Project description:Codon usage bias is a universal feature of eukaryotic and prokaryotic genomes and has been proposed to regulate translation efficiency, accuracy and protein folding based on the assumption that codon usage affects translation dynamics. The role of codon usage in regulating translation, however, is not clear and has been challenged by recent ribosome profiling studies. Here we used a Neurospora cell-free translation system to directly monitor the velocity of mRNA translation. We demonstrated that the use of preferred codons enhances the rate of translation elongation, whereas non-optimal codons slow translation. In addition, codon usage regulates ribosome traffic on the mRNA. These conclusions were supported by ribosome profiling results in vitro and in vivo with substrate mRNAs manipulated to increase signal over background noise. We further show that codon usage plays an important role in regulating protein function by affecting co-translational protein folding. Together, these results resolve a long-standing fundamental question and demonstrate the importance of codon usage on protein folding.

2015-07-18 | GSE71032 | GEO

Tertiary interactions within the ribosomal exit tunnel.

Project description: Not available

| S-EPMC2670549 | biostudies-literature

A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae.

Project description: Not available

| S-EPMC7797049 | biostudies-literature

Codon usage regulates protein structure and function by affecting translation elongation speed in Drosophila cells.

Project description: Not available

| S-EPMC5737824 | biostudies-other

The ribosome modulates folding inside the ribosomal exit tunnel.

Project description: Not available

| S-EPMC8100117 | biostudies-literature

Codon usage and protein length-dependent feedback from translation elongation to translation initiation and kinetics

Project description:In yeast and mammals, activated GCN2 can phosphorylate its substrate eIF2α, which is a part of the eIF2-GTP-Met-tRNAiMet ternary complex. The eIF2α phosphorylation blocks the ternary complex formation and therefore inhibits translation initiation. Meanwhile, GCN2 activation associates with ribosomes and some translation elongation factors such as eEF1A. In Neurospora crassa, the homolog of GCN2 is CPC-3. Ribosome profiling and accompanying RNA-seq experiments in this project were used to explore the effects of CPC-3 on translation kinetics. Here we show that poor codon usage of mRNAs with long CDS preferentially causes CPC-3 activation, which in turn suppresses the translation initiation and elongation in both codon usage and CDS length dependent manner.

2021-08-10 | GSE168595 | GEO

Cysteine oxidation and disulfide formation in the ribosomal exit tunnel.

Project description: Not available

| S-EPMC7642426 | biostudies-literature