Roadblocks and resolutions in eukaryotic translation

Abstract

During protein synthesis, ribosomes encounter many roadblocks, the outcomes of which are largely determined by substrate availability, amino acid features and reaction kinetics. Prolonged ribosome stalling is likely to be resolved by ribosome rescue or quality control pathways, whereas shorter stalling is likely to be resolved by ongoing productive translation. How ribosome function is affected by such hindrances can therefore have a profound impact on the translational output (yield) of a particular mRNA. In this Review, we focus on these roadblocks and the resumption of normal translation elongation rather than on alternative fates wherein the stalled ribosome triggers degradation of the mRNA and the incomplete protein product. We discuss the fundamental stages of the translation process in eukaryotes, from elongation through ribosome recycling, with particular attention to recent discoveries of the complexity of the genetic code and regulatory elements that control gene expression, including ribosome stalling during elongation, the role of mRNA context in translation termination and mechanisms of ribosome rescue that resemble recycling.

Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing

“…It has long been known that elongating ribosomes can pause in response to 595 obstacles that they encounter, and most pauses are assumed to occur in a transitory fashion and to be resolved in a productive manner (Schuller and Green, 2018). For certain cases, there is good evidence that the translational pause is even an integral, possibly obligatory part of the mechanism of nascent polypeptide synthesis, as exemplified by the pausing seen on signal peptide-encoding 600 transcripts that require targeting to the secretory pathway (Wolin and Walter, 1988).…”

“…An early ribosome profiling study in mouse embryonic stem cells (mESCs) already addressed the question of how to extract potential pause sites from footprint data (Ingolia et al, 2011), which resulted in the identification of thousands of alleged pauses in the body of genes as well as an enrichment at termination 65 codons. In combination with quantitative modelling approaches, subsequent studies have identified parameters that can impinge on local translation speed and pausing (reviewed in Schuller and Green (2018)). Among these are, notably, specific amino acids (Charneski and Hurst, 2013), codon pairs (Gamble et al, 2016), tRNA availability (Darnell et al, 2018;Guydosh and Green, 2014), 70 RNA secondary structures (Zhang et al, 2017;Pop et al, 2014), or the folding (Doring et al, 2017) and exit tunnel interactions (Dao Duc and Song, 2018;Charneski and Hurst, 2013) of the nascent peptide.…”

Human NMD ensues independently of stable ribosome stalling

“…In cases of faulty mRNAs that are degraded due to a lack of a TC (nonstop decay) or due to a strong secondary structure or the absence of a cognate tRNA (no-go decay), the activating signal is the ribosome stalling during elongation. In this scenario, ribosome stalling marks a dead-end event and the rescue of an otherwise trapped ribosome is crucial (reviewed in 17,43,44 ). The term "stalling" is used broadly to describe increased ribosome density, without distinguishing between transient pauses and stable stalls.…”

“…An important feature of NMD is that it is dependent on translation, either on the first or a later round [9][10][11][12] . Evidence supporting the formation of complexes containing NMD and translation termination factors suggested a functional connection between the two processes [13][14][15][16][17] . In view of this data, a currently prevailing working model for NMD activation suggests that NMD ensues when translation termination is aberrant, either because it requires additional factors for ribosome release or because it is not fast enough.…”

USP21 and OTUD3 Antagonize Regulatory Ribosomal Ubiquitylation and Ribosome-Associated Quality Control

“…Cellular protein homeostasis must continuously adapt to changing environmental conditions and exposure to extrinsic proteotoxic stressors that challenge cellular, tissue, and organismal health. A prominent source of proteotoxic stress arises during translation where transcriptional or mRNA processing errors can result in the translation of defective or truncated proteins and lead to the accumulation of toxic nascent protein products (Brandman and Hegde, 2016;Schuller and Green, 2018). Failure to remove these deleterious proteins can lead to aggregation which contribute to human pathologies including a wide range of neurodegenerative disorders (Gestwicki and Garza, 2012).…”