The Ribosome Uses Two Active Mechanisms to Unwind mRNA During Translation

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 slows the peptide elongation rate, as the ribosome must disrupt structures it encounters in the mRNA at its entry site to enable translocation to the next codon. Such structures are exploited by the cell to create diverse strategies for translation regulation, such as programmed frameshifting(1,2), protein expression levels(3,4), ribosome localization(5), and cotranslational protein folding(6). Although strand separation activity is inherent to the ribosome, requiring no exogenous helicases(7), 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 center is greatly influenced by the G•C content of folded structures at the mRNA entry site. Furthermore, force applied to the ends of the hairpin to favor 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: (i) it destabilizes the helical junction at the mRNA entry site by biasing its thermal fluctuations toward the open state, increasing the probability for the ribosome to translocate unhindered; and (ii) it also mechanically pulls apart the mRNA single-strands of the closed junction during the conformational changes that accompany ribosome translocation. Our results establish a quantitative mechanical basis for understanding the mechanism of regulation of the elongation rate of translation by structured mRNAs.