HIV-1 Packaging Visualised by In-Gel SHAPE

Structural and computational studies of HIV-1 RNA

Viruses remain a global threat to animals, plants, and humans. The type 1 human immunodeficiency virus (HIV-1) is a member of the retrovirus family and carries an RNA genome, which is reverse transcribed into viral DNA and further integrated into the host-cell DNA for viral replication and proliferation. The RNA structures from the HIV-1 genome provide valuable insights into the mechanisms underlying the viral replication cycle. Moreover, these structures serve as models for designing novel therapeutic approaches. Here, we review structural data on RNA from the HIV-1 genome as well as computational studies based on these structural data. The review is organized according to the type of structured RNA element which contributes to different steps in the viral replication cycle. This is followed by an overview of the HIV-1 transactivation response element (TAR) RNA as a model system for understanding dynamics and interactions in the viral RNA systems. The review concludes with a description of computational studies, highlighting the impact of biomolecular simulations in elucidating the mechanistic details of various steps in the HIV-1's replication cycle.

Structural diversity of the region encompassing DIS, SD and Psi hairpins in HIV and SIV genomes

We investigated in silico the secondary structure of the region encompassing DIS, SD and Psi hairpins in HIV-1 genomes of rare groups N, O and P, HIV-2 genomes and SIV genomes from chimpanzees, gorillas and monkeys. We found that the structure of this region in SIVcpzptt genomes of the 1st and the 2nd clusters is similar to that in HIV-1 genomes of groups M and N, respectively. Further, the structure of the region encompassing DIS, SD and Psi hairpins is similar in HIV-1 genomes of groups O and P and SIVgor genomes. Here we report that the DIS hairpin and truncated Psi hairpin are conserved in all HIV-1 and SIVcpz/gor genomes studied, while only the sequence of the splice donor site, but not the architecture of the SD hairpin involving this signal is conserved in HIV-1N/O/P and SIVcpz/gor genomes. A study on the 5' leader structure in genomes of 28 different SIV lineages infecting monkeys showed that the domain closed by U5-AUG duplex can form in all these genomes. This domain mainly consists of 2 subdomains, one of which includes the signal PBS (PBS subdomain) and another contains a putative DIS hairpin (DIS subdomain). DIS subdomains contain 1-8 hairpins. None of them is similar to those in HIV-1 or SIVcpz/gor genomes. The palindrome GUGCAC was found only in SIVdrl/mnd-2, the GACGC-GCGUC duplex (Sakuragi et al., 2012) - only in SIVrcm/drl/mnd-2 and a putative 5' G-quadruplex - in SIVdeb/drl/rcm/stm genomes. In genomes of eight SIV lineages, DIS hairpin has palindrome UGCGCA. Studies on the 5' leader in 64 HIV-2 genomes of different subtypes showed, in particular, that this region has sequences of a putative 5' G-quadruplex and a putative duplex similar to the GACGC-GCGUC duplex. The secondary structures of the region encompassing DIS, SD and Psi hairpins in HIV-2 genomes of subtype B and recombinant 01_AB are similar and differ from that in genomes of subtype A.

Initiation of HIV-1 Gag lattice assembly is required for recognition of the viral genome packaging signal

The encapsidation of HIV-1 gRNA into virions is enabled by the binding of the nucleocapsid (NC) domain of the HIV-1 Gag polyprotein to the structured viral RNA packaging signal (Ψ) at the 5' end of the viral genome. However, the subcellular location and oligomeric status of Gag during the initial Gag-Ψ encounter remain uncertain. Domains other than NC, such as capsid (CA), may therefore indirectly affect RNA recognition. To investigate the contribution of Gag domains to Ψ recognition in a cellular environment, we performed protein-protein crosslinking and protein-RNA crosslinking immunoprecipitation coupled with sequencing (CLIP-seq) experiments. We demonstrate that NC alone does not bind specifically to Ψ in living cells, whereas full-length Gag and a CANC subdomain bind to Ψ with high specificity. Perturbation of the Ψ RNA structure or NC zinc fingers affected CANC:Ψ binding specificity. Notably, CANC variants with substitutions that disrupt CA:CA dimer, trimer, or hexamer interfaces in the immature Gag lattice also affected RNA binding, and mutants that were unable to assemble a nascent Gag lattice were unable to specifically bind to Ψ. Artificially multimerized NC domains did not specifically bind Ψ. CA variants with substitutions in inositol phosphate coordinating residues that prevent CA hexamerization were also deficient in Ψ binding and second-site revertant mutants that restored CA assembly also restored specific binding to Ψ. Overall, these data indicate that the correct assembly of a nascent immature CA lattice is required for the specific interaction between Gag and Ψ in cells.

Differing coronavirus genres alter shared host signaling pathways upon viral infection

Coronaviruses are important viral pathogens across a range of animal species including humans. They have a high potential for cross-species transmission as evidenced by the emergence of COVID-19 and may be the origin of future pandemics. There is therefore an urgent need to study coronaviruses in depth and to identify new therapeutic targets. This study shows that distant coronaviruses such as Alpha-, Beta-, and Deltacoronaviruses can share common host immune associated pathways and genes. Differentially expressed genes (DEGs) in the transcription profile of epithelial cell lines infected with swine acute diarrhea syndrome, severe acute respiratory syndrome coronavirus 2, or porcine deltacoronavirus, showed that DEGs within 10 common immune associated pathways were upregulated upon infection. Twenty Three pathways and 21 DEGs across 10 immune response associated pathways were shared by these viruses. These 21 DEGs can serve as focused targets for therapeutics against newly emerging coronaviruses. We were able to show that even though there is a positive correlation between PDCoV and SARS-CoV-2 infections, these viruses could be using different strategies for efficient replication in their cells from their natural hosts. To the best of our knowledge, this is the first report of comparative host transcriptome analysis across distant coronavirus genres.