The packaging signal of simian immunodeficiency virus is upstream of the major splice donor at a distance from the RNA cap site similar to that of human immunodeficiency virus types 1 and 2

Strappe, Pádraig; Greatorex, Jane; Thomas, James A.; Biswas, Parthapratim; McCann, E.; Lever, Andrew

doi:10.1099/vir.0.19185-0

Cited by 20 publications

(13 citation statements)

References 30 publications

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“…It is possible that these purine motifs might be involved in the specific RNA-protein interactions taking place during genomic RNA selection and encapsidation. Likewise, deletion mutagenesis studies suggest that an extended SL1 element is involved in encapsidation and dimerization of the SIVmac239 genomic RNA (Strappe et al 2003;Whitney and Wainberg 2006).…”

Section: Discussionmentioning

confidence: 99%

HIV-2 RNA dimerization is regulated by intramolecular interactions in vitro

Baig

Lanchy

Lodmell

2007

RNA

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Genomic RNA dimerization is an essential process in the retroviral replication cycle. In vitro, HIV-2 RNA dimerization is mediated at least in part by direct intermolecular interaction at stem-loop 1 (SL1) within the 59-untranslated leader region (UTR). RNA dimerization is thought to be regulated via alternate presentation and sequestration of dimerization signals by intramolecular base-pairings. One of the proposed regulatory elements is a palindrome sequence (pal) located upstream of SL1. To investigate the role of pal in the regulation of HIV-2 dimerization, we randomized this motif and selected in vitro for dimerization-competent and dimerization-impaired RNAs. Energy minimization folding analysis of these isolated sequences suggests the involvement of pal region in several short-distance intramolecular interactions with other upstream and downstream regions of the UTR. Moreover, the consensus predicted folding patterns indicate the altered presentation of SL1 depending on the interactions of pal with other regions of RNA. The data suggest that pal can act as a positive or negative regulator of SL1-mediated dimerization and that the modulation of base-pairing arrangements that affect RNA dimerization could coordinate multiple signals located within the 59-UTR.

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Section: Discussionmentioning

confidence: 99%

HIV-2 RNA dimerization is regulated by intramolecular interactions in vitro

Baig

Lanchy

Lodmell

2007

RNA

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“…Similar to the case with human immunodeficiency virus, simian immunodeficiency virus, and Mason-Pfizer monkey virus (4,5,9,11), this region folded into several stem-loops, of which four were stable, named stemloops 1 to 4 (SL1 to SL4). Folding of the mutant vector RNAs revealed that most of the conformation of the wild-type UTR was destroyed in the vectors with only 90 and 120 bp of the UTR, except for SL1, which was conserved in all transfer vector RNAs (Fig.…”

mentioning

confidence: 83%

Sequences Intervening between the Core Packaging Determinants Are Dispensable for Maintaining the Packaging Potential and Propagation of Feline Immunodeficiency Virus Transfer Vector RNAs

Mustafa¹,

Ghazawi

Jayanth

et al. 2005

J Virol

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The packaging determinants of feline immunodeficiency virus (FIV) consist of two discontinuous core regions, extending from R to ϳ150 bp of the 5 untranslated region and the first ϳ100 bp of gag. However, the role of sequences intervening between the core regions in packaging has not been clear. A mutational analysis was conducted to determine whether the intervening sequences played a role in FIV RNA packaging, using an in vivo packaging assay complemented with semiquantitative reverse transcriptase PCR. Our analyses reveal that the intervening sequences are dispensable not only for vector RNA packaging but also for propagation, confirming the discontinuous nature of the FIV packaging signal.A series of recent studies have suggested that the packaging determinants of feline immunodeficiency virus (FIV) are complex and multipartite, consisting of at least two discontinuous core regions, one located upstream of the major splice donor sequence from R/U5 at the 5Ј end to the first ϳ150 bp of the 5Ј untranslated region (UTR), while the other is within the first 100 bp of gag (2, 3, 6, 7). To determine whether the region intervening between the core determinants was required for maintaining the stability of the FIV packaging signal, we modified our previously described vector, MB15 (2), and constructed a series of transfer vectors, AG002 to AG004, that maintained the R/U5 and 100 bp of gag but kept only the first 90, 120, or 150 bp of the 5Ј UTR, generating incremental deletions between the core packaging determinants (Fig. 1). In a second series, AG013 to AG015, the deletions were replaced with heterologous sequences of the same lengths to further determine whether the deleted/substituted region had a role at the structural level or acted only as a spacer (Fig. 1).The two series of mutant vector RNAs were tested for their ability to be packaged by FIV proteins, using our well-established in vivo packaging assay along with TR394, which contains the entire 270-bp UTR with a 333-bp gag sequence (1-3). The amount of transfer vector RNA packaged into viral particles was analyzed by reverse transcriptase PCR (RT-PCR) (10) for variable cycle numbers, and the resulting products were Southern blotted and hybridized using an R/U5 probe. All mutant vector RNAs, either with deletions or deletion/ substitution, were packaged into the virus particles but with different efficiencies, while the control vectors, MB15 and TR394, were packaged at similar levels ( Fig. 2A). This was despite the fact that all cultures produced similar levels of viral particles and the transfection efficiencies were within twofold of each other ( Fig. 2B and C). Since the PCRs were conducted across the deleted or deleted/substituted region, the size of the PCR fragment varied with each construct, confirming that correct packaging constructs were being expressed in each transfection.To determine the packaging efficiencies of the various constructs accurately, RT-PCRs were repeated using primers within the R/U5 region that would result in same-sized fragme...

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“…Lentiviral vectors derived from HIV-1, HIV-2, and SIVmac251 have been described previously (48)(49)(50)(51)(52). These vectors were originally engineered from NL4-3, ROD, and SIVmac251 viral strains.…”

Section: Methodsmentioning

confidence: 99%

Evidence for a Different Susceptibility of Primate Lentiviruses to Type I Interferons

Cordeil

Nguyen

Berger

et al. 2013

J Virol

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Type I interferons induce a complex transcriptional program that leads to a generalized antiviral response against a large panel of viruses, including human immunodeficiency virus type 1 (HIV-1). However, despite the fact that interferons negatively regulate HIV-1 ex vivo, a chronic interferon state is linked to the progression of AIDS and to robust viral replication, rather than protection, in vivo. To explain this apparent contradiction, we hypothesized that HIV-1 may have evolved a partial resistance to interferon, and to test this hypothesis, we analyzed the effects of alpha interferon (IFN-␣) on the infectivity of HIV-1, human immunodeficiency virus type 2 (HIV-2), and rhesus monkey simian immunodeficiency virus (SIVmac). The results we obtained indicate that HIV-1 is more resistant to an IFN-␣-induced response than are HIV-2 and SIVmac. Our data indicate that the accumulation of viral DNA is more compromised following the infection of IFN-␣-treated cells with HIV-2 and SIVmac than with HIV-1. This defect correlates with a faster destabilization of HIV-2 viral nucleoprotein complexes (VNCs), suggesting a link between VNC destabilization and impaired viral DNA (vDNA) accumulation. The differential susceptibilities to IFN-␣ of the primate lentiviruses tested here do not map to the capsid protein (CA), excluding de facto a role for human tripartite motif protein isoform 5 alpha (Trim5␣) in this restriction; this also suggests that an additional restriction mechanism differentially affects primate lentivirus infection. The different behaviors of HIV-1 and HIV-2 with respect to IFN-␣ responses may account at least in part for the differences in pathogenesis observed between these two virus types.

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The packaging signal of simian immunodeficiency virus is upstream of the major splice donor at a distance from the RNA cap site similar to that of human immunodeficiency virus types 1 and 2

Cited by 20 publications

References 30 publications

HIV-2 RNA dimerization is regulated by intramolecular interactions in vitro

HIV-2 RNA dimerization is regulated by intramolecular interactions in vitro

Sequences Intervening between the Core Packaging Determinants Are Dispensable for Maintaining the Packaging Potential and Propagation of Feline Immunodeficiency Virus Transfer Vector RNAs

Evidence for a Different Susceptibility of Primate Lentiviruses to Type I Interferons

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