Measurement of average decoding rates of the 61 sense codons in vivo

Elife. 2014 Oct 27;3:e03735. doi: 10.7554/eLife.03735.

Abstract

Most amino acids can be encoded by several synonymous codons, which are used at unequal frequencies. The significance of unequal codon usage remains unclear. One hypothesis is that frequent codons are translated relatively rapidly. However, there is little direct, in vivo, evidence regarding codon-specific translation rates. In this study, we generate high-coverage data using ribosome profiling in yeast, analyze using a novel algorithm, and deduce events at the A- and P-sites of the ribosome. Different codons are decoded at different rates in the A-site. In general, frequent codons are decoded more quickly than rare codons, and AT-rich codons are decoded more quickly than GC-rich codons. At the P-site, proline is slow in forming peptide bonds. We also apply our algorithm to short footprints from a different conformation of the ribosome and find strong amino acid-specific (not codon-specific) effects that may reflect interactions with the exit tunnel of the ribosome.

Keywords: S. cerevisiae; biochemistry; codon bias; codon usage; decoding; evolutionary biology; genomics; ribosome; synonymous codons; translation.

Publication types

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

MeSH terms

  • Algorithms*
  • Anisomycin / pharmacology
  • Codon / genetics*
  • Dipeptides / metabolism
  • Escherichia coli / drug effects
  • Escherichia coli / genetics
  • Reproducibility of Results
  • Ribosomes / drug effects
  • Ribosomes / genetics
  • Saccharomyces cerevisiae / drug effects
  • Saccharomyces cerevisiae / genetics
  • Serine / deficiency
  • Time Factors

Substances

  • Codon
  • Dipeptides
  • Serine
  • Anisomycin