Accurate design of translational output by a neural network model of ribosome distribution

Nat Struct Mol Biol. 2018 Jul;25(7):577-582. doi: 10.1038/s41594-018-0080-2. Epub 2018 Jul 2.


Synonymous codon choice can have dramatic effects on ribosome speed and protein expression. Ribosome profiling experiments have underscored that ribosomes do not move uniformly along mRNAs. Here, we have modeled this variation in translation elongation by using a feed-forward neural network to predict the ribosome density at each codon as a function of its sequence neighborhood. Our approach revealed sequence features affecting translation elongation and characterized large technical biases in ribosome profiling. We applied our model to design synonymous variants of a fluorescent protein spanning the range of translation speeds predicted with our model. Levels of the fluorescent protein in budding yeast closely tracked the predicted translation speeds across their full range. We therefore demonstrate that our model captures information determining translation dynamics in vivo; that this information can be harnessed to design coding sequences; and that control of translation elongation alone is sufficient to produce large quantitative differences in protein output.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Codon / genetics
  • Genes, Fungal
  • Kinetics
  • Luminescent Proteins / genetics
  • Luminescent Proteins / metabolism
  • Models, Biological*
  • Models, Genetic
  • Neural Networks, Computer
  • Peptide Chain Elongation, Translational
  • Protein Biosynthesis*
  • RNA Stability
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Ribosomes / genetics*
  • Ribosomes / metabolism*
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism


  • Bacterial Proteins
  • Codon
  • Luminescent Proteins
  • RNA, Messenger
  • Recombinant Proteins
  • citrine protein, bacteria