Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates

Abstract

Although protein synthesis dynamics has been studied both with theoretical models and by profiling ribosome footprints, the determinants of ribosome flux along open reading frames (ORFs) are not fully understood. Combining measurements of protein synthesis rate with ribosome footprinting data, we here inferred translation initiation and elongation rates for over a 1,000 ORFs in exponentially growing wild-type yeast cells. We found that the amino acid composition of synthesized proteins is as important a determinant of translation elongation rate as parameters related to codon and transfer RNA (tRNA) adaptation. We did not find evidence of ribosome collisions curbing the protein output of yeast transcripts, either in high translation conditions associated with exponential growth, or in strains in which deletion of individual ribosomal protein (RP) genes leads to globally increased or decreased translation. Slow translation elongation is characteristic of RP-encoding transcripts, which have markedly lower protein output compared with other transcripts with equally high ribosome densities.

Inferring efficiency of translation initiation and elongation from ribosome profiling

“…We base our method on a well-established stochastic model for mRNA translation, the totally asymmetric simple exclusion process (TASEP) 11,28 . Over the years, the model has been improved in many ways to better match real translation 29, 30 and has been repeatedly used to interpret experimental data 16,18,24,[31][32][33][34] .…”

“…quantification such as RNA-seq with spike-ins 1 and pulsed stable isotope labelling of amino acids 18 . Future developments of NEAR will include these data to obtain a more detailed view on translation dynamics.…”

“…On the one hand, this definition implicitly assumes that ribosome interference is absent. On the other hand, the extent to which ribosome queuing affects translation has been frequently debated (Li, 2015;Diament et al, 2018;Riba et al, 2019).…”

“…However, a large body of work based on mathematical modelling of ribosome dynamics suggests that the protein synthesis rate is negatively affected by increased ribosome density due to ribosome collisions [11][12][13] . To which extent ribosome collisions can be found using ribosome profiling has been an active topic of research [14][15][16][17][18] One of the goals of ribosome profiling is to understand how the elongation rate along the transcript depends on the choice of codons. Codon elongation rates are usually estimated assuming that the ribosome density at codon i is proportional to the ribosome's dwell time on that particular codon 15,16,[19][20][21][22][23][24] ; this assumption follows from the conservation of the ribosome current assuming no ribosome drop-off.…”

Inferring translational heterogeneity from ribosome profiling data

“…Specific sequence motifs can stall translating ribosomes such as select codon pairings (19), or successive proline residues that require the specialized translation factor EF-P for their translation (20). Moreover, these determinants of translation elongation kinetics (21)(22)(23) are selectively placed along mRNA and protein sequences to prevent ribosome traffic jams and overall optimize translation (24)(25)(26).…”