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

Ajeet K. Sharma, Pietro Sormanni, Nabeel Ahmed, Prajwal Ciryam, Ulrike A. Friedrich, Günter Kramer, Edward P. O'Brien

Research output: Contribution to journalArticle

1 Citation (Scopus)

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.

Original languageEnglish (US)
Article numbere1007070
JournalPLoS computational biology
Volume15
Issue number5
DOIs
StatePublished - Jan 1 2019

Fingerprint

Chemical Kinetics
Elongation
Profiling
ribosomes
Stem cells
Ribosomes
Reaction kinetics
Codon
translation (genetics)
kinetics
Bioinformatics
codons
Chemical reactions
Physics
Molecules
Stem Cells
embryonic stem cells
Computational Biology
Transcriptome
Saccharomyces cerevisiae

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Modeling and Simulation
  • Ecology
  • Molecular Biology
  • Genetics
  • Cellular and Molecular Neuroscience
  • Computational Theory and Mathematics

Cite this

Sharma, Ajeet K. ; Sormanni, Pietro ; Ahmed, Nabeel ; Ciryam, Prajwal ; Friedrich, Ulrike A. ; Kramer, Günter ; O'Brien, Edward P. / A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data. In: PLoS computational biology. 2019 ; Vol. 15, No. 5.
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A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data. / Sharma, Ajeet K.; Sormanni, Pietro; Ahmed, Nabeel; Ciryam, Prajwal; Friedrich, Ulrike A.; Kramer, Günter; O'Brien, Edward P.

In: PLoS computational biology, Vol. 15, No. 5, e1007070, 01.01.2019.

Research output: Contribution to journalArticle

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