Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

Abstract
Article and author information
Metrics

Abstract

During translation elongation, the ribosome ratchets along its mRNA template, incorporating each new amino acid and translocating from one codon to the next. The elongation cycle requires dramatic structural rearrangements of the ribosome. We show here that deep sequencing of ribosome-protected mRNA fragments reveals not only the position of each ribosome but also, unexpectedly, its particular stage of the elongation cycle. Sequencing reveals two distinct populations of ribosome footprints, 28-30 nucleotides and 20-22 nucleotides long, representing translating ribosomes in distinct states, differentially stabilized by specific elongation inhibitors. We find that the balance of small and large footprints varies by codon and is correlated with translation speed. The ability to visualize conformational changes in the ribosome during elongation, at single-codon resolution, provides a new way to study the detailed kinetics of translation and a new probe with which to identify the factors that affect each step in the elongation cycle.

Article and author information

Author details

Liana F Lareau

California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States

For correspondence
lareau@berkeley.edu

Competing interests
The authors declare that no competing interests exist.
Dustin H Hite

Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States

Competing interests
The authors declare that no competing interests exist.
Gregory J Hogan

Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States

Competing interests
The authors declare that no competing interests exist.
Patrick O Brown

Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States

Competing interests
The authors declare that no competing interests exist.

Copyright

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.