Life depends on the precise functioning of different proteins synthesized in cells by ribosomes. This diverse set of proteins, known as the proteome, is maintained by the robust translation elongation of amino acid sequences that occurs in ribosomes. The translation mechanisms that ensure that nascent chains of polypeptides – long chains of amino acids – elongate without detaching are conserved in all living organisms. However, the elongation rates are not constant. Elongation is often disrupted by interactions between the positively charged nascent polypeptides and the negatively charged ribosomal RNA.
Studies have found that in prokaryotes Escherichia coli cells, the nascent peptide chains not only interrupt the elongation process, but also destabilize the ribosomes themselves. This type of premature termination of translation is called intrinsic ribosome destabilization (IRD). Evidence shows that IRD was primarily triggered by nascent N-terminus peptides rich in aspartic and glutamic acid sequences. Because translation mechanisms are conserved, researchers began to wonder whether a similar phenomenon could be observed in the cells of eukaryotic organisms, such as plants, fungi and animals.
Recently, a team of Japanese researchers, led by Prof Hideki Taguchi of the Tokyo Institute of Technology (Tokyo Tech), managed to provide some answers to this question. In their recent study published in Nature communications, the team used budding yeast cells and a reconstituted cell-free translation system to study the IRD phenomenon in eukaryotes. “Previous studies have explored the impact of aspartic acid and glutamic acid sequences on bacterial ribosomal translation. However, eukaryotic cells are not talked about much. Therefore, we chose a eukaryotic organism such as yeast to investigate premature termination of translation and whether there were mechanisms present to counter IRD,” explains Prof. Taguchi, one of the study’s corresponding authors.
The team found that, similar to bacteria, nascent peptide chains enriched in aspartic acid (D) or glutamic acid (E) in their N-terminal regions led to the IRD interrupting translation in yeast cells. They also found that accumulation of peptidyl-tRNA inhibited cell growth in yeast lacking peptidyl-tRNA hydrolase, an essential cellular enzyme. “The peptidyl tRNAs produced by IRD are cleaved by peptidyl tRNA hydrolase, which recycles the peptidyl tRNAs out of the ribosomal complex. The accumulation of these aborted peptidyl tRNAs is toxic, as yeast lacking the enzyme will not can grow when IRD-prone sequences are overexpressed,” says Prof. Taguchi.
The bioinformatic analysis conducted by the team, however, revealed a unique way that yeast cells reduce the risk of IRD. They found that the proteomes had a skewed amino acid distribution, where the translation elongation process disfavoured amino acid sequences with D/E runs in their N-terminal region.
This study provides new insights into the elongation dynamics of eukaryotic cells and the contrast mechanisms at work to reduce translation defects during protein synthesis. “Understanding the factors that influence the overall utilization of amino acids in proteomes can help us improve the expression of recombinant proteins. This is essential for the production of useful proteins that can have clinical and industrial applications,” concludes Prof . Taguchi.
Tokyo Institute of Technology