Abstract
The ribosome can translate through the duplex region or secondary structure of mRNA. Recent single-molecule experimental data showed that downstream mRNA secondary structures have more sensitive effects on deacylated tRNA dissociation from the E site than on tRNA translocation in the 50S subunit. However, it is unclear how the downstream mRNA secondary structure can affect the tRNA dissociation from the E site, which is distant from the secondary structure. Here, based on our proposed ribosomal translocation model, we theoretically study the dynamics of tRNA translocation in the 50S subunit, mRNA translocation and tRNA dissociation, giving quantitative explanations of the single-molecule experimental data. It is shown that the effect of the downstream mRNA secondary structure on tRNA dissociation is via the effect on mRNA translocation, while the mRNA secondary structure has no effect on the rate of deacylated tRNA dissociation from the posttranslocation state. The slow mRNA translocation, which results in slow tRNA dissociation, derives from the occurrence of the futile transition, which is induced by the energy barrier from base pair unwinding to resist the forward translocation. The reduced translation rate through the mRNA secondary structure is induced by the slow mRNA translocation rather than the slow tRNA dissociation.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Notes
Zavialov et al. (2005) found that EF-G.GDP catalyzes movement of tRNAs into the hybrid state. Experimental data of Spiegel et al. (2007) also showed that binding of EF-G.GDP in the presence of fusidic acid stabilizes the hybrid state. It is noted however that in the experiments of Spiegel et al. (2007), no stable EF-G.GDP binding to the pretranslocation state was detected in the absence of fusidic acid. This can be understood by considering that EF-G.GDP alone has a lower affinity than EF-G.GDPNP to the pretranslocation state, as demonstrated by the recent single-molecule data of Chen et al. (2013b), showing that EF-G.GDP binds infrequently, whereas EF-G.GDPNP binds frequently to the pretranslocation state. However, Chen et al. (2013b) showed that EF-G.GDP has a much higher affinity to the pretranslocation state than to the posttranslocation state. Note also that studies by Wilden et al. (2006) have concluded that EF-G.GDP translocates a pretranslocation complex at rates similar to those of EF-G.GDPNP. As explained by Zavialov et al. (2005), this is due to the contamination of GDP with trace amounts of GTP. Indeed, Spiegel et al. (2007) found that commercially available GDP preparations contain significant levels of GTP, and they further showed that when using GDP that was purified by ion-exchange chromatography, no mRNA translocation was detected.
References
Blanchard SC, Kim HD, Gonzalez RL Jr, Puglisi JD, Chu S (2004) tRNA dynamics on the ribosome during translation. Proc Natl Acad Sci USA 101:12893–12898
Chen C, Stevens B, Kaur J, Cabral D, Liu H, Wang Y, Zhang H, Rosenblum G, Smilansky Z, Goldman YE, Cooperman B (2011a) Single-molecule fluorescence measurements of ribosomal translocation dynamics. Mol Cell 42:367–377
Chen C, Stevens B, Kaur J, Smilansky Z, Cooperman BS, Goldman YE (2011b) Allosteric vs. spontaneous exit-site (E-site) tRNA dissociation early in protein synthesis. Proc Natl Acad Sci USA 108:16980–16985
Chen C, Zhang H, Broitman SL, Reiche M, Farrell I, Cooperman BS, Goldman YE (2013a) Dynamics of translation by single ribosomes through mRNA secondary structures. Nature Struct Mol Biol 20:582–588
Chen J, Petrov A, Tsai A, O’Leary SE, Puglisi JD (2013b) Coordinated conformational and compositional dynamics drive ribosome translocation. Nature Struct Mol Biol 20:718–727
Cornish PV, Ermolenko DN, Noller HF, Ha T (2008) Spontaneous intersubunit rotation in single ribosomes. Mol Cell 30:578–588
Fei J, Kosuri P, MacDougall DD, Gonzalez RL Jr (2008) Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. Mol Cell 30:348–359
Feinberg JS, Joseph S (2001) Identification of molecular interactions between P-site tRNA and the ribosome essential for translocation. Proc Natl Acad Sci USA 98:11120–11125
Fischer N, Konevega AL, Wintermeyer W, Rodnina MV, Stark H (2010) Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy. Nature 466:329–333
Frank J, Agrawal RK (2000) A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature 406:318–322
Frank J, Gao H, Sengupta J, Gao N, Taylor DJ (2007) The process of mRNA–tRNA translocation. Proc Natl Acad Sci USA 104:19671–19678
Green R, Noller HF (1997) Ribosomes and translation. Annu Rev Biochem 66:679–716
Lill R, Robertson JM, Wintermeyer W (1989) Binding of the 30-terminus of tRNA to 23S rRNA in the ribosomal exit site actively promotes translocation. EMBO J 8:3933–3938
Moazed D, Noller HF (1989) Intermediate states in the movement of transfer RNA in the ribosome. Nature 342:142–148
Petrov A, Kornberg G, O’Leary S, Tsai A, Uemura S, Puglisi JD (2011) Dynamics of the translational machinery. Curr Opin Struct Biol 21:137–145
Qu X, Wen J-D, Lancaster L, Noller HF, Bustamante C, Tinoco I Jr (2011) The ribosomeuses two activemechanisms to unwind messenger RNA during translation. Nature 475:118–121
Savelsbergh A, Katunin VI, Mohr D, Peske F, Rodnina MV, Wintermeyer W (2003) An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation. Mol Cell 11:1517–1523
Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JHD (2005) Structures of the bacterial ribosome at 3.5 Å resolution. Science 310:827–834
Shoji S, Walker SE, Fredrick K (2009) Ribosomal translocation: one step closer to the molecular mechanism. ACS Chem Biol 4:93–107
Spiegel PC, Ermolenko DN, Noller HF (2007) Elongation factor G stabilizes the hybrid-state conformation of the 70S ribosome. RNA 13:1473–1482
Takyar S, Hickerson RP, Noller HF (2005) mRNA helicase activity of the ribosome. Cell 120:49–58
Valle M (2011) Almost lost in translation. Cryo-EM of a dynamic macromolecular complex: the ribosome. Eur Biophys J 40:589–597
Valle M, Zavialov A, Sengupta J, Rawat U, Ehrenberg M, Frank J (2003) Locking and unlocking of ribosomal motions. Cell 114:123–134
Wen J-D, Lancaster L, Hodges C, Zeri A-C, Yoshimura SH, Noller HF, Bustamante C, Tinoco I Jr (2008) Following translation by single ribosomes one codon at a time. Nature 452:598–604
Wilden B, Savelsbergh A, Rodnina MV, Wintermeyer W (2006) Role and timing of GTP binding and hydrolysis during EF-G–dependent tRNA translocation on the ribosome. Proc Natl Acad Sci 103:13670–13675
Wintermeyer W, Peske F, Beringer M, Gromadski KB, Savelsbergh A, Rodnina MV (2004) Mechanisms of elongation on the ribosome: dynamics of a macromolecular machine. Biochem Soc Trans 32:733–737
Xie P (2013a) Model of ribosome translation and mRNA unwinding. Eur Biophys J 42:347–354
Xie P (2013b) Dynamics of forward and backward translocation of mRNA in the ribosome. PLoS One 8:e70789
Xie P (2013c) A dynamical model of programmed-1 ribosomal frameshifting. J Theor Biol 336:119–131
Xie P (2014) An explanation of biphasic characters of mRNA translocation in the ribosome. Biosystems 118:1–7
Zavialov AV, Ehrenberg M (2003) Peptidyl-tRNA regulates the GTPase activity of translation factors. Cell 114:113–122
Zavialov AV, Hauryliuk VV, Ehrenberg M (2005) Guaninenucleotide exchange on ribosome-bound elongation factor G initiates the translocation of tRNAs. J. Biol 4:9
Acknowledgments
This work was supported by the National Natural Science Foundation of China (grant No. 11374352).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Xie, P. Dynamics of tRNA translocation, mRNA translocation and tRNA dissociation during ribosome translation through mRNA secondary structures. Eur Biophys J 43, 229–240 (2014). https://doi.org/10.1007/s00249-014-0957-x
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00249-014-0957-x