Table 2.
Functions of invasiveness and virulence of individual proteins of SARS-CoV-2.
| Proteins | Functions |
|---|---|
| Nsp1 | Suppresses the host protein synthesis (including IFN-I and RIG-I) through association with ribosomes [155,156]. Inhibits IRF3 phosphorylation and IFN production; suppresses ISG induction due to Tyk2 and STAT2 depletion and inhibition of STAT1 phosphorylation [40,157]. Changes the structure and function of the cytoskeleton [158]. |
| Nsp2 | Can participate in the binding of nucleic acids and the regulation of intracellular signaling pathways [159]. Participates in the processes of viral replication [160]. Proteins that interact with nsp2 are involved in several biological processes, such as endosomal transport and translation [161]. Changes the synthesis and modification of lipids [158]. |
| Nsp3 | Papain-like protease (PLpro) and deubiquitinase. Participates in the proteolysis of 1a/1ab polyproteins [10,162]. Cleaves IRF3 [163]. By removing ubiquitin in the structures of signaling pathways, they disrupt the development of antiviral cellular stress, including translocation of IRF3 into the cell nucleus and inhibition of RIG-I, STING, TRAF3, TBK1, IRF3 [164]. Nsp3 SARS-CoV-1 c promotes inactivation of conjugated ubiquitin-like molecules such as interferon, which is involved in different pathways of the innate antiviral immune response regulation [165,166]. However, the deubiquitinase and IFN-blocking functions of nsp3 SARS-CoV-2 seem to be significantly lower than that of nsp3 SARS-CoV-1 [150]. Participates in the RTC formation [167]. |
| Nsp4 | An ER-localized transmembrane protein (as nsp3 and nsp6), is considered to be involved in the assembly of virus-induced cytoplasmic double-membrane vesicles [168]. Participates in the RTC formation [167]. |
| Nsp5 | 3-chymotrypsin-like “main” protease (3CLpro) is involved in the proteolysis of 1a/1ab polyproteins [10]. Inhibits the translocation of IRF3 into the cell nucleus and promotes the degradation of IRF3 [169]. It regulates (by proteolysis) the development of pro-inflammatory stress in different directions: activating the formation of NLRP12 by inflammasomes and inhibiting kinase - TGF-beta activated kinase 1 (MAP3K7 - mitogen-activated protein kinase 7) binding protein 1 (TAB1) [163]. Participates in the RTC formation [167]. |
| Nsp6 | Inhibits the phosphorylation of IRF3, STAT1, and STAT2 [110]. Potentially contributes to SARS-CoV-2 infection by impairing the ability of autophagosomes to deliver viral components to lysosomes for degradation [170,171]. Probably, along with orf7a, can interact with sigma receptors, which are involved in lipid remodeling and the ER stress response [161]. Participates in the RTC formation [167]. |
| Nsp7 | During viral RNA replication, the nsp12 cofactor forms a primase complex with nsp8 [167,172]. Participates in the RTC formation [167,173]. |
| Nsp8 | The nsp12 cofactor in viral RNA replication [162]. Participates in the formation of the RTC [167,173]. Forms a primase complex with nsp7, which plays a decisive role in the regulation of the activity of RNA-dependent RNA polymerase (RdRP) nsp12. [174,175]. Suppresses the transport of membrane proteins in cells infected with SARS-CoV-2, disrupts IFN secretion [176]. |
| Nsp9 | RNA-binding protein, interacting with nsp12, is one of the key factors of RTC [173,175]. Suppresses the transport of membrane proteins in cells infected with SARS-CoV-2, disrupts the secretion of IFN and some other cytokines [176]. Interferes with the activation of IRF3 and the induction of IFN synthesis by inhibiting TBK1 [20,138]. |
| Nsp10 | The cofactor of nsp14 and nsp16 forms functional complexes with them upon methylation of viral RNA [154,172]. Acting on NKRF (NF-κB-repressive factor), can regulate the levels of IL-8, NKRF and form a unique immune signature in COVID-19 [177]. Participates in the RTC formation [167]. |
| Nsp11 | Includes only 13 amino acid residues [178]. The role of the nsp11 protein in cells infected with CoV has not yet been studied [179]. |
| Nsp12 | RNA-dependent RNA polymerase is a key enzyme mediating the synthesis of all viral RNA molecules [162]. A key component of RTC [167,173,175]. |
| Nsp13 | Helicase, 5′-triphosphatase. Inhibits the phosphorylation of TBK1, which leads to a decrease in IRF3 activation, inhibits the phosphorylation of STAT1 and STAT2 [40]. Participates in viral replication [170]. Changes the structure and function of the cytoskeleton [158]. Participates in the RTC formation [167,173,175]. |
| Nsp14 | 3′-5 ′exoribonuclease and N-7-methyltransferase. Inhibits nuclear translocation of IRF3 [150]. Participates in the RTC formation [167,175]. As an exonuclease, it provides the ability to correct errors in the RNA synthesis complex, which allows SARS-CoV-2 to maintain its large genome [180]. |
| Nsp15 | NendoU, a uridylate-specific endoribonuclease. Inhibits nuclear translocation of IRF3 [150]. Participates in the RTC formation [167,175]. Meanwhile, nsp15-deficient CoVs are viable and can replicate [181], but with some delay and errors [182]. Another possible mechanism of nsp15 action is an evasion of viral double-stranded RNA recognition by host sensors in macrophages, including MDA5, PKR, and OAS/RNaseL [182]. |
| Nsp16 | 2-Oʹ-methyltransferase, which blocks the recognition of viral RNA by PRR [183,184] by forming the morpho-functional complexes with nsp10 [174]. Participates in the RTC formation [167,175]. |
| Orf3a | Disrupts the IFN signaling pathways by inhibiting STAT1 phosphorylation [40,177]. Can regulate the effects of IL-6 action by inhibiting STAT3 and STAT5 [177]. Promotes lysosomal degradation of the α-chain of the IFN-I receptor (IFNAR1) and induces ER stress (shown in SARS-CoV-1) [185,186]. Forms transmembrane ionic potassium-specific channels that facilitate the release of the virus from the cell [187]. It is assumed that viral ion channels can also promote membrane fusion and regulate viral replication and/or the packaging of genomic RNA into viral particles [187]. Activates NF-kB, NLRP3 inflammasomes, promoting cytokine storm [188,189]. Blocks the fusion of autophagosomes with lysosomes, contributing to the survival of the virus [136]. |
| Orf3b | Interferes with nuclear translocation of IRF3 [190]. Can cause a specific antibody response as N and orf8 proteins [191]. Orf3b is not expressed in many strains of SARS-CoV-2 [150], however, SARS-CoV-2 orf3b can suppress IFN-I induction more efficiently than its orthologue SARS-CoV-1 [190]. |
| Orf6 | Inhibits IRF3 (via action on TBK1) phosphorylation [177]. Binds to KPNA2 (karyopherin subunit alpha 2) and the Nup98-Rae1 complex, which inhibits nuclear translocation of IRF3 and STAT1 [40,150,192]. Causes changes in signaling pathways that include the activation of apoptosis through caspase-3-mediated, ER stress, and JNK-dependent pathways (JNK-c-Jun N-terminal kinases) [158]. Inhibition of STAT1 causes compensatory hyperactivation of STAT3 in cells infected with SARS-CoV-2, which promotes overproduction and activation of plasminogen activator inhibitor-1 (PAI-1) and can lead to coagulopathy [193]. |
| Orf7a | Inhibits the STAT2 phosphorylation [40]. According to the results of in silico calculations, can interact with sigma receptors, as nsp6 [194]. Has structural homology to ICAM-1, binds to Mac-1 and the integrin receptor LFA-1 on leukocytes. The orf7a expression leads to apoptosis, blocking the cell cycle, activation of NF-kB, and mitogen-activated protein kinase (MAPK) [195]. Binds to CD14 (TLR4 cofactor), promoting the production of proinflammatory cytokines [196]. Promotes the release of SARS-CoV-2 from the cell membrane by inhibiting the membrane protein BST-2 [197]. |
| Orf7b | Inhibits STAT1 and STAT2 phosphorylation [40]. |
| Orf8 | Interacts with a variety of host proteins and blocks the class 1 major histocompatibility complex (MHC-I) protein in the ER lumen [198,199]. Inhibits IFN signaling pathways and activation of ISG promoters [200]. Orf8, being secreted into the extracellular space can activate the IL-17 signaling pathway by interacting with the host’s IL17RA [201]. Forms cation channels upon assembly in the lipid bilayer, like orf3a and E-protein [202]. |
| Orf9b | Blocks the signaling pathways from TNF receptors by acting on TRAF3 and TRAF6 (TNF receptor-associated factor 3 and 6), disrupts IFN-I synthesis, and induces ATG5-mediated autophagy in host cells [189]. Blocks TOM70, a key adapter that transmits an antiviral signal from the mitochondrial RLR/MAVS pathway to TBK1/IRF3 to induce an IFN response [203,204]. Interacts with RIG-I, MDA-5, MAVS, STING, and TBK1, prevents phosphorylation and nuclear translocation of IRF3, NF-κB activation, and inhibits TRIF (TLR adapter) [205,206]. |
| S | Plays a key role in the process of receptor recognition and cell membrane fusion [207]. The structure of this protein allows it to interact with many receptors in host cells (Table 1). |
| E | Promotes the assembly and release of the virus, has the properties of a viroporin membrane channel, which can contribute to damage to the epithelial barrier, the pathogenesis, and the severity of COVID-19 [208]. The function of the ion channel is associated with the activation of inflammasomes and the development of hyperinflammation in the lungs [209,210]. These effects of E-protein are capable of initiating a cytokine storm and the development of an experimental analog of ARDS [211]. |
| M | The dominant structural protein can bind to other structural proteins such as S and E and determines the shape of the viral envelope [210]. Participates in the packaging of the genome in the viral particle, structures the viral particle [172]. Inhibits STAT1 phosphorylation [40]. M interacts with RIG-I, MAVS, and TBK1, thus preventing the formation of a multiprotein complex containing RIG-I, MAVS, TRAF3, and TBK1, and subsequently preventing phosphorylation, nuclear translocation, and activation of IRF3 [212]. |
| N | Binds viral RNA and protects the viral genome, participates in the assembly of the genomic RNA of the virus [172]. Modifies the signaling pathway of the cytokine TGF-β, blocking the apoptosis of infected host cells, but can also induce apoptosis by activating the mitochondrial pathway [158]. Promotes hyperinflammation by activating NLRP3 inflammasome [213]. It interferes with RIG-I activation, interferes with the association between TBK1 and IRF3, and prevents nuclear translocation of IRF3 [214]. Inhibits the formation of G3BP1-dependent stress granules during the development of the cell’s antiviral response and blocks the host mRNA [215]. |
RTC—replication/transcription complex includes: nsp3, nsp4 and nsp6, which are involved in the formation of viral RNA synthesis sites, basic protease (nsp5), nsp nsp8 primase complex, RNA-binding protein nsp9, basic RNA-dependent RNA polymerase (nsp12), helicase/triphosphatase (nsp13), exoribonuclease (nsp14), endonuclease (nsp15), and N7- and 2’O-methyltransferase (nsp10/nsp16), ER—endoplasmic reticulum.