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Structure of the HIV-1 RNA packaging signal

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Science  22 May 2015:
Vol. 348, Issue 6237, pp. 917-921
DOI: 10.1126/science.aaa9266
  • Fig. 1 HIV-1 5′ leader and ΨCES RNA construct.

    (A) Predicted secondary structure of the HIV-1 (NL4-3 strain) 5′ leader (16); gray shading denotes elements detected in the intact leader by NMR (13, 15); dark letters denote ΨCES (nonnative residues colored red; see text). (B and C) Substitution of the native DIS loop residues (DIS-native) by GAGA (DIS-GAGA) prevents dimerization (B) but does not affect NC binding (C). ppm, parts per million. (D) Representative NOESY spectra for G8A-ΨCES (black) and G-ΨCES (green); lines connect H8 (vertical labels) and H1′ (horizontal labels) signals. (E) Representative very-long-range NOE (A268-H2 to C252-H1′; ~7 Å separation) obtained for A2rCrCES.

  • Fig. 2 Fragmentation-based 2H-edited NMR approach and observed ΨCES secondary structure.

    (A) The DIS loop of ΨCES served as the fragmentation site and was substituted by a stretch of intermolecular G-C base pairs. (B) Fragment-annealing efficiency as measured by native agarose gel electrophoresis. (C) The 2D NOESY spectra of uniformly labeled A2rCr-, A2rUr-, and A2rCrUrCES and segmentally labeled fr-A2r:Ur- and fr-A2rCr:UrCES samples used to make long-range NOE assignments. (D) Similarities in NOESY spectra obtained for A2rCrUr-labeled [5′-LΔPBS]2 and ΨCES confirm that the tandem three-way junction structure is present in both constructs. (E) NMR-derived secondary structure of ΨCES. Black and blue arrows denote A-H2 NOEs observable in ΨCES and fr-ΨCES samples, respectively; red arrows highlight NOEs shown in (C) and (D); thin arrows denote very-long-range NOEs. (F) Packaging of native HIV-1NL4-3 5′-L and 5′-LΔPBS RNAs under competition conditions assayed by means of ribonuclease protection. P, undigested probe; M, RNA sizes marker. Lanes 1 and 2 show native HIV-1NL4-3 helper versus test vectors containing 5′-LΔPBS (1) or native HIV-1NL4-3 (2). Lane 3 contains HIV-1NL4-3 helper expressed without test RNA. Lane 4 is mock transfected cells. Samples obtained from transfected cells (Cells) or viral-containing media (Virus) are indicated. Bands corresponding to host 7SL RNA, HIV-1NL4-3 helper RNA (Ψ+), and copackaged test RNAs (Test) are labeled.

  • Fig. 3 Three-dimensional structure of ΨCES.

    (A) Ensemble of 20 refined structures (residues 105 to 344 shown). (B and C) Expanded views of the (B) three-way-1 and (C) three-way-2 junctions. (D) Surface representation of ΨCES highlighting U5 (blue):AUG (green) base pairing and the integral participation of SD residues (pink) in the tandem three-way junction structure. (E) Severe line broadening indicative of slow (millisecond) conformational averaging was observed for stacked, mismatched pyrimidines in the extended DIS stem [yellow in (D); broadened C287-H1′ signal boxed in (E)]. NOE patterns and sharp NMR signals also indicate that the ψ hairpin loop is unstructured [red in (D)].

  • Fig. 4 Junction guanosines mediate NC binding and packaging.

    (A) ΨCES contains 17 unpaired or weakly paired guanosines (red) that serve as potential NC binding sites. (B) Mutation of the three-way-2 (green) or ψ (magenta) guanosines to adenosines modestly reduces NC binding (N = 7.0 ± 0.3 and 7.0 ± 0.5, respectively) relative to wild-type ΨCES (black; N = 8.0 ± 0.3). Mutation of ψ and three-way-1 guanosines to adenosines (blue) severely inhibits high-affinity NC binding (N = 2.0 ± 0.1). (C) Competitive packaging of HIV-1NL4-3 vectors containing native and mutant 5′ leader sequences, assayed by means of ribonuclease protection. Lanes 1 to 4 are native HIV-1NL4-3 versus test vectors containing 5′-L3way2-G/A (1), 5′-L3way1-G/A (2), 5′-L3way1,2-G/A (3), and 5′-L (4). Lane 5 is HIV-1NL4-3 helper expressed without test RNA. Lane 6 is mock transfected cells. Samples obtained from transfected cells (Cells) or viral containing media (Virus) are indicated. Bands corresponding to host 7SL RNA, HIV-1NL4-3 helper RNA (Ψ+), and copackaged test RNAs (Test) are labeled.

Supplementary Materials

  • Structure of the HIV-1 RNA packaging signal

    Sarah C. Keane, Xiao Heng, Kun Lu, Siarhei Kharytonchyk, Venkateswaran Ramakrishnan, Gregory Carter, Shawn Barton, Azra Hosic, Alyssa Florwick, Justin Santos, Nicholas C. Bolden, Sayo McCowin, David A. Case, Bruce A. Johnson, Marco Salemi, Alice Telesnitsky, Michael F. Summers

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Figs. S1 to S4
    • Tables S1 and S2
    • Full Reference List

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