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 thousand ORFs in exponentially-growing wildtype 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 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 genes leads to globally increased or decreased translation. Slow translation elongation is characteristic of RP-encoding transcripts, which have markedly lower protein output than other transcripts with equally high ribosome densities. Significance StatementAlthough sequencing of ribosome footprints has uncovered new aspects of mRNA translation, the determinants of ribosome flux remain incompletely understood. Combining ribosome footprint data with measurements of protein synthesis rates, we here inferred translation initiation and elongation rates for over a thousand ORFs in yeast strains with varying translation capacity. We found that the translation elongation rate varies up to ~20-fold among yeast transcripts, and is significantly correlated with the rate of translation initiation. Furthermore, the amino acid composition of synthesized proteins impacts the rate of translation elongation to the same extent as measures of codon and tRNA adaptation. Transcripts encoding ribosomal proteins are translated especially slow, having markedly lower protein output than other transcripts with equally high ribosome densities.

Building blocks are synthesized on demand during the yeast cell cycle

“…2E). Recently, Riba et al (23) found that the rate of protein translation can be impacted by amino acid composition of synthesized proteins as much as codon and transfer RNA adaptation. In particular, they show that negatively charged proteins are translated faster than positively charged protein.…”

So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes

“…The less efficient translation initiation may have an essential role in the overall efficiency of the translation process. In yeast, for example, the relative inefficiency of translation of ribosomal proteins was suggested to at least partially stem from the positive charge of their protein products, which may interact more strongly with the negatively charged exit tunnel (Riba et al, 2019). Therefore, TOP elements may coordinate and optimize the rates of translation initiation and elongation to prevent potential collision of ribosomes and premature termination of translation (Racle et al, 2015).…”

Ribosome exit tunnel electrostatics

“…Although the average codon translation rate is rather constant transcriptome wide, estimated at 5.6 amino acid residues per second in eukaryotes, codon translation rates have been shown to vary up to 100-fold across a single transcript [8,9]. Many factors influence translation speeds across a single transcript (mRNA), including differences in cognate, near-cognate and non-cognate tRNA relative abundance, nascentchain charged residues inside the ribosome exit tunnel, mRNA secondary structure, proline residues at either A or P site of the ribosome, steric hindrance between contiguous ribosomes translating the same mRNA molecule, and the finite resource of the ribosome pool available in the cell [10][11][12][13][14][15][16][17][18][19][20][21][22]. The individual contributions of each of the previous factors to the rate of the translation are difficult to assess quantitatively and separately.…”