CAPÍTULO 3: El modelo clásico de regresión lineal: inferencia y predicción
3.2. Intervalos de confianza
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
38 VIRUS STRUCTURE
Some herpesviruses T phages
Adenoviruses Tectiviruses (phages)
Some parvoviruses
Retroviruses
Influenza viruses Bunyaviruses
Examples Type of
repeat1 Nucleic acid
DTR
DTR ITR
ITR ITR
XY XY
xy
yx YX
yx XY
dsDNA
dsDNA
ssDNA xy
XY xy
ssRNA(+) ssRNA(+) XY
XY XYXY
XY yx
yx YX ssRNA(–)
Figure 3.7 Terminal repeats in virus genomes.
1DTR: direct terminal repeat ITR: inverted terminal repeat
X and x represent complementary sequences.
Y and y represent complementary sequences.
ssRNA (+) has the same sequence as the virus mRNA.
ssRNA (−) has the sequence complementary to the virus mRNA.
The RNAs of single-stranded RNA viruses with ITRs can circularize; a ‘panhandle’ is formed by base pairing between the complementary sequences at the termini.
herpes simplex virus 1, and over 100 in the virion of the algal virus Paramecium bursaria Chlorella virus 1.
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).
CAPSIDS 39
Virus proteins may have additional roles, some of which may be carried out by structural proteins, and 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.
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).
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.
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 rec-ognize 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.
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. 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
helix
icosahedron
rod
cone
Figure 3.8 Symmetrical structures. All these types of symmetry are seen amongst viruses. The most common are helical and icosahedral symmetries.
40 VIRUS STRUCTURE
vast majority of viruses the capsid symmetry is either helical or icosahedral.
3.4.1 Capsids with helical symmetry
The capsids of many ssRNA viruses have helical sym-metry; 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.
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; 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.
3.4.2 Capsids with icosahedral symmetry Before proceeding further, a definition of the term
‘icosahedron’ is required.
RNA
(a) (b) (c)
100 nm protein
molecules
Figure 3.9 Helical symmetry. (a) Structure of a capsid with helical symmetry. The ssRNA coils are coated with repeated copies of a protein. (b) Part of measles virus nucleocapsid. The complete nucleocapsid is folded and enclosed within an envelope. Reconstructed image from cryo-electron microscopy, courtesy of Dr. David Bhella (MRC Virology Unit, Glasgow). Reinterpretation of data in Bhella et al. (2004) Journal of Molecular Biology, 340, 319 (by permission of Elsevier Limited). (c) Beet yellows virus particle. The virion is a long flexible rod, at one end of which there is a ‘tail’ (arrow) composed of a minor capsid protein, detected here by specific antibodies labelled with gold.
Image courtesy of Professor Valerian Dolja, originally published in Alzhanova et al. (2001) The EMBO Journal, 20, 6997. Reproduced by permission of Nature Publishing Group.
CAPSIDS 41
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).
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)).
In capsids composed of more than 60 protein molecules it is impossible for all the molecules to be arranged completely symmetrically with equiva-lent bonds to all their neighbours. In 1962 Don-ald Caspar and Aaron Klug proposed a theory of quasi-equivalence, where the molecules do not interact equivalently with one another, but nearly equivalently.
Viewing towards:
Figure 3.10 The three axes of symmetry of an icosahedron.
(a) (b)
Figure 3.11 Capsid constructed from sixty protein molecules. (a) Arrangement of protein molecules, with three per triangular face. (b) Virions of satellite tobacco mosaic virus. The bar represents 5 nm.
Image created with the molecular graphics program UCSF Chimera from the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco. Courtesy of Tom Goddard.
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 com-posed 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 ver-tices of the icosahedron (12× 5 = 60 copies) and the other is present as ‘hexamers’ on the faces. Each ‘hex-amer’ 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. The satellite tobacco mosaic virus capsid is about 17 nm in diameter, whereas 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).
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
42 VIRUS STRUCTURE
Cowpea mosaic virus capsid
Figure 3.12 Capsid constructed from two protein species. The cowpea mosaic virus capsid is constructed from one protein species (blue) that forms 12
‘pentamers’, and from a second protein species with two domains (green and red) that forms 20
‘hexamers’. The football is similarly constructed from 12 ‘pentamers’ and 20 ‘hexamers’. The cowpea mosaic virus image is from the VIPER database (Shepherd et al., 2006). The image was reconstructed using the data of Lin et al. (1999) Virology, 265, 20. Reproduced by permission of Elsevier Limited.
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 and 190 nm across when measured along the five-fold axes. Capsids that have an icosahedral shape have an angular outline in electron micrographs (Figure 3.14).
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 viri-ons are often described as isometric, such as those of densoviruses and foot and mouth disease virus (Figure 3.13).
Some capsids with icosahedral symmetry are elon-gated. 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 elon-gated as a result of insertions of a protein lattice
between a half icosahedral structure at each end of the capsid.
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: pentons, which are found at the vertices of the icosahedron, and 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.
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, while 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.
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
CAPSIDS 43
Ribgrass
Mosaic Virus Cowpea Chlorotic Mottle Virus
Feline
Panleukopenia Virus Bacteriophage MS2
Hepatitis B Virus Foot and Mouth
Disease Virus Bacteriophage G4
Human Papillomavirus L1 Capsid
Human Rhinovirus 16
& cellular receptor
Nudaurelia Capensis Omega Virus
Reovirus Core Bacteriophage PRD1
Bacteriophage HK97
Rice Dwarf Virus
Paramecium Bursaria Chlorella Virus Dengue Virus Bluetongue Virus
inner layer Human Papillomavirus Bacteriophage
Phi-X174 procapsid Norwalk Virus Densovirus
Satellite Tobacco Mosaic Virus
50nm
Figure 3.13 Capsids with icosahedral symmetry. Some of the wide ranges of capsid architectures and sizes are illustrated. The images were created with the molecular graphics program UCSF Chimera using data from cryo-electron microscopy and X-ray diffraction. From Goddard et al. (2005) Structure, 13, 473. Reproduced by permission of Elsevier Limited.
44 VIRUS STRUCTURE
Figure 3.14 Transmission electron micrograph of negatively stained virions of Tipula iridescent virus.
Figure 3.15 Papillomavirus capsid reconstruction.
From Trus et al. (1997) Nature Structural Biology, 4, 413, with the permission of the authors and Nature Publishing Group.
may be specialized structures such as fibres and/or a baseplate.
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.
penton penton fibre
Figure 3.16 Adenovirus virion. At each of the 12 vertices of the virion there is a penton, and attached to each penton there is a protein fibre with a knob at the end. The rest of the capsid is constructed from hexons. Please see Figure 12.1 for an electron micrograph of an adenovirus.
head
internal core
connector tail fibres
tail
Figure 3.17 Structure of phage T7. Each of the components is composed of one or more distinct proteins.
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).
VIRION MEMBRANES 45
HIV-1 Capsids Baculovirus Virions
100 nm
Figure 3.18 Conical and rod-shaped capsids.
e: envelope n: nucleocapsid
HIV-1 capsids from Kotov et al. (1999) Journal of Virology, 73, 8824. Reproduced by permission of the American Society for Microbiology. Baculovirus virions are those of Aglais urticae nucleopolyhedrovirus. From Harrap (1972) Virology, 50, 124. Reproduced by permission of Elsevier Limited