Post-translational modifications of coronavirus proteins: roles and function

Abstract

Post-translational modifications (PTMs) refer to the covalent modifications of polypeptides after they are synthesized, adding temporal and spatial regulation to modulate protein functions. Being obligate intracellular parasites, viruses rely on the protein synthesis machinery of host cells to support replication, and not surprisingly, many viral proteins are subjected to PTMs. Coronavirus (CoV) is a group of enveloped RNA viruses causing diseases in both human and animals. Many CoV proteins are modified by PTMs, including glycosylation and palmitoylation of the spike and envelope protein, N- or O-linked glycosylation of the membrane protein, phosphorylation and ADP-ribosylation of the nucleocapsid protein, and other PTMs on nonstructural and accessory proteins. In this review, we summarize the current knowledge on PTMs of CoV proteins, with an emphasis on their impact on viral replication and pathogenesis. The ability of some CoV proteins to interfere with PTMs of host proteins will also be discussed.

Keywords: coronavirus; deubiquitination; glycosylation; innate immunity; pathogenesis; phosphorylation; post-translational modification; replication; ubiquitination; virus–host interaction.

Figure 1.. Schematic diagram depicting the replication cycle of coronavirus.

Coronavirus replication starts with the binding of the virion to the cognate cell surface receptor, which triggers the fusion between the virus envelope and the cellular membrane, allowing the nucleocapsid to enter the cytoplasm (attachment and entry). After uncoating, the genomic RNA is translated to produce pp1a and pp1ab, which are cleaved to form numerous Nsps. Some of the Nsps induce the formation of DMVs, on which the RTC is assembled. Both gRNA and sgRNA are synthesized via negative sense intermediates. The sgRNAs encode structural proteins and accessory proteins. Virion assembly occurs in the ERGIC. Mature virus particles are transported in smooth-walled vesicles and released via the secretary pathway. DMV: Double membrane vesicle; ER: Endoplasmic reticulum; ERGIC: ER–Golgi intermediate compartment; gRNA: Genomic RNA species; Nsp: Nonstructural protein; pp: Polyprotein; RTC: Replication transcription complex; sgRNA: Subgenomic RNA species.

Figure 2.. Schematic diagram showing the membrane topology and PTMs of coronavirus S protein.

(A) Membrane topology of coronavirus S protein. The trimeric S protein, the six-helix bundle of S2 and the globular S1 domains are illustrated. (B) Major functional domains and PTMs on coronavirus S protein (not to scale). Protein–protein interactions involving some of the modified residues are also indicated. Endo: Endodomain; FP: Fusion peptide; HR: Heptad repeat; N-gly: N-glycosylation; Palm: Palmitoylation; RBD: Receptor-binding domain; S: Spike; TM: Transmembrane domain.

Figure 3.. Schematic diagram showing the membrane topology and PTMs of coronavirus E protein.

(A) Membrane topology of coronavirus E protein. The exterior, interior and transmembrane domains of the protein are shown. (B) Major functional domains and PTMs on coronavirus E protein (not to scale). Endo: Endodomain; MHV: Mouse hepatitis virus; N-gly: N-glycosylation; Palm: Palmitoylation; PTM: Post-translational modification; SARS-CoV: Severe acute respiratory syndrome coronavirus; TM: Transmembrane domain.

Figure 4.. Schematic diagram showing the membrane topology and PTMs of coronavirus M protein.

(A) Membrane topology of coronavirus M protein. The exterior, interior and transmembrane domains of the protein are shown. (B) Major functional domains and PTMs on coronavirus M protein (not to scale). Endo: Endodomain; IBV: Infectious bronchitis virus; MHV: Mouse hepatitis virus; N-gly: N-glycosylation; O-gly: O-glycosylation; Palm: Palmitoylation; PTM: Post-translational modification; SARS-CoV: Severe acute respiratory syndrome coronavirus; TM: Transmembrane domain.

Figure 5.. Schematic diagram showing major functional domains and post-translational modifications on coronavirus N protein (not to scale).

Protein–protein interactions involving some of the modified residues are also indicated. CTD: C-terminal domain; IBV: Infectious bronchitis virus; MHV: Mouse hepatitis virus; NTD: N-terminal domain; phos: Phosphorylation; PTM: Post-translational modification; SARS-CoV: Severe acute respiratory syndrome coronavirus; SR: Serine arginine-rich domain; TGEV: Transmissible gastroenteritis virus.

Figure 6.. Schematic diagram showing the post-translational modifications on coronavirus nonstructural proteins and accessory proteins.

The cleavage sites of PLPro and Mpro are indicated by empty circles and reverse triangles, respectively. IBV: Infectious bronchitis virus; MHV: Mouse hepatitis virus; N-gly: N-glycosylation; nsp: Nonstructural protein; O-gly: O-glycosylation; PLPro: Papain-like protease; pp: Polyprotein; SARS: Severe acute respiratory syndrome; TGEV: Transmissible gastroenteritis virus; Ubi: Ubiquitination.

Figure 7.. Schematic diagram summarizing the known mechanisms by which coronavirus proteins interfere with the post-translational modifications of host proteins.

Proteins in blue are pattern recognition receptors, and proteins in purple are E3 ubiquitin ligases. Green ellipses and rectangles are transcription factors and response elements involved in type I interferon induction and signaling, respectively. Black pointed arrows indicate activation, and blunt-ended red lines indicate inhibition. See text for detail.