Correlated Conformational Events in EF-G and the Ribosome Regulate Translocation

Overview

Journal Nat Struct Mol Biol

Specialties Cell Biology
Molecular Biology

Date 2010 Nov 9

PMID 21057527

Citations 69

Authors

James B Munro

Michael R Wasserman

Roger B Altman

Leyi Wang

Scott C Blanchard

Affiliations

Soon will be listed here.

Abstract

In bacteria, the translocation of tRNA and mRNA with respect to the ribosome is catalyzed by the conserved GTPase elongation factor-G (EF-G). To probe the rate-determining features in this process, we imaged EF-G-catalyzed translocation from two unique structural perspectives using single-molecule fluorescence resonance energy transfer. The data reveal that the rate at which the ribosome spontaneously achieves a transient, 'unlocked' state is closely correlated with the rate at which the tRNA-like domain IV-V element of EF-G engages the A site. After these structural transitions, translocation occurs comparatively fast, suggesting that conformational processes intrinsic to the ribosome determine the rate of translocation. Experiments conducted in the presence of non-hydrolyzable GTP analogs and specific antibiotics further reveal that allosterically linked conformational events in EF-G and the ribosome mediate rapid, directional substrate movement and EF-G release.

Citing Articles

Alternate conformational trajectories in ribosome translocation.

Alejo J, Girodat D, Hammerling M, Willi J, Jewett M, Engelhart A PLoS Comput Biol. 2024; 20(8):e1012319.

PMID: 39141679 PMC: 11346969. DOI: 10.1371/journal.pcbi.1012319.

β-Amino Acids Reduce Ternary Complex Stability and Alter the Translation Elongation Mechanism.

Cruz-Navarrete F, Griffin W, Chan Y, Martin M, Alejo J, Brady R ACS Cent Sci. 2024; 10(6):1262-1275.

PMID: 38947208 PMC: 11212133. DOI: 10.1021/acscentsci.4c00314.

Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers.

Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H Chem Rev. 2024; 124(10):6444-6500.

PMID: 38688034 PMC: 11122139. DOI: 10.1021/acs.chemrev.3c00894.

β-amino acids reduce ternary complex stability and alter the translation elongation mechanism.

Cruz-Navarrete F, Griffin W, Chan Y, Martin M, Alejo J, Natchiar S bioRxiv. 2024; .

PMID: 38464221 PMC: 10925103. DOI: 10.1101/2024.02.24.581891.

Partial spontaneous intersubunit rotations in pretranslocation ribosomes.

Huang T, Choi J, Prabhakar A, Puglisi J, Petrov A Proc Natl Acad Sci U S A. 2023; 120(41):e2114979120.

PMID: 37801472 PMC: 10576065. DOI: 10.1073/pnas.2114979120.

References

Bergemann K, Nierhaus K . Spontaneous, elongation factor G independent translocation of Escherichia coli ribosomes. J Biol Chem. 1983; 258(24):15105-13. View

Qin F, Auerbach A, Sachs F . Estimating single-channel kinetic parameters from idealized patch-clamp data containing missed events. Biophys J. 1996; 70(1):264-80. PMC: 1224925. DOI: 10.1016/S0006-3495(96)79568-1. View

Agirrezabala X, Lei J, Brunelle J, Ortiz-Meoz R, Green R, Frank J . Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome. Mol Cell. 2008; 32(2):190-7. PMC: 2614368. DOI: 10.1016/j.molcel.2008.10.001. View

Ticu C, Nechifor R, Nguyen B, Desrosiers M, Wilson K . Conformational changes in switch I of EF-G drive its directional cycling on and off the ribosome. EMBO J. 2009; 28(14):2053-65. PMC: 2718289. DOI: 10.1038/emboj.2009.169. View

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

Katunin V, Savelsbergh A, Rodnina M, Wintermeyer W . Coupling of GTP hydrolysis by elongation factor G to translocation and factor recycling on the ribosome. Biochemistry. 2002; 41(42):12806-12. DOI: 10.1021/bi0264871. 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

Julian P, Konevega A, Scheres S, Lazaro M, Gil D, Wintermeyer W . Structure of ratcheted ribosomes with tRNAs in hybrid states. Proc Natl Acad Sci U S A. 2008; 105(44):16924-7. PMC: 2579354. DOI: 10.1073/pnas.0809587105. View

Savelsbergh A, Katunin V, Mohr D, Peske F, Rodnina M, Wintermeyer W . An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation. Mol Cell. 2003; 11(6):1517-23. DOI: 10.1016/s1097-2765(03)00230-2. View

10.

Walker S, Shoji S, Pan D, Cooperman B, Fredrick K . Role of hybrid tRNA-binding states in ribosomal translocation. Proc Natl Acad Sci U S A. 2008; 105(27):9192-7. PMC: 2453706. DOI: 10.1073/pnas.0710146105. View

11.

Cornish P, Ermolenko D, Noller H, Ha T . Spontaneous intersubunit rotation in single ribosomes. Mol Cell. 2008; 30(5):578-88. PMC: 2491453. DOI: 10.1016/j.molcel.2008.05.004. View

12.

Munro J, Sanbonmatsu K, Spahn C, Blanchard S . Navigating the ribosome's metastable energy landscape. Trends Biochem Sci. 2009; 34(8):390-400. PMC: 2914510. DOI: 10.1016/j.tibs.2009.04.004. View

13.

Aitken C, Marshall R, Puglisi J . An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments. Biophys J. 2007; 94(5):1826-35. PMC: 2242739. DOI: 10.1529/biophysj.107.117689. View

14.

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

15.

Wen J, Lancaster L, Hodges C, Zeri A, Yoshimura S, Noller H . Following translation by single ribosomes one codon at a time. Nature. 2008; 452(7187):598-603. PMC: 2556548. DOI: 10.1038/nature06716. View

16.

Wintermeyer W, Peske F, Beringer M, Gromadski K, Savelsbergh A, Rodnina M . Mechanisms of elongation on the ribosome: dynamics of a macromolecular machine. Biochem Soc Trans. 2004; 32(Pt 5):733-7. DOI: 10.1042/BST0320733. View

17.

Dave R, Terry D, Munro J, Blanchard S . Mitigating unwanted photophysical processes for improved single-molecule fluorescence imaging. Biophys J. 2009; 96(6):2371-81. PMC: 2907709. DOI: 10.1016/j.bpj.2008.11.061. View

18.

Connell S, Takemoto C, Wilson D, Wang H, Murayama K, Terada T . Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors. Mol Cell. 2007; 25(5):751-64. DOI: 10.1016/j.molcel.2007.01.027. View

19.

Cukras A, Southworth D, Brunelle J, Culver G, Green R . Ribosomal proteins S12 and S13 function as control elements for translocation of the mRNA:tRNA complex. Mol Cell. 2003; 12(2):321-8. DOI: 10.1016/s1097-2765(03)00275-2. View

20.

Agirrezabala X, Frank J . Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu. Q Rev Biophys. 2009; 42(3):159-200. PMC: 2832932. DOI: 10.1017/S0033583509990060. View