Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins

Area of Science:

• Genomics
• Evolutionary Biology
• Molecular Biology

Background:

• Codon bias influences mRNA translation speed and protein abundance.
• Differences in codon bias may play an evolutionary role within and between species.

Purpose of the Study:

• To investigate the evolutionary role of codon bias by comparing genome-wide patterns across six eukaryotic species.
• To explore relationships between codon bias and protein function within and between lineages.

Main Methods:

• Acquired complete protein-coding sequences for six diverse eukaryotic species.
• Computed genome-wide codon bias for all genes in each organism.
• Analyzed correlations between codon bias and protein function, considering evolutionary lineages.

Main Results:

• Identified five coordinated patterns of extreme codon bias linked to lineage-specific traits.
• Observed distinct codon bias patterns for transcription factors, ribosomal proteins, hair, cell wall, chloroplasts, and mitochondrial proteins.
• Noted specific extreme codon bias in Homo sapiens (transcription factors), mammals (hair), Arabidopsis thaliana (cell wall/chloroplasts), and Gallus gallus (mitochondrial/Ciliary Neurotrophic Factor).

Conclusions:

• Extreme codon bias is pronounced in functionally related gene groups characteristic of specific lineages.
• Propose a pathway-level energetic explanation for the observed extreme codon bias patterns.
• Codon bias variation reflects evolutionary adaptations and lineage-specific biological innovations.