Ribosomes slide on lysine-encoding homopolymeric A stretches

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Abstract

Protein output from synonymous codons is thought to be equivalent if appropriate tRNAs are sufficiently abundant. Here we show that mRNAs encoding iterated lysine codons, AAA or AAG, differentially impact protein synthesis: insertion of iterated AAA codons into an ORF diminishes protein expression more than insertion of synonymous AAG codons. Kinetic studies in E. coli reveal that differential protein production results from pausing on consecutive AAA-lysines followed by ribosome sliding on homopolymeric A sequence. Translation in a cell free-expression system demonstrates that diminished output from AAA-codon-containing reporters results from premature translation termination on out of frame stop codons following ribosome sliding. In eukaryotes, these premature termination events target the mRNAs for Nonsense-Mediated-Decay (NMD). The finding that ribosomes slide on homopolymeric A sequences explains bioinformatic analyses indicating that consecutive AAA codons are under-represented in gene-coding sequences. Ribosome 'sliding' represents an unexpected type of ribosome movement possible during translation.

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Kristin S Koutmou

Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States

Competing interests
No competing interests declared.
Anthony P Schuller

Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States

Competing interests
No competing interests declared.
Julie L Brunelle

Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States

Competing interests
No competing interests declared.
Aditya Radhakrishnan

Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States

Competing interests
No competing interests declared.
Sergej Djuranovic

Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, United States

Competing interests
No competing interests declared.
Rachel Green

Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States

For correspondence
ragreen@jhmi.edu

Competing interests
Rachel Green, Reviewing editor, eLife.

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