Diffusion properties of transfer RNAs in the yeast cytoplasm under normal and osmotic stress conditions

• Published in: Biochimica et biophysica acta. General subjects Vol. 1869; no. 6; p. 130798
• Main Authors: Kompella, Vijay Phanindra Srikanth, Romano, Maria Carmen, Stansfield, Ian, Mancera, Ricardo L.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.05.2025
• Subjects: Brownian dynamics; Cytoplasm - metabolism; Diffusion; Macromolecular crowding; Osmotic Pressure; Osmotic stress; Protein Biosynthesis; Ribosomes - metabolism; RNA, Transfer - chemistry; RNA, Transfer - metabolism; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Subdiffusion; Yeast cytoplasm; Macromolecular crowding; Brownian dynamics; Yeast cytoplasm; Subdiffusion; Osmotic stress
• DOI: 10.1016/j.bbagen.2025.130798
• ISSN: 0304-4165; 1872-8006

The mechanism by which aminoacyl-tRNAs are supplied to translating ribosomes for protein synthesis is likely to involve a process of diffusion within the cellular environment, which is inevitably impacted by macromolecular crowding. Osmotic stress leading to cell shrinkage increases the concentration of macromolecules in the cytoplasm, reducing protein diffusion. The impact of macromolecular crowding on the translation machinery in eukaryotes remains uncharacterised. In this study Brownian dynamics simulation were used for the first time to study the effect of macromolecular crowding on the microsecond-time scale diffusion properties of tRNAs and their ternary complexes within a model yeast cytoplasmic environment. Under normal cell-like conditions, the diffusion of tRNAs and ternary complexes was predicted to be reduced by up to 8-fold (compared with dilute conditions), whilst diffusion under severe osmotic stress conditions decreased by up to a remarkable 80-fold. All molecules exhibited sub-diffusive behaviour, which was stronger under osmotic stress. These findings may be readily used to predict protein translation dynamics, including the crucial process of tRNA delivery to the ribosome, under a variety of conditions. •Macromolecular crowding induces sub-diffusive dynamics in the microsecond-time scale.•Diffusion of tRNAs and their complexes are reduced 8-fold in the yeast cytoplasm.•Diffusion under severe osmotic stress decreases by 80-fold.•Macromolecular concentration, composition and size distribution affect diffusion.