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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.


Preferential encapsidation of messenger RNA (mRNA) molecules with long 3′ UTRs. The log fold changes between messenger RNA (mRNA) measurements in the cellular and viral components were divided into groups of 1000 genes. The 1000 most excluded RNA species, labeled low; an “average” group representing the middle 1000 genes; and the 1000 most enriched mRNAs, the “high” group, are represented by different colored density plots. The plot depicts the log10 (UTR length) on the x-axis and the density on the y-axis. Upper panel: HIV-1; lower panel, MLV.
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viruses-08-00246-f003: Preferential encapsidation of messenger RNA (mRNA) molecules with long 3′ UTRs. The log fold changes between messenger RNA (mRNA) measurements in the cellular and viral components were divided into groups of 1000 genes. The 1000 most excluded RNA species, labeled low; an “average” group representing the middle 1000 genes; and the 1000 most enriched mRNAs, the “high” group, are represented by different colored density plots. The plot depicts the log10 (UTR length) on the x-axis and the density on the y-axis. Upper panel: HIV-1; lower panel, MLV.

Mentions: The data was also analyzed by selecting the 1000 mRNAs with the highest fold change, the 1000 species with the average fold-change, and the 1000 species with the lowest fold-change, i.e., those with the most preferential, average, and most excluded encapsidation efficiencies. Figure 3 shows the “density plot” (frequency distribution) of the 3′-UTR lengths for these three subsets of the mRNAs (for both HIV-1 and MLV). This analysis shows that the preferentially packaged mRNAs have unusually long 3′-UTRs, while there is little difference in the mean 3′-UTR lengths between the other two classes. A t-test between the UTR lengths in the “average fold-change” group and the “high fold-change” group was highly significant, with a p-value < 10−15. This relationship was observed for both HIV-1 and MLV Gag, suggesting that this apparent selectivity for long 3′-UTR RNAs is a general property of the retroviral assembly pathway, not unique to HIV-1 (a member of the lentivirus genus) or MLV (a gammaretrovirus). One possible explanation is that the 3′-UTR is a stretch of mRNA that is unoccupied by ribosomes; perhaps this provides sites to which Gag can bind in the absence of gRNA. Thus, RNAs with longer 3′-UTRs have a larger number of available Gag binding sites than RNAs with shorter 3′-UTRS. It is interesting to notice that the gRNA of retroviruses has an extremely long 3′-UTR.


On the Selective Packaging of Genomic RNA by HIV-1
Preferential encapsidation of messenger RNA (mRNA) molecules with long 3′ UTRs. The log fold changes between messenger RNA (mRNA) measurements in the cellular and viral components were divided into groups of 1000 genes. The 1000 most excluded RNA species, labeled low; an “average” group representing the middle 1000 genes; and the 1000 most enriched mRNAs, the “high” group, are represented by different colored density plots. The plot depicts the log10 (UTR length) on the x-axis and the density on the y-axis. Upper panel: HIV-1; lower panel, MLV.
© Copyright Policy
Related In: Results  -  Collection

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

viruses-08-00246-f003: Preferential encapsidation of messenger RNA (mRNA) molecules with long 3′ UTRs. The log fold changes between messenger RNA (mRNA) measurements in the cellular and viral components were divided into groups of 1000 genes. The 1000 most excluded RNA species, labeled low; an “average” group representing the middle 1000 genes; and the 1000 most enriched mRNAs, the “high” group, are represented by different colored density plots. The plot depicts the log10 (UTR length) on the x-axis and the density on the y-axis. Upper panel: HIV-1; lower panel, MLV.
Mentions: The data was also analyzed by selecting the 1000 mRNAs with the highest fold change, the 1000 species with the average fold-change, and the 1000 species with the lowest fold-change, i.e., those with the most preferential, average, and most excluded encapsidation efficiencies. Figure 3 shows the “density plot” (frequency distribution) of the 3′-UTR lengths for these three subsets of the mRNAs (for both HIV-1 and MLV). This analysis shows that the preferentially packaged mRNAs have unusually long 3′-UTRs, while there is little difference in the mean 3′-UTR lengths between the other two classes. A t-test between the UTR lengths in the “average fold-change” group and the “high fold-change” group was highly significant, with a p-value < 10−15. This relationship was observed for both HIV-1 and MLV Gag, suggesting that this apparent selectivity for long 3′-UTR RNAs is a general property of the retroviral assembly pathway, not unique to HIV-1 (a member of the lentivirus genus) or MLV (a gammaretrovirus). One possible explanation is that the 3′-UTR is a stretch of mRNA that is unoccupied by ribosomes; perhaps this provides sites to which Gag can bind in the absence of gRNA. Thus, RNAs with longer 3′-UTRs have a larger number of available Gag binding sites than RNAs with shorter 3′-UTRS. It is interesting to notice that the gRNA of retroviruses has an extremely long 3′-UTR.

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&ndash;gRNA complex will nucleate particle assembly more efficiently than other Gag&ndash;RNA complexes. New data shows that among cellular mRNAs, those with long 3&prime;-untranslated regions (UTR) are selectively packaged. It seems plausible that the 3&prime;-UTR, a stretch of RNA not occupied by ribosomes, offers a favorable binding site for Gag.

No MeSH data available.