Causes and effects of N-terminal codon bias in bacterial genes

Science. 2013 Oct 25;342(6157):475-9. doi: 10.1126/science.1241934. Epub 2013 Sep 26.


Most amino acids are encoded by multiple codons, and codon choice has strong effects on protein expression. Rare codons are enriched at the N terminus of genes in most organisms, although the causes and effects of this bias are unclear. Here, we measure expression from >14,000 synthetic reporters in Escherichia coli and show that using N-terminal rare codons instead of common ones increases expression by ~14-fold (median 4-fold). We quantify how individual N-terminal codons affect expression and show that these effects shape the sequence of natural genes. Finally, we demonstrate that reduced RNA structure and not codon rarity itself is responsible for expression increases. Our observations resolve controversies over the roles of N-terminal codon bias and suggest a straightforward method for optimizing heterologous gene expression in bacteria.

Publication types

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

MeSH terms

  • Codon, Terminator / chemistry
  • Codon, Terminator / genetics*
  • Escherichia coli / genetics*
  • Gene Expression Regulation, Bacterial*
  • Gene Library
  • Genes, Bacterial*
  • Genes, Reporter*
  • Nucleic Acid Conformation
  • Protein Biosynthesis / genetics
  • Recombinant Proteins / biosynthesis*
  • Recombinant Proteins / genetics


  • Codon, Terminator
  • Recombinant Proteins