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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.


Related in: MedlinePlus

The Rous sarcoma virus (RSV) Gag polyprotein domain organization and functional sequences in the 5′ untranslated region (UTR) of the genomic RNA. (a) The RSV Gag protein is made of multiple domains: matrix (MA; green) contains the membrane binding motif (M) and a non-canonical nuclear localization signal (NLS); p2 (orange) contains the late (L) motif. p10 (gold) contains a chromosome region maintenance 1 (CRM1)-dependent nuclear export signal (NES); capsid (CA; blue) contains a multimerization interface (MI) that extends from p10; spacer peptide (SP; yellow); nucleocapsid (NC; pink) binds nucleic acids and proteins via interaction motifs (I) and Cys-His boxes (CH; translucent grey) and also contains an NLS; and protease (PR; blue). The Cys-His boxes contain zinc finger domains (red) required for the binding of the Ψ packaging sequence located in the 5′ UTR of the viral RNA (vRNA); (b) The primer binding site (PBS) is required for reverse transcription (nts 102–119). The entire RSV packaging sequence AΨ extends from nucleotides 126–395. The MΨ sequence extends from nucleotides 156–215. The minimal functional packaging element, identified as µΨ, is 82 nucleotides in length, extending from 156 to 238. Because the splice donor (SD) is located downstream of the packaging sequence at nucleotide 397, the Ψ sequence is contained in both spliced and unspliced vRNAs. DR: direct repeat; RU5: repeat-unique 5’; U3: unique 3’.
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viruses-08-00257-f001: The Rous sarcoma virus (RSV) Gag polyprotein domain organization and functional sequences in the 5′ untranslated region (UTR) of the genomic RNA. (a) The RSV Gag protein is made of multiple domains: matrix (MA; green) contains the membrane binding motif (M) and a non-canonical nuclear localization signal (NLS); p2 (orange) contains the late (L) motif. p10 (gold) contains a chromosome region maintenance 1 (CRM1)-dependent nuclear export signal (NES); capsid (CA; blue) contains a multimerization interface (MI) that extends from p10; spacer peptide (SP; yellow); nucleocapsid (NC; pink) binds nucleic acids and proteins via interaction motifs (I) and Cys-His boxes (CH; translucent grey) and also contains an NLS; and protease (PR; blue). The Cys-His boxes contain zinc finger domains (red) required for the binding of the Ψ packaging sequence located in the 5′ UTR of the viral RNA (vRNA); (b) The primer binding site (PBS) is required for reverse transcription (nts 102–119). The entire RSV packaging sequence AΨ extends from nucleotides 126–395. The MΨ sequence extends from nucleotides 156–215. The minimal functional packaging element, identified as µΨ, is 82 nucleotides in length, extending from 156 to 238. Because the splice donor (SD) is located downstream of the packaging sequence at nucleotide 397, the Ψ sequence is contained in both spliced and unspliced vRNAs. DR: direct repeat; RU5: repeat-unique 5’; U3: unique 3’.

Mentions: The RSV Gag polyprotein is translated in the cytoplasm from unspliced viral mRNA. Gag is comprised of multiple functional domains that are cleaved upon proteolytic cleavage by the protease domain (PR) during virion maturation (Figure 1). The domains of RSV Gag are matrix (MA), p2, p10, capsid (CA), spacer peptide (SP), nucleocapsid (NC), and PR. MA contains the plasma membrane targeting and binding motif (M) and a non-canonical nuclear localization signal (NLS) [6,7,8]. The p2 domain contains the late (L) motif and is involved in the pinching off of virions from the plasma membrane during budding [9,10,11]. The p10 domain contains a chromosome region maintenance 1 (CRM1)-dependent nuclear export signal (NES) and contains structural elements that influence mature virion morphology [6,12,13,14]. CA encompasses the major homology region (MHR) and the multimerization interface (MI), which facilitates Gag–Gag interactions in the immature and mature virus particle [5,14,15,16,17]. SP is required for the proper assembly of the immature virion [18]. NC contains two interaction (I) domains that mediate Gag–Gag and Gag–nucleic acid interactions, and NC contains both an NLS and a nucleolar localization signal [7,15,19,20].


Orchestrating the Selection and Packaging of Genomic RNA by Retroviruses: An Ensemble of Viral and Host Factors
The Rous sarcoma virus (RSV) Gag polyprotein domain organization and functional sequences in the 5′ untranslated region (UTR) of the genomic RNA. (a) The RSV Gag protein is made of multiple domains: matrix (MA; green) contains the membrane binding motif (M) and a non-canonical nuclear localization signal (NLS); p2 (orange) contains the late (L) motif. p10 (gold) contains a chromosome region maintenance 1 (CRM1)-dependent nuclear export signal (NES); capsid (CA; blue) contains a multimerization interface (MI) that extends from p10; spacer peptide (SP; yellow); nucleocapsid (NC; pink) binds nucleic acids and proteins via interaction motifs (I) and Cys-His boxes (CH; translucent grey) and also contains an NLS; and protease (PR; blue). The Cys-His boxes contain zinc finger domains (red) required for the binding of the Ψ packaging sequence located in the 5′ UTR of the viral RNA (vRNA); (b) The primer binding site (PBS) is required for reverse transcription (nts 102–119). The entire RSV packaging sequence AΨ extends from nucleotides 126–395. The MΨ sequence extends from nucleotides 156–215. The minimal functional packaging element, identified as µΨ, is 82 nucleotides in length, extending from 156 to 238. Because the splice donor (SD) is located downstream of the packaging sequence at nucleotide 397, the Ψ sequence is contained in both spliced and unspliced vRNAs. DR: direct repeat; RU5: repeat-unique 5’; U3: unique 3’.
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Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC5035971&req=5

viruses-08-00257-f001: The Rous sarcoma virus (RSV) Gag polyprotein domain organization and functional sequences in the 5′ untranslated region (UTR) of the genomic RNA. (a) The RSV Gag protein is made of multiple domains: matrix (MA; green) contains the membrane binding motif (M) and a non-canonical nuclear localization signal (NLS); p2 (orange) contains the late (L) motif. p10 (gold) contains a chromosome region maintenance 1 (CRM1)-dependent nuclear export signal (NES); capsid (CA; blue) contains a multimerization interface (MI) that extends from p10; spacer peptide (SP; yellow); nucleocapsid (NC; pink) binds nucleic acids and proteins via interaction motifs (I) and Cys-His boxes (CH; translucent grey) and also contains an NLS; and protease (PR; blue). The Cys-His boxes contain zinc finger domains (red) required for the binding of the Ψ packaging sequence located in the 5′ UTR of the viral RNA (vRNA); (b) The primer binding site (PBS) is required for reverse transcription (nts 102–119). The entire RSV packaging sequence AΨ extends from nucleotides 126–395. The MΨ sequence extends from nucleotides 156–215. The minimal functional packaging element, identified as µΨ, is 82 nucleotides in length, extending from 156 to 238. Because the splice donor (SD) is located downstream of the packaging sequence at nucleotide 397, the Ψ sequence is contained in both spliced and unspliced vRNAs. DR: direct repeat; RU5: repeat-unique 5’; U3: unique 3’.
Mentions: The RSV Gag polyprotein is translated in the cytoplasm from unspliced viral mRNA. Gag is comprised of multiple functional domains that are cleaved upon proteolytic cleavage by the protease domain (PR) during virion maturation (Figure 1). The domains of RSV Gag are matrix (MA), p2, p10, capsid (CA), spacer peptide (SP), nucleocapsid (NC), and PR. MA contains the plasma membrane targeting and binding motif (M) and a non-canonical nuclear localization signal (NLS) [6,7,8]. The p2 domain contains the late (L) motif and is involved in the pinching off of virions from the plasma membrane during budding [9,10,11]. The p10 domain contains a chromosome region maintenance 1 (CRM1)-dependent nuclear export signal (NES) and contains structural elements that influence mature virion morphology [6,12,13,14]. CA encompasses the major homology region (MHR) and the multimerization interface (MI), which facilitates Gag–Gag interactions in the immature and mature virus particle [5,14,15,16,17]. SP is required for the proper assembly of the immature virion [18]. NC contains two interaction (I) domains that mediate Gag–Gag and Gag–nucleic acid interactions, and NC contains both an NLS and a nucleolar localization signal [7,15,19,20].

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.


Related in: MedlinePlus