A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data

Analysis methods based on simulations and optimization have been previously developed to estimate relative translation rates from next-generation sequencing data. Translation involves molecules and chemical reactions, hence bioinformatics methods consistent with the laws of chemistry and physics are more likely to produce accurate results. Here, we derive simple equations based on chemical kinetic principles to measure the translation-initiation rate, transcriptome-wide elongation rate, and individual codon translation rates from ribosome profiling experiments. Our methods reproduce the known rates from ribosome profiles generated from detailed simulations of translation. By applying our methods to data from S. cerevisiae and mouse embryonic stem cells, we find that the extracted rates reproduce expected correlations with various molecular properties, and we also find that mouse embryonic stem cells have a global translation speed of 5.2 AA/s, in agreement with previous reports that used other approaches. Our analysis further reveals that a codon can exhibit up to 26-fold variability in its translation rate depending upon its context within a transcript. This broad distribution means that the average translation rate of a codon is not representative of the rate at which most instances of that codon are translated, and it suggests that translational regulation might be used by cells to a greater degree than previously thought. Author summary The process of translating the genetic information encoded in an mRNA molecule to a protein is crucial to cellular life and plays a role in regulating gene expression. The translation initiation rate of a transcript is a direct measure of the rate of protein synthesis and is the key kinetic parameter defining translational control of the gene's expression. Translation rates of individual codons play a considerable role in coordinating co-translational processes like protein folding and protein secretion and thus contribute to the proper functioning of the encoded protein. Direct measurement of these rates in vivo is nontrivial and recent next generation sequencing methods like ribosome profiling offer an opportunity to quantify these rates for the entire translatome. In this study, we develop chemical kinetic models to measure absolute rates and quantify the influence of different molecular factors in shaping the variability of these rates at codon resolution. These new analysis methods are significant because they allow scientists to measure absolute rates of translation from Next-Generation Sequencing data, provide analysis tools rooted in the physical sciences rather than heuristic or ad hoc approaches, and allow for the quantitative, rather than qualitative study of translation kinetics.