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Structural basis for packaging the dimeric genome of Moloney murine leukaemia virus

Abstract

All retroviruses specifically package two copies of their genomes during virus assembly, a requirement for strand-transfer-mediated recombination during reverse transcription1,2. Genomic RNA exists in virions as dimers, and the overlap of RNA elements that promote dimerization and encapsidation suggests that these processes may be coupled3,4,5. Both processes are mediated by the nucleocapsid domain (NC) of the retroviral Gag polyprotein3. Here we show that dimerization-induced register shifts in base pairing within the Ψ-RNA packaging signal of Moloney murine leukaemia virus (MoMuLV) expose conserved UCUG elements that bind NC with high affinity (dissociation constant = 75 ± 12 nM). These elements are base-paired and do not bind NC in the monomeric RNA. The structure of the NC complex with a 101-nucleotide ‘core encapsidation’ segment of the MoMuLV Ψ site6 reveals a network of interactions that promote sequence- and structure-specific binding by NC's single CCHC zinc knuckle. Our findings support a structural RNA switch mechanism for genome encapsidation, in which protein binding sites are sequestered by base pairing in the monomeric RNA and become exposed upon dimerization to promote packaging of a diploid genome.

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Figure 1: MoMuLV Ψ site and structure of the NC–mΨCES complex.
Figure 2: Comparison of the guanosine binding sites of the MoMuLV and HIV-1 zinc knuckles.
Figure 3: NC binds to dimeric forms of DIS-1 and DIS-2.
Figure 4: Structural changes in the Ψ-site that seem to serve as a switch for the selective binding of NC to the dimer.

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Acknowledgements

We thank the HHMI staff and colleagues at UMBC for technical support. This research was supported by a grant from the NIH to M.F.S.

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Correspondence to Michael F. Summers.

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The authors declare that they have no competing financial interests.

Supplementary information

Supplementary Figures (DOC 2090 kb)

Supplementary Table

Statistical information associated with the structure calculations for the MLV NC-mCES complex (DOC 21 kb)

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D'Souza, V., Summers, M. Structural basis for packaging the dimeric genome of Moloney murine leukaemia virus. Nature 431, 586–590 (2004). https://doi.org/10.1038/nature02944

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