Nascent peptide-induced translation discontinuation in eukaryotes impacts biased amino acid usage in proteomes

Abstract

Robust translation elongation of any given amino acid sequence is required to shape proteomes. Nevertheless, nascent peptides occasionally destabilize ribosomes, since consecutive negatively charged residues in bacterial nascent chains can stochastically induce discontinuation of translation, in a phenomenon termed intrinsic ribosome destabilization (IRD). Here, using budding yeast and a human factor-based reconstituted translation system, we show that IRD also occurs in eukaryotic translation. Nascent chains enriched in aspartic acid (D) or glutamic acid (E) in their N-terminal regions alter canonical ribosome dynamics, stochastically aborting translation. Although eukaryotic ribosomes are more robust to ensure uninterrupted translation, we find many endogenous D/E-rich peptidyl-tRNAs in the N-terminal regions in cells lacking a peptidyl-tRNA hydrolase, indicating that the translation of the N-terminal D/E-rich sequences poses an inherent risk of failure. Indeed, a bioinformatics analysis reveals that the N-terminal regions of ORFs lack D/E enrichment, implying that the translation defect partly restricts the overall amino acid usage in proteomes.

Global regulation via modulation of ribosome pausing by the ABC-F protein EttA

“…Our results echo the work of the Taguchi lab, who have shown that repeats of acidic residues when polymerized by the ribosome, before the nascent peptide fills the NPET, can induce Intrinsic Ribosome Destabilization (IRD) in prokaryotes 2,3 and eukaryotes 1 . They showed that the effect of the acidic residues depends on the bulkiness of the nascent chain 2 .…”

“… Abstract Having multiple rounds of translation of the same mRNA is a key feature of the Central Dogma that creates substantial dynamic complexities along with opportunities for regulation related to ribosome pausing and stalling at specific sequences 1–5 . The molecular mechanisms controlling these critical processes and the principles guiding their evolution remain among the least understood facets of cellular physiology.…”

The ABCF proteins inEscherichia coliindividually alleviate nascent peptide-induced noncanonical translations

“…Given the arrest-releasing activity of YheS, we aimed to investigate whether other ABCFs also play a role in coping with nascent peptide-dependent noncanonical translations. Our previous research has demonstrated that the translation of poly-acidic sequences triggers intrinsic ribosome destabilization (IRD), leading to Pth-mediated premature termination (11, 13). For instance, over 50% of the synthesized product from a model GFP mRNA containing the 20D poly-acidic sequence accumulated as Pth-sensitive peptidyl-tRNA ( Fig.…”

“…The interaction between EttA and tRNA might indeed impose constraints on the movement of the P-site tRNA, potentially leading to an inhibition of IRD. Our previous studies have shown that IRD is inhibited in situations where the dynamics of P-site tRNA is restricted by the preceding nascent chain (12, 13). Additionally, molecular simulations have indicated the possibility of P-site tRNA adopting a different positioning due to the translation of polyacidic sequence (40).…”

“…When a polypeptide chain passing through the ribosome tunnel contains an abundance of positively charged amino acids, translation elongation can be hindered due to interactions with the negatively charged tunnel structure (9,10). Conversely, the translation of poly-acidic sequences can lead to difficulties in maintaining the intact ribosome complex conformation, resulting in stochastic premature termination termed intrinsic ribosome destabilization (IRD) (11)(12)(13). Thus, the growing nascent peptide can impact ribosomal activity through the interplay of ribosome structure and chemical properties.…”