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. 2011 Jul 6;475(7354):118-21.
doi: 10.1038/nature10126.

The ribosome uses two active mechanisms to unwind messenger RNA during translation

Affiliations

The ribosome uses two active mechanisms to unwind messenger RNA during translation

Xiaohui Qu et al. Nature. .

Abstract

The ribosome translates the genetic information encoded in messenger RNA into protein. Folded structures in the coding region of an mRNA represent a kinetic barrier that lowers the peptide elongation rate, as the ribosome must disrupt structures it encounters in the mRNA at its entry site to allow translocation to the next codon. Such structures are exploited by the cell to create diverse strategies for translation regulation, such as programmed frameshifting, the modulation of protein expression levels, ribosome localization and co-translational protein folding. Although strand separation activity is inherent to the ribosome, requiring no exogenous helicases, its mechanism is still unknown. Here, using a single-molecule optical tweezers assay on mRNA hairpins, we find that the translation rate of identical codons at the decoding centre is greatly influenced by the GC content of folded structures at the mRNA entry site. Furthermore, force applied to the ends of the hairpin to favour its unfolding significantly speeds translation. Quantitative analysis of the force dependence of its helicase activity reveals that the ribosome, unlike previously studied helicases, uses two distinct active mechanisms to unwind mRNA structure: it destabilizes the helical junction at the mRNA entry site by biasing its thermal fluctuations towards the open state, increasing the probability of the ribosome translocating unhindered; and it mechanically pulls apart the mRNA single strands of the closed junction during the conformational changes that accompany ribosome translocation. The second of these mechanisms ensures a minimal basal rate of translation in the cell; specialized, mechanically stable structures are required to stall the ribosome temporarily. Our results establish a quantitative mechanical basis for understanding the mechanism of regulation of the elongation rate of translation by structured mRNAs.

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Figures

Figure 1
Figure 1
Experimental setup. a, Schematic drawing showing the attachment of the ends of the mRNA hairpin to the two beads. The mRNA sequences are shown in Figure S1. b, A trajectory for translation of hpValGC50 mRNA under 18 pN force (gray: 1000 Hz; red: 10 Hz). Extension change is in units of number of base pairs (bp) opened. Hopping of the residual hairpin is observed at the end of the trajectory due to its instability under force. Inset: zoomed-in view of step-wise extension change for two steps (100 Hz).
Figure 2
Figure 2
Dependence of translation rate on force and mRNA G•C content. a, Schematic drawing showing that when the ith codon in the A site (magenta) is translated, the subsequent translocation corresponds to unwinding the (i+4)th codon downstream (green) because the ribosome covers about 13 bases of single-stranded mRNA from its P site to the mRNA entry site. Only the sequence in the hairpin region is shown. b, Left panel: translation rate dependence on force for hpValGC50 mRNA (∼50% G•C unwinding). (i) Blue circles: experimental data. (ii) Black solid, dashed, and dot-dashed lines: predicted force dependence by the Betterton model, v = vss·fopen, with ΔGd = 0, 1.1, and 2.2 kcal/mole per bp, respectively. The three lines represent (solid) a totally passive helicase, (dashed) the best fit to FM and the high-force plateau, and (dot-dashed) the best fit to the two plateaus, respectively. (iii) Blue line: best fit by Equation 1: v = vss·fopen + vds·(1-fopen). The three fitting parameters, vss, vds, and ΔGd, largely determine the high-force plateau, the low-force plateau, and ΔFM (the shift in FM relative to a totally passive helicase), respectively. Right panel: Translation rate dependence on force for hpValGC100 mRNA with 100% G•C unwinding (red circles) and the best fit by Equation 1 (red line). The data and best fit for hpValGC50 mRNA (blue; from the left panel) is shown again for reference. The fitting results for both mRNAs are summarized in Table S1. n = 39-120 ribosomes for hpValGC50 and 16-29 ribosomes for hpValGC100, respectively, at each force. The error bars are the s.e.m.
Figure 3
Figure 3
The molecular arrangement of a translocating ribosome. a, The structure of the 30S subunit viewed from the mRNA entry site. About 30 nucleotides of single-stranded mRNA (orange) enter the ring-shaped mRNA entry site formed by the three colored ribosomal proteins, and wrap around the neck domain between the head and body. Secondary structures of the mRNA are excluded from the ribosome. b, Proposed ribosome unwinding mechanisms. The ribosome is rendered transparent so that the mRNA and the tRNAs inside can be clearly seen. Several base pairs (red) are destabilized by the ribosomal proteins at the entry site, which biases junction thermal fluctuations toward opening. Before translocation, the tRNAs (yellow) shift to the hybrid state (dashed). Then driven by ribosomal conformational changes, the tRNA anticodons translocate from the P and A sites on the 30S subunit to the E and P sites, and pull the mRNA along (black arrow). When encountering an open junction, translocation rectifies the junction opening events. Upon encountering a closed junction, the pulling force on the mRNA breaks open the mRNA junction at the entry site. The 50S and 30S subunits are from PDB files 2AW4 and 2AVY, respectively, and are modeled using PyMOL. The tRNAs and mRNA are for illustration purpose only.
Scheme 1
Scheme 1

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