title: Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation.
abstract: In the absence of elongation factor EF-G, ribosomes undergo spontaneous, thermally driven fluctuation between the pre-translocation (classical) and intermediate (hybrid) states of translocation. These fluctuations do not result in productive mRNA translocation. Extending previous findings that the antibiotic sparsomycin induces translocation, we identify additional peptidyl transferase inhibitors that trigger productive mRNA translocation. We find that antibiotics that bind the peptidyl transferase A site induce mRNA translocation, whereas those that do not occupy the A site fail to induce translocation. Using single-molecule FRET, we show that translocation-inducing antibiotics do not accelerate intersubunit rotation, but act solely by converting the intrinsic, thermally driven dynamics of the ribosome into translocation. Our results support the idea that the ribosome is a Brownian ratchet machine, whose intrinsic dynamics can be rectified into unidirectional translocation by ligand binding.
authors.affiliation: Department of Biochemistry and Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA. Dmitri_Ermolenko@urmc.rochester.edu
authors.forename: Dmitri N
authors.initials: DN
authors.lastname: Ermolenko
authors.forename: Peter V
authors.initials: PV
authors.lastname: Cornish
authors.forename: Taekjip
authors.initials: T
authors.lastname: Ha
authors.forename: Harry F
authors.initials: HF
authors.lastname: Noller
mesh_terms: D000900:Anti-Bacterial Agents / Q000378:metabolism / Q000494:pharmacology*; D002701:Chloramphenicol / Q000378:metabolism / Q000494:pharmacology; D002981:Clindamycin / Q000378:metabolism / Q000494:pharmacology; D004791:Enzyme Inhibitors / Q000378:metabolism / Q000494:pharmacology; D004926:Escherichia coli / Q000187:drug effects* / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000187:drug effects / Q000378:metabolism; D031541:Fluorescence Resonance Energy Transfer; D008034:Lincomycin / Q000378:metabolism / Q000494:pharmacology; D020653:Peptide Elongation Factor G / Q000187:drug effects / Q000378:metabolism; D010458:Peptidyl Transferases / Q000187:drug effects / Q000378:metabolism; D014176:Protein Biosynthesis / Q000187:drug effects*; D034443:RNA Transport / Q000187:drug effects*; D012329:RNA, Bacterial / Q000187:drug effects / Q000378:metabolism; D012333:RNA, Messenger / Q000187:drug effects* / Q000378:metabolism; D012343:RNA, Transfer / Q000187:drug effects / Q000378:metabolism; D054681:Ribosome Subunits, Large, Bacterial / Q000187:drug effects* / Q000378:metabolism; D013033:Sparsomycin / Q000378:metabolism / Q000494:pharmacology
chemical_list: D000900:Anti-Bacterial Agents; D004791:Enzyme Inhibitors; D029968:Escherichia coli Proteins; D020653:Peptide Elongation Factor G; D012329:RNA, Bacterial; D012333:RNA, Messenger; D002981:Clindamycin; D002701:Chloramphenicol; D013033:Sparsomycin; D012343:RNA, Transfer; D008034:Lincomycin; D010458:Peptidyl Transferases