly valuable for analyzing genomes with high G+C content.