Mechanism of ribosome stalling during translation of a poly(A) tail

• Published in: Nature structural & molecular biology Vol. 26; no. 12; pp. 1132 - 1140
• Main Authors: Chandrasekaran, Viswanathan, Juszkiewicz, Szymon, Choi, Junhong, Puglisi, Joseph D., Brown, Alan, Shao, Sichen, Ramakrishnan, V., Hegde, Ramanujan S.
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.12.2019; Nature Publishing Group
• Subjects: 631/337/574/1789; 631/45/500; 631/535/1258/1259; Biochemistry; Biodegradation; Biological Microscopy; Biomedical and Life Sciences; Damage detection; Decoding; Elongation; Eukaryotes; Genetic translation; HEK293 Cells; Homeostasis; Humans; Life Sciences; Lysine; Membrane Biology; Messenger RNA; Models, Molecular; mRNA turnover; Nucleic Acid Conformation; Peptides - chemistry; Peptides - metabolism; Poly A - chemistry; Poly A - metabolism; Polyadenine; Polyadenylation; Polylysine - chemistry; Polylysine - metabolism; Protein Biosynthesis; Protein research; Protein Structure; Proteolysis; Quality control; Ribosomal RNA; Ribosomes; Ribosomes - chemistry; Ribosomes - metabolism; RNA Stability; RNA, Messenger - chemistry; RNA, Messenger - metabolism; RNA, Transfer - chemistry; RNA, Transfer - metabolism; RNA, Transfer, Amino Acyl - chemistry; RNA, Transfer, Amino Acyl - metabolism; rRNA; Stalling; Structure; Transfer RNA; tRNA; United Kingdom
• ISSN: 1545-9993; 1545-9985
• DOI: 10.1038/s41594-019-0331-x

Faulty or damaged messenger RNAs are detected by the cell when translating ribosomes stall during elongation and trigger pathways of mRNA decay, nascent protein degradation and ribosome recycling. The most common mRNA defect in eukaryotes is probably inappropriate polyadenylation at near-cognate sites within the coding region. How ribosomes stall selectively when they encounter poly(A) is unclear. Here, we use biochemical and structural approaches in mammalian systems to show that poly-lysine, encoded by poly(A), favors a peptidyl-transfer RNA conformation suboptimal for peptide bond formation. This conformation partially slows elongation, permitting poly(A) mRNA in the ribosome’s decoding center to adopt a ribosomal RNA-stabilized single-stranded helix. The reconfigured decoding center clashes with incoming aminoacyl-tRNA, thereby precluding elongation. Thus, coincidence detection of poly-lysine in the exit tunnel and poly(A) in the decoding center allows ribosomes to detect aberrant mRNAs selectively, stall elongation and trigger downstream quality control pathways essential for cellular homeostasis. Biochemical and structural analysis demonstrate that simultaneous detection of poly-lysine in the exit tunnel and poly(A) in the decoding center allows ribosomes to detect aberrant mRNAs, stall elongation and trigger downstream quality control pathways.