RNA flexibility in the dimerization domain of a gamma retrovirus


Retroviruses are the causative agents of serious diseases, such as acquired immunodeficiency syndromes and several cancers, and are also useful gene therapy vectors. Retroviruses contain two sense-strand RNA genomes, which become linked at their 5′ ends to form an RNA dimer. Understanding the molecular basis for dimerization may yield new approaches for controlling viral infectivity. Because this RNA domain is highly conserved within retrovirus groups, it has not been possible to define a consensus structure for the 5′ dimerization domain by comparative sequence analysis. Here, we defined a 170-nucleotide minimal dimerization active sequence (MiDAS) for a representative gamma retrovirus, the Moloney murine sarcoma virus, by stringent competitive dimerization. We then analyzed the structure at every nucleotide in the MiDAS monomeric starting state with quantitative selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry. Notably, SHAPE analysis demonstrated that the RNA monomer contains an extensive flexible domain spanning 50 nucleotides. These findings support a structural model in which RNA flexibility directly facilitates retroviral genome dimerization by reducing the energetic cost of disrupting pre-existing base pairings in the monomer.

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Figure 1: 5′-untranslated region of MuSV.
Figure 2: Competitive-dimerization assay for stringent definition of RNA structures essential for dimerization.
Figure 3: The MiDAS for MuSV defined by competitive dimerization.
Figure 4: SHAPE analysis of the MuSV MiDAS RNA and of the PALSTB and Δ289–300 mutants.
Figure 5: Secondary structure model of the MuSV MiDAS RNA.
Figure 6: Quantitative difference maps for the effects of mutations on MiDAS structure.
Figure 7: Structural model for overall flexibility in the 231–315 domain.


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This work was supported by a grant from the US National Institutes of Health (GM64803 to K.M.W. and A. Kaplan). We are indebted to A. Kaplan, C. Gherghe and A. Rein for many helpful discussions; to E. Merino and K. Wilkinson for assistance with SHAPE chemistry; and to D. Mathews for extensive advice with the RNAStructure program.

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Correspondence to Kevin M Weeks.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Dimerization activity of 3′ and 5′ truncation mutants. (PDF 398 kb)

Supplementary Fig. 2

Proposed secondary structures for MuLV and HaSV dimerization domains. (PDF 242 kb)

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Badorrek, C., Weeks, K. RNA flexibility in the dimerization domain of a gamma retrovirus. Nat Chem Biol 1, 104–111 (2005). https://doi.org/10.1038/nchembio712

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