Destabilization of the P site codon-anticodon helix results from movement of tRNA into the P/E hybrid state within the ribosome

Abstract

Retention of the reading frame in ribosomal complexes after single-round translocation depends on the acylation state of the tRNA. When tRNA lacking a peptidyl group is translocated to the P site, the mRNA slips to allow re-pairing of the tRNA with a nearby out-of-frame codon. Here, we show that this ribosomal activity results from movement of tRNA into the P/E hybrid state. Slippage of mRNA is suppressed by 3' truncation of the translocated tRNA, increased MgCl2 concentration, and mutation C2394A of the 50S E site, and each of these conditions inhibits P/E-state formation. Mutation G2252U of the 50S P site stimulates mRNA slippage, suggesting that decreased affinity of tRNA for the P/P state also destabilizes mRNA in the complex. The effects of G2252U are suppressed by C2394A, further implicating the P/E state in mRNA destabilization. This work uncovers a functional attribute of the P/E state crucial for understanding translation.

Figure 1. Deacylation of N-Acetyl-Aminoacyl-tRNA in the Posttranslocation Complex Results in mRNA Slippage The position of mRNA in ribosomal complexes was mapped by toe-printing after each of several additions

(A) A pretranslocation complex was made by incubating ribosomes with message m299 and tRNA^fMet to fill the P site (lane P) and then adding N-acetyl-Tyr-tRNA^Tyr2 to fill the A site (lane A). Next, this pretranslocation complex was incubated with either GTP alone as a control (− lane) or with EF-G plus GTP to form the posttranslocation complex (+ lane). Finally, this posttranslocation complex was further incubated without or with addition of puromycin (1.7 mM) as indicated. (B) In an analogous experiment, a posttranslocation complex was formed by translocation of N-acetyl-Val-tRNA^Val1 paired to the GUA codon of m291, and slippage of the mRNA was observed after addition of puromycin.

Figure 2. The Destabilization of mRNA Observed Is Hypothesized to Result from Movement of tRNA into the P/E Hybrid State

Translocation of tRNA within the ribosome is believed to occur in a step-wise fashion (Pathway 1). After peptide bond formation, the newly deacylated tRNA and newly formed peptidyl-tRNA move first with respect to the 50S subunit into the hybrid P/E and A/P states, respectively. EF-G (+GTP) then catalyzes the movement of tRNA and mRNA with respect to the 30S subunit. Because interaction of tRNA in the E/E state is kinetically labile (Robertson and Wintermeyer, 1987; Semenkov et al., 1996), peptidyl-tRNA bound to the P/P state is presumably sufficient to retain stable mRNA interaction in this posttranslocation complex. EF-G(+GTP) can also catalyze the translocation of deacylated tRNA within the ribosome (Pathway 2), although it is unclear whether this reaction involves the hybrid state intermediate. In this posttranslocation complex, tRNA can occupy either the P/P or the P/E state. It is hypothesized that movement of tRNA into the P/E state destabilizes mRNA in this posttranslocation complex, which results in slippage of mRNA. Deacylation of peptidyl-tRNA in the posttranslocation complex of Pathway 1 by addition of puromycin also allows movement of tRNA into the P/E state, and destabilization of mRNA is also observed in this case (see Figure 1).

Figure 3. Slippage of mRNA Conferred by Translocation of Deacylated tRNA Is Suppressed by Its 3′ Truncation

(A) Preparations of 3′-truncated tRNAs (tRNA^Val1Δ3′ and tRNA^Tyr2Δ3′ ) were made by limited digestion with snake venom phosphodiesterase. Denaturing PAGE and methylene blue staining indicates that in each of these preparations, ~60% of the molecules lack nucleotides C74–A76 and ~40% lack C75–A76. Analytical digests were loaded in adjacent lanes to provide size markers. (B) Toeprinting was used to map the position of mRNA within the ribosome before and after EF-G-dependent translocation of several forms of tRNA^Tyr2. Pretranslocation complexes were made by incubating ribosomes with m299 and tRNA^fMet to fill the P site (P lanes) and then adding N-acetyl-Tyr-tRNA^Tyr2, tRNA^Tyr2, tRNA^Tyr2Δ3′, or ASL^Tyr2 to bind the A site (− lanes) as indicated. Complexes were then incubated in the presence of GTP alone (2 lanes) or EF-G plus GTP (+ lanes). In parallel, mRNA was mapped in complexes formed by binding N-acetyl-Tyr-tRNA^Tyr2, tRNA^Tyr2, tRNA^Tyr2Δ3′, or ASL^Tyr2 directly to the P site (lanes 17–20). (C) Slippage of mRNA conferred by the translocation of deacylated tRNA is partially suppressed by increasing the concentration of MgCl₂ in the translocation reaction. Pretranslocation complexes containing either N-acetyl-aminoacyl-tRNA (open symbols) or deacylated tRNA (closed symbols) bound to the A site were mixed into translocation reactions containing EF-G and GTP such that the final concentration of MgCl₂ differed as indicated. Reading-frame retention was determined after translocation of m291 with N-acetyl-Val-tRNA^Val1 (○) or tRNA^Val1 (●), m299 with N-acetyl-Tyr-tRNA^Tyr2 (□) or tRNA^Tyr2 (■), and m301 (Fredrick and Noller, 2003) with N-acetyl-Phe-tRNA^Phe (△) or tRNA^Phe (▲).

Figure 4. Effects of 23S rRNA Mutations C2394A, G2252U, and G2553U on Reading-Frame Retention after Translocation of Several Forms of tRNA^Tyr2

Pretranslocation complexes were made by incubating ribosomes with m299 and tRNA^fMet to fill the P site (P lanes) and then adding N-acetyl-Tyr-tRNA^Tyr2, Tyr-tRNA^Tyr2, tRNA^Tyr2, or tRNA^Tyr2Δ3′ to bind the A site (A lanes), as indicated. Complexes were then incubated in the presence of GTP (− lanes) or EF-G plus GTP (+ lanes). At each stage of the experiment, the position of mRNA was mapped by toeprinting.

Figure 5. Effect of G2252U on Deacylation of tRNA within the Ribosome

(A) G2252U increases the extent of deacylation of Tyr-[3′-³²P]-tRNA^Tyr2 in the posttranslocation complex. Pretranslocation complexes were formed by incubating programmed ribosomes with tRNA^fMet to fill the P site and subsequently adding either deacyl-[3′-³²P]-tRNA^Tyr2 (da) or Tyr-[3′-³²P]-tRNA^Tyr2 (aa) to bind the A site. Then, EF-G and GTP were added to catalyze translocation, and the resulting complexes were purified from free tRNA and subjected to acid gel electrophoresis to resolve aminoacylated from deacylated tRNA (as indicated). (B) G2252U does not affect the extent of deacylation of Val-[3′-³²P]-tRNAVal1 in the posttranslocation complex. This experiment is similar to that of (A), although in this case, either deacyl-[3′-³²P]-tRNA^Val1 (da) or Val-[3′-³²P]-tRNA^Val1 (aa) was translocated to the P site prior to complex purification and acid gel electrophoresis. Values represent the mean ± SEM of three independent experiments.

Figure 6. Summary of Data to Support the Model that Movement of tRNA into the P/E State Destabilizes the Codon-Anticodon Helix

For each condition predicted to increase the relative affinity for the P/P state, an increase in reading-frame retention was observed. On the other hand, mutation G2252U, predicted to increase the relative affinity for the P/E state, decreased frame retention.