Protein post-translational modification in SARS-CoV-2 and host interaction

Abstract

SARS-CoV-2 can cause lung diseases, such as pneumonia and acute respiratory distress syndrome, and multi-system dysfunction. Post-translational modifications (PTMs) related to SARS-CoV-2 are conservative and pathogenic, and the common PTMs are glycosylation, phosphorylation, and acylation. The glycosylation of SARS-CoV-2 mainly occurs on spike (S) protein, which mediates the entry of the virus into cells through interaction with angiotensin-converting enzyme 2. SARS-CoV-2 utilizes glycans to cover its epitopes and evade the immune response through glycosylation of S protein. Phosphorylation of SARS-CoV-2 nucleocapsid (N) protein improves its selective binding to viral RNA and promotes viral replication and transcription, thereby increasing the load of the virus in the host. Succinylated N and membrane(M) proteins of SARS-CoV-2 synergistically affect virus particle assembly. N protein regulates its affinity for other proteins and the viral genome through acetylation. The acetylated envelope (E) protein of SARS-CoV-2 interacts with bromodomain-containing protein 2/4 to influence the host immune response. Both palmitoylation and myristoylation sites on S protein can affect the virus infectivity. Papain-like protease is a domain of NSP3 that dysregulates host inflammation by deubiquitination and impinges host IFN-I antiviral immune responses by deISGylation. Ubiquitination of ORF7a inhibits host IFN-α signaling by blocking STAT2 phosphorylation. The methylation of N protein can inhibit the formation of host stress granules and promote the binding of N protein to viral RNA, thereby promoting the production of virus particles. NSP3 macrodomain can reverse the ADP-ribosylation of host proteins, and inhibit the cascade immune response with IFN as the core, thereby promoting the intracellular replication of SARS-CoV-2. On the whole, PTMs have fundamental roles in virus entry, replication, particle assembly, and host immune response. Mutations in various SARS-CoV-2 variants, which lead to changes in PTMs at corresponding sites, cause different biological effects. In this paper, we mainly reviewed the effects of PTMs on SARS-CoV-2 and host cells, whose application is to inform the strategies for inhibiting viral infection and facilitating antiviral treatment and vaccine development for COVID-19.

Keywords: ADP-ribosylation; SARS-CoV-2; acylation; glycosylation; methylation; phosphorylation; ubiquitination.

Figure 1

Distribution of SARS-CoV-2 structural proteins post-translational modification sites in 2D and 3D structural models. (A) Distribution of SARS-CoV-2 spike protein post-translational modification sites. (B) Distribution of SARS-CoV-2 envelope protein post-translational modification sites. (C) Distribution of SARS-CoV-2 membrane protein post-translational modification sites. (D) Distribution of SARS-CoV-2 nucleocapsid protein post-translational modification sites. In 2D structural models, the post-translational modifications represented by the different colors are shown in the figure legends. NTD, N-terminal domain; CTD, C-terminal domain; RBD, receptor binding domain; SD1/2, subdomain 1/2; FP, fusion peptide; HR1/2, heptad repeat region 1/2; CH, central helix; CD, connector domain; TM, transmembrane region; Ext., external; Intra., intravirion. (Sites with * indicate that various protein post-translational modifications have occurred.) In 3D structural models, different colors were used to represent different post-translational modifications occurring at a certain site. Green: N-linked glycosylation; Orange: O-linked glycosylation; Cyan: phosphorylation; Magenta: succinylation; Pink: acetylation; Blue: methylation; Gray 90: succinylation and acetylation; Bluewhite: O-linked glycosylation and phosphorylation. Due to the limitations of the 3D model, some sites could not be marked. We used the open source software PyMOL for mapping, and data were obtained from the RCSB PDB database (https://www.rcsb.org/).

Figure 2

Mechanism of SARS-CoV-2 on PTMs of host proteins. ①Spike proteins recognize and bind to host cell surface receptors (ACE2, GAGS), TMPRSS2 and furin cleave the S1 and S2 subunits. ②Membrane fusion. ③The production of IFN: RIG-I and MAD5 recognize viral RNA and expose the CARD domain, through which RIG-I or MDA5 could interact with MAVS to activate the inhibitor of IκBϵ and TBK1, thereby phosphorylating IRF3 and phosphorylated IRF3 enters into the nucleus to activate IFN-I gene expression. ④The signaling process of IFN: Secreted IFN-α/β binds and activates JAK1 and TYK2, then they phosphorylate STAT1 and STAT2. Phosphorylated STAT1 and STAT2 can form heterodimers, which then bind to IRF9 to form a transcriptional complex IRF3 that translocates to the nucleus to induce the expression of ISG. ⑤NSP3 macrodomain reverses PARP9/DTX3L-dependent ADP-ribosylation of host proteins induced by IFN signaling. ⑥H3K27 can be methylated by EZH2 to form H3K27me3, then inhibits ACE2 expression in host cells. ⑦Highly expressed ACE2 receptors increase the risk of SARS-CoV-2 infection. ⑧NSP14 interacts with SIRT5 to reduce the level of protein succinylation in the host TCA cycle. The blue bars represent the metabolic enzymes in the TCA cycle.