Histone mimicry: How a SARS-CoV-2 protein functions as an H3 mimic to disrupt host cell epigenetic regulation

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first recognized at the beginning of 2020 and is responsible for the ongoing COVID-19 pandemic.  The persistence of the virus has been partly accredited to its effective suppression of host cell responses.  As such, continued research in elucidating the dynamics of the SARS-CoV-2 life cycle is essential to facilitate the design and development of novel diagnostics and suitable therapies.  Although reports suggest that SARS-CoV-2 can dysregulate the host’s gene expression and innate immune response, the underlying mechanism has remained somewhat elusive, until now.

SARS-CoV-2 consists of a positive-sense single-stranded RNA genome and 4 different types of structural proteins.  The N, or nucleocapsid, protein encapsidates the genome, while the S (spike), E (envelope), and M (membrane) proteins comprise the surrounding lipid bilayer envelope.  Several open reading frames (ORFs) within the SARS-CoV-2 genome have been identified, corresponding to viral structural elements (S, E, M, and N proteins) and accessory genes (ORF1a, 1b, 3a, 6, 7a, 7b, 8, and 10).  In particular, the protein encoded by ORF8 has garnered some attention of late.

The ORF8 viral protein is highly expressed during infection, with a small enough size (15 kDa) to accommodate diffusion into the nucleus.  It was recently shown that ORF8 can modify the epigenome of host cells and disrupt chromatin, consequently impeding the host transcriptional response.  This process is facilitated by a specific amino acid (aa) sequence known as the ARKS (alanine, arginine, lysine, serine) motif.  Situated at aa 50 of ORF8, the motif is identical to that of two separate sites considered critical regulatory regions within the histone H3 N-terminal tail.  It also mediates an interaction between ORF8 and chromatin proteins, including nuclear architectural proteins, histones, histone-modifying enzymes, and transcription factors.

Similar to H3, the ARKS motif of ORF8 contains an acetylated lysine.  Such homology affords ORF8 the ability to act as a histone mimic.  Accordingly, the viral protein can perturb histone post-translational modification (PTM) regulation.  Histone PTMs are well-associated with chromatin structure (euchromatin versus heterochromatin), which in turn impacts transcriptional activation/silencing.  For instance, histone acetylation (e.g., H3K9ac, H3K14ac, H3K27ac) has been linked to an open chromatin configuration and active gene expression state.  Methylated histone marks like H3K4me1/2/3, H3K36me3, and H3K79me2 have been identified as transcription activators, while tri-methylated H3K9 and H3K27 are known to play repressive roles.

Cells expressing ORF8 were found to display increased repressive marks (H3K9me3, H3K27me3) and decreased active marks (H3K9ac) within their H3 ARKS motifs, which correlated with a heterochromatic remodeling of the host DNA and a lower expression of highly accessible genes.  Coincidentally, it was also found that ORF8 induces the degradation of KAT2A, an H3K9-targeting acetyltransferase that is likely responsible for lysine acetylation of the ARKS histone mimic site.

By deleting either ORF8 from the SARS-CoV-2 genome or the histone mimic site from the ORF8 protein, both the SARS-CoV-2 genome copy number and the virus’s ability to disrupt host cell chromatin were diminished.  Such promising results could lead to alternate routes in stemming SARS-CoV-2 infectivity and transmissibility that are predicated on epigenetic processes governing the viral life cycle.

References

Kee J, Thudium S, Renner DM, et al. SARS-CoV-2 disrupts host epigenetic regulation via histone mimicry. Nature. 2022;610(7931):381-388. doi:10.1038/s41586-022-05282-z

Kim D, Lee JY, Yang JS, Kim JW, Kim VN, Chang H. The Architecture of SARS-CoV-2 Transcriptome. Cell. 2020;181(4):914-921.e10. doi:10.1016/j.cell.2020.04.011

Tsai K, Cullen BR. Epigenetic and epitranscriptomic regulation of viral replication. Nat Rev Microbiol. 2020;18(10):559-570. doi:10.1038/s41579-020-0382-3