title: The antibiotic viomycin traps the ribosome in an intermediate state of translocation.
abstract: During protein synthesis, transfer RNA and messenger RNA undergo coupled translocation through the ribosome's A, P and E sites, a process catalyzed by elongation factor EF-G. Viomycin blocks translocation on bacterial ribosomes and is believed to bind at the subunit interface. Using fluorescent resonance energy transfer and chemical footprinting, we show that viomycin traps the ribosome in an intermediate state of translocation. Changes in FRET efficiency show that viomycin causes relative movement of the two ribosomal subunits indistinguishable from that induced by binding of EF-G with GDPNP. Chemical probing experiments indicate that viomycin induces formation of a hybrid-state translocation intermediate. Thus, viomycin inhibits translation through a unique mechanism, locking ribosomes in the hybrid state; the EF-G-induced 'ratcheted' state observed by cryo-EM is identical to the hybrid state; and, since translation is viomycin sensitive, the hybrid state may be present in vivo.
authors.affiliation: Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA.
authors.forename: Dmitri N
authors.initials: DN
authors.lastname: Ermolenko
authors.forename: P Clint
authors.initials: PC
authors.lastname: Spiegel
authors.forename: Zigurts K
authors.initials: ZK
authors.lastname: Majumdar
authors.forename: Robyn P
authors.initials: RP
authors.lastname: Hickerson
authors.forename: Robert M
authors.initials: RM
authors.lastname: Clegg
authors.forename: Harry F
authors.initials: HF
authors.lastname: Noller
mesh_terms: D031541:Fluorescence Resonance Energy Transfer; D008958:Models, Molecular; D020653:Peptide Elongation Factor G / Q000378:metabolism; D014176:Protein Biosynthesis / Q000187:drug effects* / Q000502:physiology; D011500:Protein Synthesis Inhibitors / Q000494:pharmacology*; D012333:RNA, Messenger / Q000378:metabolism*; D012343:RNA, Transfer / Q000378:metabolism*; D054657:Ribosome Subunits / Q000378:metabolism*; D014756:Viomycin / Q000494:pharmacology*
chemical_list: D020653:Peptide Elongation Factor G; D011500:Protein Synthesis Inhibitors; D012333:RNA, Messenger; D012343:RNA, Transfer; D014756:Viomycin