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Other Double-Stranded DNA Viruses
Published in Paul Pumpens, Peter Pushko, Philippe Le Mercier, Virus-Like Particles, 2022
Paul Pumpens, Peter Pushko, Philippe Le Mercier
As reviewed by the most recent ICTV report (Wilson et al. 2012), the virions of the Phycodnaviridae family, a sole member of the order Algavirales, which covers 6 genera, were assumed to be large icosahedral structures of 120–220 nm in diameter with a multilaminate shell surrounding an electron-dense core and lacking an external membrane, as shown in Figure 5.5. In addition, one of the vertices in the representative Paramecium bursaria chlorella virus 1 (PBCV-1) of the genus Chlorovirus has a cylindrical spike or tail, 250 Å long and 50 Å wide. Generally, PBCV-1 has a 330-kb genome that encodes 416 predicted proteins and 11 tRNA molecules and involves 149 different proteins in the mature virion (Dunigan et al. 2012).
Mass spectrometric analysis of glycosylated viral proteins
Published in Expert Review of Proteomics, 2018
The initial stage in N-glycan biosynthesis involves attachment of the glycan Glc3Man9GlcNAc2 (1) (Figure 1) to the consensus sequence asparagine of the glycoprotein in the endoplasmic reticulum (ER) followed by cleavage of the glucose residues to give Man9GlcNAc2 (2). A series of α-mannosidases, located in the ER and later in the Golgi, cleaves the α-linked mannose residues to give first Man8GlcNAc2 (3) and eventually Man5GlcNAc2 (4). These glycans are known as high-mannose glycans. In the most common pathways, a GlcNAc residue is then attached at the 2-position of the mannose residue which is linked to the 3-position of the branching mannose to give glycan 5 followed by attachment of a 4-linked galactose (6) and N-acetylneuraminic (sialic) acid, in either the 3- (7) or 6-linked positions. These glycans are known as hybrid glycans. Glycan 5 is also a substrate for additional mannosidases which cleave the remaining α-linked mannose residues to give glycan 8 which undergoes further processing to the biantennary glycan 11 (3-linked sialic acid shown) via 9 and 10. Additional GlcNAc-Gal-Neu5Ac chains can be attached at position 4 in the 3-antenna and position 6 in the 6-antenna to give triantennary glycans 12 and 13, respectively, and tetra-antennary glycans (16). Further processing can involve attachment of fucose residues, usually to the 6-position of the reducing-terminal GlcNAc residue (14) and/or to the GlcNAc (17) or galactose (18) residues of the antenna. GlcNAc can also be added to the 4-position of branching mannose residues (15, known as bisecting GlcNAc), antennae can be extended by addition to the galactose residues of further Gal-GlcNAc units, galactose can sometimes be replaced with GalNAc, and the antennae can be further decorated with phosphate or sulfate groups. These more highly processed glycans are known as complex glycans. Biosynthesis can stop at any point with the result that a large number of N-glycans can be found at many of the glycosylated sites. Although complicated, these pathways are ubiquitous in eukaryotes and some prokaryotes making structural analysis of the glycans reasonably straightforward. All, for example, contain the same Man3GlcNAc2 core. However, the large chloroviruses, which have their own glycosylation machinery, synthesize a totally different type of N-glycan [7,8]. These glycans lack the Man3GlcNAc2 core and are attached to asparagine via glucose. Some typical structures are shown in Figure 2. The giant virus Mimivirus encodes an autonomous glycosylation system and incorporates the rare N-acetylated dideoxyhexose, viosamine (2,6-dideoxy-d-glucose) in complex glycans present in fibers surrounding its icosahedral capsid [9] and the giant virus Megavirus chilensis encodes N-acetylrhamnosamine for incorporation into its glycans [10].