Discrepancy among the synonymous codons with respect to their selection as optimal codon in bacteria

Area of Science:

• Genomics and Molecular Biology
• Bioinformatics
• Evolutionary Biology

Background:

• Synonymous codons, encoding the same amino acid, exhibit unequal abundance within genomes.
• Factors like G+C content and tRNA availability influence codon abundance.
• The specific nucleotide sequence within a codon may also affect its usage frequency.

Purpose of the Study:

• To investigate the selection of optimal codons (OCs) for 18 amino acids across 221 bacterial species.
• To determine if amino acid sequence and phylogenetic relationships influence OC selection.
• To explore the role of nucleotide order in codon usage bias.

Main Methods:

• Comparative analysis of optimal codon usage for 18 amino acids.
• Examination of 221 diverse bacterial species.
• Statistical evaluation of codon abundance in relation to G+C content and phylogeny.

Main Results:

• Optimal codon selection demonstrates a significant amino acid-specific pattern.
• Phylogenetic influence on OC choice is evident for specific amino acids (Glu, Gln, Lys, Leu).
• Codon bias is supported by comparative abundance studies of synonymous codons with identical G+C content.

Conclusions:

• The selection of optimal codons is influenced by both the specific amino acid and the organism's evolutionary history.
• Evidence suggests that the nucleotide order within a codon plays a role in codon usage bias.
• Further research into the impact of nucleotide sequence on codon bias is warranted.