1. Biochemistry and Chemical Biology
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Measurement of average decoding rates of the 61 sense codons in vivo

  1. Justin Gardin
  2. Rukhsana Yeasmin
  3. Alisa Yurovsky
  4. Ying Cai
  5. Steve Skiena
  6. Bruce Futcher  Is a corresponding author
  1. Stony Brook University, United States
Research Article
  • Cited 114
  • Views 4,822
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Cite this article as: eLife 2014;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. Here, 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.

Article and author information

Author details

  1. Justin Gardin

    Stony Brook University, Stony Brook, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Rukhsana Yeasmin

    Stony Brook University, Stony Brook, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Alisa Yurovsky

    Stony Brook University, Stony Brook, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Ying Cai

    Stony Brook University, Stony Brook, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Steve Skiena

    Stony Brook University, Stony Brook, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Bruce Futcher

    Stony Brook University, Stony Brook, United States
    For correspondence
    bfutcher@gmail.com
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. Nahum Sonenberg, McGill University, Canada

Publication history

  1. Received: June 19, 2014
  2. Accepted: October 24, 2014
  3. Accepted Manuscript published: October 27, 2014 (version 1)
  4. Version of Record published: December 3, 2014 (version 2)

Copyright

© 2014, Gardin et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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