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Orchestrating the Selection and Packaging of Genomic RNA by Retroviruses: An Ensemble of Viral and Host Factors

View Article: PubMed Central - PubMed

ABSTRACT

Infectious retrovirus particles contain two copies of unspliced viral RNA that serve as the viral genome. Unspliced retroviral RNA is transcribed in the nucleus by the host RNA polymerase II and has three potential fates: (1) it can be spliced into subgenomic messenger RNAs (mRNAs) for the translation of viral proteins; or it can remain unspliced to serve as either (2) the mRNA for the translation of Gag and Gag–Pol; or (3) the genomic RNA (gRNA) that is packaged into virions. The Gag structural protein recognizes and binds the unspliced viral RNA to select it as a genome, which is selected in preference to spliced viral RNAs and cellular RNAs. In this review, we summarize the current state of understanding about how retroviral packaging is orchestrated within the cell and explore potential new mechanisms based on recent discoveries in the field. We discuss the cis-acting elements in the unspliced viral RNA and the properties of the Gag protein that are required for their interaction. In addition, we discuss the role of host factors in influencing the fate of the newly transcribed viral RNA, current models for how retroviruses distinguish unspliced viral mRNA from viral genomic RNA, and the possible subcellular sites of genomic RNA dimerization and selection by Gag. Although this review centers primarily on the wealth of data available for the alpharetrovirus Rous sarcoma virus, in which a discrete RNA packaging sequence has been identified, we have also summarized the cis- and trans-acting factors as well as the mechanisms governing gRNA packaging of other retroviruses for comparison.

No MeSH data available.


Models for unspliced retroviral RNA utilization. (a) Nuclear determination of vRNA fate for simple retroviruses: The cytoplasmic utilization of unspliced vRNAs may be determined by the co-transcriptional binding of specific factors that “mark” the unspliced vRNA for either packaging or translation, and the vRNAs are not interchangeable. The mechanism by which the unspliced RNA is exported from the nucleus could determine the cytoplasmic utilization of the unspliced retroviral RNA. Models include: (i) Nuclear Gag binds to the vRNA to mark it for packaging; (ii) Nuclear Gag and a host factor bind to the vRNA to mark it for packaging; or (iii) Nuclear host factors bind to the unspliced vRNA to determine its fate; (b) Nuclear determination of fate for complex retroviruses: Complex retroviruses encode accessory proteins that facilitate the nuclear export of unspliced or incompletely spliced retroviral RNA, such as HIV-1 Rev. In addition to Rev-like proteins, other host and viral factors also bind to the unspliced vRNA co-transcriptionally and may contribute to the fate of unspliced vRNA. Models include: (i) Nuclear viral export factor and Gag bind to the vRNA to mark it as a genome for packaging; (ii) Nuclear viral export factor, Gag, and a host factor bind to the vRNA to sort it for packaging; or (iii) Nuclear viral export factor and specific host factors bind to the unspliced vRNA to determine its cytoplasmic fate; (c) Cytoplasmic determination of fate: The fate of unspliced vRNAs may be defined in the cytoplasm. An unspliced vRNA can be used for either translation or packaging. A previously translated RNA can subsequently be packaged. In this scenario, host and viral factors may be bound to the unspliced vRNA in the nucleus, but their presence does not determine cytoplasmic utilization of the vRNA.
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viruses-08-00257-f002: Models for unspliced retroviral RNA utilization. (a) Nuclear determination of vRNA fate for simple retroviruses: The cytoplasmic utilization of unspliced vRNAs may be determined by the co-transcriptional binding of specific factors that “mark” the unspliced vRNA for either packaging or translation, and the vRNAs are not interchangeable. The mechanism by which the unspliced RNA is exported from the nucleus could determine the cytoplasmic utilization of the unspliced retroviral RNA. Models include: (i) Nuclear Gag binds to the vRNA to mark it for packaging; (ii) Nuclear Gag and a host factor bind to the vRNA to mark it for packaging; or (iii) Nuclear host factors bind to the unspliced vRNA to determine its fate; (b) Nuclear determination of fate for complex retroviruses: Complex retroviruses encode accessory proteins that facilitate the nuclear export of unspliced or incompletely spliced retroviral RNA, such as HIV-1 Rev. In addition to Rev-like proteins, other host and viral factors also bind to the unspliced vRNA co-transcriptionally and may contribute to the fate of unspliced vRNA. Models include: (i) Nuclear viral export factor and Gag bind to the vRNA to mark it as a genome for packaging; (ii) Nuclear viral export factor, Gag, and a host factor bind to the vRNA to sort it for packaging; or (iii) Nuclear viral export factor and specific host factors bind to the unspliced vRNA to determine its cytoplasmic fate; (c) Cytoplasmic determination of fate: The fate of unspliced vRNAs may be defined in the cytoplasm. An unspliced vRNA can be used for either translation or packaging. A previously translated RNA can subsequently be packaged. In this scenario, host and viral factors may be bound to the unspliced vRNA in the nucleus, but their presence does not determine cytoplasmic utilization of the vRNA.

Mentions: Retroviruses depend on the unspliced vRNA for dual roles: to serve as the mRNA for translation of Gag and Gag–Pol, and as the gRNA for encapsidation into virions. Presumably, these RNAs are biochemically identical, therefore the mechanism whereby retroviruses distinguish between the RNA used for translation versus the RNA used for packaging remains a mystery. Two models have been proposed as potential explanations for how retroviruses distinguish between the two unspliced vRNAs for use as gRNA or mRNA. There may be separate pools of unspliced vRNA, one for translation and the other for packaging, or a single population of vRNA may be used interchangeably, as either gRNA or mRNA (Figure 2). If the “two pools” hypothesis is correct, then the question arises as to how, when, and where the vRNAs are sorted into separate pools? One possibility is that a single metabolic pool of unspliced vRNAs exists, and the RNAs are “marked,” by viral or cellular proteins, directing them to either the translation or packaging pathways. Alternatively, two separate pools of vRNA could be physically segregated into distinct populations in the cell. The “one pool” model can be explained by two different scenarios. A vRNA can serve as either mRNA or gRNA, without translation being a prerequisite for packaging, or translation of the vRNA may be required prior to packaging [98,99]. Different retroviruses may adopt mechanisms represented by each of the models.


Orchestrating the Selection and Packaging of Genomic RNA by Retroviruses: An Ensemble of Viral and Host Factors
Models for unspliced retroviral RNA utilization. (a) Nuclear determination of vRNA fate for simple retroviruses: The cytoplasmic utilization of unspliced vRNAs may be determined by the co-transcriptional binding of specific factors that “mark” the unspliced vRNA for either packaging or translation, and the vRNAs are not interchangeable. The mechanism by which the unspliced RNA is exported from the nucleus could determine the cytoplasmic utilization of the unspliced retroviral RNA. Models include: (i) Nuclear Gag binds to the vRNA to mark it for packaging; (ii) Nuclear Gag and a host factor bind to the vRNA to mark it for packaging; or (iii) Nuclear host factors bind to the unspliced vRNA to determine its fate; (b) Nuclear determination of fate for complex retroviruses: Complex retroviruses encode accessory proteins that facilitate the nuclear export of unspliced or incompletely spliced retroviral RNA, such as HIV-1 Rev. In addition to Rev-like proteins, other host and viral factors also bind to the unspliced vRNA co-transcriptionally and may contribute to the fate of unspliced vRNA. Models include: (i) Nuclear viral export factor and Gag bind to the vRNA to mark it as a genome for packaging; (ii) Nuclear viral export factor, Gag, and a host factor bind to the vRNA to sort it for packaging; or (iii) Nuclear viral export factor and specific host factors bind to the unspliced vRNA to determine its cytoplasmic fate; (c) Cytoplasmic determination of fate: The fate of unspliced vRNAs may be defined in the cytoplasm. An unspliced vRNA can be used for either translation or packaging. A previously translated RNA can subsequently be packaged. In this scenario, host and viral factors may be bound to the unspliced vRNA in the nucleus, but their presence does not determine cytoplasmic utilization of the vRNA.
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Related In: Results  -  Collection

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viruses-08-00257-f002: Models for unspliced retroviral RNA utilization. (a) Nuclear determination of vRNA fate for simple retroviruses: The cytoplasmic utilization of unspliced vRNAs may be determined by the co-transcriptional binding of specific factors that “mark” the unspliced vRNA for either packaging or translation, and the vRNAs are not interchangeable. The mechanism by which the unspliced RNA is exported from the nucleus could determine the cytoplasmic utilization of the unspliced retroviral RNA. Models include: (i) Nuclear Gag binds to the vRNA to mark it for packaging; (ii) Nuclear Gag and a host factor bind to the vRNA to mark it for packaging; or (iii) Nuclear host factors bind to the unspliced vRNA to determine its fate; (b) Nuclear determination of fate for complex retroviruses: Complex retroviruses encode accessory proteins that facilitate the nuclear export of unspliced or incompletely spliced retroviral RNA, such as HIV-1 Rev. In addition to Rev-like proteins, other host and viral factors also bind to the unspliced vRNA co-transcriptionally and may contribute to the fate of unspliced vRNA. Models include: (i) Nuclear viral export factor and Gag bind to the vRNA to mark it as a genome for packaging; (ii) Nuclear viral export factor, Gag, and a host factor bind to the vRNA to sort it for packaging; or (iii) Nuclear viral export factor and specific host factors bind to the unspliced vRNA to determine its cytoplasmic fate; (c) Cytoplasmic determination of fate: The fate of unspliced vRNAs may be defined in the cytoplasm. An unspliced vRNA can be used for either translation or packaging. A previously translated RNA can subsequently be packaged. In this scenario, host and viral factors may be bound to the unspliced vRNA in the nucleus, but their presence does not determine cytoplasmic utilization of the vRNA.
Mentions: Retroviruses depend on the unspliced vRNA for dual roles: to serve as the mRNA for translation of Gag and Gag–Pol, and as the gRNA for encapsidation into virions. Presumably, these RNAs are biochemically identical, therefore the mechanism whereby retroviruses distinguish between the RNA used for translation versus the RNA used for packaging remains a mystery. Two models have been proposed as potential explanations for how retroviruses distinguish between the two unspliced vRNAs for use as gRNA or mRNA. There may be separate pools of unspliced vRNA, one for translation and the other for packaging, or a single population of vRNA may be used interchangeably, as either gRNA or mRNA (Figure 2). If the “two pools” hypothesis is correct, then the question arises as to how, when, and where the vRNAs are sorted into separate pools? One possibility is that a single metabolic pool of unspliced vRNAs exists, and the RNAs are “marked,” by viral or cellular proteins, directing them to either the translation or packaging pathways. Alternatively, two separate pools of vRNA could be physically segregated into distinct populations in the cell. The “one pool” model can be explained by two different scenarios. A vRNA can serve as either mRNA or gRNA, without translation being a prerequisite for packaging, or translation of the vRNA may be required prior to packaging [98,99]. Different retroviruses may adopt mechanisms represented by each of the models.

View Article: PubMed Central - PubMed

ABSTRACT

Infectious retrovirus particles contain two copies of unspliced viral RNA that serve as the viral genome. Unspliced retroviral RNA is transcribed in the nucleus by the host RNA polymerase II and has three potential fates: (1) it can be spliced into subgenomic messenger RNAs (mRNAs) for the translation of viral proteins; or it can remain unspliced to serve as either (2) the mRNA for the translation of Gag and Gag–Pol; or (3) the genomic RNA (gRNA) that is packaged into virions. The Gag structural protein recognizes and binds the unspliced viral RNA to select it as a genome, which is selected in preference to spliced viral RNAs and cellular RNAs. In this review, we summarize the current state of understanding about how retroviral packaging is orchestrated within the cell and explore potential new mechanisms based on recent discoveries in the field. We discuss the cis-acting elements in the unspliced viral RNA and the properties of the Gag protein that are required for their interaction. In addition, we discuss the role of host factors in influencing the fate of the newly transcribed viral RNA, current models for how retroviruses distinguish unspliced viral mRNA from viral genomic RNA, and the possible subcellular sites of genomic RNA dimerization and selection by Gag. Although this review centers primarily on the wealth of data available for the alpharetrovirus Rous sarcoma virus, in which a discrete RNA packaging sequence has been identified, we have also summarized the cis- and trans-acting factors as well as the mechanisms governing gRNA packaging of other retroviruses for comparison.

No MeSH data available.