Novel Protein and Coding Determinants of Protein Biosynthesis Speed and Accuracy: The Role of Scp160p in Translational Efficiency and Fidelity of Suboptimally tRNA Re-Use Encoded Yeast mRNAs

Abstract

In balancing accuracy versus speed in protein synthesis, numerous parameters serve to increase translational efficiency by optimizing the binding kinetics of translation factors to the ribosome. On the one hand, use of frequent codons, recognized by higher-abundance tRNAs, correlates with lower mistranslation rates. On the other hand, autocorrelation, the re-use of tRNAs by different synonymous codons, is a proven predictor of translational velocity. Factors that limit diffusion of ribosome interacting molecules, e.g. aminoacyl tRNA synthetases, can also contribute to higher efficiency. Additionally, accumulation of positively charged amino acids in the peptide exit tunnel is a reliable predictor of translational stalling. The budding yeast multi-KH domain RNA-binding protein Scp160p binds to over 1000 mRNAs as well as polyribosomes, and its mammalian homolog vigilin binds tRNAs and translation elongation factor EF1alpha. Despite its implication in translation, studies on Scp160p's molecular function are lacking to date. Our lab previously applied translational profiling approaches and demonstrated that the association of a specific subset of mRNAs with ribosomes or heavy polysomes depends on Scp160p. Interaction of Scp160p with these mRNAs requires the conserved K homology (KH) domains 13 and 14. Transfer RNA pairing index (TPI) analysis of Scp160p target mRNAs had indicated a higher degree of consecutive use of iso-decoding codons in more depletion-affected messages. As shown previously for one target mRNA encoding the glycoprotein Pry3p, Scp160p depletion results in translational downregulation but increased association with polysomes, suggesting that it is required for efficient translation elongation. In my study, depletion of Scp160p decreased the relative abundance of ribosome-associated tRNAs whose codons show low potential for autocorrelation on depletion-affected mRNAs. Conversely, tRNAs with highly autocorrelated codons in mRNAs are less impaired. The data indicates that Scp160p might increase the efficiency of tRNA recharge, or prevent diffusion of discharged tRNAs, both of which were also proposed to be the likely basis for the translational fitness effect of codon autocorrelation. Yeast Scp160p also interacts with Asc1p, the homolog of mammalian RACK1, on the ribosomal small subunit - which in turn has been shown to interact physically with kinases, and genetically with aminoacyl-tRNA synthetases. After analyzing the role of Scp160p and Asc1p in translational efficiency and fidelity in yeast in my study, more insights were gained: scp160Δ and asc1Δ mutants decode stop codons with increased fidelity, consistent with the proteins’ roles in promoting elongation velocity. Loss of Scp160p or Asc1p increases rates of both programmed and nonprogrammed -1 ribosomal frameshifting but not +1 frameshifting, consistent with roles for both these proteins in enhancing elongation speeds. Differential mistranslation of codons for tRNAs with low or high abundances by the respective mutants on the other hand matches their proposed roles in limiting tRNA diffusion and boosting tRNA recycling, respectively. In conjunction with their known physical interactions with other components of the ribosome and trans-acting factors, a biophysical model is presented describing how these two proteins might stabilize polysomes and help to channel tRNAs between successive ribosomes during translation elongation.