title: Ribosomes slide on lysine-encoding homopolymeric A stretches.
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.
authors.affiliation: Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States.
authors.forename: Kristin S
authors.initials: KS
authors.lastname: Koutmou
authors.affiliation: Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States.
authors.forename: Anthony P
authors.initials: AP
authors.lastname: Schuller
authors.affiliation: Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States.
authors.forename: Julie L
authors.initials: JL
authors.lastname: Brunelle
authors.affiliation: Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States.
authors.forename: Aditya
authors.initials: A
authors.lastname: Radhakrishnan
authors.affiliation: Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, United States.
authors.forename: Sergej
authors.initials: S
authors.lastname: Djuranovic
authors.affiliation: Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States.
authors.forename: Rachel
authors.initials: R
authors.lastname: Green
mesh_terms: D001483:Base Sequence; D015153:Blotting, Western; D003062:Codon / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D017353:Gene Deletion; D008164:Luminescent Proteins / Q000235:genetics / Q000378:metabolism; D008239:Lysine / Q000235:genetics*; D008969:Molecular Sequence Data; D011061:Poly A / Q000235:genetics; D014176:Protein Biosynthesis / Q000235:genetics*; D020365:RNA Helicases / Q000235:genetics / Q000378:metabolism; D020871:RNA Stability / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012270:Ribosomes / Q000235:genetics* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D000097573:Red Fluorescent Protein
chemical_list: D003062:Codon; D008164:Luminescent Proteins; D008239:Lysine; D011061:Poly A; D020365:RNA Helicases; D012333:RNA, Messenger; D029701:Saccharomyces cerevisiae Proteins; D000097573:Red Fluorescent Protein; C074151:NAM7 protein, S cerevisiae
keywords: E. coli; S. cerevisiae; biochemistry; poly(A); ribosome; sliding