The role of tRNA and ribosome competition in coupling the expression of different mRNAs in Saccharomyces cerevisiae

Abstract

Protein synthesis translates information from messenger RNAs into functional proteomes. Because of the finite nature of the resources required by the translational machinery, both the overall protein synthesis activity of a cell and activity on individual mRNAs are controlled by the allocation of limiting resources. Upon introduction of heterologous sequences into an organism—for example for the purposes of bioprocessing or synthetic biology—limiting resources may also become overstretched, thus negatively affecting both endogenous and heterologous gene expression. In this study, we present a mean-field model of translation in Saccharomyces cerevisiae for the investigation of two particular translational resources, namely ribosomes and aminoacylated tRNAs. We firstly use comparisons of experiments with heterologous sequences and simulations of the same conditions to calibrate our model, and then analyse the behaviour of the translational system in yeast upon introduction of different types of heterologous sequences. Our main findings are that: competition for ribosomes, rather than tRNAs, limits global translation in this organism; that tRNA aminoacylation levels exert, at most, weak control over translational activity; and that decoding speeds and codon adaptation exert strong control over local (mRNA specific) translation rates.

Charting the dynamics of translation

“…Consequently, the elongation time depends primarily on the ratio of cognate to nearcognates rather than on the absolute number of cognates. This model of cognate/near-cognate interaction has recently been corroborated experimentally (Chu et al, 2011).…”

“…Even though each near-cognate occupies the ribosome only for a short time, collectively they cause a major bottleneck for translation as a whole (Chu et al, 2011). Consequently, the elongation time depends primarily on the ratio of cognate to nearcognates rather than on the absolute number of cognates.…”

“…Given that ribosomes are metabolically costly (Chu et al, 2011), it would seem natural to assume that there is a strong adaptive pressure towards faster mRNAs.…”

“…For one, the original authors based their model on careful measurements of the interactions between cognate and near-cognate tRNA. Then, more recently Chu et al (2011) showed for Firefly Luciferase in a yeast host system that simulations based on the Gromadski-Rodnina model can to a very good degree of accuracy predict the effect of synonymous codon substitutions and changes in the aa-tRNA abundance on the overall expression rate. This corroborates the Gromadski-Rodnina model.…”

The Herpes Simplex Virus 1 Virion Host Shutoff Protein Enhances Translation of Viral Late mRNAs by Preventing mRNA Overload

“…Recent studies in yeast stress that maintaining proper mRNA levels is vital for a cell by demonstrating that regulation of transcription, translation, and mRNA decay are linked (55,56). Furthermore, computational modeling in yeast suggests that ribosomes are the limiting component of the translation apparatus (57)(58)(59). This configuration is thought to combine efficient use of resources with flexibility in terms of changes in expression levels.…”