Ribosomes slide on lysine-encoding homopolymeric A stretches
Kristin S Koutmou,
Anthony P Schuller,
Julie L Brunelle,
Aditya Radhakrishnan,
Sergej Djuranovic,
Rachel Green
Affiliations
Kristin S Koutmou
Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States
Anthony P Schuller
Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States
Julie L Brunelle
Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States; Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, United States
Aditya Radhakrishnan
Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States
Sergej Djuranovic
Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, United States
Rachel Green
Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States; Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, United States
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.
