COVID-19 was first identified in January 2020. A patient in the state of Washington was given a diagnosis of coronavirus infection on 20 January. A group of scientists based at the Centers for Disease Control and Prevention in Atlanta, Georgia isolated the virus from nasopharyngeal and oropharyngeal swabs and were able to characterize the genomic sequence, replication properties and cell culturetropism from the swabs. They made available the virus to the wider scientific community shortly thereafter "by depositing it into two virus reagent repositories".[6]
Both the N-terminal and C-terminal domains are capable of binding RNA. The C-terminal domain forms a dimer that is likely to be the native functional state.[2] Parts of the IDR, particularly a conservedsequence motif rich in serine and arginine residues (the SR-rich region), may also be implicated in dimer formation, though reports on this vary.[2][3] Although higher-order oligomers formed through the C-terminal domain have been observed crystallographically, it is unclear if these structures have a physiological role.[2][9]
The C-terminal dimer has been structurally characterized by X-ray crystallography for several coronaviruses and has a highly conserved structure.[7] The N-terminal domain - sometimes known as the RNA-binding domain, though other parts of the protein also interact with RNA - has also been crystallized and has been studied by nuclear magnetic resonance spectroscopy in the presence of RNA.[10]
Post-translational modifications
The N protein is post-translationally modified by phosphorylation at sites located in the IDR, particularly in the SR-rich region.[2][11] SARS-CoV-2
nucleocapsid (N) protein is arginine methylated by protein arginine methyltransferase 1 (PRMT1) at residues R95 and R177. Type I PRMT inhibitor (MS023) or substitution of R95 or R177 with lysine inhibited interaction of N protein with the 5’-UTR of SARS-CoV-2 genomic RNA, a property required for viral packaging | doi: 10.1016/j.jbc.2021.100821 | PMID 34029587. In several coronaviruses, ADP-ribosylation of the N protein has also been reported.[12][11] With unclear functional significance, the SARS-CoV N protein has been observed to be SUMOylated and the N proteins of several coronaviruses including SARS-CoV-2 have been observed to be proteolytically cleaved.[11][13][14]
Expression and localization
The N protein is the most highly expressed in host cells of the four major structural proteins.[2] Like the other structural proteins, the gene encoding the N protein is located toward the 3' end of the genome.[3]
Illustration of a coronavirus virion in the respiratory mucosa, showing the positions of the four structural proteins and components of the extracellular environment.[16]NMR structure of the SARS-CoV-2 N protein N-terminal domain (red) in complex with double-stranded RNA (orange and yellow).[10]
The N protein binds to RNA to form ribonucleoprotein (RNP) structures for packaging the genome into the viral capsid.[2][3] The RNP particles formed are roughly spherical and are organized in flexible helical structures inside the virus.[2][3] Formation of RNPs is thought to involve allosteric interactions between RNA and multiple RNA-binding regions of the protein.[2][9]Dimerization of N is important for assembly of RNPs. Encapsidation of the genome occurs through interactions between N and M.[2][3] N is essential for viral assembly.[3] N also serves as a chaperone protein for the formation of RNA structure in the genomic RNA.[3][9]
Genomic and subgenomic RNA synthesis
Synthesis of genomic RNA appears to involve participation by the N protein. N is physically colocalized with the viral RNA-dependent RNA polymerase early in the replication cycle and forms interactions with non-structural protein 3, a component of the replicase-transcriptase complex.[3] Although N appears to facilitate efficient replication of genomic RNA, it is not required for RNA transcription in all coronaviruses.[3][17] In at least one coronavirus, transmissible gastroenteritis virus (TGEV), N is involved in template switching in the production of subgenomic mRNAs, a process that is a distinctive feature of viruses in the order Nidovirales.[3][17][18]
Cell cycle effects
Coronaviruses manipulate the cell cycle of the host cell through various mechanisms. In several coronaviruses, including SARS-CoV, the N protein has been reported to cause cell cycle arrest in S phase through interactions with cyclin-CDK.[3][4] In SARS-CoV, a cyclin box-binding region in the N protein can serve as a cyclin-CDK phosphorylation substrate.[3] Trafficking of N to the nucleolus may also play a role in cell cycle effects.[4] More broadly, N may be involved in reduction of host cell protein translation activity.[3]
The sequences and structures of N proteins from different coronaviruses, particularly the C-terminal domains, appear to be well conserved.[2][7][23] Similarities between the structure and topology of the N proteins of coronaviruses and arteriviruses suggest a common evolutionary origin and supports the classification of these two groups in the common order Nidovirales.[2][3]
Examination of SARS-CoV-2 sequences collected during the COVID-19 pandemic found that missense mutations were most common in the central linker region of the protein, suggesting this relatively unstructured region is more tolerant of mutations than the structured domains.[7] A separate study of SARS-CoV-2 sequences identified at least one site in the N protein under positive selection.[24]
The N protein's properties of being well conserved, not appearing to recombine frequently, and producing a strong T-cell response have led to it being studied as a potential target for coronavirus vaccines.[25][26][23][27] The vaccine candidate UB-612 is one such experimental vaccine that targets the N protein, along with other viral proteins, to attempt to induce broad immunity.[28][29]
^Wang CY, Hwang KP, Kuo HK, Peng WJ, Shen YH, Kuo BS, Huang JH, Liu H, Ho YH, Lin F, Ding S, Liu Z, Wu HT, Huang CT, Lee YJ, Liu MC, Yang YC, Lu PL, Tsai HC, Lee CH, Shi ZY, Liu CE, Liao CH, Chang FY, Chen HC, Wang FD, Hou KL, Cheng J, Wang MS, Yang YT, Chiu HC, Jiang MH, Shih HY, Shen HY, Chang PY, Lan YR, Chen CT, Lin YL, Liang JJ, Liao CC, Chou YC, Morris MK, Hanson CV, Guirakhoo F, Hellerstein M, Yu HJ, King CC, Kemp T, Heppner DG, Monath TP (May 2022). "A multitope SARS-CoV-2 vaccine provides long-lasting B cell and T cell immunity against Delta and Omicron variants". Journal of Clinical Investigation. 132 (10). doi:10.1172/JCI157707. PMC9106357. PMID35316221.
