Ribosome occupancy profiles are conserved between structurally and evolutionarily related yeast domains

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• Protein synthesis is a non-equilibrium process where translation speed impacts protein folding and function.
• Evolutionary conservation of translation speed profiles is hypothesized for structurally similar proteins to ensure correct folding.
• Previous evidence relied on codon rarity as a proxy for translation speed, overlooking other factors.

Purpose of the Study:

• To directly test the evolutionary conservation of translation speed profiles between related protein domains.
• To investigate if entire ribosome occupancy profiles, not just rare codons, are conserved.

Main Methods:

• Utilized ribosome profiling data from five large-scale yeast studies.
• Compared ribosome occupancy profiles between paralogous and non-paralogous protein domains.
• Analyzed conservation trends independent of domain length, structure, amino acid composition, or sequence similarity.

Main Results:

• Ribosome occupancy profiles of paralogous domains showed significantly higher similarity compared to non-paralogous domains.
• This conservation was observed across even distantly related yeast domains.
• The findings were consistent regardless of domain length, structural class, amino acid composition, or sequence similarity.

Conclusions:

• The study provides direct evidence for the conservation of entire ribosome occupancy profiles between related protein domains in yeast.
• This supports the hypothesis that translation schedules are evolutionarily conserved to maintain protein folding pathways and facilitate efficient folding.
• Ribosome occupancy profiling offers a more direct measure of translation speed conservation than codon rarity.