Sequence-dependent elongation dynamics on macrolide-bound ribosomes.
The traditional view of macrolide antibiotics as plugs inside the ribosomal nascent peptide exit tunnel (NPET) has lately been challenged in favor of a more complex, heterogeneous mechanism, where drug-peptide interactions determine the fate of a translating ribosome. To investigate these highly dynamic processes, we applied single-molecule tracking of elongating ribosomes during inhibition of elongation by erythromycin of several nascent chains, including ErmCL and H-NS, which were shown to be, respectively, sensitive and resistant to erythromycin. Peptide sequence-specific changes were observed in translation elongation dynamics in the presence of a macrolide-obstructed NPET. Elongation rates were not severely inhibited in general by the presence of the drug; instead, stalls or pauses were observed as abrupt events. The dynamic pathways of nascent-chain-dependent elongation pausing in the presence of macrolides determine the fate of the translating ribosome stalling or readthrough.
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.
Magnus
M
Johansson
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305-4090, USA.
Jin
J
Chen
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305-4090, USA.
Albert
A
Tsai
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.
Guy
G
Kornberg
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA; Stanford Magnetic Resonance Laboratory, Stanford University School of Medicine, Stanford, CA 94305-5126, USA. Electronic address: puglisi@stanford.edu.
Joseph D
JD
Puglisi
D000595:Amino Acid Sequence; D000890:Anti-Infective Agents / Q000494:pharmacology*; D001665:Binding Sites; D018388:Codon, Terminator / Q000235:genetics; D004917:Erythromycin / Q000494:pharmacology*; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics / Q000378:metabolism; D008780:Methyltransferases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D010441:Peptide Chain Elongation, Translational; D011485:Protein Binding; D011500:Protein Synthesis Inhibitors / Q000494:pharmacology*; D012270:Ribosomes / Q000737:chemistry / Q000187:drug effects / Q000378:metabolism*
D000890:Anti-Infective Agents; D018388:Codon, Terminator; D011500:Protein Synthesis Inhibitors; D004917:Erythromycin; D008780:Methyltransferases; C035181:rRNA (adenosine-O-2'-)methyltransferase