Interpreting ribosome dynamics during mRNA translation

Abstract

Translation takes a central position in gene expression, and its swift response to environmental stress is evolutionarily conserved. Upon chemical damage to the messenger RNA (mRNA) or the lack of building blocks, the ribosome stalls during elongation and halts the production line. Even under normal growth conditions, the translation machinery encounters constant hindrances such as varied codon composition or nascent chains with distinct features. However, it is challenging to define these kinetics experimentally, partly due to the inherent variations of ribosome behavior during mRNA translation. To ensure the flow of ribosomal traffic, cells employ several mechanisms to circumvent the traffic jam. When the roadblock is not resolved timely, trailing ribosomes can collide with stalled ribosomes. However, the boundary between physiological queuing and pathological collision is often blurred, representing a fundamental gap in our understanding of ribosome dynamics. To cope with translational barriers, several signaling pathways are activated to adjust the rate of global translation and rescue the local stalled ribosome. Deficiencies in cellular response to translational stress have been associated with a wide array of human diseases. In this review, we focus on fundamental aspects of the ribosome dynamics during mRNA translation. We provide an overview of causes, outcomes, and cellular responses to ribosome stalling and collision on mRNA. We highlight questions that may clarify the biological roles of distinct ribosome behavior during mRNA translation and emphasize the mechanistic connection between altered ribosome dynamics and human diseases.

Keywords: codon; mRNA; protein synthesis; ribosome; stress response; tRNA; translation.

Figure 1

A wide range of ribosome dynamics during mRNA translation. An elongating ribosome could exhibit different kinetics ranging from slowdown, temporary pause, persistent stall, to collision (top panel). These distinct ribosome stages are context-dependent, and their definition is often ambiguous if judged by the A-site ribosome density (bottom panel). During ribosome pausing, the deacylated tRNA (light blue t) likely dissociates from the E-site due to prolonged dwell time. Upon persistent stalling, additional factors like eIF5A (blue oval) could bind to the empty E-site. When the trailing ribosome collides with the stalled ribosome, the collided ribosome takes on a rotated state and the disome interface can be occupied with collision factors (orange oval). Ribosome collision also leads to elevated A-site ribosome peaks (blue line) upstream of the stall site. The size of single ribosome and disome is shown with light blue lines as codons of ribosome footprints.

Figure 2

The central role of tRNA in ribosome dynamics. The availability and functional integrity of tRNAs are key determinants of ribosome dynamics during translation. Besides differential gene expressions of tRNA isoacceptors and isodecoders, tRNA molecules are subject to cleavage by endonucleases. Aminoacyl synthetase (ARS)-mediated tRNA charging is central to the decoding process and tRNA modification also modulates decoding fidelity by influencing codon-anticodon base pairing. Amino acids are depicted as orange.

Figure 3

Intrinsic mRNA features influence ribosome dynamics. The rate of translation elongation is modulated by codon optimality. Optimal codons (blue) are typically translated more efficiently, accurately, and rapidly than the non-optimal ones (orange). mRNA modifications and secondary structures affect elongation rates directly or indirectly. Certain nascent peptides enriched in specific amino acids can significantly influence ribosome dynamics during translation.

Figure 4

Translational outcomes of altered ribosome dynamics. To ensure the flow of ribosomal traffic, cells employ several mechanisms to overcome the non-productive stalling, such as ribosomal frameshifting, codon reassignment, codon bypassing, or translation abortion. In many cases, these translational products are non-functional and subject to degradation. While mRNA is depicted in light blue, protein products are shown in dark green. A light green line indicates a different frame. An orange dot refers to an altered amino acid, whereas the sign of “v” indicates the missing amino acid. Dark triangle, start codon; dark square, stop codon.

Figure 5

Cellular response to altered ribosome dynamics. In response to ribosome pausing and collision, cells activate several signaling pathways to cope with the translational hinderance. While single ribosome pausing or stalling triggers integrated stress response (ISR) and ribotoxic stress response (RSR), ribosome collision exacerbates such global responses. Ribosome collision also induces ribosome collision response (RCR) or ribosome-associated quality control (RQC) pathways to clear the roadblock by acting locally, resulting in ribosome splitting, nascent chain degradation and mRNA decay.