Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate.
Bottom Line: Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation elongation rate, but recent genome-wide ribosome profiling experiments have not observed significant influence of either on translation efficiency.Here we provide evidence that this results from an inherent trade-off between these factors.The trade-off between secondary structure and tRNA-concentration based codon choice allows for compensation of their independent effects on translation, helping to smooth overall translational speed and reducing the chance of potentially detrimental points of excessively slow or fast ribosome movement.
Affiliation: DSM Biotechnology Center, P.O. Box 1, 2600 MA Delft, The Netherlands email@example.com.Show MeSH
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Mentions: Finally we assessed the amino acid composition of high and low structured regions (Supplementary Figure S4). We found a slight enrichment of some amino acids in high or low structured regions. Alanine was commonly found in high structured regions and lysine, asparagine, phenylalanine and isoleucine in low structured regions across both organisms. This may be partially due to the sequences of the codons encoding each amino acid. For example, amino acids found in high-structured regions are coded for by codons that are G/C rich, while amino acids found in low-structured regions are coded for by A/T rich codons (Figure 4).
Affiliation: DSM Biotechnology Center, P.O. Box 1, 2600 MA Delft, The Netherlands firstname.lastname@example.org.