title: Critical 23S rRNA interactions for macrolide-dependent ribosome stalling on the ErmCL nascent peptide chain.
abstract: The nascent peptide exit tunnel has recently been identified as a functional region of ribosomes contributing to translation regulation and co-translational protein folding. Inducible expression of the erm resistance genes depends on ribosome stalling at specific codons of an upstream open reading frame in the presence of an exit tunnel-bound macrolide antibiotic. The molecular basis for this translation arrest is still not fully understood. Here, we used a nucleotide analog interference approach to unravel important functional groups on 23S rRNA residues in the ribosomal exit tunnel for ribosome stalling on the ErmC leader peptide. By replacing single nucleobase functional groups or even single atoms we were able to demonstrate the importance of A2062, A2503 and U2586 for drug-dependent ribosome stalling. Our data show that the universally conserved A2062 and A2503 are capable of forming a non-Watson-Crick base pair that is critical for sensing and transmitting the stalling signal from the exit tunnel back to the peptidyl transferase center of the ribosome. The nucleobases of A2062, A2503 as well as U2586 do not contribute significantly to the overall mechanism of protein biosynthesis, yet their elaborate role for co-translational monitoring of nascent peptide chains inside the exit tunnel can explain their evolutionary conservation.
authors.affiliation: Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
authors.forename: Miriam
authors.initials: M
authors.lastname: Koch
authors.affiliation: Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
authors.forename: Jessica
authors.initials: J
authors.lastname: Willi
authors.affiliation: Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland.
authors.forename: Ugo
authors.initials: U
authors.lastname: Pradère
authors.affiliation: Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Hall
authors.affiliation: Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
authors.forename: Norbert
authors.initials: N
authors.lastname: Polacek
mesh_terms: D000900:Anti-Bacterial Agents / Q000737:chemistry*; D029968:Escherichia coli Proteins / Q000096:biosynthesis / Q000737:chemistry; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D018942:Macrolides / Q000737:chemistry*; D014176:Protein Biosynthesis / Q000187:drug effects; D012329:RNA, Bacterial / Q000737:chemistry; D012338:RNA, Ribosomal, 23S / Q000737:chemistry*; D013824:Thermus
chemical_list: D000900:Anti-Bacterial Agents; D029968:Escherichia coli Proteins; D018942:Macrolides; D012329:RNA, Bacterial; D012338:RNA, Ribosomal, 23S