Viruses and Virology
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9 Viruses and Virology Bacterial viruses such as the I Virus Structure and Growth 237 Escherichia coli bacterio- 9.1 General Properties of Viruses 237 phage T4 have long been 9.2 Nature of the Virion 238 used as model systems for 9.3 The Virus Host 241 studying viral infection and 9.4 Quantification of Viruses 241 replication processes. II Viral Replication 243 9.5 General Features of Virus Replication 243 9.6 Viral Attachment and Penetration 244 9.7 Production of Viral Nucleic Acid and Protein 245 III Viral Diversity 247 9.8 Overview of Bacterial Viruses 247 9.9 Virulent Bacteriophages and T4 250 9.10 Temperate Bacteriophages, Lambda and P1 251 9.11 Overview of Animal Viruses 254 9.12 Retroviruses 255 IV Subviral Entities 257 9.13 Defective Viruses 257 9.14 Viroids 257 9.15 Prions 258 CHAPTER 9 • Viruses and Virology 237 iruses are genetic elements that cannot replicate indepen- provide the energy and materials needed for replicating their Vdently of a living cell, called the host cell. However, viruses do genomes and synthesizing their proteins. Consequently, viruses possess their own genetic information and are thus independent cannot replicate unless the virus genome has gained entry into a of the host cell’s genome. Viruses rely on the host cell for energy, suitable host cell. metabolic intermediates, and protein synthesis. Viruses are Viruses can exist in either extracellular or intracellular forms. therefore obligate intracellular parasites that rely on entering a In its extracellular form, a virus is a microscopic particle contain- suitable living cell to carry out their replication cycle. However, ing nucleic acid surrounded by a protein coat and sometimes, unlike genetic elements such as plasmids ( Section 6.6), depending on the specific virus, other macromolecules. The viruses have an extracellular form, the virus particle, that enables virus particle, or virion, is metabolically inert and cannot gener- them to exist outside the host and that facilitates transmission ate energy or carry out biosynthesis. The virus genome moves from one host cell to another. To multiply, viruses must enter a from the cell in which it was produced to another cell inside the cell in which they can replicate, a process called infection. virion. Once in the new cell, the intracellular state begins and the Viruses can replicate in a way that is destructive to the host virus replicates. New copies of the virus genome are produced, cell, and this accounts for the fact that some viruses are agents of and the components of the virus coat are synthesized. Certain disease. We cover a number of human diseases caused by viruses animal viruses (such as polio and respiratory syncytial virus) may in Chapters 33 and 34. However, viruses may also inhabit a cell skip the extracellular stage when moving from cell to cell within and replicate in step with the cell without destroying it. Like plas- the same organism. Instead, they mediate the fusion of infected mids and transposable elements, viruses may confer important cells with uninfected cells and transfer themselves in this way. new properties on their host cells. These properties will be inher- However, when moving from one organism to another they are UNIT 4 ited when the host cell divides if each new cell also inherits the truly extracellular. viral genome. These changes are not always harmful and may Viral genomes are usually very small, and they encode primar- even be beneficial. ily proteins whose functions viruses cannot usurp from their The study of viruses is called virology, and we introduce the hosts. Therefore, during replication inside a cell, viruses depend essentials of the field here. There are four parts in this chapter. heavily on host cell structural and metabolic components. The The first part introduces basic concepts of virus structure, infec- virus redirects host metabolic functions to support virus replica- tion of the host cell, and how viruses can be detected and quanti- tion and the assembly of new virions. Eventually, new viral parti- fied. The second part deals with the basic molecular biology of cles are released, and the process can repeat itself. virus replication. The third part provides an overview of some key viruses that infect bacteria and animals; further coverage of Viral Genomes viral diversity can be found in Chapter 21. The fourth part deals All cells contain double-stranded DNA genomes. By contrast, with subviral entities. viruses have either DNA or RNA genomes. (One group of viruses Viruses outnumber the living cells on our planet by at least 10- does use both DNA and RNA as their genetic material but at dif- fold, and infect all types of cellular organisms. Therefore, they are ferent stages of their replication cycle.) Virus genomes can be interesting in their own right. However, scientists also study classified according to whether the nucleic acid in the virion is viruses for what they reveal about the genetics and biochemistry of DNA or RNA and further subdivided according to whether the cellular processes and, for many viruses, the development of dis- nucleic acid is single- or double-stranded, linear, or circular ease. Furthermore, as we shall see in Chapters 10 and 11, viruses (Figure 9.1). Some viral genomes are circular, but most are linear. are also important in microbial genetics and genetic engineering. Although those viruses whose genome consists of DNA follow the central dogma of molecular biology (DNA S RNA S protein, I Virus Structure and Growth Section 6.1), RNA viruses are exceptions to this rule. Nonetheless, genetic information still flows from nucleic acid to protein. Moreover, all viruses use the cell’s translational machin- 9.1 General Properties of Viruses ery, and so regardless of the genome structure of the virus, mes- Although viruses are not cells and thus are nonliving, they senger RNA (mRNA) must be generated that can be translated nonetheless possess a genome encoding the information they on the host cell ribosomes. need in order to replicate. However, viruses rely on host cells to RNA DNA Viral Class DNA viruses RNA viruses viruses ssRNA dsDNA ssDNA dsDNA ssRNA dsRNA Viral Genome (Retroviruses) (Hepadnaviruses) Figure 9.1 Viral genomes. The genomes of viruses can be either DNA or RNA, and some use both as their genomic material at different stages in their replication cycle. However, only one type of nucleic acid is found in the virion of any particular type of virus. This can be single-stranded (ss), double-stranded (ds), or in the hepadnaviruses, partially double-stranded. Some viral genomes are circular, but most are linear. 238 UNIT 4 • Virology, Genetics, and Genomics Viral Hosts and Taxonomy 9.2 Nature of the Virion Viruses can be classified on the basis of the hosts they infect as Virions come in many sizes and shapes. Most viruses are smaller well as by their genomes. Thus, we have bacterial viruses, than prokaryotic cells, ranging in size from 0.02 to 0.3 m archaeal viruses, animal viruses, plant viruses, and viruses that (20–300 nm). A common unit of measure for viruses is the infect other kinds of eukaryotic cells. Bacterial viruses, some- nanometer, which is one-thousandth of a micrometer. Smallpox times called bacteriophages (or phage for short; from the virus, one of the largest viruses, is about 200 nm in diameter Greek phagein, meaning “to eat”), have been intensively stud- (about the size of the smallest cells of Bacteria). Poliovirus, one ied as model systems for the molecular biology and genetics of of the smallest viruses, is only 28 nm in diameter (about the size virus replication. Species of both Bacteria and Archaea are of a ribosome). Consequently, viruses could not be properly infected by specific viruses. Indeed, many of the basic concepts characterized until the invention of the electron microscope in of virology were first worked out with bacterial viruses and the 1930s. subsequently applied to viruses of higher organisms. Because Viral genomes are smaller than those of most cells. Most bac- of their frequent medical importance, animal viruses have terial genomes are between 1000 and 5000 kilobase pairs (kbp) of been extensively studied, whereas plant viruses, although of DNA, with the smallest known being about 500 kbp. (Interest- enormous importance to modern agriculture, have been less ingly, Bacteria with the smallest genomes are, like viruses, para- well studied. sites that replicate in other cells; Table 12.1.) The largest A formal system of viral classification exists that groups known viral genome, that of Mimivirus, consists of 1.18 Mbp of viruses into various taxa, such as orders, families, and even genus double-stranded DNA. This virus, which infects protists such as and species. The family taxon seems particularly useful. Mem- Amoeba, is one of a few viruses currently known whose genome bers of a family of viruses all have a similar virion morphology, is larger than some cellular genomes. More typical virus genome genome structure, and strategy of replication. Virus families have sizes are listed in Table 9.1. Some viruses have genomes so small names that include the suffix -viridae (as in Poxviridae). We dis- they contain fewer than five genes. Also, as can be seen in the cuss a few of these in Chapter 21. table, the genome of some viruses, such as reovirus or influenza virus, is segmented into more than one molecule of nucleic acid. MiniQuiz • How does a virus differ from a plasmid? Viral Structure • How does a virion differ from a cell? The structures of virions are quite diverse, varying widely in size, • What is a bacteriophage? shape, and chemical composition. The nucleic acid of the virion is • Why does a virus need a host cell? always located within the particle, surrounded by a protein shell called the capsid.