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bioRxiv · 10.1101/2025.08.28.672766

Structural insights into YheS-mediated release of SecM-arrested ribosome.

Iso, K.·Ikeda, T.·Yamasaki, K.·Ando, Y.·Sano, F. K.·Furuta, T.·Taguchi, H.·Nureki, O.·Chadani, Y.·Itoh, Y.
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Abstract

ATPase-binding cassette subfamily F (ABCF) proteins interact with the ribosome to resolve translation defects near the peptidyl-transferase center, induced by ribosome-targeting antibiotics or "hard-to-translate" nascent peptides. In Escherichia coli, four ABCF proteins resolve the translation of distinct problematic sequences, but their molecular mechanisms remain unclear. Here, we present a 2.8-[A] cryo-EM structure of the SecM-stalled ribosome in complex with an ATPase-deficient mutant of YheS, an ABCF protein that releases ribosomes stalled during the translation of SecM, a representative ribosome-arresting peptide. YheS is bound to the E-site and relocates the P-site tRNA (P-tRNA) by displacing its CCA-end. Notably, the density of the SecM nascent chain mostly disappeared upon YheS binding. Molecular dynamics simulations support that the P-tRNA relocation generates a pulling force that disrupts key intratunnel interactions essential for arrest. This mechanism is functionally analogous to, yet mechanistically distinct from, the translocon-mediated external pulling force for SecM release. TeaserThe release mechanism of the SecM-arrested ribosome by the ABCF protein YheS was elucidated by structure-based analyses.

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Iso, K., Ikeda, T., Yamasaki, K., Ando, Y., Sano, F. K., Furuta, T., Taguchi, H., Nureki, O., Chadani, Y., Itoh, Y.. 2025-08-30. Structural insights into YheS-mediated release of SecM-arrested ribosome.. https://doi.org/10.1101/2025.08.28.672766

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