HIV-1 Sequence Necessary and Sufficient to Package Non-viral RNAs into HIV-1 Particles

Liu, Yang; Nikolaitchik, Olga A.; Rahman, Sheikh Abdul; Chen, Jianbo; Pathak, Vinay K.; Hu, Wei-Shau

doi:10.1016/j.jmb.2017.06.018

Cited by 30 publications

(39 citation statements)

References 77 publications

(75 reference statements)

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“…Additionally, this study does not investigate how Gag assembly is mediated by cellular RNAs, which can also bind to Gag to form VLPs, particularly in the absence of vRNA ( 9 – 11 ). Nonetheless, our results should still be relevant to understanding the HIV-1 assembly process, as vRNA is the dominant RNA species that drives Gag assembly ( 5 , 6 , 34 , 35 ).…”

Section: Discussionmentioning

confidence: 92%

Roles of Gag-RNA interactions in HIV-1 virus assembly deciphered by single-molecule localization microscopy

Yang

Tan

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

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SignificanceSingle-molecule localization microscopy (SMLM) is useful for deciphering dynamic organizations of structures densely labeled by specific proteins in the cellular context with nanoscopic resolution not attainable by conventional imaging tools. Here we employed SMLM to investigate the mechanism by which the HIV-1 viral RNA (vRNA) mediates the assembly of thousands of Gag proteins into a virus particle at the plasma membrane. In contrast to the general notion that vRNA only triggers Gag assembly and is dispensable for subsequent assembly, we found that vRNA is indispensable throughout assembly, scaffolding the formation of assembly intermediates and maintaining their architectures via balancing of external forces acting on the assembly environment. These previously unidentified features may facilitate understanding of HIV-1 and, potentially, other retroviruses.

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Section: Discussionmentioning

confidence: 92%

Roles of Gag-RNA interactions in HIV-1 virus assembly deciphered by single-molecule localization microscopy

Yang

Tan

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

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“…Together, these findings suggest that upon binding of monomeric Gag to the viral genome through Ψ, multimerization-dependent changes in the RNA binding specificity of Gag may drive the selective packaging of the A-rich viral genome. In line with this model, a recent study has shown that longer segments of the Gag ORF, but not Ψ alone, can gradually increase the packaging of heterologous RNAs into virions [ 80 ]. Thus as part of the selective RNA packaging process, the role of Gag-Ψ interaction may be to nucleate further assembly of Gag oligomers on the viral genome [ 81 ].…”

Section: Application Of Clip Techniques In Retrovirologymentioning

confidence: 90%

CLIP-related methodologies and their application to retrovirology

Bieniasz

Kutluay

2018

Retrovirology

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Virtually every step of HIV-1 replication and numerous cellular antiviral defense mechanisms are regulated by the binding of a viral or cellular RNA-binding protein (RBP) to distinct sequence or structural elements on HIV-1 RNAs. Until recently, these protein–RNA interactions were studied largely by in vitro binding assays complemented with genetics approaches. However, these methods are highly limited in the identification of the relevant targets of RBPs in physiologically relevant settings. Development of crosslinking-immunoprecipitation sequencing (CLIP) methodology has revolutionized the analysis of protein–nucleic acid complexes. CLIP combines immunoprecipitation of covalently crosslinked protein–RNA complexes with high-throughput sequencing, providing a global account of RNA sequences bound by a RBP of interest in cells (or virions) at near-nucleotide resolution. Numerous variants of the CLIP protocol have recently been developed, some with major improvements over the original. Herein, we briefly review these methodologies and give examples of how CLIP has been successfully applied to retrovirology research.

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“…Deletion of nt 22 to 378 in gag does not substantially decrease infectious-virus production (15,47), indicating that there are no essential cis-acting elements in the region. However, altering the RNA sequence could modulate the local RNA structure in ways that a large deletion did not, and the 5= region of gag has been shown to indirectly regulate gRNA packaging by regulating the structure of the 5= UTR (48,49).…”

Section: Ficarelli Et Almentioning

confidence: 99%

CpG Dinucleotides Inhibit HIV-1 Replication through Zinc Finger Antiviral Protein (ZAP)-Dependent and -Independent Mechanisms

Ficarelli

Antzin-Anduetza

Hugh-White

et al. 2020

J Virol

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CpG dinucleotides are suppressed in the genomes of many vertebrate RNA viruses, including HIV-1. The cellular antiviral protein ZAP (zinc finger antiviral protein) binds CpGs and inhibits HIV-1 replication when CpGs are introduced into the viral genome. However, it is not known if ZAP-mediated restriction is the only mechanism driving CpG suppression. To determine how CpG dinucleotides affect HIV-1 replication, we increased their abundance in multiple regions of the viral genome and analyzed the effect on RNA expression, protein abundance, and infectious-virus production. We found that the antiviral effect of CpGs was not correlated with their abundance. Interestingly, CpGs inserted into some regions of the genome sensitize the virus to ZAP antiviral activity more efficiently than insertions into other regions, and this sensitivity can be modulated by interferon treatment or ZAP overexpression. Furthermore, the sensitivity of the virus to endogenous ZAP was correlated with its sensitivity to the ZAP cofactor KHNYN. Finally, we show that CpGs in some contexts can also inhibit HIV-1 replication by ZAP-independent mechanisms, and one of these is the activation of a cryptic splice site at the expense of a canonical splice site. Overall, we show that the location and sequence context of the CpG in the viral genome determines its antiviral activity. IMPORTANCE Some RNA virus genomes are suppressed in the nucleotide combination of a cytosine followed by a guanosine (CpG), indicating that they are detrimental to the virus. The antiviral protein ZAP binds viral RNA containing CpGs and prevents the virus from multiplying. However, it remains unknown how the number and position of CpGs in viral genomes affect restriction by ZAP and whether CpGs have other antiviral mechanisms. Importantly, manipulating the CpG content in viral genomes could help create new vaccines. HIV-1 shows marked CpG suppression, and by introducing CpGs into its genome, we show that ZAP efficiently targets a specific region of the viral genome, that the number of CpGs does not predict the magnitude of antiviral activity, and that CpGs can inhibit HIV-1 gene expression through a ZAP-independent mechanism. Overall, the position of CpGs in the HIV-1 genome determines the magnitude and mechanism through which they inhibit the virus.

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HIV-1 Sequence Necessary and Sufficient to Package Non-viral RNAs into HIV-1 Particles

Cited by 30 publications

References 77 publications

Roles of Gag-RNA interactions in HIV-1 virus assembly deciphered by single-molecule localization microscopy

Roles of Gag-RNA interactions in HIV-1 virus assembly deciphered by single-molecule localization microscopy

CLIP-related methodologies and their application to retrovirology

CpG Dinucleotides Inhibit HIV-1 Replication through Zinc Finger Antiviral Protein (ZAP)-Dependent and -Independent Mechanisms

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