Virus Assembly

Abstract

Viral genomes are sequestered by capsid proteins to form nucleocapsids with icosahedral (pseudospherical) or helical symmetry. Mature virus particles (virions) may be naked (i.e. composed of nucleic acid and protein only) or enveloped within a lipid bilayer(s). There is great diversity in size and complexity across the virus spectrum; recently discovered giant viruses are larger than some bacteria. Virions assemble from relatively large numbers of a few identical subunits but may include additional proteins required for specialised functions. Various mechanisms ensure that only viral genomic nucleic acids are packaged. Virion components are transported by cellular processes to sites of assembly. Basic functions of virions are protection of the genome from environmental damage during extracellular existence and delivery to a susceptible cell to initiate a new infection. Proteolytic cleavage of specific proteins during virus maturation commonly induces a quasi‐stable ‘triggered’ state to allow conformational changes necessary for cell penetration and genome release.

Key Concepts

  • For genetic economy, virions are assembled from large numbers of a few components.
  • Nucleocapsids comprise the viral genomic nucleic acid sequestered within a protein coat.
  • The symmetry of nucleocapsids is usually icosahedral or helical.
  • Virions are either nonenveloped (i.e. a naked nucleocapsid) or enveloped by a lipid membrane.
  • Virus‐specific nucleic acids are selectively packaged within nucleocapsids.
  • Intracellular transport mechanisms are hijacked by viruses to ensure that components are delivered to sites of assembly.
  • Postassembly proteolytic cleavages are often used to induce a quasi‐stable state primed for cell entry.

Keywords: nucleocapsid; envelope; icosahedral; helical; packaging signals; intracellular transport; maturation

Figure 1. Virus gallery: A range of viruses are illustrated differing in their capsid architectures and their genome types. (a) Electron micrograph of TMV, the classical helical virus; (b) examples of spherical viruses with icosahedral capsids with differing triangulation numbers (Reproduced with permission from Fontana and Steven (2015) © Elsevier.); (c) viruses known to assemble using multiple RNA‐based PSs, STNV (left) and bacteriophage MS2 (right), see Figure; (d) the large (T = 25) bacteriophage PRD1 showing a front view with its major CPs removed to highlight the roles of ‘ruler’ proteins, shown as extended chains, to define the locations of its symmetry axes. PRD1 also encompasses a membrane bilayer (yellow/orange layers), as seen in the adjacent cross section (Reproduced with permission from Cockburn et al. (2004) © Dr Joseph Cockburn, Leeds/Nature Publishing Group.); (e) Top – cartoon of the mature HIV nucleocapsid, which has the geometry of a fullerene cone. The latter is a closed structure composed of hexameric and pentameric assemblies. Closure, as with icosahedral particles, requires that it contains 12 fivefold capsomeres, highlighted in red. The asymmetry is generated by the large end having 7/12 fivefolds. Bottom – cryo‐EM images of HIV infected cells showing the formation of the Fullerene cone as the particles mature (i–iii) (Reproduced from Briggs et al. (2006) © Elsevier.). False colour is added in (iii) to ease interpretation.
Figure 2. Molecular mechanisms of packaging signal‐mediated assembly: (a) Mechanism of TMV assembly. A self‐assembled two‐layer symmetrical disk of the CP interacts with a specific sequence within the TMV genome leading to dislocation of the disk into the assembly‐competent ‘lock washer’ with growth points at both ends. Simultaneously, the RNA assembly initiation site structure is denatured allowing each CP to contact three nucleotides along the central pore of the virion. As the initiation site is internal within the genome, this creates assembly intermediates in which both RNA ends enter the growing helical rod from the same end. The red cartoons to the right of the assembly intermediates illustrate the presumed RNA structures present during these steps. (b) An illustration of the packaging problems faced by ssRNA spherical viruses. The RNA shown below the cartoon of the capsid into which it is packaged is drawn roughly to scale. (c) A solution to the challenge shown in (b) is the presence of multiple PSs distributed throughout viral genomes. For MS2, a T = 3 virion composed of 180 CP subunits organised as two types of noncovalent dimer, 60 A/B and 30 C/C. PS–CP interactions regulate the conformation of the dimeric capsomere during assembly favouring the A/B conformer. Both types of dimers are required for higher order assembly of intermediates on the pathway to complete the capsid. The CPs are shown as ribbon diagrams, while the highest affinity PS, a 19‐nt stem‐loop is shown as a framework structure. Crosslinking of the CPs and genomic RNA in infectious virions confirms that this mechanism is used in vivo. (d) The same PS‐mediated mechanism occurs for assembly of the T = 1 STNV, a virus having a CP with a canonical ‘jelly roll’ globular domain with a positively charged N‐terminal arm. There is no need to define the CP conformer in this case because all 60 CPs in the capsid are identical. Capsid assembly is still dependent on binding PSs. The CP recognition sequences (highlighted in red in the loops) and relative placement of PS sites, like the five predicted to occur in the 5′ 127 nts genomic segment illustrated, promote cooperative assembly while neutralising electrostatic repulsions between the N termini of the CP monomers, allowing a trimer capsomere to form. (e) Left: The X‐ray structure of an STNV T = 1 virus‐like particle (PDB 2BUK), assembled around one of its PS RNAs, viewed along a twofold axis. Right: Ribbon diagram of the STNV CP subunit structure seen in virions (PDB 3S4G) with the disordered N‐terminal amino acid sequence shown dashed, with the sequence of the first 25 amino acids below. When this assembles around a PS RNA, there is additional ordering of the CP N‐terminal region (magenta helical turn) in response to binding the preferred RNA sequence.
Figure 3. Hepatitis B core: An example of a VLP: (a) Ribbon diagram of the assembled HBc particle showing the prominent surface ‘spikes’ formed from coat protein dimers. (b) Structural dimer of the HBc protein. MIR is the major immunogenic region preferred for antigen insertion. Linker is a sequence replacing the C‐terminal domain of an upstream HBc protein and linking it to the N terminus of a downstream copy, thus defining the HBc protein dimer association. Reproduced from Peyret et al. (2015) © Creative Commons Attribution (CC BY) license.
Figure 4. Examples of proteolytic cleavages associated with viral maturation: (a) Conversion of the herpesvirus procapsid into the DNA‐filled C‐capsid involves the cleavage and release of proteins forming the assembly scaffold and filling of the internal space with DNA via the pore and motor indicated by UL6. (Reproduced from Trus et al. () © Cell Press (Elsevier).). (b) Maturation cleavage of VP0 in poliovirus allows the rearrangement of the VP4 component to form an internal stabilising network on the inner surface of the virion. On the left is a stereo view from the inside of the capsid fivefold axis, showing the overlay of VP4 (red) and the first 78 residues of VP0 (blue). The scission point on VP0 is marked with a yellow sphere (arrowed). The remaining capsid proteins are shown in grey for context. On the right is an overlay of the crystal structures of VP0 (blue) and VP4, and the first few residues of VP2 (Red) show the difference between the two structures. The scission site (yellow sphere) at residue 69 of VP0 extends farther from the fivefold axis in the native (cleaved) structure. Paler‐coloured ribbons of the neighbouring symmetry copies of VP0 and VP4 are shown for context (Courtesy of J. Hogle and M. Strauss.). (c) Cleavage of HA0, the precursor to the influenza receptor‐binding glycoprotein, into HA1 and HA2 allows the molecule to undergo the massive conformational changes induced by reduction in pH that are necessary for fusion with the cell membrane during cell entry. Note: only HA2 is shown in the acid‐induced form for clarity. Courtesy of I. Wilson and P. Lee.
Figure 5. Acquisition of membranes and intracellular transport as exemplified by the herpesviruses: (a) Herpesvirus capsids assemble and mature in the nucleus and then bud through first the inner nuclear membrane and then the outer nuclear membrane, first gaining and then shedding a membrane in the process. (b) The glycoproteins present at the surface of mature herpesvirus particles are synthesised in the endoplasmic reticulum (ER) and transported to the plasma membrane via the Golgi apparatus (GA) and trans‐Golgi network (TGN). They are then internalised in early endosomes (EE) where they associate with c‐capsids together with tegument protein. These bud into the endosomes to form mature enveloped particles which are transported to the cell surface and released via the recycling endosome route. Reproduced from Hollinshead et al. (2012)© European Molecular Biology Organization.
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Further Reading

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Zlotnick A (2004) Viruses and the physics of soft condensed matter. Proceedings of the National Academy of Sciences 101: 15549–15550. DOI: 10.1073/pnas.0406935101.

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Rowlands, David J, and Stockley, Peter G(Jun 2016) Virus Assembly. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0024782]