Interaction Between the Ribosome and the Nascent Peptide Shapes the Proteome

Gene expression is the process by which the protein coding potential inscribed in the DNA is converted into proteins. Gene translation is a central stage of gene expression, in which the ribosome synthesizes new proteins from amino acids building blocks. During translation, the nascent peptide emerges out from the ribosome through a cramped exit tunnel. Specific sequences within the nascent peptide might undergo biochemical interactions with the tunnel and lead to ribosome stalling. Using new experimental data from the baker`s yeast, Saccharomyces cerevisiae, we detect short peptide sequences that can slow down ribosomes and show that they tend to be underrepresented in the proteome. The computational approach described here can be further used for various biomedical and biotechnological applications such as gene engineering and vaccine developments.