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

Ajeet K Sharma,Pietro Sormanni,Günter Kramer,Edward P O’Brien,Nabeel Ahmed,Ulrike A Friedrich,Prajwal Ciryam,Tamir Tuller

doi:10.1371/journal.pcbi.1007070

Abstract

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.

Highlights

Translation-associated rates influence in vivo protein abundance, structure and function
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

Summary

Introduction

Translation-associated rates influence in vivo protein abundance, structure and function. The ribosome synthesizes a protein in three steps namely initiation, elongation, and termination [1,2,3]. The ribosome moves along the mRNA transcript decoding individual codons and adding residues to the growing nascent chain. The initiation and elongation phases of translation contribute to protein levels inside a cell; alteration of their rates can cause protein abundance to vary by up to five orders of magnitude [6,7,8], and alter protein structure and function [9]. Termination does not influence the cellular concentration of proteins as it is not a rate limiting step [10]. Knowledge of translation initiation and codon translation rates are important to understand the regulation of gene expression

Methods

Results

Discussion

Conclusion