Chapter 10: Genetics of Viruses Student Learning Objectives Upon completion of this chapter you should be able to: 1. Understand the structure and genomic composition of viruses. 2. Distinguish between the different reproductive cycles of viruses. 3. Recognize the significance of plaque morphology to the genetic study of viruses. 4. Understand the molecular basis and interpretation of the complementation test. 5. Understand the process of intragenic mapping in bacteriophages. 10.1 Virus Structure and Genetic Composition Overview The first section of this chapter introduces us to viruses. So what is a virus? Well, it is a small infectious particle that consists of one type of nucleic acid enclosed in a protein coat. While viruses share this feature, they are a very diverse group of organisms that differ in several other features, including: 1) Host range, which refers to the number of species and cell types they can infect (Refer to Table 10.1); 2) Structure: for example, some viruses are helical, such as the tobacco moasaic virus (the first virus to be discovered); others are polyhedral (e.g.: adenovirus); still others have complex shapes, including the T4 bacteriophage which has separate head and tail components (Refer to Figure 10.1); 3) Genome composition, which may be DNA or RNA, single-stranded or double-stranded, circular or linear (See Table 10.1). Outline of Key Terms Virus Host cell Host range Bacteriophage (phage) Capsid Capsomers Viral envelope Viral genome Focal Points Variations in the structure of viruses (Figure 10.1) Hosts and characteristics of selected viruses (Table 10.1) Exercises and Problems For questions 1 to 6, complete the sentence with the most appropriate term(s): 1. A cell that is infected by a virus is called a cell. 2. All viruses have a protein coat called a, which is made up of subunits called. 79
3. Many viruses that infect animal cells have a viral enclosing its protein coat. 4. The lipid layer surrounding many animal viruses has glycoproteins sticking out of it. 5. Viruses that infect bacteria are called. 6. All living organisms have a genome consisting of ; viral genomes, on the other hand, may be or. 10.2 Viral Reproductive Cycles Overview A viral reproductive cycle refers to the series of steps involved in the production of new viruses. While the details of these steps may vary among the different types of viruses, researchers have determined that the vast majority of reproductive cycles consist of five or six steps. These include: 1) attachment; 2) entry; 3) integration (not in all viruses); 4) synthesis of viral components; 5) viral assembly; and 6) release (Refer to Figure 10.2A). This section also discusses the phenomenon of latency, where viruses remain inactive inside their host cells. For example, some bacteriophages, such as phage, can alternate between lytic and lysogenic cycles (Refer to Figure 10.3). Latency is also possible among animal viruses, including HIV, the causative agent of AIDS. HIV is a retrovirus whose reproductive cycle involves the integration of the viral genome into a chromosome in the host cell (Figure10.2B) Outline of Key Terms Viral reproductive cycle Virulent phage Lytic cycle Phage Temperate phage Lysogenic cycle Latent Lysogeny Prophage Human immunodeficiency virus (HIV) Reverse transcriptase Episome Integrase Provirus Emerging viruses Focal Points Comparison of the steps of two viral reproductive cycles (Figure 10.2) The lytic and lysogenic reproductive cycles (Figure 10.3) Exercises and Problems For questions 1 to 4, complete the sentence with the most appropriate word or phrase: 1. Viruses that can insert their genomes into host chromosomes carry an enzyme called. 2. HIV uses its enzyme to convert its RNA genome into double stranded DNA. 3. HIV leaves its host cell by from the plasma membrane. 4. Bacteriophages produce the enzyme which lyses the cell, thus releasing new phages. 80
For questions 5 to 11, match the definition provided with its label on the diagram below. Some answers may be used more than once. 5. This life cycle immediately begins to reproduce new phage 6. The bacterial chromosome 7. A bacteriophage 8. The lysogenic life cycle 9. Virulent phages are active only in this cycle 10. The prophage of the lysogenic cycle 11. The life cycle that is used exclusively by temperate phages 10.3 Plaque Formation and Intergenic Complementation in Bacteriophages Overview As mentioned in the earlier section, bacteriophages (also called phages) are viruses that infect bacteria. The genomes of bacteriophages are much smaller than those of bacteria. In many cases, the genome consists of less than 100 genes. While not living, viruses are important to biologists due to their ability to infect cells and cause disease. Thus, there is an interest in mapping viral genomes. This section examines the growth properties of bacteriophages in the laboratory and explores how mutations in phage genes are analyzed. It is important to recognize that even though viruses are submicroscopic, they have phenotypes that can be scored for mutations. This has to do with the way that viral colonies, called plaques, look under a microscope. The differences in plaque phenotype are due to variations in certain viral genes (Refer to Figures 10.7 and 10.8). Complementation tests can determine if similar plaque phenotypes are associated with the same gene. Figure 10.9 demonstrates the process by which a complementation test is performed. Basically, bacterial cells are coinfected with an excess of two different strains of mutant T4 bacteriophages. If, for example, the two mutations are in the same gene, the coinfected cell cannot make the normal viral product, and so there will be be cell lysis or plaque formation. This phenomenon is called noncomplementation. 81
Outline of Key Terms Plaques Complementation test Complementation Noncomplementation Cistron Focal Points Structure of the T4 virus (Figure 10.6) The formation of phage plaques on a lawn of bacteria (Figure 10.7) The complementation test (Figure 10.9) Exercises and Problems For questions 1 to 6, complete the sentence with the most appropriate word or phrase: 1. Bacteriophage T4 packages its viral genome in its. 2. Bacteriophage T4 attaches to host cells via its. 3. When bacteriophages are added to bacteria on a petri dish, repeated cycles of infection and lysis produce an observable clear area called a. 4. You perform a complementation test, and observe complementation. This indicates that the phage mutations are. 5. You perform a complementation test, and observe no complementation. This indicates that the phage mutations are. 6. The smallest genetic unit that gives a negative complementation test is called a. 10.4 Intragenic Mapping in Bacteriophages Overview In chapters 7 and 9, we discussed mapping studies in eukaryotes and bacteria, respectively. These are examples of intergenic mapping, which aim to determine the distance between two different genes. This section deals with intragenic mapping, which seeks to establish distances between two or more mutations within the same gene. Two techniques are discussed: intragenic mapping (Figure 10.11), and deletion mapping (Figure 10.12). It should be noted that the technological advances in DNA sequencing have reduced the use of these procedures, since it is often faster simply to sequence the entire genome. However, an understanding of these procedures is important in recognizing the structure of viral genomes. Outline of Key Terms Intergenic mapping Intragenic mapping (Fine structure mapping) Homoallelic mutations Deletion mapping Hot spots 82
Focal Points Intragenic recombination (Figure 10.10) Intragenic mapping (Figure 10.11) Deletion mapping (Figure 10.12) Exercises and Problems For questions 1 to 5, explain which experimental procedure the statement applies to. a. intragenic mapping b. complementation test c. deletion mapping d. all of the above 1. Can be used to determine if two mutations are homoallelic. 2. Can be used to determine the location of mutation hot spots in a gene. 3. The procedure that establishes whether two similar phenotypes are the result of mutations in the same, or different, genes. 4. Examines the rate of rare crossovers within a gene to determine the location of mutations. 5. Used to map genes within viruses. For questions 6 to 13, indicate whether the statement is True (T) or False (F). If false, change the statement to make it true. 6. The determination of the distance between two different genes is called intergenic mapping. 7. Hot spots are areas of a gene that have a higher rate of mutation than is found in neighboring areas of the gene. 8. Two mutations found at the same location in the same gene are called homoallelic. 9. Intragenic mapping involves the removal of segments of a gene to isolate the location of a specific mutation. 10. Two strains of mutated bacteriophages that coinfect bacteria and cause lysis are said to be in complementation. 11. In bacteria and eukaryotes, mapping studies are typically intragenic. 12. Intergenic mapping is also called fine-structure mapping. 13. The technique of intragenic mapping was developed by James Watson and Francis Crick. 84
Chapter Quiz 1. phages can undergo a lytic or lysogenic cycle. a. Virulent b. Temperate c. Competent d. Integrating 2. Which of the following is NOT possible in a viral genome? a. single-stranded DNA b. double-stranded DNA c. single-stranded RNA d. double-stranded RNA e. choose this answer if all of the above are possible 3. Use the following key to select the sequence of events during replication of viruses. 1 = entry ; 2 = release ; 3 = attachment ; 4 = assembly ; 5 = synthesis a. 1, 2, 3, 4, 5 b. 3, 1, 5, 2, 4 c. 3, 1, 4, 5, 2 d. 2, 5, 4, 1, 3 e. 3, 1, 5, 4, 2 4. An envelope is acquired during which of the following steps? a. entry into host cell b. attachment to host cell c. synthesis of viral components d. release of viral particles e. viral assembly 5. Which of the following BEST describes viral DNA that has integrated into the bacterial chromosome? a. prophage b. plasmid c. lysogenic phage d. episome e. virulent phage 6. A complementation test is performed and the results are recorded as Noncomplementation. This indicates that the a. phages cannot attach to the bacteria b. bacteria are resistant to phage infection c. bacteria are sensitive to phage infection d. phage mutations are in the same gene e. phage mutations are in different genes 85
7. Intragenic mapping is used to determine which of the following? a. the sequence of genes on a bacterial chromosome b. the location of genes in a viral genome c. the distance between closely-linked genes d. the distance between mutations in a single gene e. the insertion site of a viral genome into the bacterial chromosome 8. All of the following are features of the human immunodeficiency virus EXCEPT a. can exist as a provirus b. contains the enzyme reverse transcriptase c. has a DNA genome d. is an enveloped virus e. choose this answer if all of the above are features of HIV 9. The swine flu (H1N1) virus can best be described as a(n) a. bacteriophage. b. transforming virus. c. emerging virus. d. lysogenic virus. 10. The enzyme integrase is required for which of the following bacteriophages cycles? a. lytic cycle b. lysogenic cycle c. both of these cycles d. neither of these cycles Answer Key for Study Guide Questions This answer key provides the answers to the exercises and chapter quiz for this chapter. Answers in parentheses ( ) represent possible alternate answers to a problem, while answers marked with an asterisk (*) indicate that the response to the question may vary. 10.1 1. host 2. capsid; capsomers 3. envelope 4. spike 5. bacteriophages 6. DNA; DNA or RNA 10.2 1. integrase 2. reverse transcriptase 3. budding 4. lysozyme 5. c 6. b 7. a 8. d 9. c 10. e 11. d 86
10.3 1. head 2. tail fibers 3. plaque 4. in different genes 5. in the same gene 6. cistron 10.4 1. a 2. c 3. b 4. a 5. d 6. T 7. T 8. T 9. F, deletion mapping 10. T 11. F, intergenic 12. F, intragenic 13. F, Seymour Benzer Quiz 1. b 2. e 3. e 4. d 5. a 6. d 7. d 8. c 9. c 10. b 84