The SecM arrest peptide traps a pre-peptide bond formation state of the ribosome

Felix Gersteuer, Martino Morici, Sara Gabrielli, Keigo Fujiwara, Haaris A. Safdari, Helge Paternoga, Lars V. Bock, Shinobu Chiba and Daniel N. Wilson ()
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Felix Gersteuer: University of Hamburg
Martino Morici: University of Hamburg
Sara Gabrielli: Max Planck Institute for Multidisciplinary Sciences
Keigo Fujiwara: Kyoto Sangyo University, Kamigamo, Motoyama
Haaris A. Safdari: University of Hamburg
Helge Paternoga: University of Hamburg
Lars V. Bock: Max Planck Institute for Multidisciplinary Sciences
Shinobu Chiba: Kyoto Sangyo University, Kamigamo, Motoyama
Daniel N. Wilson: University of Hamburg

Nature Communications, 2024, vol. 15, issue 1, 1-16

Abstract: Abstract Nascent polypeptide chains can induce translational stalling to regulate gene expression. This is exemplified by the E. coli secretion monitor (SecM) arrest peptide that induces translational stalling to regulate expression of the downstream encoded SecA, an ATPase that co-operates with the SecYEG translocon to facilitate insertion of proteins into or through the cytoplasmic membrane. Here we present the structure of a ribosome stalled during translation of the full-length E. coli SecM arrest peptide at 2.0 Å resolution. The structure reveals that SecM arrests translation by stabilizing the Pro-tRNA in the A-site, but in a manner that prevents peptide bond formation with the SecM-peptidyl-tRNA in the P-site. By employing molecular dynamic simulations, we also provide insight into how a pulling force on the SecM nascent chain can relieve the SecM-mediated translation arrest. Collectively, the mechanisms determined here for SecM arrest and relief are also likely to be applicable for a variety of other arrest peptides that regulate components of the protein localization machinery identified across a wide range of bacteria lineages.

Date: 2024
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DOI: 10.1038/s41467-024-46762-2

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