Single-molecule study of ribosome hierarchic dynamics at the peptidyl transferase center

Abstract

During protein biosynthesis the ribosome moves along mRNA in steps of precisely three nucleotides. The mechanism for this ribosome motion remains elusive. Using a classification algorithm to sort single-molecule fluorescence resonance energy transfer data into subpopulations, we found that the ribosome dynamics detected at the peptidyl transferase center are highly inhomogeneous. The pretranslocation complex has at least four subpopulations that sample two hybrid states, whereas the posttranslocation complex is mainly static. We observed transitions among the ribosome subpopulations under various conditions, including 1), in the presence of EF-G; 2), spontaneously; 3), in different buffers, and 4), bound to antibiotics. Therefore, these subpopulations represent biologically active ribosomes. One key observation indicates that the Hy2 hybrid state only exists in a fluctuating ribosome subpopulation, which prompts us to propose that ribosome dynamics are hierarchically arranged. This proposal may have important implications for the regulation of cellular translation rates.

Figure 1

(a) The relative labeling positions of the FRET pairs on the ribosome L27 and the tRNAs at the A-site (left plot) and P-site (right plot). (b) Illustration of the ribosome complexes studied in this work. The triangle represents the N-acetyl-capped phenylalanine, and the circles represent the elongated phenylalanines.

Figure 2

FRET distributions of the signals between the L27 protein and the A-/P-site tRNAs in the (a) Pre-complex (951 particles) and (b) Post-complex (743 particles). The sketches beneath the histogram plots show the relative position of the FRET pairs. (c) One representative trace of the real-time observation of the translocation process. Imaging began immediately after EF-G·GTP (200 nM) was loaded onto the surface-bound Pre-complex. Translocation happened after ∼14 s.

Figure 3

FRET efficiency histograms of the Pre-complex. Four horizontally arranged plots are shown. The top-tier plots show the FRET histogram of the total ribosomes (951 particles, as shown in the parentheses) and a cartoon of the Pre-complex. The second-tier plots show the FRET histograms of the ribosomes separated into fluctuating (F, 640 particles) and nonfluctuating (NF, 311 particles) groups. The third-tier plots show the FRET histograms of the ribosomes further separated into groups of fluctuations that were above or below a FRET value of 0.6 (F-low contained 327 particles and F-high contained 313 particles). Similar thresholds (as discussed in the text) were applied to the NF ribosomes to separate them into stable FRET states that were below or above 0.6 (NF-low contained 262 particles and NF-high contained 49 particles). The fourth-tier plots display the representative fluorescence traces of the donor and acceptor species and their corresponding FRET traces (both the original and the truncated data) from each of the four subpopulations. Legends are shown in the individual plots.

Figure 4

Possible configurations of the FRET states observed in the Pre-complex. C is the classical state corresponding to the FRET efficiency of 0.44. Hy1 and Hy2 are the two possible hybrid states. The Hy1 state is assigned to the FRET state of 0.2 formed by the independent movement of the P-site tRNA. The Hy2 state is assigned to the FRET state of 0.63. Hy2 is most likely coupled with the ribosome intersubunit ratcheting.

Figure 5

Real-time stochastic transitions of ribosome subpopulations in the Pre-complex. The dotted lines separate the different types of dynamics. Although the exact points of the transitions are hard to identify, the overall transitions among the different ribosome subpopulations are obvious.

Figure 6

Redistribution of the Pre-complex subpopulations in 10 mM Mg²⁺ or 4.5 mM Mg²⁺ buffers, or bound with Viomycin. The color codes for the subpopulations are shown in the plot. With decreasing Mg²⁺ concentrations, F-High increases mainly at the expense of decreasing NF-Low, whereas in the presence of Viomycin, F-High increases mainly at the expense of decreasing F-Low. The error bars are calculated from at least three independent measurements.

Figure 7

The expanded, rugged, qualitative energy potential in the Pre-complex. The Post- and Pre-complexes are separated by first-level kinetic barriers. After deacylation of the P-site tRNA, the Pre-complex is able to sample a rugged potential surface. A second-level barrier separates the fluctuating and nonfluctuating conformations, and a third-level barrier further separates the fluctuations between C and Hy1 or C, Hy1, and Hy2. The motions of tRNAs to form A/P state and the P/E state are not coupled.