Table 1.
Description of the viral proteins encoded by SARS-CoV-2 genome highlighting their role in the viral lifecycle and immune pathogenicity.
| Viral proteins | Characteristics | Molecular functions | References | |
|---|---|---|---|---|
| Structural protein | Spike-like surface glycoprotein | MW ~ 150 kDa; 1273 amino acids; Rich in glutamine, asparagine, leucine, phenylalanine and serine amino acids | S1 subunit facilitates hACE2-mediated virus attachment; S2 subunit promotes membrane fusion process into the host cell; help in promoting adhesion of infected cells with adjacent non-infected cells | Astuti & Ysrafil, 2020; Bianchi et al., 2020; Chen et al., 2020; Satarker & Nampoothiri, 2020 |
| Envelope glycoprotein | MW ~ 8–12 kDa; 76–109 amino acids; Contains N Terminal Domain (NTD) and hydrophilic C Terminal Domain (CTD) | Forms viriporins which is required for virion assembly and release | ||
| Membrane glycoprotein | 220–260 amino acids; Contains hydrophilic C terminal and amphipathic N terminal | Determine the shape of the virus envelope; helps to stabilize nucleocapsids and promotes completion of viral assembly by stabilizing N protein-RNA complex, inside the internal virion | ||
| Nucleocapsid protein | Composed of a serine-rich linker region between NTD and CTD | NTD forms orthorhombic crystals and binds to the viral genome; linker region regulate self- functioning; CTD promotes nucleocapsid formation; promotes the activation of COX-2 leading to inflammation in the lungs; inhibits IFN-1 causing restrictions in immune responses | ||
| Non-structural proteins | NSP1 (Leader protein) | Inhibit host mRNA translation, antagonize IFN signalling and induce inflammatory cytokines and chemokines | Astuti & Ysrafil, 2020; Min et al., 2020; Samaddar et al., 2020; Yoshimoto, 2020, Zhang et al., 2020 | |
| NSP2 | Binding to prohibitin-1 (PHB1) and prohibitin-2 (PHB2) leads to disruption of the host cell environment | |||
| NSP3 | Encode papain-like protease (PLpro) that helps to cleave the site between NSP2 and NSP3 and release essential viral proteins for viral activity | |||
| NSP4 (Transmembrane domain 2) | Interacting with NSP3 causes rearrangement of the host cell membrane | |||
| NSP5 | Encode chymotrypsin-like protease (3CLpro/Mpro) that cleaves at 11 different sites to produce mature and intermediate viral polyproteins | |||
| NSP6 (Putative Transmembrane domain) | Restricting autophagolysosome development cause hindrance of autophagosomes from transporting viral components for degradation in lysosomes | |||
| NSP7 (Peptide cofactor) | Forms a complex NSP8 and NSP12 to yield RNA polymerase activity | |||
| NSP8 (Peptide cofactor) | Forms hexadecameric complex of RNA polymerase | |||
| NSP9 | Encode RNA-binding protein phosphatase that helps in viral genome replication and transcription | |||
| NSP10 | Interacting with NSP14 and NSP16 to stimulate SAM-dependent methyltransferase activity and 2′-O-Ribosemethyltransferase activity respectively | |||
| NSP11 | Unknown activity yet | |||
| NSP12 (RdRP) | Encodes RNA-dependent RNA polymerase that replicates viral RNA | |||
| NSP13 (Helicase) | Unwinds duplex RNA; elicits 5′-triphosphatase activity to introduce a 5′-terminal cap of mRNA | |||
| NSP14 (N7-methyltransferase) | Proofreading of viral genome by endonuclease and methyltransferase activity | |||
| NSP15 (Endoribonuclease) | Cleaves RNA at 3′-uridylates to form a 2′-3′ cyclic phosphodiester product that protects viral RNA from host recognition and inhibit innate response | |||
| NSP16 (2′-O-Ribosemethyltransferase) | Methylate 2′-hydroxyadenine using SAM as methyl pool thereby avoid MDA5 recognition of viral RNA and inhibit innate immunity regulation | |||