Journal Article

Structural basis for stop codon recognition in eukaryotes

Murray, Jason, Hegde, Ramanujan S., Brown, Alan, Ramakrishnan, V., Shao, Sichen

2015

Overview

All eukaryotes utilize a single termination factor, eRF1, to halt translation when the ribosome encounters one of three possible stop codons; here electron cryo-microscopy structures of ribosome–eRF1 complexes in the process of recognizing each stop codon reveal how stop codons are discriminated from sense codons. How mRNA knows when to stop Mammalian messenger RNAs utilize three stop codons, but have a single termination factor, eRF1, that can recognize all three. To understand how eRF1 can distinguish stop codons from sense codons, Alan Brown et al . determined the structures of the mammalian 80S ribosome bound to eRF1 and mRNAs containing each of the stop codons. They find that two nucleotides from the 18S rRNA are stacked with two of the stop codon nucleotides, and the next nucleotide, to compact the mRNA, a conformation that favours stop codons to the exclusion of sense codons. Termination of protein synthesis occurs when a translating ribosome encounters one of three universally conserved stop codons: UAA, UAG or UGA. Release factors recognize stop codons in the ribosomal A-site to mediate release of the nascent chain and recycling of the ribosome. Bacteria decode stop codons using two separate release factors with differing specificities for the second and third bases 1 . By contrast, eukaryotes rely on an evolutionarily unrelated omnipotent release factor (eRF1) to recognize all three stop codons 2 . The molecular basis of eRF1 discrimination for stop codons over sense codons is not known. Here we present cryo-electron microscopy (cryo-EM) structures at 3.5–3.8 Å resolution of mammalian ribosomal complexes containing eRF1 interacting with each of the three stop codons in the A-site. Binding of eRF1 flips nucleotide A1825 of 18S ribosomal RNA so that it stacks on the second and third stop codon bases. This configuration pulls the fourth position base into the A-site, where it is stabilized by stacking against G626 of 18S rRNA. Thus, eRF1 exploits two rRNA nucleotides also used during transfer RNA selection to drive messenger RNA compaction. In this compacted mRNA conformation, stop codons are favoured by a hydrogen-bonding network formed between rRNA and essential eRF1 residues that constrains the identity of the bases. These results provide a molecular framework for eukaryotic stop codon recognition and have implications for future studies on the mechanisms of canonical and premature translation termination 3 , 4 .

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 101/28 / 631/337/574/1789 / 631/45/612/1249 / 631/535/1258/1259 / Adenosine / Amino Acid Motifs / Atoms & subatomic particles / Bacteria / Binding Sites / Cell research / Codon / Codon - chemistry / Codon - genetics / Codon - metabolism / Codon, Terminator - chemistry / Codon, Terminator - genetics / Codon, Terminator - metabolism / Cryoelectron Microscopy / Eukaryota / Eukaryotes / Humanities and Social Sciences / Humans / Hydrogen Bonding / letter / Models, Molecular / multidisciplinary / Nucleic Acid Conformation / Nucleotides - chemistry / Nucleotides - metabolism / Peptide Termination Factors - chemistry / Peptide Termination Factors - metabolism / Physiological aspects / Polypeptides / Protein Biosynthesis / Protein Conformation / Protein synthesis / Ribosomes - chemistry / Ribosomes - metabolism / RNA, Messenger - chemistry / RNA, Messenger - genetics / RNA, Messenger - metabolism / RNA, Ribosomal, 18S - genetics / Science / Structure-Activity Relationship / Substrate Specificity