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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

Relationship between bins of similar log2 (fold change) on the x-axis and the log10 (UTR length) on the y-axis. A, mRNAs encapsidated in HIV-1 virus-like particles (VLPs); AC, mRNAs in cells producing HIV-1 VLPs; B, mRNAs encapsidated in murine leukemia virus (MLV) VLPs; BC, mRNAs in cells producing MLV VLPs.
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viruses-08-00246-f002: Relationship between bins of similar log2 (fold change) on the x-axis and the log10 (UTR length) on the y-axis. A, mRNAs encapsidated in HIV-1 virus-like particles (VLPs); AC, mRNAs in cells producing HIV-1 VLPs; B, mRNAs encapsidated in murine leukemia virus (MLV) VLPs; BC, mRNAs in cells producing MLV VLPs.

Mentions: As mentioned before, in the absence of the gRNA, HIV-1 Gag, as well as murine leukemia virus (MLV) Gag, packages cellular mRNAs without any obvious specificity [35]. However, although the concentration of the vast majority of the cellular mRNAs that are packaged in the absence of the gRNA is a reflection of their concentration in the cell, some mRNAs are preferentially packaged. One of these mRNA species is ankyrin repeat and SOCS box containing 1 (ASB-1) mRNA [35]. We noted that this mRNA has an unusually long 3′-UTR, and wondered whether this might contribute to the relatively efficient encapsidation of this mRNA. We have now explored this question by re-analyzing our earlier microarray data [35] on the mRNA species packaged in HIV-1 and MLV particles in the absence of Ψ-containing RNA. All data analyses were carried out using the R statistical programming language (R: A Language and Environment for Statistical Computing. R Core Team. Vienna Austria. https://www.R-project.org) and Bioconductor [38]. The raw data was normalized using Robust Multi-array Average (RMA) from the affy package [39]. As we did not have biological replicates, fold changes between the cellular and viral compartments were used for further analyses. The entire set of mRNAs was divided into bins according to the “fold change”, a measure of the selectivity of encapsidation of each species. Figure 2 shows the relationship between log2 (fold change) in each bin and the log10 (median 3′-UTR length) for the mRNAs in the bin. As can be seen, the mRNAs that are encapsidated with higher-than-average efficiency possess, on average, a significantly longer 3′-UTR than other mRNAs.


On the Selective Packaging of Genomic RNA by HIV-1
Relationship between bins of similar log2 (fold change) on the x-axis and the log10 (UTR length) on the y-axis. A, mRNAs encapsidated in HIV-1 virus-like particles (VLPs); AC, mRNAs in cells producing HIV-1 VLPs; B, mRNAs encapsidated in murine leukemia virus (MLV) VLPs; BC, mRNAs in cells producing MLV VLPs.
© Copyright Policy
Related In: Results  -  Collection

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

viruses-08-00246-f002: Relationship between bins of similar log2 (fold change) on the x-axis and the log10 (UTR length) on the y-axis. A, mRNAs encapsidated in HIV-1 virus-like particles (VLPs); AC, mRNAs in cells producing HIV-1 VLPs; B, mRNAs encapsidated in murine leukemia virus (MLV) VLPs; BC, mRNAs in cells producing MLV VLPs.
Mentions: As mentioned before, in the absence of the gRNA, HIV-1 Gag, as well as murine leukemia virus (MLV) Gag, packages cellular mRNAs without any obvious specificity [35]. However, although the concentration of the vast majority of the cellular mRNAs that are packaged in the absence of the gRNA is a reflection of their concentration in the cell, some mRNAs are preferentially packaged. One of these mRNA species is ankyrin repeat and SOCS box containing 1 (ASB-1) mRNA [35]. We noted that this mRNA has an unusually long 3′-UTR, and wondered whether this might contribute to the relatively efficient encapsidation of this mRNA. We have now explored this question by re-analyzing our earlier microarray data [35] on the mRNA species packaged in HIV-1 and MLV particles in the absence of Ψ-containing RNA. All data analyses were carried out using the R statistical programming language (R: A Language and Environment for Statistical Computing. R Core Team. Vienna Austria. https://www.R-project.org) and Bioconductor [38]. The raw data was normalized using Robust Multi-array Average (RMA) from the affy package [39]. As we did not have biological replicates, fold changes between the cellular and viral compartments were used for further analyses. The entire set of mRNAs was divided into bins according to the “fold change”, a measure of the selectivity of encapsidation of each species. Figure 2 shows the relationship between log2 (fold change) in each bin and the log10 (median 3′-UTR length) for the mRNAs in the bin. As can be seen, the mRNAs that are encapsidated with higher-than-average efficiency possess, on average, a significantly longer 3′-UTR than other mRNAs.

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