Proteomics-Based Insights Into the SARS-CoV-2-Mediated COVID-19 Pandemic: A Review of the First Year of Research

Abstract

In late 2019, a virus subsequently named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in China and led to a worldwide pandemic of the disease termed coronavirus disease 2019. The global health threat posed by this pandemic led to an extremely rapid and robust mobilization of the scientific and medical communities as evidenced by the publication of more than 10,000 peer-reviewed articles and thousands of preprints in the first year of the pandemic alone. With the publication of the initial genome sequence of SARS-CoV-2, the proteomics community immediately joined this effort publishing, to date, more than 100 peer-reviewed proteomics studies and submitting many more preprints to preprint servers. In this review, we focus on peer-reviewed articles published on the proteome, glycoproteome, and glycome of SARS-CoV-2. At a basic level, proteomic studies provide valuable information on quantitative aspects of viral infection course; information on the identities, sites, and microheterogeneity of post-translational modifications; and, information on protein-protein interactions. At a biological systems level, these studies elucidate host cell and tissue responses, characterize antibodies and other immune system factors in infection, suggest biomarkers that may be useful for diagnosis and disease-course monitoring, and help in the development or repurposing of potential therapeutics. Here, we summarize results from selected early studies to provide a perspective on the current rapidly evolving literature.

Keywords: COVID-19; MS; SARS-CoV-2; glycosylation; review.

Graphical abstract

Fig. 1

The SARS-CoV-2 proteome and its post-translational modifications (PTMs). The SARS-CoV-2 NCBI reference sequence proteome delineated along its genome (A). The 28 proteins annotated in the NCBI reference sequence are represented as boxes with the starting base corresponding to each protein in the genome listed later along with most protein names (pp1ab and pp1a are labeled inside boxes). Note that the nsp proteins are expressed as parts of large polyproteins (pp1ab and pp1a), which are subsequently cleaved by proteases contained in the polyproteins themselves. A summary of PTMs detected in proteomics studies is listed above each protein except for N and S, which are shown in detail in panels B and C. Numbers in parentheses indicate the residue number in pp1ab as given in the study by Klann et al. (102). The PTMs of S. A partial domain structure is shown for orientation with coloring for contrast and start residue numbers. The most abundant N-glycans from the most abundant Oxford class at each site are shown as reported by Zhao et al. (86). The class abundances at each site reported by Watanabe et al. (83) are similar although the protein they aonalyzed showed a small but clear tendency toward slightly less processed glycoforms. Articles have reported varying amounts of O-glycosylation on S almost exclusively at T323, occupancy generally ~10% or less. Note also that Davidson et al. (14) identified 13 sites of phosphorylation on S; however, most were not cytoplasmic. Secretory pathway kinases have been confirmed (e.g., FAM20C), but it is not clear that these sites fit with known specificity determinants. The PTMs of N and ORF9b. Domain structure shown with coloring for contrast and start residue numbers. ORF9b is an alternative ORF in the N coding sequence that is not annotated in the NCBI reference sequence. FP, fusion peptide; HR1, heptad repeat 1; HR2, heptad repeat 2; NCBI, National Center for Biotechnology Information; nsp, nonstructural protein; RBD, receptor binding domain; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Fig. 2

Views of the SARS-CoV-2 spike protein and its glycosylation. Images courtesy of Oliver C. Grant (unused graphics from Zhao et al. (86)). Protein models courtesy of Professor Bing Chen. A, the interface of SARS-CoV-2 S (white) bound to ACE2 (red) showing glycans involved in glycan–peptide and glycan–glycan interactions. B, the postfusion structure of SARS-CoV-2 S showing its distinctive columnar structure and regular spacing of N-glycans. ACE2, angiotensin-converting enzyme 2; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Fig. 3

The SARS-CoV-2 viral life cycle and selected host proteins involved. The viral life cycle is displayed proceeding from host cell entry through new virion synthesis, packaging, and export. Host cell proteins are labeled in green, and SARS-CoV-2 proteins are labeled in blue. Red arrows (→) indicate protease cleavage. The representation of virus shows ribonucleoproteins (RNPs) (consisting of five dimers of N) in the tetrahedral geometry recently reported (Yao et al. (99)). This article reported an average of 26 ± 15 copies of prefusion S per virion and 26 ± RNPs per virion. The life cycle in a given cell begins with host cell entry mediated by ACE2 (the receptor), TMPRSS2 (or alternatively CatB/L—CSTB/CTSL—fusion priming enzymes), and proceeds with trafficking through endosomes. Endosomal maturation required for viral–host–cell membrane fusion involves the proteins PIKfyve and TPC2. After fusion and uncoating of the viral RNA, the replication-transcription complex is expressed, and new viral genomic RNAs (gRNAs, + and − sense) and subgenomic RNAs (sgRNAs, + and − sense) are produced. The translation of viral proteins and modulation of host protein translation is affected by protein–protein interactions (Nsp2-eIFE2/GIGYF2, Nsp9-eIF4H, and N-LARP1 are shown) and signaling. New virion structural protein N is phosphorylated (CK2, PKC, and CDK), forms RNPs, winds gRNAs, and collects at the ERGIC membrane for envelopment. Viral proteins E, M, and S traffic through the secretory pathway for further processing including addition of glycans. Filopodia formation is enhanced (proposed to be CK2 driven by Bouhaddou et al. (101)) and may improve transmission of egressing virus between cells. ACE2, angiotensin-converting enzyme 2; CTSL, cathepsin L; ERGIC, endoplasmic reticulum golgi intermediate compartment; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; TMPRSS2, transmembrane serine protease 2.