Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation

RNA. 2013 Feb;19(2):158-66. doi: 10.1261/rna.035964.112. Epub 2012 Dec 17.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Anti-Bacterial Agents / metabolism
  • Anti-Bacterial Agents / pharmacology*
  • Chloramphenicol / metabolism
  • Chloramphenicol / pharmacology
  • Clindamycin / metabolism
  • Clindamycin / pharmacology
  • Enzyme Inhibitors / metabolism
  • Enzyme Inhibitors / pharmacology
  • Escherichia coli / drug effects*
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / drug effects
  • Escherichia coli Proteins / metabolism
  • Fluorescence Resonance Energy Transfer
  • Lincomycin / metabolism
  • Lincomycin / pharmacology
  • Peptide Elongation Factor G / drug effects
  • Peptide Elongation Factor G / metabolism
  • Peptidyl Transferases / drug effects
  • Peptidyl Transferases / metabolism
  • Protein Biosynthesis / drug effects*
  • RNA Transport / drug effects*
  • RNA, Bacterial / drug effects
  • RNA, Bacterial / metabolism
  • RNA, Messenger / drug effects*
  • RNA, Messenger / metabolism
  • RNA, Transfer / drug effects
  • RNA, Transfer / metabolism
  • Ribosome Subunits, Large, Bacterial / drug effects*
  • Ribosome Subunits, Large, Bacterial / metabolism
  • Sparsomycin / metabolism
  • Sparsomycin / pharmacology

Substances

  • Anti-Bacterial Agents
  • Enzyme Inhibitors
  • Escherichia coli Proteins
  • Peptide Elongation Factor G
  • RNA, Bacterial
  • RNA, Messenger
  • Clindamycin
  • Chloramphenicol
  • Sparsomycin
  • RNA, Transfer
  • Lincomycin
  • Peptidyl Transferases