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Characterization of a small tRNA-binding protein that interacts with the archaeal proteasome complex

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Date
11/07/2022
Author
Hogrel, Gaëlle
Marino-Puertas, Laura
Laurent, Sébastien
Ibrahim, Ziad
Covès, Jacques
Girard, Eric
Gabel, Frank
Fenel, Daphna
Daugeron, Marie-Claire
Clouet-d’Orval, Béatrice
Basta, Tamara
Flament, Didier
Franzetti, Bruno
Keywords
Proteasome
Ribosome-associated quality control
Protein-protein interaction
Archaea
tRNA binding
OB-fold
QH301 Biology
QH426 Genetics
NDAS
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Abstract
The proteasome system allows the elimination of functional or structurally impaired proteins. This includes the degradation of nascent peptides. In Archaea, how the proteasome complex interacts with the translational machinery remains to be described. Here, we characterised a small orphan protein, Q9UZY3 (Uniprot ID) conserved in Thermococcales. The protein was identified in native pull-down experiments using the proteasome regulatory complex (PAN) as bait. X-ray crystallography and SAXS experiments revealed that the protein is monomeric and adopts a β-barrel core structure with an Oligonucleotide/oligosaccharide-Binding (OB) fold, typically found in translation elongation factors. Mobility shift experiment showed that Q9UZY3 displays tRNA binding properties. Pull-downs, co-immunoprecipitation and ITC studies revealed that Q9UZY3 interacts in vitro with PAN. Native pull-downs and proteomic analysis using different versions of Q9UZY3 showed that the protein interacts with the assembled PAN-20S proteasome machinery in Pyrococcus abyssi cellular extracts. The protein was therefore named Pbp11, for Proteasome Binding Protein of 11 kDa. Interestingly, the interaction network of Pbp11 also includes ribosomal proteins, tRNA processing enzymes and exosome subunits dependent on Pbp11's N-terminal domain that was found to be essential for tRNA binding. Together these data suggest that Pbp11 participates in an interface between the proteasome and the translational machinery.
Citation
Hogrel , G , Marino-Puertas , L , Laurent , S , Ibrahim , Z , Covès , J , Girard , E , Gabel , F , Fenel , D , Daugeron , M-C , Clouet-d’Orval , B , Basta , T , Flament , D & Franzetti , B 2022 , ' Characterization of a small tRNA-binding protein that interacts with the archaeal proteasome complex ' , Molecular Microbiology , vol. 118 , no. 1-2 , pp. 16-29 . https://doi.org/10.1111/mmi.14948
Publication
Molecular Microbiology
Status
Peer reviewed
DOI
https://doi.org/10.1111/mmi.14948
ISSN
0950-382X
Type
Journal article
Rights
Copyright © 2022 The Authors. Molecular Microbiology published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
Description
Authors acknowledge financial support from the French Agence Nationale de la Recherche (grant [ANR-18-CE11-0018-01] to B.F. and [ANR-16-CE12-0016-01] to B.C.O). This work used the platforms of the Grenoble Instruct-ERIC Centre (ISBG: UMS3518 CNRS-CEA-UGA-EMBL) with support from FRISBI (ANR-10-INBS-05-02) and GRAL, a project of the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003) within the Grenoble Partnership for Structural Biology. The IBS Electron Microscope facility is supported by the Auvergne Rhône-Alpes Region, the Fonds Feder, the Fondation pour la Recherche Médicale and GIS-IBiSA.
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URI
http://hdl.handle.net/10023/25552

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