The E3 ubiquitin ligase and RNA-binding protein ZNF598 commences ribosome quality control of premature polyadenylated mRNAs

Cryptic polyadenylation within coding sequences or after incomplete removal of introns during splicing produces aberrant transcripts that lack in-frame stop codons and are subject to ribosome-associated quality control (RQC). Premature polyadenylated mRNAs trigger ribosome stalling and activation of the RQC pathway, leading to degradation of the aberrant mRNA and nascent polypeptide, ribosome disassembly and recycling of its subunits. While ribosomal subunit dissociation and nascent peptide degradation are well-understood, the molecular sensors of aberrant mRNAs and their mechanism of action, especially in mammalian cells, remain largely unknown. In yeast the E3 ubiquitin ligase Hel2 has been implicated in facilitating RQC. Here, we studied its human ortholog, Zinc Finger Protein 598 (ZNF598) using PAR-CLIP and revealed crosslinking to tRNAs, mRNAs, and rRNAs, thereby placing the protein on translating ribosomes. Crosslinked reads originating from AAA-decoding tRNALys(UUU) were 10-fold enriched over its cellular abundance, and poly-lysine encoded by poly(AAA), but not poly(AAG), induced RQC in a ZNF598-dependent manner. Sensing of premature polyA tails by ZNF598 triggered ubiquitination of the ribosomal proteins RPS3A, RPS10, and RPS20 requiring the E2 ubiquitin ligase UBE2D3 and thereby initiating RQC. Considering that human coding sequences are devoid of >4 repeated AAA codons, sensing of premature polyA by a specialized RNA-binding protein is a novel nucleic-acid-based surveillance mechanism for engendering RQC.