Structure and Function of Major SARS-CoV-2 and SARS-CoV Proteins

Abstract

SARS-CoV-2 virus, the causative agent of COVID-19 pandemic, has a genomic organization consisting of 16 nonstructural proteins (nsps), 4 structural proteins, and 9 accessory proteins. Relative of SARS-CoV-2, SARS-CoV, has genomic organization, which is very similar. In this article, the function and structure of the proteins of SARS-CoV-2 and SARS-CoV are described in great detail. The nsps are expressed as a single or two polyproteins, which are then cleaved into individual proteins using two proteases of the virus, a chymotrypsin-like protease and a papain-like protease. The released proteins serve as centers of virus replication and transcription. Some of these nsps modulate the host’s translation and immune systems, while others help the virus evade the host immune system. Some of the nsps help form replication-transcription complex at double-membrane vesicles. Others, including one RNA-dependent RNA polymerase and one exonuclease, help in the polymerization of newly synthesized RNA of the virus and help minimize the mutation rate by proofreading. After synthesis of the viral RNA, it gets capped. The capping consists of adding GMP and a methylation mark, called cap 0 and additionally adding a methyl group to the terminal ribose called cap1. Capping is accomplished with the help of a helicase, which also helps remove a phosphate, two methyltransferases, and a scaffolding factor. Among the structural proteins, S protein forms the receptor of the virus, which latches on the angiotensin-converting enzyme 2 receptor of the host and N protein binds and protects the genomic RNA of the virus. The accessory proteins found in these viruses are small proteins with immune modulatory roles. Besides functions of these proteins, solved X-ray and cryogenic electron microscopy structures related to the function of the proteins along with comparisons to other coronavirus homologs have been described in the article. Finally, the rate of mutation of SARS-CoV-2 residues of the proteome during the 2020 pandemic has been described. Some proteins are mutated more often than other proteins, but the significance of these mutation rates is not fully understood.

A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19

“…The SARS-CoV-2 genome is approximately 29.9 kb in length, with 12 open reading frames (ORFs). It encodes two large polyproteins, four structural proteins, and eight accessory proteins [ 5 ]. The two large polyproteins are ORF1a and ORF1b, which proteolytically cleave to form 16 non-structural proteins (NSPs) [ 6 ].…”

Human Coronaviruses: Genetics, Virulence Factors and Pathophysiology, Diseases’ Epidemiology

“…Nsp2 and nsp3 of SARS-CoV are detected not only as mature processed proteins but also as precursors of nsp1 and nsp3, which conferred them a role as precursors in replication. These results suggest that nsp2 may be involved in the regulation of nsp1 and nsp3 functions [47] .…”

Innate Immunity Evasion Strategies of Highly Pathogenic Coronaviruses: SARS-CoV, MERS-CoV, and SARS-CoV-2

“…In addition, NSP14 of HP-hCoVs possesses guanine N7-MTase activity coupled with exonuclease activity, involving RNA cap formation and cleaving RNA-PAMPs, also contributing to immune evasion (Chen et al, 2009;Ramasamy and Subbian, 2021). NSP16 of all HP-hCoVs, with its activating cofactor nsp10, can form a 2 -O-methylated cap for immune evasion in which the conserved D130 is critical (Gorkhali et al, 2021). Taken together, the 5 cap modification of viral RNA impairs the recognition by cytosolic PRRs, thereby resisting the IFN-mediated antiviral response.…”