Chapter 3: Introduction to Virus Structure PDF

10/28/2015 John B. Carter and Venetia A. Saunders Chapter 3 Dr. Nadeem Sheikh © 2012 John Wiley & Sons Ltd....

10/28/2015 John B. Carter and Venetia A. Saunders Chapter 3 Dr. Nadeem Sheikh © 2012 John Wiley & Sons Ltd. 1 www.wiley.com/college/carter 3.1 Introduction to virus structure Outside their host cells, viruses survive as virus particles, also known as virions. The virion is a gene delivery system. It contains the virus genome, and its functions are to protect the genome and to aid its entry into a host cell, where it can be replicated and packaged into new virions. The genome is packaged in a protein structure known as a capsid. © 2012 John Wiley & Sons Ltd. 2 www.wiley.com/college/carter 1  10/28/2015 Many viruses also have a lipid component, generally present at the surface of the virion forming an envelope. Envelope also contains proteins with roles in aiding entry into host cells. A few viruses form protective protein occlusion bodies around their virions. Before looking at these virus structures we shall consider characteristics of the nucleic acid and protein molecules that are the main components of virions. © 2012 John Wiley & Sons Ltd. 3 www.wiley.com/college/carter 3.2 Virus genomes A virion contains the genome of a virus in the form of one or more molecules of nucleic acid. For any one virus the genome is composed of either RNA or DNA. If a new virus is isolated, one way to determine whether it is an RNA virus or a DNA virus is to test its susceptibility to a ribonuclease and a deoxyribonuclease. The virus nucleic acid will be susceptible to degradation by only one of these enzymes. © 2012 John Wiley & Sons Ltd. 4 www.wiley.com/college/carter 2  10/28/2015 Each nucleic acid molecule is either single-stranded (ss) or double-stranded (ds). Giving four categories of virus genome: dsDNA ssDNA dsRNA ssRNA. The dsDNA viruses encode their genes in the same kind of molecule as animals, plants, bacteria and other cellular organisms, while the other three types of genome are unique to viruses. © 2012 John Wiley & Sons Ltd. 5 www.wiley.com/college/carter It is interesting to note that most fungal viruses have dsRNA genomes. Most plant viruses have ssRNA genomes. Most prokaryotic viruses have dsDNA genomes. The reasons for these distributions presumably concern diverse origins of the viruses in these very different host types. A further categorization of a virus nucleic acid can be made on the basis of whether the molecule is linear, with free 5 and 3 ends, or circular, as a result of the strand(s) being covalently closed. © 2012 John Wiley & Sons Ltd. 6 www.wiley.com/college/carter 3  10/28/2015 Examples of each category are given in Figure 3.1. In this figure, and indeed throughout the book, molecules of DNA and RNA are colour coded. Dark blue and light blue depict (+) RNA and (−) RNA respectively; these terms are explained in Section 6.2. It should be noted that some linear molecules may be in a circular conformation as a result of base pairing between complementary sequences at their ends (see Figure 3.7 below). This applies, for example, to the DNA in hepadnavirus virions and to the RNA in influenza virions. © 2012 John Wiley & Sons Ltd. 7 www.wiley.com/college/carter © 2012 John Wiley & Sons Ltd. 8 www.wiley.com/college/carter 4  10/28/2015 © 2012 John Wiley & Sons Ltd. 9 www.wiley.com/college/carter 3.2.1 Genome size Virus genomes span a large range of sizes. Porcine circovirus (ssDNA) and hepatitis delta virus (ssRNA) each have a genome of about 1.7 kilobases (kb), While at the other end of the scale there are viruses with dsDNA genomes comprised of over 1000 kilobase pairs (kbp). The maximum size of a virus genome is subject to constraints, which vary with the genome category. As the constraints are less severe for dsDNA all of the large virus genomes are composed of dsDNA. The largest RNA genomes known are those of some coronaviruses, which are 33 kb of ssRNA. The largest virus genomes, such as that of the mimivirus, are larger than the smallest genomes of cellular organisms, such as some mycoplasmas (Figure 3.2). © 2012 John Wiley & Sons Ltd. 10 www.wiley.com/college/carter 5  10/28/2015 © 2012 John Wiley & Sons Ltd. 11 www.wiley.com/college/carter 3.2.2 Secondary and tertiary structure As well as encoding the virus proteins (and in some cases untranslated RNAs) to be synthesized in the infected cell. The virus genome carries additional information. Such as signals for the control of gene expression. Some of this information is contained within the nucleotide sequences. While for the single-stranded genomes some of it is contained within structures formed by intramolecular base pairing. © 2012 John Wiley & Sons Ltd. 12 www.wiley.com/college/carter 6  10/28/2015 In ssDNA complementary sequences may base pair through G–C and A–T hydrogen bonding. In ssRNA weaker G–U bonds may form in addition to G–C and A–U base pairing. Intramolecular base pairing results in regions of secondary structure with stemloops and bulges (Figure 3.3(a)). In some ssRNAs intramolecular base pairing results in structures known as pseudoknots, the simplest form of which is depicted in Figure 3.3(b). © 2012 John Wiley & Sons Ltd. 13 www.wiley.com/college/carter © 2012 John Wiley & Sons Ltd. 14 www.wiley.com/college/carter 7  10/28/2015 Regions of secondary structure in single-stranded nucleic acids are folded into tertiary structures with specific shapes. Many of which are important in molecular interactions during virus replication. For an example see Figure 14.6, which depicts the 5 end of poliovirus RNA, where there is an internal ribosome entry site to which cell proteins bind to initiate translation. Some pseudoknots have enzyme activity, while others play a role in ribosomal frameshifting (Section 6.4.2). © 2012 John Wiley & Sons Ltd. 15 www.wiley.com/college/carter 3.2.3 Modifications at the ends of virus genomes It is interesting to note that the genomes of some DNA viruses and many RNA viruses are modified at one or both ends (Figures 3.4 and 3.5). Some genomes have a covalently linked protein at the 5 end. In at least some viruses this is a vestige of a primer that was used for initiation of genome synthesis (Section 7.3.1). Some genome RNAs have one or both of the modifications that occur in eukaryotic messenger RNAs (mRNAs). A methylated nucleotide cap at the 5 end (Section 6.3.4) and a sequence of adenosine residues (a polyadenylate tail; poly(A) tail) at the 3 end (Section 6.3.5). © 2012 John Wiley & Sons Ltd. 16 www.wiley.com/college/carter 8  10/28/2015 © 2012 John Wiley & Sons Ltd. 17 www.wiley.com/college/carter © 2012 John Wiley & Sons Ltd. 18 www.wiley.com/college/carter 9  10/28/2015 The genomes of many RNA viruses function as mRNAs after they have infected host cells. A cap and a poly(A) tail on a genome RNA may indicate that the molecule is ready to function as mRNA. But neither structure is essential for translation. All the ssRNAs in Figure 3.5 function as mRNAs, but not all have a cap and a poly(A) tail. The genomes of some ssRNA plant viruses are base paired and folded near their 3 ends to form structures similar to transfer RNA. These structures contain sequences that promote the initiation of RNA synthesis. © 2012 John Wiley & Sons Ltd. 19 www.wiley.com/college/carter 3.2.4 Proteins non-covalently associated with virus genomes Many nucleic acids packaged in virions have proteins bound to them non-covalently. These proteins have regions that are rich in the basic amino acids lysine, arginine and histidine, which are positively charged and able to bind strongly to the negatively charged nucleic acids. Papillomaviruses and polyomaviruses, which are DNA viruses, have cell histones bound to the virus genome. Most proteins associated with virus genomes, however, are virus coded. Such as the HIV-1 nucleocapsid protein that coats the virus RNA; 29 per cent of its amino acid residues are basic. © 2012 John Wiley & Sons Ltd. 20 www.wiley.com/college/carter 10  10/28/2015 As well as their basic nature, nucleic-acid- binding proteins may have other characteristics, such as zinc fingers (Figure 3.6). The HIV-1 nucleocapsid protein has two zinc fingers. In some viruses, such as tobacco mosaic virus (Section 3.4.1), the protein coating the genome constitutes the capsid of the virion. © 2012 John Wiley & Sons Ltd. 21 www.wiley.com/college/carter © 2012 John Wiley & Sons Ltd. 22 www.wiley.com/college/carter 11  10/28/2015 3.2.5 Segmented genomes Most virus genomes consist of a single molecule of nucleic acid. But the genes of some viruses are encoded in two or more nucleic acid molecules. These segmented genomes are much more common amongst RNA viruses than DNA viruses. Examples of ssRNA viruses with segmented genomes are the influenza viruses (see Figure 3.20 below), which package the segments in one virion, and brome mosaic virus, which packages the segments in separate virions. © 2012 John Wiley & Sons Ltd. 23 www.wiley.com/college/carter Most dsRNA viruses, such as members of the family Reoviridae (Chapter 13), have segmented genomes. The possession of a segmented genome provides a virus with the possibility of new gene combinations, and hence a potential for more rapid evolution (Section 20.3.3.c). For those viruses with the segments packaged in separate virions, however, there may be a price to pay for this advantage. A new cell becomes infected only if all genome segments enter the cell, which means that at least one of each of the virion categories must infect. © 2012 John Wiley & Sons Ltd. 24 www.wiley.com/college/carter 12  10/28/2015 3.2.6 Repeat sequences The genomes of many viruses contain sequences that are repeated. These sequences include promoters, enhancers, origins of replication and other elements that are involved in the control of events in virus replication. Many linear virus genomes have repeat sequences at the ends (termini), in which case the sequences are known as terminal repeats (Figure 3.7). If the repeats are in the same orientation they are known as direct terminal repeats (DTRs). If they are in the opposite orientation they are known as inverted terminal repeats (ITRs). © 2012 John Wiley & Sons Ltd. 25 www.wiley.com/college/carter Strictly speaking, the sequences referred to as ‘ITRs’ in single-stranded nucleic acids are not repeats until the second strand is synthesized during replication. In the single-stranded molecules the ‘ITRs’ are, in fact, repeats of the complementary sequences (see ssDNA and ssRNA (−) in (Figure 3.7). © 2012 John Wiley & Sons Ltd. 26 www.wiley.com/college/carter 13  10/28/2015 © 2012 John Wiley & Sons Ltd. 27 www.wiley.com/college/carter 3.3 Virus proteins The virion of tobacco mosaic virus contains only one protein species and the virions of parvoviruses contain two to four protein species. These are viruses with small genomes. As the size of the genome increases, so the number of protein species tends to increase. 39 Protein species have been reported in the virion of herpes simplex virus 1. Over 100 in the virion of the algal virus Paramecium bursaria Chlorella virus 1. © 2012 John Wiley & Sons Ltd. 28 www.wiley.com/college/carter 14  10/28/2015 Proteins that are components of virions are known as structural proteins. They have to carry out a wide range of functions, including: protection of the virus genome attachment of the virion to a host cell (for many viruses) fusion of the virion envelope to a cell membrane (for enveloped viruses). © 2012 John Wiley & Sons Ltd. 29 www.wiley.com/college/carter Virus proteins may have additional roles, Some of which may be carried out by structural proteins. Some by non-structural proteins (proteins synthesized by the virus in an infected cell but they are not virion components). These additional roles include enzymes (e.g. protease, reverse transcriptase) transcription factors primers for nucleic acid replication interference with the immune response of the host. © 2012 John Wiley & Sons Ltd. 30 www.wiley.com/college/carter 15  10/28/2015 In a virion the virus genome is enclosed in a protein coat, known as a capsid. For some viruses the genome and the capsid constitute the virion. While for other viruses there are additional components. There may be an envelope at the surface of the virion, in which case there may be protein between the envelope and the capsid, or there may be an internal lipid membrane. A few viruses produce protein occlusion bodies in which virions become embedded. We shall consider each of these components in turn. © 2012 John Wiley & Sons Ltd. 31 www.wiley.com/college/carter Nomenclature of virus proteins There is no standard system of nomenclature for virus proteins. With different systems having evolved for different groups of viruses. For quite a number of viruses the following system has been adopted, the proteins being numbered in decreasing order of size: Structural proteins VP1, VP2, VP3,... (VP = virus protein) Non-structural proteins: NSP1, NSP2, NSP3,.... Many virus proteins are known by an abbreviation of one or two letters, which may indicate A structural characteristic G (glycoprotein) P (phosphoprotein) Or a function F (fusion) P (polymerase) RT (reverse transcriptase © 2012 John Wiley & Sons Ltd. 32 www.wiley.com/college/carter 16  10/28/2015 3.4 Capsids Virus genomes removed from their capsids are more susceptible to inactivation. So a major function of the capsid is undoubtedly the protection of the genome. A second major function of many capsids is to recognize and attach to a host cell in which the virus can be replicated. Although the capsid must be stable enough to survive in the extracellular environment. It must also have the ability to alter its conformation so that, at the appropriate time, it can release its genome into the host cell. © 2012 John Wiley & Sons Ltd. 33 www.wiley.com/college/carter For many viruses the capsid and the genome that it encloses constitute the virion. For other viruses a lipid envelope (Section 3.5.1), and sometimes another layer of protein, surrounds this structure, which is referred to as a nucleocapsid. Capsids are constructed from many molecules of one or a few species of protein. The individual protein molecules are asymmetrical, but they are organized to form symmetrical structures. Some examples of symmetrical structures are shown in Figure 3.8. © 2012 John Wiley & Sons Ltd. 34 www.wiley.com/college/carter 17  10/28/2015 © 2012 John Wiley & Sons Ltd. 35 www.wiley.com/college/carter A symmetrical object, including a capsid, has the same appearance when it is rotated through one or more angles, or when it is seen as a mirror image. For the vast majority of viruses the capsid symmetry is either helical or icosahedral. © 2012 John Wiley & Sons Ltd. 36 www.wiley.com/college/carter 18  10/28/2015 3.4.1 Capsids with helical symmetry The capsids of many ssRNA viruses have helical symmetry. The RNA is coiled in the form of a helix and many copies of the same protein species are arranged around the coil (Figure 3.9(a), (b)). This forms an elongated structure, Which may be a rigid rod if strong bonds are present between the protein molecules in successive turns of the helix, or a flexible rod (Figure 3.9(c)) if these bonds are weak. The length of the capsid is determined by the length of the nucleic acid. © 2012 John Wiley & Sons Ltd. 37 www.wiley.com/college/carter © 2012 John Wiley & Sons Ltd. 38 www.wiley.com/college/carter 19  10/28/2015 For many ssRNA viruses, such as measles and influenza viruses, the helical nucleic acid coated with protein forms a nucleocapsid, which is inside an envelope (see Figure 3.20 below). The nucleocapsid may be coiled or folded to form a compact structure. The virions of some plant viruses that have helical symmetry (e.g. tobacco mosaic virus) are hollow tubes. © 2012 John Wiley & Sons Ltd. 39 www.wiley.com/college/carter © 2012 John Wiley & Sons Ltd. 40 www.wiley.com/college/carter 20  10/28/2015 This allows the entry of negative stain, making the centre of the virion appear dark in electron micrographs. The rod-shaped tobacco rattle virus has a segmented genome with two RNAs of different sizes packaged in separate virions, resulting in two lengths of virion. The virions of a few DNA viruses, such as the filamentous phages (Section 19.4.2), also have helical symmetry. © 2012 John Wiley & Sons Ltd. 41 www.wiley.com/college/carter 3.4.2 Capsids with icosahedral symmetry Before proceeding further, a definition of the term ‘icosahedron’ is required. An icosahedron is an object with 20 faces, each an equilateral triangle; 12 vertices, each formed where the vertices of five triangles meet; 30 edges, at each of which the sides of two triangles meet. An icosahedron has five-, three- and two-fold axes of rotational symmetry (Figure 3.10). © 2012 John Wiley & Sons Ltd. 42 www.wiley.com/college/carter 21  10/28/2015 © 2012 John Wiley & Sons Ltd. 43 www.wiley.com/college/carter Capsids with icosahedral symmetry consist of a shell built from protein molecules that appear to have been arranged on scaffolding in the form of an icosahedron. They have less contact with the virus genome than the capsid proteins of viruses with helical symmetry. To construct an icosahedron from identical protein molecules the minimum number of molecules required is three per triangular face, giving a total of 60 for the icosahedron (Figure 3.11(a)). The capsid of satellite tobacco mosaic virus is constructed in this way (Figure 3.11(b)). © 2012 John Wiley & Sons Ltd. 44 www.wiley.com/college/carter 22  10/28/2015 © 2012 John Wiley & Sons Ltd. 45 www.wiley.com/college/carter In capsids composed of more than 60 protein molecules it is impossible for all the molecules to be arranged completely symmetrically with equivalent bonds to all their neighbours. In 1962 Donald Caspar and Aaron Klug proposed a theory of quasi-equivalence, where the molecules do not interact equivalently with one another, but nearly equivalently. © 2012 John Wiley & Sons Ltd. 46 www.wiley.com/college/carter 23  10/28/2015 Hence, the capsid of a virus built from 180 identical protein molecules. Such as tomato bushy stunt virus, contains three types of bonding between the molecules. The capsids of many icosahedral viruses are composed of more than one protein species. That of cowpea mosaic virus is composed of two proteins (Figure 3.12). One is present as ‘pentamers’ at the vertices of the icosahedron (12 × 5 = 60 copies) and the other is present as ‘hexamers’ on the faces. © 2012 John Wiley & Sons Ltd. 47 www.wiley.com/college/carter Each ‘hexamer’ is composed of three copies of a protein with two domains. The arrangement is similar to that of the panels on the surface of the football in Figure 3.12. It was pointed out in Section 3.2.1 that there is a huge range in the sizes of virus genomes, with all the large genomes being dsDNA. There is also a huge range in the sizes of icosahedral capsids. © 2012 John Wiley & Sons Ltd. 48 www.wiley.com/college/carter 24  10/28/2015 © 2012 John Wiley & Sons Ltd. 49 www.wiley.com/college/carter The satellite tobacco mosaic virus capsid is about 17 nm in diameter. The diameter of the Paramecium bursaria Chlorella virus 1 capsid is about ten times greater than this (Figure 3.13) and the mimivirus capsid is about 300 nm in diameter (Figure 1.3). © 2012 John Wiley & Sons Ltd. 50 www.wiley.com/college/carter 25  10/28/2015 3.4.2.a Capsid shapes It is clear from the images in Figure 3.13 that capsid surfaces vary in their topography. There may be canyons, hollows, ridges and/or spikes present. It is also clear that some capsids actually have the shape of an icosahedron. Such as that of Paramecium bursaria Chlorella virus 1, which is 165 nm across when measured along the two- and three- fold axes 190 nm across when measured along the fivefold axes. Capsids that have an icosahedral shape have an angular outline in electron micrographs (Figure 3.14). © 2012 John Wiley & Sons Ltd. 51 www.wiley.com/college/carter © 2012 John Wiley & Sons Ltd. 52 www.wiley.com/college/carter 26  10/28/2015 An icosahedral shape is not an inevitable outcome of icosahedral symmetry. The football in Figure 3.12 is constructed in the form of icosahedral symmetry, but the structure is spherical. Many small viruses that have capsids with icosahedral symmetry appear to be spherical, or almost spherical, and their virions are often described as isometric, such as those of densoviruses and foot and mouth disease virus (Figure 3.13). © 2012 John Wiley & Sons Ltd. 53 www.wiley.com/college/carter Some capsids with icosahedral symmetry are elongated. The capsids of geminiviruses (plant viruses) are formed from two incomplete icosahedra. Another plant virus, alfalfa mosaic virus, has four sizes of virion. All are 19 nm diameter, but three are elongated as a result of insertions of a protein lattice between a half icosahedral structure at each end of the capsid. © 2012 John Wiley & Sons Ltd. 54 www.wiley.com/college/carter 27  10/28/2015 3.4.2.b Capsomeres The capsids of some viruses, such as papillomaviruses (Figure 3.15), are clearly constructed from discrete structures. These structures are called capsomeres and each is built from several identical protein molecules. The capsids of papillomaviruses are constructed from 72 capsomeres, which are all identical. But the capsids of some viruses are constructed from two types of capsomere: © 2012 John Wiley & Sons Ltd. 55 www.wiley.com/college/carter Pentons, which are found at the vertices of the icosahedron. Hexons, which make up the remainder of the capsid. In these viruses there are always 12 pentons (one at each vertex). But the number of hexons varies. For example, the capsids of herpesviruses and adenoviruses contain 150 and 240 hexons, respectively. © 2012 John Wiley & Sons Ltd. 56 www.wiley.com/college/carter 28  10/28/2015 © 2012 John Wiley & Sons Ltd. 57 www.wiley.com/college/carter 3.4.2.c Structures at capsid vertices Some icosahedral viruses have a structure such as a knob, projection or fibre at each of the 12 vertices of the capsid. For example, the virions of some phages (e.g. G4; Figure 3.13) have projections. The adenovirus virion has a fibre, with a knob attached, at each of the 12 pentons (Figure 3.16). These structures at the capsid vertices are composed of distinct proteins that are involved in attachment of the virion to its host cell and in delivery of the virus genome into the cell. © 2012 John Wiley & Sons Ltd. 58 www.wiley.com/college/carter 29  10/28/2015 © 2012 John Wiley & Sons Ltd. 59 www.wiley.com/college/carter © 2012 John Wiley & Sons Ltd. 60 www.wiley.com/college/carter 30  10/28/2015 3.4.2.d Tailed bacteriophages The majority of the known phages are constructed in the form of a tail attached to a head, which contains the virus genome. All of these phages have dsDNA genomes. The head has icosahedral symmetry and may be isometric as in phage lambda (λ). Or elongated as in phage T4. The tail, which is attached to one of the vertices of the head via a connector, may be long as in phage λ, or short as in phage T7. Attached to the tail there may be specialized structures such as fibres and/or a baseplate. © 2012 John Wiley & Sons Ltd. 61 www.wiley.com/college/carter Some of the tailed phages have been objects of intensive study and a lot of the detail of their structures has been uncovered. One such phage is T7 (Figure 3.17). Inside the head of phage T7 is a cylindrical structure (the internal core) around which the DNA is wound. The connector has a wider region inserted into one of the vertices of the head and a narrower region to which the tail is attached. The tail is very short and tapers from the connector to the tip; attached to the tail are six tail fibres. Further details about the structure of tailed phages are given in Section 19.5. © 2012 John Wiley & Sons Ltd. 62 www.wiley.com/college/carter 31  10/28/2015 © 2012 John Wiley & Sons Ltd. 63 www.wiley.com/college/carter 3.4.3 Conical and rod-shaped capsids HIV-1 and baculoviruses have capsids that are conical and rod shaped, respectively (Figure 3.18). Inside each capsid is a copy of the virus genome coated in a highly basic protein. Both of these viruses have enveloped virions (Section 3.5.1). © 2012 John Wiley & Sons Ltd. 64 www.wiley.com/college/carter 32  10/28/2015 © 2012 John Wiley & Sons Ltd. 65 www.wiley.com/college/carter s3.5 Virion membrane Many viruses have a lipid membrane component. In most of these viruses the membrane is at the virion surface and is associated with one or more species of virus protein. This lipid–protein structure is known as an envelope and it encloses the nucleocapsid (nucleic acid plus capsid). The virions of most enveloped viruses, such as herpesviruses, are spherical or roughly spherical, but other shapes exist (Figure 3.19). Some viruses have a membrane located not at the virion surface, but within the capsid. © 2012 John Wiley & Sons Ltd. 66 www.wiley.com/college/carter 33  10/28/2015 © 2012 John Wiley & Sons Ltd. 67 www.wiley.com/college/carter 3.5.1 Enveloped virions Many animal viruses are enveloped. Including all those with helical symmetry. e.g. influenza viruses. A significant number of those with icosahedral symmetry. e.g. herpesviruses. Enveloped virions are much less common amongst the viruses that infect plants (e.g. potato yellow dwarf virus). They are extremely rare amongst the viruses that infect prokaryotes (e.g. Pseudomonas phage ϕ6). © 2012 John Wiley & Sons Ltd. 68 www.wiley.com/college/carter 34  10/28/2015 Associated with the membranes of an enveloped virus are one or more species of protein. Most of these proteins are integral membrane proteins and most are O- and/or N-glycosylated (Section 6.4.3.a). Many of the glycoproteins in virion envelopes are present as multimers. The envelope of influenza A virus (Figure 3.20). For example, contains two glycoprotein species: a haemagglutinin present as trimers and aneuraminidase present as tetramers. There is also a third protein species (M2) that is not glycosylated. © 2012 John Wiley & Sons Ltd. 69 www.wiley.com/college/carter © 2012 John Wiley & Sons Ltd. 70 www.wiley.com/college/carter 35  10/28/2015 Some envelope proteins span the membrane only once. Some, such as those of hepatitis B virus (Section 18.3.4), span the membrane several times. The polypeptide chain is highly hydrophobic at each membrane anchor. Some surface glycoproteins of enveloped viruses perform the function of fusing the virion membrane to a cell membrane during the infection process (Section 5.2.4.b). These fusion proteins have an additional hydrophobic region that plays a major role in the fusion process. © 2012 John Wiley & Sons Ltd. 71 www.wiley.com/college/carter Many enveloped viruses, including influenza viruses (Figure 3.20) and retroviruses, have a layer of protein between the envelope and the nucleocapsid. This protein is often called a matrix protein. In some viruses, however, such as yellow fever virus, there is no such layer and the nucleocapsid interacts directly with the internal tails of the integral membrane protein molecules. © 2012 John Wiley & Sons Ltd. 72 www.wiley.com/college/carter 36  10/28/2015 © 2012 John Wiley & Sons Ltd. 73 www.wiley.com/college/carter 3.5.2 Virions with internal membranes There are several viruses that have a lipid membrane within the virion rather than at the surface (Figure 3.19). These membranes have proteins associated with them and are present in the virions of, for example, Paramecium bursaria Chlorella virus 1 (Figure 3.13). The iridoviruses (Figure 3.14) and the tectiviruses (phages). © 2012 John Wiley & Sons Ltd. 74 www.wiley.com/college/carter 37  10/28/2015 © 2012 John Wiley & Sons Ltd. 75 www.wiley.com/college/carter © 2012 John Wiley & Sons Ltd. 76 www.wiley.com/college/carter 38  10/28/2015 © 2012 John Wiley & Sons Ltd. 77 www.wiley.com/college/carter 3.5.3 Membrane lipids Most virion membranes are derived from host cell membranes that undergo modification before incorporation into virions. For example, the HIV-1 envelope is derived from the plasma membrane of the host cell, But the virus envelope contains more cholesterol and sphingomyelin, and less phosphatidylcholine and phosphatidylinositol. Some viruses are able to replicate in more than one kind of host cell. For example, alphaviruses replicate in both mammalian cells and insect cells. © 2012 John Wiley & Sons Ltd. 78 www.wiley.com/college/carter 39  10/28/2015 When progeny virions are released from cells the lipid composition of the envelope may reflect that of the cell. Virions of Semliki Forest virus produced in hamster kidney cells contain about five times more cholesterol than virions produced in mosquito cells. © 2012 John Wiley & Sons Ltd. 79 www.wiley.com/college/carter 3.6 Occlusion bodies Some viruses provide added protection to the virions whilst outside their hosts by occluding them in protein crystals. These occlusion bodies, as they are known, are produced by many of the viruses that infect invertebrates, including most baculoviruses. There are two major types of occlusion body in which baculoviruses embed their rod-shaped virions (Figure 3.18). The granuloviruses form small granular occlusion bodies, generally with a single virion in each (Figure 3.21(a)), while the nucleopolyhedroviruses form large occlusion bodies with many virions in each (Figure 3.21(b), (c)). © 2012 John Wiley & Sons Ltd. 80 www.wiley.com/college/carter 40  10/28/2015 © 2012 John Wiley & Sons Ltd. 81 www.wiley.com/college/carter © 2012 John Wiley & Sons Ltd. 82 www.wiley.com/college/carter 41  10/28/2015 3.7 Other virion components 3.7.1 Virus RNA in DNA viruses Virus RNA is present in the virions of a number of DNA viruses. The hepadnaviruses and the caulimoviruses have short RNA sequences covalently attached to their DNAs. These RNAs have functioned as primers for DNA synthesis and remain attached to the genome in the mature virion. There is evidence that virus mRNAs are packaged in the virions of herpesviruses, but the roles of these molecules are not clear. © 2012 John Wiley & Sons Ltd. 83 www.wiley.com/college/carter 3.7.2 Cell molecules The incorporation of cell lipids into virions has already been discussed. Other cell molecules that become incorporated into virions include the following. Transfer RNA molecules. These are present in the virions of retroviruses. Proteins. When a virion is assembled some cell protein may be incorporated. There are reports of HIV-1 incorporating several cell proteins, including cyclophilin A in association with the capsid and human leukocyte antigens in the envelope. © 2012 John Wiley & Sons Ltd. 84 www.wiley.com/college/carter 42  10/28/2015 Polyamines. Spermidine and other polyamines have been reported in a variety of viruses. Cations, such as Na+, K+, Zn2+ and Mg2+ have also been reported as components of virions. One likely role for polyamines and cations is the neutralization of negative charges on the virus genome. © 2012 John Wiley & Sons Ltd. 85 www.wiley.com/college/carter 43