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

• Published in: Molecular microbiology Vol. 118; no. 1-2; pp. 16 - 29
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01-07-2022; Wiley
• Series: Bacterial macromolecular machineries
• Subjects: Archaea; Baits; Biochemistry, Molecular Biology; Calorimetry; Crystallography; Electrophoretic mobility; Elongation; Immunoprecipitation; Life Sciences; Nucleotidase; OB‐fold; Oligonucleotides; Oligosaccharides; Peptides; proteasome; Proteasomes; Proteins; protein–protein interaction; Proteomics; Ribonucleic acid; Ribosomal proteins; ribosome‐associated quality control; RNA; Structural Biology; Titration; Titration calorimetry; Transfer RNA; Translation; Translation elongation; tRNA; tRNA binding; protein-protein interaction; ribosome-associated quality control; tRNA binding; OB-fold; Archaea; Proteasome; proteasome
• ISSN: 0950-382X; 1365-2958
• DOI: 10.1111/mmi.14948

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.
Partner of the archaeal proteasome PAN:20S complex in Thermococcales, Pbp11 directly interacts with the unfoldase PAN. From the cellular extract, Pbp11 pulls down the proteasome system and other macromolecular assemblies related to RNA processes. These last interactions are dependent on the presence of the flexible N‐terminal tail of Pbp11, a key feature of Pbp11 to bind transfer ribonucleic acids. Pbp11 becomes an interesting candidate to study tight connections between these nanomachines in the context of extremophilic Archaea.