N

Virus Nucleocapsid

Nucleocapsids containing partly reverse transcribed DNA that have associated with cytoplasmically located pre S domains of the L envelope protein may then bud into the ER as maturing virions, or alternatively may be transported to the nucleus, thereby increasing the pool of cccDNA.

From: Virus Taxonomy, 2005

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Family Bornaviridae

Susan Payne, in Viruses, 2017

Assembly, Release, and Maturation

Bornavirus nucleocapsids contain N and RNA, associated with P and L proteins. M is also part of the nucleocapsid. While the details are lacking, the process of nucleocapsid formation is presumed to be similar to other members of the order Mononegavirales. Nucleocapsid formation occurs in the nucleus and the RNP must be exported from the nucleus for the assembly of complete virions. In addition to transmission by extracellular virions, it is likely that nucleocapsids are also the transmissible particle from cell to cell (Fig. 22.3). This is most clearly seen in cultured cells where BoDV nucleocapsids associate tightly with chromatin to segregate into daughter cells during cell division.

Figure 22.3. Fluorescent antibody labeling of duck embryo fibroblasts persistently infected an avian bornavirus. A focus of infected cells (green) sits amidst uninfected cells. The uninfected cells are visualized by DAPI staining (blue) of their nuclei.

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Structure and Composition of Viruses

FRANK FENNER, ... DAVID O. WHITE, in Veterinary Virology, 1987

Helical Symmetry

The nucleocapsids of several RNA viruses have a different type of symmetry: the capsomers and nucleic acid molecule(s) self-assemble as a helix (Fig. 1-1C,D; Plate 1-1C). In all such viruses each capsomer consists of a single polypeptide molecule. The plant viruses with helical nucleocapsids are rod shaped and naked (nonenveloped). However, in all animal viruses helical nucleocapsids are wound into a coil and enclosed within a lipoprotein envelope (see Plate 27-1), possibly to give the very long nucleocapsids stability.

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The Structure of Viruses

JAMES H. STRAUSS, ELLEN G. STRAUSS, in Viruses and Human Disease (Second Edition), 2008

The Nucleocapsid

The nucleocapsids of enveloped RNA viruses are fairly simple structures that contain only one major structural protein, often referred to as the nucleocapsid protein or core protein. This protein is usually quite basic or has a basic domain. It binds to the viral RNA and encapsidates it to form the nucleocapsid. For most RNA viruses, nucleocapsids can be recognized as distinct structures within the infected cell and can be isolated from virions by treatment with detergents that dissolve the envelope. The nucleocapsids of alphaviruses, and probably flaviviruses and arteriviruses as well, are regular icosahedral structures, and there are no other proteins within the nucleocapsid other than the nucleocapsid protein. In contrast, the nucleocapsids of all minus-strand viruses are helical and contain, in addition to the major nucleocapsid protein, two or more minor proteins that possess enzymatic activity. As described, the nucleocapsids of minus-strand RNA viruses remain intact within the cell during the entire infection cycle and serve as machines that make viral RNA. The coronaviruses also have helical nucleocapsids, but being plus-strand RNA viruses they do not need to carry enzymes in the virion to initiate infection. The helical nucleocapsids of (-) RNA viruses appear disordered within the envelope of all viruses except the rhabdoviruses, in which they are coiled in a regular fashion (see later).

The nucleocapsids of retroviruses also appear to be fairly simple structures. They are formed from one major precursor protein, the Gag polyprotein, that is cleaved during maturation into four or five components. The precursor nucleocapsid is spherically symmetric but lacks icosahedral symmetry. The mature nucleocapsid produced by cleavage of Gag may or may not be spherical symmetric. The nucleocapsid also contains minor proteins, produced by cleavage of Gag–Pro–Pol, as described in Chapter 1. These minor proteins include the protease, RT, RNase H, and integrase that are required to cleave the polyprotein precursors, to make a cDNA copy of the viral RNA, and to integrate this cDNA copy into the host chromosome.

The two families of enveloped DNA viruses that we consider here, the poxviruses and the herpesviruses, contain large genomes and complicated virus structures. The nucleocapsids of herpesviruses are regular icosahedrons but those of poxviruses are complicated structures containing a core and associated lateral bodies.

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Virion Structure and Composition

Christopher J. Burrell, ... Frederick A. Murphy, in Fenner and White's Medical Virology (Fifth Edition), 2017

Helical Symmetry

The nucleocapsid of many RNA viruses self-assembles very differently, forming a cylindrical structure in which the protein structural units are spatially arranged as a helix, hence the term helical symmetry. The occurrence of identical protein–protein interfaces on the structural units promotes the symmetrical assembly of the helix. In helically symmetrical nucleocapsids, the RNA genome forms a spiral within the nucleocapsid (Fig. 3.7). Many plant viruses with helical nucleocapsids are rod-shaped, flexible or rigid, and non-enveloped. The helical structure of tobacco mosaic virus was among the first viral structures determined by negative staining electron microscopy—its detailed structure was resolved by X-ray crystallography. However, in all viruses of vertebrates with helical symmetry, the nucleocapsid is wound into a secondary coil and enclosed within a lipoprotein envelope, for example rhabdoviruses (see Fig. 27.1); and paramyxoviruses (see Fig. 26.2).

Figure 3.7. Helical symmetry. (A) Model of tobacco mosaic virus virion, showing interlocking capsid subunits and internal helical RNA. (B) Negative contrast electron micrograph of TMV particle.

(A) From David S. Goodsell, RCSB. (B) Reproduced from Williams, R.C. and Fisher, H.W. (1974). An electron micrographic atlas of viruses. Charles C. Thomas, Springfield, Il, with permission.

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CYTOMEGALOVIRUSES (HERPERSVIRIDAE) | Murine Cytomegaloviruses

John Staczek, in Encyclopedia of Virology (Second Edition), 1999

Assembly Site, Uptake, Release, Cytopathology

Nucleocapsid self-assembly occurs in the nucleus. Concatemeric viral DNA is cleaved and packaged into preassembled capsids. The association of the nucleocapsids with the nuclear membrane is facilitated by the viral tegument proteins. Viral glycoproteins are targeted to the nuclear membrane and aid in virion assembly. The virion buds out into the cisternae of the Golgi apparatus where further modifications of the glycoproteins may occur.

Infected cells display a cytopathology that is characterized by the enlargement (cytomegaly) of the cell. The enlarged cells have characteristic intranuclear inclusion bodies, marginated chromatin, and large cytoplasmic vacuoles.

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Families Paramyxoviridae and Pneumoviridae

Susan Payne, in Viruses, 2017

Assembly, Release, and Maturation

Nucleocapsid assembly occurs in the cytoplasm. The nucleocapsid consists of genomic RNA, N, P, and L proteins. The nucleocapsid travels to the plasma membrane and interacts with M. Virions bud from the PM. Virions containing uncleaved F0 are noninfectious unless F0 is cleaved by extracellular, trypsin-like proteases. Recall that F cleavage is a necessary maturation step as it releases the hydrophobic fusion peptide at the N-terminus of F2, a process critical for fusion to an uninfected cell.

The cellular location of F cleavage is determined by the amino acid sequence at the cleavage site. Measles and canine distemper viruses have F proteins that are cleaved in the ER/Golgi by furin-like or cathepsin-like proteases. Thus these viruses have a wide tissue tropism in the infected animal. In contrast, human parainfluenza virus F0 is cleaved by extracellular proteases found in the respiratory tract.

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Control

B.C. Bonning, in Comprehensive Molecular Insect Science, 2005

6.8.2.1 Nucleocapsids

Nucleocapsids are tubular in shape with cap structures at each end (Figure 2). The genome is condensed to about 100-fold within the inner nucleoprotein core (Bud and Kelly, 1980). The supercoiled, circular genome of double-stranded DNA is complexed with a highly basic protein, P6.9 in NPV and VP12 in GV (Tweeten et al., 1980; Wilson et al., 1987). Binding of these arginine-rich molecules to the DNA produces a compact, insoluble DNA complex. The viral genomes appear to be prepackaged within the virogenic stroma (an electron-dense structure produced within the nucleus at the onset of viral DNA synthesis), before incorporation into the capsid shells (Fraser, 1986) (Figure 3). The end structures of nucleocapsids consist of a flat disk at the basal end and nipple structures at the apical end (Federici, 1986). Nucleocapsids attach to membranes at the apical end of the capsid. VP39 is the major component of the nucleocapsid in BV and OB of AcMNPV (Pearson et al., 1988; Thiem and Miller, 1989). P80 and P24 are also associated with the capsid and PP78/83 is associated with the basal end complexed with EC27 and C42 (Braunagel et al., 2001) (Figure 2). VP1054 and VP91 are associated with both BV and OB (Olszewski and Miller, 1997a; Russell and Rohrmann, 1997).

Figure 2. Structure of budded and occlusion-derived virus. (a) Transmission electron micrograph (TEM) of budded virus (BV) of Lymantria dispar MNPV showing glycoprotein spikes, or peplomers at the anterior end. Scale bar = 50 nm. (Reproduced with permission from Adams, J.R., Goodwin, R.H., Wilcox, T.A., 1977. Electron microscopic investigations on invasion and replication of insect baculoviruses in vivo and in vitro. Biol. Cellulaire 28, 261–268.) (b) TEM of occlusion-derived virus (ODV) of Agrotis ipsilon MNPV (AgipMNPV) in a hemocyte of Agrotis ipsilon. Scale bar 100 nm. (c) Schematic representation of BV and ODV indicating virus-encoded structural components common to both or unique to each structure (after Funk et al., 1997). References for structural proteins: P6.9 (Wilson et al., 1987); VP39 (Thiem and Miller, 1989); P80 (Lu and Carstens, 1992); PP78/83 (Vialard and Richardson, 1993); ODV-E25 (Russell and Rohrmann, 1993); ODV-E66 (Hong et al., 1994); ODV-E56 (Braunagel et al., 1996a; Theilmann et al., 1996); ODV-E18, -E35, and -E27 (Braunagel et al., 1996b); GP41 (Whitford and Faulkner, 1992); p74 (Kuzio et al., 1989); GP64 (group I NPVs: Whitford et al., 1989) or F protein (group II NPVs and GVs: Pearson et al., 2001).

Figure 3. (a) Detail of the virogenic stroma (VS) and polyhedra (PH) within the nucleus of an AgipMNPV-infected hemocyte of Agrotis ipsilon. Scale bar = 1 μm. (b) Rod-shaped nucleocapsids (NC) produced within the virogenic stroma (VS). Scale bar = 500 nm.

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PARAINFLUENZA VIRUSES (PARAMYXOVIRIDAE) | Animal

Kailash C. Gupta, in Encyclopedia of Virology (Second Edition), 1999

Genetic Manipulation

Purified nucleocapsids associated with P and L proteins are capable of initiating virus infection. Recently, success has been achieved in constructing nucleocapsids from synthetic RNA and viral proteins in vitro. These nucleocapsids contained a reporter gene flanked by 5′ and 3′ termini of the regulatory virus genome sequences. These RNA minigenomes were rescued on transfection of virus-infected cells. Similarly, cDNA minigenomes were rescued on cotransfection with NP, P and L genes. Now infectious virus cDNA clones have been produced. Mutant virus can be derived from these clones. These experimental approaches make it possible to alter specifically the virus gene or regulatory sequences to define their function more precisely and to create virus strains that could be potentially useful for vaccine development.

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BACULOVIRUSES (BACULOVIRIDAE) | NUCLEOPOLYHEDROVIRUS

George F. Rohrmann, in Encyclopedia of Virology (Second Edition), 1999

Structural proteins of the nucleocapsid

The nucleocapsids of BV and ODV appear to be very similar in composition. The nucleocapsid is composed of at least one small putative DNA binding protein, a protein apparently specific to the basal end structure, and a number of capsid proteins, and the viral genome (Fig. 1).

Baculoviruses have large genomes that must be highly condensed to be efficiently packaged within a nucleocapsid. Histones do not appear to be associated with DNA packaging within nucleocapsids. In AcMNPV, a small gene has been identified that encodes an arginine/serine–threonine rich protein of 54 amino acids (termed p6.9) that is thought to be a DNA-binding protein. Homologues of the AcMNPV p6.9 gene have been isolated from other NPVs. These proteins consist of more than 40% arginine and approximately 30% serine or threonine residues. It has been suggested that the basic arginine residues of the DNA-binding protein neutralize the acidic residues of the viral DNA to enable condensation of the viral genome. Upon entry into an insect cell, serine and threonine residues on the DNA binding protein may become phosphorylated by a protein kinase . This would result in the unpackaging of the viral DNA. This hypothesis is supported by the observation that protein kinase activity is associated with purified capsids of granulosis viruses and with both BV and ODV of AcMNPV.

In addition to a DNA-binding protein, a protein of approximately 39 kDa (vp39) has been identified that appears to be a major component of the nucleocapsid of NPVs. This protein is present in both BV and ODV virions at a relatively high concentration. Immunoelectron microscopy confirmed that the vp39 protein is a component of the nucleocapsid and showed that it was randomly distributed over the entire surface of the nucleocapsid . In addition to vp39, vp80 (p87 in OpMNPV), p24 (OpMNPV) and vp91 (OpMNPV) have been found associated with nucleocapsids (Fig. 1). A phosphoprotein called ORF 1629 or pp78/83 has been shown to be associated with capsid basal end structures.

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Icosahedral Enveloped dsRNA Bacterial Viruses

R. Tuma, in Encyclopedia of Virology (Third Edition), 2008

Membrane Acquisition and Host Cell Lysis

NC is enveloped with a lipid bilayer, which is derived from the host cell plasma membrane. It contains only the viral membrane proteins. The virion-associated lytic enzyme P5 is also incorporated at this stage. Structural protein P9 and the nonstructural protein P12 are essential and sufficient for membrane envelopment in ϕ6. These two proteins alone can produce lipid vesicles inside the host cell suggesting that envelopment takes place within the cytoplasm. The envelope is subsequently decorated with P3 receptor binding spike which is anchored by the integral membrane protein P6. Virions are released by host cell lysis which is assisted by phage-encoded lytic proteins P5 and P10.

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Virus Research

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