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A proposal for a new HIV-1 DLS structural model.

Sakuragi J, Ode H, Sakuragi S, Shioda T, Sato H - Nucleic Acids Res. (2012)

Bottom Line: Interestingly, the study revealed a previously unnoticed stem formation between two distantly positioned regions.Based on this and other findings on functional base pairing in vivo, we propose new 3D models of the HIV-1 DLS which contain a unique pseudoknot-like conformation.Since this pseudoknot-like conformation appears to be thermodynamically stable, forms a foundational skeleton for the DLS and sterically restricts the spontaneous diversification of DLS conformations, its unique shape may contribute to the viral life cycle and potentially serve as a novel target for anti-HIV-1 therapies.

View Article: PubMed Central - PubMed

Affiliation: Department of Viral Infections, RIMD, Osaka Univ. 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan. sakuragi@biken.osaka-u.ac.jp

ABSTRACT
The dimer initiation site/dimer linkage sequence (DIS/DLS) region of the human immunodeficiency virus type 1 (HIV-1) RNA genome is suggested to play essential roles at various stages of the viral life cycle. Through a novel assay we had recently developed, we reported on the necessary and sufficient region for RNA dimerization in the HIV-1 virion. Using this system, we performed further detailed mapping of the functional base pairs necessary for HIV-1 DLS structure. Interestingly, the study revealed a previously unnoticed stem formation between two distantly positioned regions. Based on this and other findings on functional base pairing in vivo, we propose new 3D models of the HIV-1 DLS which contain a unique pseudoknot-like conformation. Since this pseudoknot-like conformation appears to be thermodynamically stable, forms a foundational skeleton for the DLS and sterically restricts the spontaneous diversification of DLS conformations, its unique shape may contribute to the viral life cycle and potentially serve as a novel target for anti-HIV-1 therapies.

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New models of 2D and 3D structure of the DLS. The 2D and 3D structures of the DLS. (A) The 2D DLS schematic model that contains a previously unknown GCGUC-GACGC duplex. Other duplexes that were proposed previously and suggested to play roles in HIV-1 RNA dimerization within the virion in this and other studies (12,41) are also indicated. (B, C) Two 3D structural models of the DLS monomer. The 3D structural models of the DLS monomer were predicted with the MC-Sym software (37) by incorporating information on the duplexes within the DLS described in Figure 5A. Only two monomer models that were thermodynamically stable were obtained, due to the pseudoknot-like conformation that was formed with the two duplexes (GCGUC-GACGC and U5-AUG) restraining the conformational flexibility of the monomer. (D, E) Two 3D structural models of the DLS dimer. The 3D structural models of the DLS dimer were constructed by superposing 3D structure of SL1 with SL1 in a reported dimer structure [PDB code: 2D19 (24)], followed by energy minimization as described in ‘Materials and Methods' section.
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gks156-F5: New models of 2D and 3D structure of the DLS. The 2D and 3D structures of the DLS. (A) The 2D DLS schematic model that contains a previously unknown GCGUC-GACGC duplex. Other duplexes that were proposed previously and suggested to play roles in HIV-1 RNA dimerization within the virion in this and other studies (12,41) are also indicated. (B, C) Two 3D structural models of the DLS monomer. The 3D structural models of the DLS monomer were predicted with the MC-Sym software (37) by incorporating information on the duplexes within the DLS described in Figure 5A. Only two monomer models that were thermodynamically stable were obtained, due to the pseudoknot-like conformation that was formed with the two duplexes (GCGUC-GACGC and U5-AUG) restraining the conformational flexibility of the monomer. (D, E) Two 3D structural models of the DLS dimer. The 3D structural models of the DLS dimer were constructed by superposing 3D structure of SL1 with SL1 in a reported dimer structure [PDB code: 2D19 (24)], followed by energy minimization as described in ‘Materials and Methods' section.

Mentions: Upon the accumulated results, we draw the two-dimensional (2D) structural schema of DLS (Figure 5A). The 2D schema shows that the DLS is characterized by a unique pseudoknot-like conformation and three stem–loops. Such a pseudoknot-like conformation was predicted to form upon performing secondary structure prediction analysis using MC-Fold, without using additional experimental information. We further attempted the 3D structural modeling of the DLS by using RNA structure prediction computer programs that have shown marked improvements as of recent. We then confirmed whether the DLS could indeed have conformations similar to our modeling, without unfavorable interactions such as steric clash. The modeling predicted only two plausible 3D structures of the DLS monomer having the pseudoknot-like conformation (Figure 5B and C). In each of the DLS structures, the SL1 loop neighbored the SL3 loop and the pseudoknot-like conformation was located near the bases of these loops. In contrast, the two structures had distinct PBS stem orientations. Furthermore, we constructed dimer predictions based on these monomer structures (Figure 5D and E). In the dimer structures, palindromic sequences within the SL1 had interactions between monomers, whereas the pseudoknot-like conformations were furthest apart from each other. We also predicted 3D structural models of the DLS without a connection region between SL3 and the 3′-end part of the pseudoknot-like conformation. The modeling continually generated more structures, suggesting the pseudoknot-like conformation in the DLS would restrict its conformation. In the two models, an AUG codon at the translation initiation site of Gag p17 ORF formed a ‘U5-AUG duplex’, which was embedded as unexposed, translation-incompetent structures.Figure 5.


A proposal for a new HIV-1 DLS structural model.

Sakuragi J, Ode H, Sakuragi S, Shioda T, Sato H - Nucleic Acids Res. (2012)

New models of 2D and 3D structure of the DLS. The 2D and 3D structures of the DLS. (A) The 2D DLS schematic model that contains a previously unknown GCGUC-GACGC duplex. Other duplexes that were proposed previously and suggested to play roles in HIV-1 RNA dimerization within the virion in this and other studies (12,41) are also indicated. (B, C) Two 3D structural models of the DLS monomer. The 3D structural models of the DLS monomer were predicted with the MC-Sym software (37) by incorporating information on the duplexes within the DLS described in Figure 5A. Only two monomer models that were thermodynamically stable were obtained, due to the pseudoknot-like conformation that was formed with the two duplexes (GCGUC-GACGC and U5-AUG) restraining the conformational flexibility of the monomer. (D, E) Two 3D structural models of the DLS dimer. The 3D structural models of the DLS dimer were constructed by superposing 3D structure of SL1 with SL1 in a reported dimer structure [PDB code: 2D19 (24)], followed by energy minimization as described in ‘Materials and Methods' section.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC3367192&req=5

gks156-F5: New models of 2D and 3D structure of the DLS. The 2D and 3D structures of the DLS. (A) The 2D DLS schematic model that contains a previously unknown GCGUC-GACGC duplex. Other duplexes that were proposed previously and suggested to play roles in HIV-1 RNA dimerization within the virion in this and other studies (12,41) are also indicated. (B, C) Two 3D structural models of the DLS monomer. The 3D structural models of the DLS monomer were predicted with the MC-Sym software (37) by incorporating information on the duplexes within the DLS described in Figure 5A. Only two monomer models that were thermodynamically stable were obtained, due to the pseudoknot-like conformation that was formed with the two duplexes (GCGUC-GACGC and U5-AUG) restraining the conformational flexibility of the monomer. (D, E) Two 3D structural models of the DLS dimer. The 3D structural models of the DLS dimer were constructed by superposing 3D structure of SL1 with SL1 in a reported dimer structure [PDB code: 2D19 (24)], followed by energy minimization as described in ‘Materials and Methods' section.
Mentions: Upon the accumulated results, we draw the two-dimensional (2D) structural schema of DLS (Figure 5A). The 2D schema shows that the DLS is characterized by a unique pseudoknot-like conformation and three stem–loops. Such a pseudoknot-like conformation was predicted to form upon performing secondary structure prediction analysis using MC-Fold, without using additional experimental information. We further attempted the 3D structural modeling of the DLS by using RNA structure prediction computer programs that have shown marked improvements as of recent. We then confirmed whether the DLS could indeed have conformations similar to our modeling, without unfavorable interactions such as steric clash. The modeling predicted only two plausible 3D structures of the DLS monomer having the pseudoknot-like conformation (Figure 5B and C). In each of the DLS structures, the SL1 loop neighbored the SL3 loop and the pseudoknot-like conformation was located near the bases of these loops. In contrast, the two structures had distinct PBS stem orientations. Furthermore, we constructed dimer predictions based on these monomer structures (Figure 5D and E). In the dimer structures, palindromic sequences within the SL1 had interactions between monomers, whereas the pseudoknot-like conformations were furthest apart from each other. We also predicted 3D structural models of the DLS without a connection region between SL3 and the 3′-end part of the pseudoknot-like conformation. The modeling continually generated more structures, suggesting the pseudoknot-like conformation in the DLS would restrict its conformation. In the two models, an AUG codon at the translation initiation site of Gag p17 ORF formed a ‘U5-AUG duplex’, which was embedded as unexposed, translation-incompetent structures.Figure 5.

Bottom Line: Interestingly, the study revealed a previously unnoticed stem formation between two distantly positioned regions.Based on this and other findings on functional base pairing in vivo, we propose new 3D models of the HIV-1 DLS which contain a unique pseudoknot-like conformation.Since this pseudoknot-like conformation appears to be thermodynamically stable, forms a foundational skeleton for the DLS and sterically restricts the spontaneous diversification of DLS conformations, its unique shape may contribute to the viral life cycle and potentially serve as a novel target for anti-HIV-1 therapies.

View Article: PubMed Central - PubMed

Affiliation: Department of Viral Infections, RIMD, Osaka Univ. 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan. sakuragi@biken.osaka-u.ac.jp

ABSTRACT
The dimer initiation site/dimer linkage sequence (DIS/DLS) region of the human immunodeficiency virus type 1 (HIV-1) RNA genome is suggested to play essential roles at various stages of the viral life cycle. Through a novel assay we had recently developed, we reported on the necessary and sufficient region for RNA dimerization in the HIV-1 virion. Using this system, we performed further detailed mapping of the functional base pairs necessary for HIV-1 DLS structure. Interestingly, the study revealed a previously unnoticed stem formation between two distantly positioned regions. Based on this and other findings on functional base pairing in vivo, we propose new 3D models of the HIV-1 DLS which contain a unique pseudoknot-like conformation. Since this pseudoknot-like conformation appears to be thermodynamically stable, forms a foundational skeleton for the DLS and sterically restricts the spontaneous diversification of DLS conformations, its unique shape may contribute to the viral life cycle and potentially serve as a novel target for anti-HIV-1 therapies.

Show MeSH
Related in: MedlinePlus