Protein Nucleotidylylation in +ssRNA Viruses

Abstract

Nucleotidylylation is a post-transcriptional modification important for replication in the picornavirus supergroup of RNA viruses, including members of the Caliciviridae, Coronaviridae, Picornaviridae and Potyviridae virus families. This modification occurs when the RNA-dependent RNA polymerase (RdRp) attaches one or more nucleotides to a target protein through a nucleotidyl-transferase reaction. The most characterized nucleotidylylation target is VPg (viral protein genome-linked), a protein linked to the 5' end of the genome in Caliciviridae, Picornaviridae and Potyviridae. The nucleotidylylation of VPg by RdRp is a critical step for the VPg protein to act as a primer for genome replication and, in Caliciviridae and Potyviridae, for the initiation of translation. In contrast, Coronaviridae do not express a VPg protein, but the nucleotidylylation of proteins involved in replication initiation is critical for genome replication. Furthermore, the RdRp proteins of the viruses that perform nucleotidylylation are themselves nucleotidylylated, and in the case of coronavirus, this has been shown to be essential for viral replication. This review focuses on nucleotidylylation within the picornavirus supergroup of viruses, including the proteins that are modified, what is known about the nucleotidylylation process and the roles that these modifications have in the viral life cycle.

Keywords: RdRp; VPg; calicivirus; coronavirus; nucleotidylylation; picornavirus; potyvirus.

Figure 1

Genome structure of representative members of the Caliciviridae, Potyviridae, Picornaviridae and Coronaviridae. The presence of a covalently attached (nucleotidylylated) 5′ VPg is shown as a yellow hexagon. The coding region for VPg proteins is shown in yellow and proteins known to be nucleotidylylated are indicated by a yellow star. Proteolytic processing of viral polyproteins are indicated by arrowheads. Potyvirus P1-Pro and HC-Pro self-cleave from the polyprotein (arrows). Viral capsid proteins are shown in green and the RNA-dependent RNA polymerases (RdRp) are shown in blue. Non-structural proteins (nsp) other than RdRp and VPg are shown in pink with the common name and/or nsp designation indicated. A second reading frame (uORF) produced by poliovirus is shown in grey. The PIPO coding region expressed as a fusion to P3 via a polymerase slippage mechanism is shown in grey for tobacco etch virus. In caliciviruses, the protease (pro) and polymerase (RdRp) are found as unprocessed precursors, analogous to 3CD in picornaviruses. The NS and VP1 genes of some calicivirus genera (e.g., lagoviruses) are a single ORF. Nucleotide lengths for the genomes depicted are indicated and genomes are not to scale.

Figure 2

Guanylylation of a calicivirus VPg. (A) For the nucleotidylylation reaction, ProPol catalyzes a nucleophilic attack by the hydroxyl of Y26 of VPg (pink) on the alpha phosphate of GTP (purple). This produces a phosphodiester bond covalently linking GMP onto Y26 of VPg. Guanylylated human norovirus VPg functions to recruit host eukaryotic initiation factors (eIF) for translation and interacts with Pol or ProPol to stimulate protein-primed transcription of the RNA genome. Structural predictions for human norovirus GII.4 VPg (KY905331) were performed with Phyre and imaged with Chimera [33,34]. (B) In addition to polymerase, a CRE RNA (AY184219) is required for nucleotidylylation of the poliovirus VPg (blue) on tyrosine 3 (Y3). The poliovirus 1 VPg structure (2BBL) was obtained from PDB and the representation of the CRE RNA stem-loop predicted using mFold [35]. Nucleotidylylation of poliovirus VPg does not contribute to translation initiation, only protein-primed transcription. Amino acid (aa) length of the VPg proteins is indicated.

Figure 3

Sequence alignment of the NiRAN domains from viruses within the order Nidovirales. Schematic diagram of nsp12 (nsp9 for Arterivirus). Sequence alignment of the N-terminal region of the RdRps from EAV (Arterivirus NP_705590.1), Dak Nong virus (Mesonivirus YP_009505590.1), Breda virus (Torovirus YP_337905.2), HCoV229E (QNT54752.1), MERS virus (YP_009047223.1), SARS-CoV-2 (QHD43415.1) and SARS virus (AER30332.1) was generated by Clustal Omega [158]. The three NiRAN motifs are designated A_n, B_n and C_n. Bolded resides denote invariant residues and a colon (:) indicates a residue that is conserved in more than 50% of the viruses aligned. The filled circles indicate positions that are lethal when mutated, and open circles indicate residues that result in impaired virus when mutated.