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On the Selective Packaging of Genomic RNA by HIV-1

View Article: PubMed Central - PubMed

ABSTRACT

Like other retroviruses, human immunodeficiency virus type 1 (HIV-1) selectively packages genomic RNA (gRNA) during virus assembly. However, in the absence of the gRNA, cellular messenger RNAs (mRNAs) are packaged. While the gRNA is selected because of its cis-acting packaging signal, the mechanism of this selection is not understood. The affinity of Gag (the viral structural protein) for cellular RNAs at physiological ionic strength is not much higher than that for the gRNA. However, binding to the gRNA is more salt-resistant, implying that it has a higher non-electrostatic component. We have previously studied the spacer 1 (SP1) region of Gag and showed that it can undergo a concentration-dependent conformational transition. We proposed that this transition represents the first step in assembly, i.e., the conversion of Gag to an assembly-ready state. To explain selective packaging of gRNA, we suggest here that binding of Gag to gRNA, with its high non-electrostatic component, triggers this conversion more readily than binding to other RNAs; thus we predict that a Gag–gRNA complex will nucleate particle assembly more efficiently than other Gag–RNA complexes. New data shows that among cellular mRNAs, those with long 3′-untranslated regions (UTR) are selectively packaged. It seems plausible that the 3′-UTR, a stretch of RNA not occupied by ribosomes, offers a favorable binding site for Gag.

No MeSH data available.


Related in: MedlinePlus

Schematic representation of the binding of HIV-1 Gag to the dimeric HIV-1 genomic RNA (gRNA) (a,b) and to non-Ψ RNA (c,d). (a) In the cytoplasm Gag binds to the HIV-1 gRNA by recognizing the RNA dimeric interface. Binding of Gag to Ψ increases the local concentration of Gag, thus promoting a conformational change in the SP1 domain from a random coil to an α-helix (green portion of Gag); (b) Once the HIV-1 Gag–dimeric gRNA complexes are bound to the plasma membrane, the specific Gag–RNA interactions promote a conformational change in Gag that enables high-order Gag–Gag interactions (blue interface); (c) In the absence of the HIV-1 gRNA Gag binds to mRNAs; however, because these interactions are non-specific, a higher Gag concentration is required to induce the conformational change in Gag; (d) When Gag–non-Ψ RNA complexes are bound to the plasma membrane, the local concentration of Gag is high enough to promote high-order Gag–Gag interactions. MA: matrix; CA-NTD: N-terminal domain of the capsid; CA-CTD: C-terminal domain of the capsid; SP1: spacer 1; NC: nucleocapsid.
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viruses-08-00246-f004: Schematic representation of the binding of HIV-1 Gag to the dimeric HIV-1 genomic RNA (gRNA) (a,b) and to non-Ψ RNA (c,d). (a) In the cytoplasm Gag binds to the HIV-1 gRNA by recognizing the RNA dimeric interface. Binding of Gag to Ψ increases the local concentration of Gag, thus promoting a conformational change in the SP1 domain from a random coil to an α-helix (green portion of Gag); (b) Once the HIV-1 Gag–dimeric gRNA complexes are bound to the plasma membrane, the specific Gag–RNA interactions promote a conformational change in Gag that enables high-order Gag–Gag interactions (blue interface); (c) In the absence of the HIV-1 gRNA Gag binds to mRNAs; however, because these interactions are non-specific, a higher Gag concentration is required to induce the conformational change in Gag; (d) When Gag–non-Ψ RNA complexes are bound to the plasma membrane, the local concentration of Gag is high enough to promote high-order Gag–Gag interactions. MA: matrix; CA-NTD: N-terminal domain of the capsid; CA-CTD: C-terminal domain of the capsid; SP1: spacer 1; NC: nucleocapsid.

Mentions: Earlier in this review, we described our findings on the SP1 domain of Gag, which led us to suggest that a conformational change in SP1 switches Gag into an assembly-ready state [23]. In some biological systems the nucleation of high-order protein complexes (e.g., immature virions) is driven by protein-protein interactions. Initiation of this process has to overcome an energetic barrier (activation energy); hence a nucleation process can be accelerated if the activation energy is lowered. This can be achieved by the presence of a nucleation site or a “seed”. In the simplest scenario, a nucleation site acts by enhancing protein-protein interactions such that the energy gained by protein multimerization overcomes the loss of entropy due to the decrease of free protein, and therefore lowers the activation energy. Based on the idea proposed by Nikolaitchick and co-workers [50], on some of the data discussed here, and on these physical principles, we can ask the following question; is selective packaging of the HIV-1 gRNA driven by Ψ acting as a nucleation site for virion assembly? A hypothesis in which selective packaging of the HIV-1 gRNA is achieved by a Ψ lowering the energy needed to nucleate virion assembly is consistent with the fact that HIV-1 VLP assembly can be efficiently supported by cellular mRNAs, but that this assembly process is completely inhibited in the presence of the gRNA. In the context of this nucleation scenario it is possible that the dimeric Ψ acts as a “seed” such that binding of just a few Gag molecules to this substrate is enough to activate the SP1 conformational switch, exposing new Gag–Gag interfaces and therefore nucleating efficient virion assembly (see Figure 4). According to this hypothesis, VLP assembly can occur in the absence of the dimeric Ψ, but this process has a higher activation energy because binding to the non-Ψ is less efficient in triggering the exposure of the interfaces in Gag that are required for efficient Gag multimerization (nucleation).


On the Selective Packaging of Genomic RNA by HIV-1
Schematic representation of the binding of HIV-1 Gag to the dimeric HIV-1 genomic RNA (gRNA) (a,b) and to non-Ψ RNA (c,d). (a) In the cytoplasm Gag binds to the HIV-1 gRNA by recognizing the RNA dimeric interface. Binding of Gag to Ψ increases the local concentration of Gag, thus promoting a conformational change in the SP1 domain from a random coil to an α-helix (green portion of Gag); (b) Once the HIV-1 Gag–dimeric gRNA complexes are bound to the plasma membrane, the specific Gag–RNA interactions promote a conformational change in Gag that enables high-order Gag–Gag interactions (blue interface); (c) In the absence of the HIV-1 gRNA Gag binds to mRNAs; however, because these interactions are non-specific, a higher Gag concentration is required to induce the conformational change in Gag; (d) When Gag–non-Ψ RNA complexes are bound to the plasma membrane, the local concentration of Gag is high enough to promote high-order Gag–Gag interactions. MA: matrix; CA-NTD: N-terminal domain of the capsid; CA-CTD: C-terminal domain of the capsid; SP1: spacer 1; NC: nucleocapsid.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC5035960&req=5

viruses-08-00246-f004: Schematic representation of the binding of HIV-1 Gag to the dimeric HIV-1 genomic RNA (gRNA) (a,b) and to non-Ψ RNA (c,d). (a) In the cytoplasm Gag binds to the HIV-1 gRNA by recognizing the RNA dimeric interface. Binding of Gag to Ψ increases the local concentration of Gag, thus promoting a conformational change in the SP1 domain from a random coil to an α-helix (green portion of Gag); (b) Once the HIV-1 Gag–dimeric gRNA complexes are bound to the plasma membrane, the specific Gag–RNA interactions promote a conformational change in Gag that enables high-order Gag–Gag interactions (blue interface); (c) In the absence of the HIV-1 gRNA Gag binds to mRNAs; however, because these interactions are non-specific, a higher Gag concentration is required to induce the conformational change in Gag; (d) When Gag–non-Ψ RNA complexes are bound to the plasma membrane, the local concentration of Gag is high enough to promote high-order Gag–Gag interactions. MA: matrix; CA-NTD: N-terminal domain of the capsid; CA-CTD: C-terminal domain of the capsid; SP1: spacer 1; NC: nucleocapsid.
Mentions: Earlier in this review, we described our findings on the SP1 domain of Gag, which led us to suggest that a conformational change in SP1 switches Gag into an assembly-ready state [23]. In some biological systems the nucleation of high-order protein complexes (e.g., immature virions) is driven by protein-protein interactions. Initiation of this process has to overcome an energetic barrier (activation energy); hence a nucleation process can be accelerated if the activation energy is lowered. This can be achieved by the presence of a nucleation site or a “seed”. In the simplest scenario, a nucleation site acts by enhancing protein-protein interactions such that the energy gained by protein multimerization overcomes the loss of entropy due to the decrease of free protein, and therefore lowers the activation energy. Based on the idea proposed by Nikolaitchick and co-workers [50], on some of the data discussed here, and on these physical principles, we can ask the following question; is selective packaging of the HIV-1 gRNA driven by Ψ acting as a nucleation site for virion assembly? A hypothesis in which selective packaging of the HIV-1 gRNA is achieved by a Ψ lowering the energy needed to nucleate virion assembly is consistent with the fact that HIV-1 VLP assembly can be efficiently supported by cellular mRNAs, but that this assembly process is completely inhibited in the presence of the gRNA. In the context of this nucleation scenario it is possible that the dimeric Ψ acts as a “seed” such that binding of just a few Gag molecules to this substrate is enough to activate the SP1 conformational switch, exposing new Gag–Gag interfaces and therefore nucleating efficient virion assembly (see Figure 4). According to this hypothesis, VLP assembly can occur in the absence of the dimeric Ψ, but this process has a higher activation energy because binding to the non-Ψ is less efficient in triggering the exposure of the interfaces in Gag that are required for efficient Gag multimerization (nucleation).

View Article: PubMed Central - PubMed

ABSTRACT

Like other retroviruses, human immunodeficiency virus type 1 (HIV-1) selectively packages genomic RNA (gRNA) during virus assembly. However, in the absence of the gRNA, cellular messenger RNAs (mRNAs) are packaged. While the gRNA is selected because of its cis-acting packaging signal, the mechanism of this selection is not understood. The affinity of Gag (the viral structural protein) for cellular RNAs at physiological ionic strength is not much higher than that for the gRNA. However, binding to the gRNA is more salt-resistant, implying that it has a higher non-electrostatic component. We have previously studied the spacer 1 (SP1) region of Gag and showed that it can undergo a concentration-dependent conformational transition. We proposed that this transition represents the first step in assembly, i.e., the conversion of Gag to an assembly-ready state. To explain selective packaging of gRNA, we suggest here that binding of Gag to gRNA, with its high non-electrostatic component, triggers this conversion more readily than binding to other RNAs; thus we predict that a Gag–gRNA complex will nucleate particle assembly more efficiently than other Gag–RNA complexes. New data shows that among cellular mRNAs, those with long 3′-untranslated regions (UTR) are selectively packaged. It seems plausible that the 3′-UTR, a stretch of RNA not occupied by ribosomes, offers a favorable binding site for Gag.

No MeSH data available.


Related in: MedlinePlus