EF-G-independent reactivity of a pre-translocation-state ribosome complex with the aminoacyl tRNA substrate puromycin supports an intermediate (hybrid) state of tRNA binding

Sharma, Divya; Southworth, Daniel R.; Green, Rachel

doi:10.1261/rna.5148704

Cited by 80 publications

(85 citation statements)

References 41 publications

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“…These data are consistent with Ͼ95% tRNA accommodation and formation of peptidyl-tRNA at the A site, which impedes puromycin reactivity (16). The observed rate, corrected for peptidyl-tRNA dissociation from the A site (49), agrees with previous studies that cite slow reaction of peptidyl-tRNA with puromycin before translocation (19,50). The residual reactivity of peptidyl-tRNA suggests that the 50S A site remains at least partially accessible to puromycin.…”

Section: Surface-immobilized Ribosomes Are Highly Active In Peptide Bondsupporting

confidence: 89%

tRNA dynamics on the ribosome during translation

Blanchard

Kim

Gonzalez

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

454

575

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Using single-molecule fluorescence spectroscopy, time-resolved conformational changes between fluorescently labeled tRNA have been characterized within surface-immobilized ribosomes proceeding through a complete cycle of translation elongation. Fluorescence resonance energy transfer was used to observe aminoacyl-tRNA (aa-tRNA) stably accommodating into the aminoacyl site (A site) of the ribosome via a multistep, elongation factor-Tu dependent process. Subsequently, tRNA molecules, bound at the peptidyl site and A site, fluctuate between two configurations assigned as classical and hybrid states. The lifetime of classical and hybrid states, measured for complexes carrying aa-tRNA and peptidyl-tRNA at the A site, shows that peptide bond formation decreases the lifetime of the classical-state tRNA configuration by Ϸ6-fold. These data suggest that the growing peptide chain plays a role in modulating fluctuations between hybrid and classical states. Single-molecule fluorescence resonance energy transfer was also used to observe aa-tRNA accommodation coupled with elongation factor G-mediated translocation. Dynamic rearrangements in tRNA configuration are also observed subsequent to the translocation reaction. This work underscores the importance of dynamics in ribosome function and demonstrates single-particle enzymology in a system of more than two components. P rotein synthesis, catalyzed by the ribosome, is rapid, processive, and highly regulated. In bacteria, two RNA-protein subunits consisting of a small 30S subunit and a large 50S subunit assemble around a mRNA template into a roughly spherical 70S particle that translates the nucleotide sequence into a polypeptide chain through repetitive, codon-dependent binding of aminoacylated tRNA.The landmark structures of the 30S (1, 2), 50S (3, 4), and 70S (5) ribosomal particles provide a molecular basis for understanding ribosome function. tRNA molecules bind to the ribosome in a solvent-accessible channel at the subunit interface. Three binding sites for tRNA, called the aminoacyl site (A site), peptidyl site (P site), and exit site (E site), have been identified on both the large and small subunit (Fig. 1). Each tRNA is separated from its neighbor at the elbow region (the site of Ϸ90°b ending) by 25-45 Å (5, 6). The anticodon stem loops of A-and P-site tRNA form Watson-Crick base pairs with adjacent mRNA codons on the 30S subunit (5, 7), whereas the 3Ј CCA terminal residues of A-and P-site tRNAs base-pair with conserved ribosomal RNA (rRNA) loops (8-10) within the 50S subunit peptidyltransferase center, the site of peptide bond formation (11). Additional interactions with rRNA and ribosomal proteins position tRNA molecules on the ribosome (5).The essential components and principal steps of translation have been delineated through genetic, biochemical, and kinetic methods (12). The process of polypeptide elongation has been most extensively characterized (13). Binding of aminoacyl-tRNA (aa-tRNA) to the A site occurs as a ''ternary complex'' with the GTPase elongation ...

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Section: Surface-immobilized Ribosomes Are Highly Active In Peptide Bondsupporting

confidence: 89%

tRNA dynamics on the ribosome during translation

Blanchard

Kim

Gonzalez

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

454

575

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“…Subunit ratcheting and the ability of the P-site tRNA to interact with the E site on the 50S subunit are essential for EF-G-promoted translocation (5,17), suggesting that the combined hybridratcheted state is an authentic early intermediate of translocation. On the other hand, the spontaneous formation of this state as such is not sufficient to move the acceptor end of peptidyltRNA into the proper posttranslocation position, as indicated by low reactivity with puromycin (15,18). Therefore, we postulate that the hybrid-ratcheted configuration is the natural substrate for EF-G, and EF-G may either bind to that state preferentially or shift the ribosomes to that state before the tRNA movement on the 30S subunit.…”

Section: Resultsmentioning

confidence: 87%

Structure of ratcheted ribosomes with tRNAs in hybrid states

Julián

Konevega

Scheres³

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

168

176

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During protein synthesis, tRNAs and mRNA move through the ribosome between aminoacyl (A), peptidyl (P), and exit (E) sites of the ribosome in a process called translocation. Translocation is accompanied by the displacement of the tRNAs on the large ribosomal subunit toward the hybrid A/P and P/E states and by a rotational movement (ratchet) of the ribosomal subunits relative to one another. So far, the structure of the ratcheted state has been observed only when translation factors were bound to the ribosome. Using cryo-electron microscopy and classification, we show here that ribosomes can spontaneously adopt a ratcheted conformation with tRNAs in their hybrid states. The peptidyl-tRNA molecule in the A/P state, which is visualized here, is not distorted compared with the A/A state except for slight adjustments of its acceptor end, suggesting that the displacement of the A-site tRNA on the 50S subunit is passive and is induced by the 30S subunit rotation. Simultaneous subunit ratchet and formation of the tRNA hybrid states precede and may promote the subsequent rapid and coordinated tRNA translocation on the 30S subunit catalyzed by elongation factor G.translocation ͉ elongation factor G ͉ cryo-electron microscopy D uring the elongation cycle, the tRNAs⅐mRNA complex is translocated to allow reading of the following codon on mRNA. Translocation is promoted by elongation factor G (EF-G) and accompanied by GTP hydrolysis. During translocation, the ribosome changes from the pretranslocation state with deacylated tRNA in the peptidyl site (P site) and peptidyltRNA in the aminoacyl site (A site) to the posttranslocation state where A-and P-site tRNAs have moved to P and exit (E) sites, respectively. The universal design of ribosomes from two subunits inspired early suggestions that translocation may involve a movement of the subunits relative to each other (1, 2). Such models imply the existence of intermediate states for the tRNAs that differ from the classic A, P, and E states. Chemical probing experiments with pretranslocation ribosomes indicated that after peptidyl transfer the acceptor ends of the tRNAs spontaneously moved on the large 50S subunit toward their posttranslocation positions (3), indicating that peptidyl-tRNA and deacylated tRNA entered hybrid A/P and P/E states, respectively. The transition was observed in the absence of EF-G, and the driving force for the movement was attributed to different affinities of the A, P, and E sites on the 50S subunit (4) for the chemically different acceptor ends of the tRNAs (5, 6). Nevertheless, cryo-electron microscopy (cryoEM) of ribosomes in the pretranslocation state showed the tRNAs in their classic A, P, and E states (7). Although this result was difficult to reconcile with the hybrid-state model, it is important to note that in that complex the occupancy of the E site by deacylated tRNA may have prevented the P-site tRNA to enter the P/E-site hybrid state.CryoEM of ribosomes in complex with EF-G revealed a relative rotation between subunits referred to as ratc...

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“…2b, lanes 11-15, or G2251 and C75G tRNA Tyr in Fig. 2c, lanes [11][12][13][14][15] or between the A loop and the A-site AcPhe-tRNA Phe (G2553C and C75G AcPhe-tRNA Phe in Fig. 2d, lanes 6-10) were not competent for sparsomycin-dependent translocation.…”

Section: Effects On Sparsomycin-dependent Translocationmentioning

confidence: 99%

The hybrid state of tRNA binding is an authentic translation elongation intermediate

Dorner

Brunelle

Sharma

et al. 2006

Nat Struct Mol Biol

Self Cite

121

140

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The GTPase elongation factor (EF)-G is responsible for promoting the translocation of the messenger RNA-transfer RNA complex on the ribosome, thus opening up the A site for the next aminoacyltRNA. Chemical modification and cryo-EM studies have indicated that tRNAs can bind the ribosome in an alternative 'hybrid' state after peptidyl transfer and before translocation, though the relevance of this state during translation elongation has been a subject of debate. Here, using pre-steady-state kinetic approaches and mutant analysis, we show that translocation by EF-G is most efficient when tRNAs are bound in a hybrid state, supporting the argument that this state is an authentic intermediate during translation.Translation elongation is the multistep process performed by the ribosome to sequentially add mRNA-encoded amino acids to the growing polypeptide chain. There are three iterated steps performed by the ribosome during the elongation cycle: (i) a tRNA-selection step in which the ribosome and elongation factor (EF)-Tu select the next aminoacyl-tRNA to enter the cycle; (ii) peptide-bond formation catalyzed in the active site of the large ribosomal subunit; and (iii) translocation of the mRNA-tRNA complex through the subunit interface region, facilitated by EF-G, with associated GTP hydrolysis. The tRNA substrates are at the heart of each of these steps, where they have key functional roles 1-3 .Early studies on the ribosome identified binding sites for two tRNA substrates, the A site for the aminoacyl-tRNA and the P site for the peptidyl-tRNA. Further biochemistry eventually identified a third site, the E or exit site, where deacylated tRNAs bind after loss of the peptidyl moiety and before release into solution 4 . An understanding of the order and timing with which tRNA substrates occupy these three sites (on both the large and small subunits) during the elongation cycle is central to a detailed molecular view of the process of translation.The hybrid state of tRNA binding on the ribosome was first proposed in the 1960s as an elegant way to understand how controlled tRNA movement through the ribosome might be accomplished 5 . The basic feature of such a hybrid state of binding is that tRNAs would move independently with respect to the two subunits of the ribosome during the steps of the translation cycle. Fluorescence studies provided early biochemical clues that such a state of tRNA binding might be populated during translation 6 , and subsequent chemical-modification analysis provided clear and detailed experimental support for the hybrid state 7 . These studies Correspondence should be addressed to R.G. (ragreen@jhmi.edu).. Note: Supplementary information is available on the Nature Structural & Molecular Biology website. COMPETING INTERESTS STATEMENTThe authors declare that they have no competing financial interests.Published online at http://www.nature.com/nsmb/ Reprints and permissions information is available online at http://www.nature.com/reprints/index.html NIH Public Access Fig. 1a). Thus, 'hybr...

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EF-G-independent reactivity of a pre-translocation-state ribosome complex with the aminoacyl tRNA substrate puromycin supports an intermediate (hybrid) state of tRNA binding

Cited by 80 publications

References 41 publications

tRNA dynamics on the ribosome during translation

tRNA dynamics on the ribosome during translation

Structure of ratcheted ribosomes with tRNAs in hybrid states

The hybrid state of tRNA binding is an authentic translation elongation intermediate

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