Tracing the evolution of RNA structure in ribosomes

Area of Science:

• Molecular Biology
• Evolutionary Biology
• Structural Biology

Background:

• Ribosome function is intrinsically linked to the dynamic interactions of its RNA components.
• Understanding ribosomal RNA (rRNA) structure is key to analyzing its evolutionary history.
• Previous studies focused on sequence-based evolution, necessitating a structure-based approach.

Purpose of the Study:

• To investigate the evolutionary origin and diversification of ribosomal RNA (rRNA) structure.
• To reconstruct a universal phylogenetic tree based on rRNA secondary structures.
• To trace the evolution of specific ribosomal structural features and their functional implications.

Main Methods:

• Phylogenetic analysis using cladistic methods applied to combined large (LSU) and small (SSU) subunit rRNA secondary structures.
• Reconstruction of a rooted universal phylogenetic tree.
• Lineage-by-lineage tracing of ribosomal structural characters and evolutionary patterns.

Main Results:

• A universal rRNA phylogenetic tree was reconstructed, revealing evolutionary trends.
• Observed tendency towards molecular simplification and homogeneous reduction of structural change over time.
• Identified patterns in inter-subunit bridge contacts and tRNA-binding sites supporting concerted evolution and ancestral origins.

Conclusions:

• Ribosome evolution is characterized by simplification and reduced structural dynamism.
• tRNA-binding sites in both subunits evolved concertedly, suggesting functional co-evolution.
• Specific structural features, like the peptidyl (P) site, are ancient and have a common origin.