Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP

. 2021 Dec 13 ; 12 (1) : 7236. [epub] 20211213

Jazyk angličtina Země Velká Británie, Anglie Médium electronic

Typ dokumentu časopisecké články, Research Support, N.I.H., Extramural, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid34903725

Grantová podpora
R35 GM134931 NIGMS NIH HHS - United States
F31 HL152650 NHLBI NIH HHS - United States
R35 GM127094 NIGMS NIH HHS - United States
R01 GM106105 NIGMS NIH HHS - United States
R01 GM107465 NIGMS NIH HHS - United States

Odkazy

PubMed 34903725
PubMed Central PMC8668904
DOI 10.1038/s41467-021-27415-0
PII: 10.1038/s41467-021-27415-0
Knihovny.cz E-zdroje

During translation, a conserved GTPase elongation factor-EF-G in bacteria or eEF2 in eukaryotes-translocates tRNA and mRNA through the ribosome. EF-G has been proposed to act as a flexible motor that propels tRNA and mRNA movement, as a rigid pawl that biases unidirectional translocation resulting from ribosome rearrangements, or by various combinations of motor- and pawl-like mechanisms. Using time-resolved cryo-EM, we visualized GTP-catalyzed translocation without inhibitors, capturing elusive structures of ribosome•EF-G intermediates at near-atomic resolution. Prior to translocation, EF-G binds near peptidyl-tRNA, while the rotated 30S subunit stabilizes the EF-G GTPase center. Reverse 30S rotation releases Pi and translocates peptidyl-tRNA and EF-G by ~20 Å. An additional 4-Å translocation initiates EF-G dissociation from a transient ribosome state with highly swiveled 30S head. The structures visualize how nearly rigid EF-G rectifies inherent and spontaneous ribosomal dynamics into tRNA-mRNA translocation, whereas GTP hydrolysis and Pi release drive EF-G dissociation.

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Ling, C. & Ermolenko, D. N. Structural insights into ribosome translocation. WIREs RNA7, 620–636 (2016). PubMed PMC

Noller HF, Lancaster L, Zhou J, Mohan S. The ribosome moves: RNA mechanics and translocation. Nat. Struct. Mol. Biol. 2017;24:1021–1027. PubMed PMC

Rodnina MV, Peske F, Peng BZ, Belardinelli R, Wintermeyer W. Converting GTP hydrolysis into motion: versatile translational elongation factor G. Biol. Chem. 2019;401:131–142. PubMed

Cornish PV, Ermolenko DN, Noller HF, Ha T. Spontaneous intersubunit rotation in single ribosomes. Mol. Cell. 2008;30:578–588. PubMed PMC

Frank J, Agrawal RK. A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature. 2000;406:318–322. PubMed

Agirrezabala X, et al. Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome. Mol. Cell. 2008;32:190–197. PubMed PMC

Wasserman MR, Alejo JL, Altman RB, Blanchard SC. Multiperspective smFRET reveals rate-determining late intermediates of ribosomal translocation. Nat. Struct. Mol. Biol. 2016;23:333–341. PubMed PMC

Blanchard SC, Kim HD, Gonzalez RL, Jr, Puglisi JD, Chu S. tRNA dynamics on the ribosome during translation. Proc. Natl Acad. Sci. USA. 2004;101:12893–12898. PubMed PMC

Julian P, et al. Structure of ratcheted ribosomes with tRNAs in hybrid states. Proc. Natl Acad. Sci. USA. 2008;105:16924–16927. PubMed PMC

Moazed D, Noller HF. Intermediate states in the movement of transfer RNA in the ribosome. Nature. 1989;342:142–148. PubMed

Ermolenko DN, Noller HF. mRNA translocation occurs during the second step of ribosomal intersubunit rotation. Nat. Struct. Mol. Biol. 2011;18:457–462. PubMed PMC

Brilot AF, Korostelev AA, Ermolenko DN, Grigorieff N. Structure of the ribosome with elongation factor G trapped in the pretranslocation state. Proc. Natl Acad. Sci. USA. 2013 doi: 10.1073/pnas.1311423110. PubMed DOI PMC

Zhou J, Lancaster L, Donohue JP, Noller HF. How the ribosome hands the A-site tRNA to the P site during EF-G-catalyzed translocation. Science. 2014;345:1188–1191. PubMed PMC

Ramrath DJ, et al. Visualization of two transfer RNAs trapped in transit during elongation factor G-mediated translocation. Proc. Natl Acad. Sci. USA. 2013;110:20964–20969. PubMed PMC

Gao YG, et al. The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Science. 2009;326:694–699. PubMed PMC

Li, W. et al. Activation of GTP hydrolysis in mRNA-tRNA translocation by elongation factor G. Sci Adv1, 1500169 (2015). PubMed PMC

Lin J, Gagnon MG, Bulkley D, Steitz TA. Conformational changes of elongation factor G on the ribosome during tRNA translocation. Cell. 2015;160:219–227. PubMed PMC

Demo, G. et al. Structural basis for +1 ribosomal frameshifting during EF-G-catalyzed translocation. Nat. Commun. 12, 4644 (2021). PubMed PMC

Zhou J, Lancaster L, Donohue JP, Noller HF. Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation. Science. 2013;340:1236086. PubMed PMC

Holtkamp W, et al. GTP hydrolysis by EF-G synchronizes tRNA movement on small and large ribosomal subunits. EMBO J. 2014;33:1073–1085. PubMed PMC

Wilden B, Savelsbergh A, Rodnina MV, Wintermeyer W. Role and timing of GTP binding and hydrolysis during EF-G-dependent tRNA translocation on the ribosome. Proc. Natl Acad. Sci. USA. 2006;103:13670–13675. PubMed PMC

Hauryliuk, V. et al. The pre-translocation ribosome is targeted by GTP-bound EF-G in partially activated form. Proc. Natl. Acad. Sci. USA, (in press) (2008). PubMed PMC

Chen J, Petrov A, Tsai A, O’Leary SE, Puglisi JD. Coordinated conformational and compositional dynamics drive ribosome translocation. Nat. Struct. Mol. Biol. 2013;20:718–727. PubMed PMC

Peske F, Matassova NB, Savelsbergh A, Rodnina MV, Wintermeyer W. Conformationally restricted elongation factor G retains GTPase activity but is inactive in translocation on the ribosome. Mol. Cell. 2000;6:501–505. PubMed

Chen C, et al. Elongation factor G initiates translocation through a power stroke. Proc. Natl Acad. Sci. USA. 2016;113:7515–7520. PubMed PMC

Yin H, Gavriliuc M, Lin R, Xu S, Wang Y. Modulation and Visualization of EF-G Power Stroke During Ribosomal Translocation. Chembiochem. 2019;20:2927–2935. PubMed PMC

Rodnina MV, Savelsbergh A, Katunin VI, Wintermeyer W. Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome. Nature. 1997;385:37–41. PubMed

Sharma H, et al. Kinetics of Spontaneous and EF-G-Accelerated Rotation of Ribosomal Subunits. Cell Rep. 2016;16:2187–2196. PubMed

Liu T, et al. Direct measurement of the mechanical work during translocation by the ribosome. Elife. 2014;3:e03406. PubMed PMC

Kaziro Y. The role of guanosine 5′-triphosphate in polypeptide chain elongation. Biochim Biophys. Acta. 1978;505:95–127. PubMed

Gavrilova LP, Kostiashkina OE, Koteliansky VE, Rutkevitch NM, Spirin AS. Factor-free (“non-enzymic”) and factor-dependent systems of translation of polyuridylic acid by Escherichia coli ribosomes. J. Mol. Biol. 1976;101:537–552. PubMed

Katunin VI, Savelsbergh A, Rodnina MV, Wintermeyer W. Coupling of GTP hydrolysis by elongation factor G to translocation and factor recycling on the ribosome. Biochemistry. 2002;41:12806–12812. PubMed

Fredrick K, Noller HF. Catalysis of ribosomal translocation by sparsomycin. Science. 2003;300:1159–1162. PubMed

Salsi E, Farah E, Ermolenko DN. EF-G Activation by Phosphate Analogs. J. Mol. Biol. 2016;428:2248–2258. PubMed PMC

Cunha CE, et al. Dual use of GTP hydrolysis by elongation factor G on the ribosome. Translation. 2013;1:e24315–24311. PubMed PMC

Loveland AB, Demo G, Korostelev AA. Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading. Nature. 2020;584:640–645. PubMed PMC

Munro JB, Altman RB, O’Connor N, Blanchard SC. Identification of two distinct hybrid state intermediates on the ribosome. Mol. Cell. 2007;25:505–517. PubMed PMC

Fu J, Munro JB, Blanchard SC, Frank J. Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation. Proc. Natl Acad. Sci. USA. 2011;108:4817–4821. PubMed PMC

Budkevich T, et al. Structure and dynamics of the mammalian ribosomal pretranslocation complex. Mol. Cell. 2011;44:214–224. PubMed PMC

Svidritskiy E, Brilot AF, Koh CS, Grigorieff N, Korostelev AA. Structures of Yeast 80S Ribosome-tRNA Complexes in the Rotated and Nonrotated Conformations. Structure. 2014;22:1210–1218. PubMed PMC

Ratje AH, et al. Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Nature. 2010;468:713–716. PubMed PMC

Flis J, et al. tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis. Cell Rep. 2018;25:2676–2688 e2677. PubMed PMC

Abeyrathne, P. D., Koh, C. S., Grant, T., Grigorieff, N. & Korostelev, A. A. Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome. Elife5, e14874 (2016). PubMed PMC

Guo Z, Noller HF. Rotation of the head of the 30S ribosomal subunit during mRNA translocation. Proc. Natl Acad. Sci. USA. 2012;109:20391–20394. PubMed PMC

Czworkowski J, Wang J, Steitz TA, Moore PB. The crystal structure of elongation factor G complexed with GDP, at 2.7 A resolution. EMBO J. 1994;13:3661–3668. PubMed PMC

Ogle JM, et al. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science. 2001;292:897–902. PubMed

Loveland AB, Demo G, Grigorieff N, Korostelev AA. Ensemble cryo-EM elucidates the mechanism of translation fidelity. Nature. 2017;546:113–117. PubMed PMC

Demeshkina N, Jenner L, Westhof E, Yusupov M, Yusupova G. A new understanding of the decoding principle on the ribosome. Nature. 2012;484:256–259. PubMed

Salsi E, Farah E, Netter Z, Dann J, Ermolenko DN. Movement of elongation factor G between compact and extended conformations. J. Mol. Biol. 2015;427:454–467. PubMed PMC

Chen Y, Koripella RK, Sanyal S, Selmer M. Staphylococcus aureus elongation factor G—structure and analysis of a target for fusidic acid. FEBS J. 2010;277:3789–3803. PubMed

Connell SR, et al. Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors. Mol. Cell. 2007;25:751–764. PubMed

Chen J, Sawyer N, Regan L. Protein-protein interactions: general trends in the relationship between binding affinity and interfacial buried surface area. Protein Sci. 2013;22:510–515. PubMed PMC

Clementi N, Chirkova A, Puffer B, Micura R, Polacek N. Atomic mutagenesis reveals A2660 of 23S ribosomal RNA as key to EF-G GTPase activation. Nat. Chem. Biol. 2010;6:344–351. PubMed

Shi X, Khade PK, Sanbonmatsu KY, Joseph S. Functional role of the sarcin-ricin loop of the 23S rRNA in the elongation cycle of protein synthesis. J. Mol. Biol. 2012;419:125–138. PubMed PMC

Evarsson A, et al. Three-dimensional structure of the ribosomal translocase: elongation factor G from Thermus thermophilus. Embo J. 1994;13:3669–3677. PubMed PMC

Voorhees RM, Schmeing TM, Kelley AC, Ramakrishnan V. The mechanism for activation of GTP hydrolysis on the ribosome. Science. 2010;330:835–838. PubMed PMC

Fenwick MK, Ealick SE. Structural basis of elongation factor 2 switching. Curr. Res. Struct. Biol. 2020;2:25–34. PubMed PMC

Pasqualato S, Cherfils J. Crystallographic evidence for substrate-assisted GTP hydrolysis by a small GTP binding protein. Structure. 2005;13:533–540. PubMed

Koripella RK, et al. A conserved histidine in switch-II of EF-G moderates release of inorganic phosphate. Sci. Rep. 2015;5:12970. PubMed PMC

Ermolenko DN, et al. Observation of intersubunit movement of the ribosome in solution using FRET. J. Mol. Biol. 2007;370:530–540. PubMed

Modolell J, Vazquez The inhibition of ribosomal translocation by viomycin. Eur. J. Biochem. 1977;81:491–497. PubMed

Pulk A, Cate JH. Control of ribosomal subunit rotation by elongation factor G. Science. 2013;340:1235970. PubMed PMC

Dubiez E, Aleksandrov A, Lazennec-Schurdevin C, Mechulam Y, Schmitt E. Identification of a second GTP-bound magnesium ion in archaeal initiation factor 2. Nucleic Acids Res. 2015;43:2946–2957. PubMed PMC

Petrychenko V, et al. Structural mechanism of GTPase-powered ribosome-tRNA movement. Nat. Commun. 2021;12:5933. PubMed PMC

Rundlet EJ, et al. Structural basis of early translocation events on the ribosome. Nature. 2021;595:741–745. PubMed PMC

Ticu C, Nechifor R, Nguyen B, Desrosiers M, Wilson KS. Conformational changes in switch I of EF-G drive its directional cycling on and off the ribosome. EMBO J. 2009;28:2053–2065. PubMed PMC

Fei J, Kosuri P, MacDougall DD, Gonzalez RL., Jr Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. Mol. Cell. 2008;30:348–359. PubMed

Chen C, et al. Single-molecule fluorescence measurements of ribosomal translocation dynamics. Mol. Cell. 2011;42:367–377. PubMed PMC

Pan D, Kirillov SV, Cooperman BS. Kinetically competent intermediates in the translocation step of protein synthesis. Mol. Cell. 2007;25:519–529. PubMed PMC

Liu G, et al. EF-G catalyzes tRNA translocation by disrupting interactions between decoding center and codon-anticodon duplex. Nat. Struct. Mol. Biol. 2014;21:817–824. PubMed

Salsi E, Farah E, Dann J, Ermolenko DN. Following movement of domain IV of elongation factor G during ribosomal translocation. Proc. Natl Acad. Sci. USA. 2014;111:15060–15065. PubMed PMC

Rodnina MV, Savelsbergh A, Wintermeyer W. Dynamics of translation on the ribosome: molecular mechanics of translocation. FEMS Microbiol Rev. 1999;23:317–333. PubMed

Hwang W, Karplus M. Structural basis for power stroke vs. Brownian ratchet mechanisms of motor proteins. Proc. Natl Acad. Sci. USA. 2019;116:19777–19785. PubMed PMC

Schuwirth BS, et al. Structures of the bacterial ribosome at 3.5 A resolution. Science. 2005;310:827–834. PubMed

Zhou J, Lancaster L, Donohue JP, Noller HF. Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state. Proc. Natl Acad. Sci. USA. 2019;116:7813–7818. PubMed PMC

Hong S, et al. Mechanism of tRNA-mediated +1 ribosomal frameshifting. Proc. Natl Acad. Sci. USA. 2018;115:11226–11231. PubMed PMC

Horan LH, Noller HF. Intersubunit movement is required for ribosomal translocation. Proc. Natl Acad. Sci. USA. 2007;104:4881–4885. PubMed PMC

Svidritskiy, E., Demo, G., Loveland, A. B., Xu, C. & Korostelev, A. A. Extensive Ribosome and RF2 Rearrangements during Translation Termination Elife8, e46850 (2019). PubMed PMC

Mastronarde DN. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 2005;152:36–51. PubMed

Kremer JR, Mastronarde DN, McIntosh JR. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 1996;116:71–76. PubMed

Grant, T., Rohou, A. & Grigorieff, N. cisTEM, user-friendly software for single-particle image processing. Elife7, 35383 (2018). PubMed PMC

Grigorieff N. Frealign: An Exploratory Tool for Single-Particle Cryo-EM. Methods Enzymol. 2016;579:191–226. PubMed PMC

Demo, G. et al. Mechanism of ribosome rescue by ArfA and RF2. Elife6, 23687 (2017). PubMed PMC

Cardone G, Heymann JB, Steven AC. One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions. J. Struct. Biol. 2013;184:226–236. PubMed PMC

Pettersen EF, et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput Chem. 2004;25:1605–1612. PubMed

DeLano, W.L The PyMOL Molecular Graphics System v. The PyMOL Molecular Graphics System (DeLano Scientific, Palo Alto, CA, USA, 2002).

Korostelev A, Bertram R, Chapman MS. Simulated-annealing real-space refinement as a tool in model building. Acta Crystallogr D. Biol. Crystallogr. 2002;58:761–767. PubMed

Korostelev A, et al. Crystal structure of a translation termination complex formed with release factor RF2. Proc. Natl Acad. Sci. USA. 2008;105:19684–19689. PubMed PMC

Adams PD, et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D. Biol. Crystallogr. 2010;66:213–221. PubMed PMC

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Structural basis for +1 ribosomal frameshifting during EF-G-catalyzed translocation

. 2021 Jul 30 ; 12 (1) : 4644. [epub] 20210730

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