Mechanism of ribosome rescue by alternative ribosome-rescue factor B

Kai-Hsin Chan, Valentyn Petrychenko, Claudia Mueller, Cristina Maracci, Wolf Holtkamp, Daniel N. Wilson, Niels Fischer () and Marina V. Rodnina ()
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Kai-Hsin Chan: Max Planck Institute for Biophysical Chemistry
Valentyn Petrychenko: Max Planck Institute for Biophysical Chemistry
Claudia Mueller: University of Hamburg
Cristina Maracci: Max Planck Institute for Biophysical Chemistry
Wolf Holtkamp: Max Planck Institute for Biophysical Chemistry
Daniel N. Wilson: University of Hamburg
Niels Fischer: Max Planck Institute for Biophysical Chemistry
Marina V. Rodnina: Max Planck Institute for Biophysical Chemistry

Nature Communications, 2020, vol. 11, issue 1, 1-11

Abstract: Abstract Alternative ribosome-rescue factor B (ArfB) rescues ribosomes stalled on non-stop mRNAs by releasing the nascent polypeptide from the peptidyl-tRNA. By rapid kinetics we show that ArfB selects ribosomes stalled on short truncated mRNAs, rather than on longer mRNAs mimicking pausing on rare codon clusters. In combination with cryo-electron microscopy we dissect the multistep rescue pathway of ArfB, which first binds to ribosomes very rapidly regardless of the mRNA length. The selectivity for shorter mRNAs arises from the subsequent slow engagement step, as it requires longer mRNA to shift to enable ArfB binding. Engagement results in specific interactions of the ArfB C-terminal domain with the mRNA entry channel, which activates peptidyl-tRNA hydrolysis by the N-terminal domain. These data reveal how protein dynamics translate into specificity of substrate recognition and provide insights into the action of a putative rescue factor in mitochondria.

Date: 2020
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DOI: 10.1038/s41467-020-17853-7

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