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An equilibrium-dependent retroviral mRNA switch regulates translational recoding


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.

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Figure 1: MLV-PK conformational-equilibrium-dependent read-through.
Figure 2: Functional data for modulation of the equilibrium.
Figure 3: Compensatory effects of the S1–L2 turn on the engineered inter-helical bend and equilibrium-based frameshifting levels.
Figure 4: Model for equilibrium-based mechanism.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Coordinates and restraints for the final ensemble of ten structures of PKinactive have been deposited in the Protein Data Bank under accession code 2LC8.


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We thank J. Atkins for the p2luc plasmid, the New York Structural Biology Center for NMR time and A. Hawkins, S. Leiman and J. Gullinger for their contributions. B.H.-L. and S.P.G. would also like to thank the late D. Wolf for his inspiration and many helpful discussions. S.P.G. acknowledges grant R37 CA30488 from the NCI/NIH and is an Investigator with the Howard Hughes Medical Institute.

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V.M.D’S., B.H.-L., M.A.D. and S.P.G. conceived of and designed the experiments. V.M.D’S., M.A.D., C.S., N.S. and B.H.-L. did the structural analysis, B.H.-L. did the recoding assays, and M.A.D. and J.M.N. did the in vivo assay for the double mutant. M.A.D. and V.M.D’S. wrote the manuscript with assistance from B.H.-L.

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Correspondence to Victoria M. D’Souza.

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The authors declare no competing financial interests.

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Houck-Loomis, B., Durney, M., Salguero, C. et al. An equilibrium-dependent retroviral mRNA switch regulates translational recoding. Nature 480, 561–564 (2011).

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