The SARS-CoV-2 Spike Glycoprotein Biosynthesis, Structure, Function, and Antigenicity: Implications for the Design of Spike-Based Vaccine Immunogens

Abstract

The ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses a grave threat to global public health and imposes a severe burden on the entire human society. Like other coronaviruses, the SARS-CoV-2 genome encodes spike (S) glycoproteins, which protrude from the surface of mature virions. The S glycoprotein plays essential roles in virus attachment, fusion and entry into the host cell. Surface location of the S glycoprotein renders it a direct target for host immune responses, making it the main target of neutralizing antibodies. In the light of its crucial roles in viral infection and adaptive immunity, the S protein is the focus of most vaccine strategies as well as therapeutic interventions. In this review, we highlight and describe the recent progress that has been made in the biosynthesis, structure, function, and antigenicity of the SARS-CoV-2 S glycoprotein, aiming to provide valuable insights into the design and development of the S protein-based vaccines as well as therapeutics.

Keywords: SARS-CoV-2; immunogen design; membrane fusion; neutralizing antibodies; receptor-binding domain; spike glycoprotein; structure; synthesis.

Figure 1

Schematic representation of the life cycle of SARS-CoV-2. The life cycle of SARS-CoV-2 begins with membrane fusion occurring at the plasma membrane or within acidified endosomes after endocytosis, which is mediated by conformational changes in the S glycoprotein triggered by angiotensin-converting enzyme 2 (ACE2) binding. Following viral entry, SARS-CoV-2 releases its genomic RNA into the host cell cytoplasm. Genome RNA is first translated into viral replicase polyproteins (pp1a and 1ab), which are further cleaved by viral proteases into a total of 16 nonstructural proteins. A replication-transcription complex (RTC) is formed based on many of these nonstructural proteins. In the process of genome replication and transcription mediated by RTC, the negative-sense (− sense) genomic RNA is synthesized and used as a template to produce positive-sense (+ sense) genomic RNA and subgenomic RNAs. The nucleocapsid (N) structural protein and viral RNA are replicated, transcribed, and synthesized in the cytoplasm, whereas other viral structural proteins, including the S protein, membrane (M) protein and envelope (E) protein, are transcribed and then translated in the rough endoplasmic reticulum (RER) and transported to the Golgi complex. In the RER and Golgi complex, the SARS-CoV-2 glycoprotein is subjected to co-translational and post-translational processing, including signal peptide removal, trimerization, extensive glycosylation and subunit cleavage. The N protein is subsequently associated with the positive sense genomic RNA to become a nucleoprotein complex (nucleocapsid), which together with S, M, and E proteins as well as other viral proteins, is further assembled and followed by budding into the lumen of the ER-Golgi intermediate compartment (ERGIC) to form mature virions. Finally, the mature virions are released from the host cell, waiting for a new life cycle to start. This figure is adapted from the template in BioRender (https://biorender.com/).

Figure 2

Overall structures of the SARS-CoV-2 S glycoprotein trimer in different conformations. (A) Schematic representation of the domain arrangement of the SARS-CoV-2 S protein precursor. SS, signal peptide; NTD: N-terminal domain; RBD: receptor-binding domain; RBM: receptor-binding motif; SD1/2: subdomain 1 and 2; FP, fusion peptide; HR1, heptad repeat 1; CH, central helix; CD, connector domain; HR2, heptad repeat 2; TM, transmembrane domain; CT, cytoplasmic tail. Arrows denote protease cleavage sites. (B) Side and top views of the prefusion structure of the SARS-CoV-2 S ectodomain trimer with all three RBDs in the down conformation (PDB ID: 6VXX). One protomer is shown in ribbon representation colored corresponding to the schematic in (A), a second protomer in light gray surface representation, and the third protomer in dark gray surface representation. (C) is identical to (B) except that a single RBD assumes the up conformation and is shown in ribbon representation (PDB ID: 6VYB). (D) Overall structure of the SARS-CoV-2 S2 trimer in the postfusion conformation is shown in ribbon representation colored corresponding to the schematic in (A) (PDB ID: 6XRA). The glycans were omitted for clarity.