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

Type Article
Date 2022-07
Language English
Author(s) Hogrel Gaëlle1, Marino‐puertas Laura1, Laurent Sebastien2, Ibrahim Ziad1, Covès Jacques1, Girard Eric1, Gabel Frank1, Fenel Daphna1, Daugeron Marie‐claire3, Clouet‐d'Orval Béatrice4, Basta Tamara3, Flament DidierORCID2, Franzetti BrunoORCID1
Affiliation(s) 1 : CNRS, CEA, IBS Univ Grenoble Alpes Grenoble, France
2 : Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F 29280, Plouzané, France
3 : Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS Université Paris‐Saclay Gif‐sur‐Yvette, France
4 : Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI) Université de Toulouse, CNRS, Université Paul Sabatier Toulouse, France
Source Molecular Microbiology (0950-382X) (Wiley), 2022-07 , Vol. 118 , N. 1-2 , P. 16-29
DOI 10.1111/mmi.14948
Note Virtual Issue: Bacterial macromolecular machineries
Keyword(s) Archaea, OB-fold, proteasome, protein-protein interaction, ribosome-associated quality control, tRNA binding

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 characterized a small orphan protein, Q9UZY3 (UniProt ID), conserved in Thermococcales. The protein was identified in native pull-down experiments using the proteasome regulatory complex (proteasome-activating nucleotidase [PAN]) as bait. X-ray crystallography and small-angle X-ray scattering 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 transfer ribonucleic acid (tRNA)-binding properties. Pull-downs, co-immunoprecipitation and isothermal titration calorimetry (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 (Pa) 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.

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Hogrel Gaëlle, Marino‐puertas Laura, Laurent Sebastien, Ibrahim Ziad, Covès Jacques, Girard Eric, Gabel Frank, Fenel Daphna, Daugeron Marie‐claire, Clouet‐d'Orval Béatrice, Basta Tamara, Flament Didier, Franzetti Bruno (2022). Characterization of a small tRNA ‐binding protein that interacts with the archaeal proteasome complex. Molecular Microbiology, 118(1-2), 16-29. Publisher's official version : , Open Access version :