Structure of ratcheted ribosomes with tRNAs in hybrid states

Abstract

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...

Insights into the molecular determinants of EF-G catalyzed translocation

“…Such observations argue for complexities in the nature of tRNA motions within the PRE complex exceeding those previously anticipated (Munro et al 2007). In line with the conclusions of recent cryo-EM investigations, such data suggest that the transition of peptidyl-tRNA from its classical to hybrid (A/P) configuration only requires motions of the 39-CCA end of peptidyl-tRNA into the P site of the large subunit, while the A-site tRNA body remains classically configured (Agirrezabala et al 2008;Julian et al 2008). Thus, the present observations suggest that the H2 FRET state, originally defined as representing an A/A; P/E hybrid PRE complex configuration (Munro et al 2007), may actually represent an ensemble of configurations that also includes the A/P; P/E hybrid configuration in which only the 39-CCA end of peptidyl-tRNA has moved into the P site.…”

“…The spontaneous exchange of A-and P-site tRNA between classical and hybrid states within the PRE complex has since been confirmed through two independent cryo-electron microscopy (EM) investigations (Agirrezabala et al 2008;Julian et al 2008). Such studies provided the first three-dimensional structural information reporting on the nature of the hybrid PRE complex configuration.…”

Taura syndrome virus IRES initiates translation by binding its tRNA-mRNA–like structural element in the ribosomal decoding center

“…In the posttranslocation state, in which peptidyl-and deacyl-tRNAs occupy the P and E sites, respectively, the ribosome adopts a "nonrotated" (classical) conformation. In the pretranslocation state, a 9-12°counterclockwise rotation of the small subunit was observed for bacterial (36,42,43) and eukaryotic (44) ribosomes. This conformation of the ribosome is referred to as "rotated.…”

“…Here, the anticodon stem loops are located in the A and P sites of the small subunit, whereas the acceptor arms on the large subunit are located in the P and E sites, respectively (41)(42)(43).…”

Following movement of domain IV of elongation factor G during ribosomal translocation

“…1A) (1). Movement of the tRNAs into the hybrid A/P and P/E states is accompanied by a rotation of the 30S subunit; translocation of the mRNA and tRNAs on the small subunit is coupled to the reverse rotation of the small subunit (2)(3)(4)(5). Hence, during the translocation cycle, the ribosome transitions between at least three different states: (i) pretranslocation ribosome in the classical, nonrotated conformation; (ii) pretranslocation ribosome in the hybrid, rotated conformation; and (iii) posttranslocation ribosome in the classical, nonrotated conformation (Fig.…”