Robust landscapes of ribosome dwell times and aminoacyl-tRNAs in response to nutrient stress in liver

Abstract

Translation depends on messenger RNA (mRNA)-specific initiation, elongation, and termination rates. While translation elongation is well studied in bacteria and yeast, less is known in higher eukaryotes. Here we combined ribosome and transfer RNA (tRNA) profiling to investigate the relations between translation elongation rates, (aminoacyl-) tRNA levels, and codon usage in mammals. We modeled codon-specific ribosome dwell times from ribosome profiling, considering codon pair interactions between ribosome sites. In mouse liver, the model revealed site- and codon-specific dwell times that differed from those in yeast, as well as pairs of adjacent codons in the P and A site that markedly slow down or speed up elongation. While translation efficiencies vary across diurnal time and feeding regimen, codon dwell times were highly stable and conserved in human. Measured tRNA levels correlated with codon usage and several tRNAs showed reduced aminoacylation, which was conserved in fasted mice. Finally, we uncovered that the longest codon dwell times could be explained by aminoacylation levels or high codon usage relative to tRNA abundance.

What determines eukaryotic translation elongation: recent molecular and quantitative analyses of protein synthesis

“…Despite this, many efforts were made to create a comprehensive view of tRNA pools. Notably, the advent of high throughput methods to study tRNA levels has provided a greater understanding of tRNA landscapes in cells under different conditions [18][19][20][21][22]. A microarray-based approach has shown that tRNA pools differ among tissues in humans [23] and that there is a significant correlation between relative tRNA abundance and codon usage of highly expressed, tissue-specific genes [23].…”

“…Codon content of a translatome is one of the factors contributing to the large variability and codon-dependent heterogeneity in ribosome elongation rates. Indeed, indirect estimates of ribosome dwell times obtained from yeast and mouse liver ribosome profiling datasets have shown that ribosome dwell times, that is the time spent by a ribosome on a specific position on a transcript, are strongly codon-specific [ 18 , 37 , 38 ]. The suggestion that frequently used codons are translated faster is frequent in the literature, in many organisms.…”

“…While there is more evidence of a relation between codon usage and ribosome occupancy in yeast, a similar relationship does not seem to be found in higher eukaryotes [ 42 ]. This was also reiterated using ribosome dwell time analysis on ribosome profiling data [ 18 ]. There was a strong correlation between dwell time and codon usage in yeast cells and this did not seem to be the case in mice.…”

“…The majority of these inhibitory codons involve wobble base-pairing leading to poor elongation. Dwell times could be influenced by codon pairs in mouse liver tissue and codon pair dwell times were found to be stable across the feeding/fasting cycle [ 18 ]. Another factor that influences translation elongation rates is amino acid composition of the peptide being synthesized.…”

“…Recently, a more detailed account of the inhibitory pair effect revealed that these codon pairs cause the ribosome to stall with an empty A-site which is caused by an alteration in the structure of the mRNA inside the decoding centre, creating an aberrant structure that precludes A-site tRNA accommodation [ 67 ]. It is so far not clear if this inhibitory pair effect is also present in mammalian cells; however, differences in elongation rate for certain codon pairs have been described in mammalian tissue [ 18 ].…”