Molecular Mechanism of Viomycin Inhibition of Peptide Elongation in Bacteria

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2016 Jan 13

PMID 26755601

Citations 25

Authors

Mikael Holm

Anneli Borg

Mans Ehrenberg

Suparna Sanyal

Affiliations

Soon will be listed here.

Abstract

Viomycin is a tuberactinomycin antibiotic essential for treating multidrug-resistant tuberculosis. It inhibits bacterial protein synthesis by blocking elongation factor G (EF-G) catalyzed translocation of messenger RNA on the ribosome. Here we have clarified the molecular aspects of viomycin inhibition of the elongating ribosome using pre-steady-state kinetics. We found that the probability of ribosome inhibition by viomycin depends on competition between viomycin and EF-G for binding to the pretranslocation ribosome, and that stable viomycin binding requires an A-site bound tRNA. Once bound, viomycin stalls the ribosome in a pretranslocation state for a minimum of ∼ 45 s. This stalling time increases linearly with viomycin concentration. Viomycin inhibition also promotes futile cycles of GTP hydrolysis by EF-G. Finally, we have constructed a kinetic model for viomycin inhibition of EF-G catalyzed translocation, allowing for testable predictions of tuberactinomycin action in vivo and facilitating in-depth understanding of resistance development against this important class of antibiotics.

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References

Thomas M, Chan Y, Ozanick S . Deciphering tuberactinomycin biosynthesis: isolation, sequencing, and annotation of the viomycin biosynthetic gene cluster. Antimicrob Agents Chemother. 2003; 47(9):2823-30. PMC: 182626. DOI: 10.1128/AAC.47.9.2823-2830.2003. View

Fei J, Kosuri P, MacDougall D, Gonzalez Jr R . Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. Mol Cell. 2008; 30(3):348-59. DOI: 10.1016/j.molcel.2008.03.012. View

Demeshkina N, Jenner L, Westhof E, Yusupov M, Yusupova G . A new understanding of the decoding principle on the ribosome. Nature. 2012; 484(7393):256-9. DOI: 10.1038/nature10913. View

Borg A, Holm M, Shiroyama I, Hauryliuk V, Pavlov M, Sanyal S . Fusidic acid targets elongation factor G in several stages of translocation on the bacterial ribosome. J Biol Chem. 2014; 290(6):3440-54. PMC: 4319013. DOI: 10.1074/jbc.M114.611608. View

Feldman M, Terry D, Altman R, Blanchard S . Aminoglycoside activity observed on single pre-translocation ribosome complexes. Nat Chem Biol. 2009; 6(1):54-62. PMC: 2914512. DOI: 10.1038/nchembio.274. View

Ermolenko D, Spiegel P, Majumdar Z, Hickerson R, Clegg R, Noller H . The antibiotic viomycin traps the ribosome in an intermediate state of translocation. Nat Struct Mol Biol. 2007; 14(6):493-7. DOI: 10.1038/nsmb1243. View

Monshupanee T, Johansen S, Dahlberg A, Douthwaite S . Capreomycin susceptibility is increased by TlyA-directed 2'-O-methylation on both ribosomal subunits. Mol Microbiol. 2012; 85(6):1194-203. PMC: 3438285. DOI: 10.1111/j.1365-2958.2012.08168.x. View

Schmeing T, Ramakrishnan V . What recent ribosome structures have revealed about the mechanism of translation. Nature. 2009; 461(7268):1234-42. DOI: 10.1038/nature08403. View

Johansson M, Bouakaz E, Lovmar M, Ehrenberg M . The kinetics of ribosomal peptidyl transfer revisited. Mol Cell. 2008; 30(5):589-98. DOI: 10.1016/j.molcel.2008.04.010. View

10.

Brilot A, Korostelev A, Ermolenko D, Grigorieff N . Structure of the ribosome with elongation factor G trapped in the pretranslocation state. Proc Natl Acad Sci U S A. 2013; 110(52):20994-9. PMC: 3876248. DOI: 10.1073/pnas.1311423110. View

11.

Cox R . Correlation of the rate of protein synthesis and the third power of the RNA : protein ratio in Escherichia coli and Mycobacterium tuberculosis. Microbiology (Reading). 2003; 149(Pt 3):729-737. DOI: 10.1099/mic.0.25645-0. View

12.

Chen J, Petrov A, Tsai A, OLeary S, Puglisi J . Coordinated conformational and compositional dynamics drive ribosome translocation. Nat Struct Mol Biol. 2013; 20(6):718-27. PMC: 3883222. DOI: 10.1038/nsmb.2567. View

13.

Antoun A, Pavlov M, Tenson T, Ehrenberg M M . Ribosome formation from subunits studied by stopped-flow and Rayleigh light scattering. Biol Proced Online. 2004; 6:35-54. PMC: 389903. DOI: 10.1251/bpo71. View

14.

Moazed D, Noller H . Intermediate states in the movement of transfer RNA in the ribosome. Nature. 1989; 342(6246):142-8. DOI: 10.1038/342142a0. View

15.

Munro J, Altman R, Tung C, Cate J, Sanbonmatsu K, Blanchard S . Spontaneous formation of the unlocked state of the ribosome is a multistep process. Proc Natl Acad Sci U S A. 2009; 107(2):709-14. PMC: 2818936. DOI: 10.1073/pnas.0908597107. View

16.

Modolell J, Vazquez . The inhibition of ribosomal translocation by viomycin. Eur J Biochem. 1977; 81(3):491-7. DOI: 10.1111/j.1432-1033.1977.tb11974.x. View

17.

Ehrlich J, Smith R, Penner M, Anderson L, BRATTON Jr A . Antimicrobial activity of Streptomyces floridae and of Viomycin. Am Rev Tuberc. 1951; 63(1):7-16. DOI: 10.1164/art.1951.63.1.7. View

18.

Schuwirth B, Borovinskaya M, Hau C, Zhang W, Vila-Sanjurjo A, Holton J . Structures of the bacterial ribosome at 3.5 A resolution. Science. 2005; 310(5749):827-34. DOI: 10.1126/science.1117230. View

19.

Kim H, Puglisi J, Chu S . Fluctuations of transfer RNAs between classical and hybrid states. Biophys J. 2007; 93(10):3575-82. PMC: 2072051. DOI: 10.1529/biophysj.107.109884. View

20.

Frank J, Agrawal R . A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature. 2000; 406(6793):318-22. DOI: 10.1038/35018597. View