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Nascent peptide assists the ribosome in recognizing chemically distinct small molecules

Nature Chemical Biology volume 12, pages 153–158 (2016)Cite this article

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Abstract

Regulation of gene expression in response to the changing environment is critical for cell survival. For instance, binding of macrolide antibiotics to the ribosome promotes translation arrest at the leader open reading frames ermCL and ermBL, which is necessary for inducing the antibiotic resistance genes ermC and ermB. Cladinose-containing macrolides such as erythromycin (ERY), but not ketolides such as telithromycin (TEL), arrest translation of ermCL, whereas either ERY or TEL stall ermBL translation. How the ribosome distinguishes between chemically similar small molecules is unknown. We show that single amino acid changes in the leader peptide switch the specificity of recognition of distinct molecules, triggering gene activation in response to ERY alone, to TEL alone or to both antibiotics or preventing stalling altogether. Thus, the ribosomal response to chemical signals can be modulated by minute changes in the nascent peptide, suggesting that protein sequences could have been optimized for rendering translation sensitive to environmental cues.

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Figure 1: The C-terminal segment of the stalled ErmBL is critical for antibiotic cofactor specificity.
Figure 2: Arg7 in ErmBL modulates recognition of macrolide stalling cofactors.
Figure 3: The C-terminal amino acid of the stalled ErmBL directs differentiation between chemically distinct molecules and determines selectivity of antibiotic-mediated gene activation.
Figure 4: Mutations in the ErmCL peptide can change antibiotic specificity of ribosome stalling.

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Acknowledgements

We thank D. Wilson and S. Arenz (Gene Center, Munich) for helpful discussions, R. Bovee for help with some experiments and P. Fernandes (Cempra Pharmaceuticals) for providing telithromycin. This work was supported by a grant from the National Science Foundation (MCB 1244455) to A.S.M. and N.V.-L. and 9P41GM104601 (to K.S.) and the National Science Foundation (PHY0822613) (to K.S.). MD modeling was facilitated by a grant from the Great Lakes Consortium for Petascale Computation on the Blue Waters Computer, financed by the National Science Foundation (OCI 07-25070) and the Oak Ridge Leadership Computing Facility at Oak Ridge National Laboratory, which is supported by the Office of Science of the Department of Energy under Contract DE-AC05-00OR22725.

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  1. Pulkit Gupta

    Present address: Present address: Merck & Co., Inc., Kenilworth, New Jersey, USA.,

Authors and Affiliations

  1. Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA

    Pulkit Gupta, Dorota Klepacki, Vrinda Gupta, Alexander S Mankin & Nora Vázquez-Laslop

  2. Beckman Institute and Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois, USA

    Bo Liu & Klaus Schulten

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Contributions

P.G., A.S.M. and N.V.-L. designed research; P.G., B.L., D.K. and V.G. performed research; P.G., B.L., K.S., A.S.M. and N.V.-L. analyzed data; P.G., N.V.-L. and A.S.M. wrote the paper.

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Correspondence to Alexander S Mankin or Nora Vázquez-Laslop.

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Gupta, P., Liu, B., Klepacki, D. et al. Nascent peptide assists the ribosome in recognizing chemically distinct small molecules. Nat Chem Biol 12, 153–158 (2016). https://doi.org/10.1038/nchembio.1998

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