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

Nat Commun. 2017 Jul 7:8:16056. doi: 10.1038/ncomms16056.

Abstract

Cryptic polyadenylation within coding sequences (CDS) triggers ribosome-associated quality control (RQC), followed by degradation of the aberrant mRNA and polypeptide, ribosome disassembly and recycling. Although ribosomal subunit dissociation and nascent peptide degradation are well-understood, the molecular sensors of aberrant mRNAs and their mechanism of action remain unknown. We studied the Zinc Finger Protein 598 (ZNF598) using PAR-CLIP and revealed that it cross-links to tRNAs, mRNAs and rRNAs, thereby placing the protein on translating ribosomes. Cross-linked reads originating from AAA-decoding tRNALys(UUU) were 10-fold enriched over its cellular abundance, and poly-lysine encoded by poly(AAA) induced RQC in a ZNF598-dependent manner. Encounter with translated polyA segments by ZNF598 triggered ubiquitination of several ribosomal proteins, requiring the E2 ubiquitin ligase UBE2D3 to initiate RQC. Considering that human CDS are devoid of >4 consecutive AAA codons, sensing of prematurely placed polyA tails by a specialized RNA-binding protein is a novel nucleic-acid-based surveillance mechanism of RQC.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Carrier Proteins / genetics*
  • Carrier Proteins / metabolism
  • Genetic Vectors / chemistry
  • Genetic Vectors / metabolism
  • HEK293 Cells
  • Humans
  • Lentivirus / genetics
  • Lentivirus / metabolism
  • Nucleic Acid Conformation
  • Plasmids / chemistry
  • Plasmids / metabolism
  • Polyadenylation
  • Protein Binding
  • Protein Biosynthesis*
  • RNA Stability
  • RNA, Messenger / chemistry
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism
  • RNA, Ribosomal / chemistry
  • RNA, Ribosomal / genetics
  • RNA, Ribosomal / metabolism
  • RNA, Transfer, Lys / chemistry
  • RNA, Transfer, Lys / genetics*
  • RNA, Transfer, Lys / metabolism
  • Ribosomes / genetics*
  • Ribosomes / metabolism
  • Ubiquitin / genetics
  • Ubiquitin / metabolism
  • Ubiquitin-Protein Ligases / genetics*
  • Ubiquitin-Protein Ligases / metabolism
  • Ubiquitination

Substances

  • Carrier Proteins
  • RNA, Messenger
  • RNA, Ribosomal
  • RNA, Transfer, Lys
  • Ubiquitin
  • ZNF598 protein, human
  • Ubiquitin-Protein Ligases