Site-specific deubiquitination of ribosomal proteins by the G3BP1-USP10 complex determines the fate of stalled ribosomes

The stalling of ribosomes at aberrant mRNAs triggers multiple molecular processes coordinating the degradation and/or recycling of its constituents. These processes include ribosome quality control (RQC) to eliminate nascent polypeptides1,2, aberrant mRNA decay3,4, subunit dissociation of stalled ribosomes5,6, and recycling of site-specifically ubiquitinated 40S subunits7-10. Here, we characterized the mRNA-bound heterodimeric complex formed between a member of the G3BP1 family of RNA-binding proteins and the deubiquitinase USP10 in site-specific deubiquitination of monoubiquitinated RPS2, RPS3, and RPS10 and in aberrant mRNA decay present at stalled ribosomes. Knockout (KO) of either USP10 or the G3BP1 protein family dramatically increased 40S ribosomal subunit degradation and imbalanced ribosomal subunit stoichiometry with 60S in excess, all of which was rescued through lysine-mutagenesis of RPS3 mutagenesis preventing monoubiquitination. KO of ZNF598, the E3 ubiquitin ligase required for sensing of stalled ribosomes at aberrant mRNAs8-11, eliminated RPS10 monoubiquitination and markedly reduced RPS2 and RPS3 monoubiquitination in USP10-KO cells, furthermore implicating RPS2 and RPS3 monoubiquitination downstream of collision-independent ribosome stalling. Our results support a model, in which mRNA-bound G3BP1-family-USP10 complexes facilitate aberrant mRNA decay at stalled ribosomes while they prevent lysosomal degradation of stalled 40S ribosomal subunits by site-specific deubiquitination.