Protein Fold Usages in Ribosomes: Another Glance to the Past

Area of Science:

• Evolutionary Biology
• Structural Biology
• Biochemistry

Background:

• Protein fold usage analysis provides insights into proteome evolution.
• Previous studies focused on modern genomes; this study examines ribosomes across kingdoms.

Purpose of the Study:

• To comparatively analyze protein fold distribution and usage in bacterial, archaeal, and eukaryotic ribosomes.
• To understand the evolutionary history and origins of ribosomal proteins.

Main Methods:

• Comparative analysis of protein fold distribution in ribosomes.
• Identification of conserved and kingdom-specific protein folds.
• Grouping ribosomal proteins into urfolds/metafolds.

Main Results:

• Identified 'super-ribosome folds' (e.g., OB fold, SH3 domain) prevalent across kingdoms.
• Observed a power-law distribution of protein folds in ribosomes.
• Found three proto-Rossmann folds in all kingdoms, indicating ancient importance.
• Highlighted molecular convergence in protein-RNA binding.
• Grouped ribosomal proteins into five ancestral urfolds/metafolds.

Conclusions:

• Ribosomal protein fold distribution reflects evolutionary trajectories and early molecular convergence.
• Proto-Rossmann folds are ancient and fundamental to ribosomal structure.
• Simple, structured folds likely preceded disordered extensions in ribosomal protein evolution.
• This analysis deepens understanding of the RNA-to-protein world transition.