An equilibrium-dependent retroviral mRNA switch regulates translational recoding

Abstract

The NMR structure of the murine leukaemia virus recoding translational signal is determined, giving insight into the mechanism of read-through in retroviruses. Retroviruses express their polymerase (Pol) and structural (Gag) proteins from a single Gag–Pol transcript during virus assembly. Although Gag can be translated on its own, Pol is produced only as a Gag–Pol fusion through recoding, a tightly controlled process involving bypass of the Gag stop codon. Victoria D'Souza and colleagues have now determined the NMR structure of the murine leukaemia virus recoding signal, a cis-acting 63-nucleotide pseudoknotted RNA, with a view to understanding how this readthrough occurs. The structure and functional data show that the RNA signal is maintained in two conformations at a ratio that correlates with the readthrough frequency. The RNA forms an equilibrium-based, protonation-dependent switch that toggles between the two conformations to maintain the required ratio. Most retroviruses require translational recoding of a viral messenger RNA stop codon to maintain a precise ratio of structural (Gag) and enzymatic (Pol) proteins during virus assembly1,2. Pol is expressed exclusively as a Gag–Pol fusion either by ribosomal frameshifting or by read-through of the gag stop codon3. Both of these mechanisms occur infrequently and only affect 5–10% of translating ribosomes, allowing the virus to maintain the critical Gag to Gag–Pol ratio4,5,6,7,8. Although it is understood that the frequency of the recoding event is regulated by cis RNA motifs, no mechanistic explanation is currently available for how the critical protein ratio is maintained. Here we present the NMR structure of the murine leukaemia virus recoding signal and show that a protonation-dependent switch occurs to induce the active conformation. The equilibrium is such that at physiological pH the active, read-through permissive conformation is populated at approximately 6%: a level that correlates with in vivo protein quantities. The RNA functions by a highly sensitive, chemo-mechanical coupling tuned to ensure an optimal read-through frequency. Similar observations for a frameshifting signal indicate that this novel equilibrium-based mechanism may have a general role in translational recoding.