Essential structural elements in tRNAPro for EF-P-mediated alleviation of translation stalling

Takayuki Katoh (), Ingo Wohlgemuth, Masanobu Nagano, Marina V. Rodnina and Hiroaki Suga ()
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Takayuki Katoh: Graduate School of Science, The University of Tokyo
Ingo Wohlgemuth: Max Planck Institute for Biophysical Chemistry
Masanobu Nagano: Graduate School of Science, The University of Tokyo
Marina V. Rodnina: Max Planck Institute for Biophysical Chemistry
Hiroaki Suga: Graduate School of Science, The University of Tokyo

Nature Communications, 2016, vol. 7, issue 1, 1-12

Abstract: Abstract The ribosome stalls on translation of polyproline sequences due to inefficient peptide bond formation between consecutive prolines. The translation factor EF-P is able to alleviate this stalling by accelerating Pro-Pro formation. However, the mechanism by which EF-P recognizes the stalled complexes and accelerates peptide bond formation is not known. Here, we use genetic code reprogramming through a flexible in-vitro translation (FIT) system to investigate how mutations in tRNAPro affect EF-P function. We show that the 9-nt D-loop closed by the stable D-stem sequence in tRNAPro is a crucial recognition determinant for EF-P. Such D-arm structures are shared only among the tRNAPro isoacceptors and tRNAfMet in Escherichia coli, and the D-arm of tRNAfMet is essential for EF-P-induced acceleration of fMet–puromycin formation. Thus, the activity of EF-P is controlled by recognition elements in the tRNA D-arm.

Date: 2016
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DOI: 10.1038/ncomms11657

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