Viruses Tomasz Kordula, Ph.D.

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1 Viruses Tomasz Kordula, Ph.D. Resources: Alberts et al., Molecular Biology of the Cell, pp. 295, 1330, ; Lehninger CD Movie A Learning Objectives: 1. Understand parasitic life cycle of viruses and bacteriophages. 2. Be aware of the variety of viral genomes. 3. Understand the variety of structural characteristics of the viruses. 4. Be able to describe the replication and life cycles of lambda phage and other viruses. 5. Appreciate the role of viruses in neoplastic transformation. 6. Know the difference between the lytic and lysogenic pathways 7. Know the viral budding process. 8. Have a sense of the life styles and genetics of the tumor viruses. I. Viral Structures A. Viruses and bacteriophages are mobile, parasitic hitchhikers containing a nucleic acid genome surrounded by at least a protective protein "coat." B. The nucleic acid component can be either DNA or RNA that exists in one of a variety of forms, depending upon the specific virus type. C. The outer coat is either protein alone, called capsid, or capsid surrounded by a membrane. This diversity contributes to the various superstructures observed among the viral types. Viral membranes are derived in part from a host cell membrane, which enshrouds the protein coated virion upon exiting from the cell. This "budding" process typically does not lyse the host cell. Budding can occur through different membranes; e.g., nuclear, ER, golgi; or through different membrane faces depending upon where the viral membrane proteins are targeted (see, for example, Fig , p.1445 of Alberts et al., fourth edition). Figure 1. Source: Alberts et al. Molecular Biology of the Cell, Garland Science 1995

2 D. Examples of Viral/Phage Shapes Figure 2. Source: Alberts et al. Molecular Biology of the Cell, Garland Science 1995 EM A: T4 phage with a linear dsdna genome EM B: Potato virus X with a ssrna genome EM C: Adenovirus with dsdna and attached primer proteins EM D: Influenza virus with a capsid plus a membrane and ssrnas genome. Figure 3. Source: Lehninger et al., Principles of Biochemistry Woth Publishers copyright 2005 EM of tobacco mosaic virus and cut away drawing detailing the relationship of the caspid proteins and the viral genome, an RNA molecule in this case.

3 II. III. Viral genes encode a selected number of viral specific proteins ranging in number from a few to several hundred. These invariably include capsid proteins and membrane proteins when a membrane is included. Depending upon the nature of the viral genome, replication enzymes such as reverse transcriptase and replicase are also viral encoded. Such enzymes are not normal components of the host cells. Viral genomes virtually every imaginable style of DNA is represented among the various viral genomes. In addition, single strand and double strand RNA genomes have been found. In the 1950's, it was shown that TMV (Tobacco Mosaic Virus) contained only RNA thus confirming that RNA as well as DNA could be infective and serve as a movable genetic element. Because of the diversity of genome types, the viral genes differ to reflect the various non host enzymes required for viral replication. See the list below for an overview of viral genome types. Do Not Memorize!! Figure 4. Source: Alberts et al., Molecular Biology of the Cell, Garland Science 2002 IV. RNA viruses A. (+) strand virus: means that its encapsulated ("traveling") RNA strand is an mrna that can directly encode for viral specific proteins, using the host cell translation apparatus. Replication of (+) strands requires the initial synthesis of a ( ) strand template. The replication enzyme is usually a replicase, or RNA dependent RNA polymerase. B. ( ) strand virus: means that its encapsulated ("traveling") RNA strand is the

4 antisense (or complement) of an mrna. Thus, the ( ) strand must be copied by a replicase to yield a complementary (+) before viralspecific proteins can be made. This (+) strand then serves as the template for new ( ) strands which are packaged in the mature virion. C. Retroviruses: These RNA viruses will be reviewed under Tumor viruses below. V. Life cycle of Bacteriophage Lambda. Figure 4. Source: Alberts et al., Molecular Biology of the Cell, Garland Science 2002 The double stranded genome of Lambda encodes about 60 proteins. Shortly after entry into the cell, the cohesive ends come together to form a circle. The circular form either (1) directs the synthesis if new viral particles, which lyse the cell upon their release (The Lytic Path), or (2) the circular DNA is integrated into the phage genome (The Lysogenic Path). The integration is a good example of sitespecific recombination. The lysogenic mode permits amplification of the phage genome as a component of the replicating bacterial chromosome. The integrated copy of viral or phage genome is referred to as a provirus or prophage. The lysogenic path can be jarred into the lytic path by treatments such as heat, organic solvents, or UV radiation.

5 VI. Neoplastic transformation (uncontrolled growth) can be induced by tumor viruses. A small percentage cancers are caused by viruses. For example, papilloma virus is associated with cervical carcinoma, hepatitis B is associated with liver cancer, and Epstein Barr virus is associated with Burkitt s Lymphoma. Some RNA viruses are also associated with cancers. You know of HIV and Kaposi s Sarcoma. The mechanisms, however are somewhat elusive. A. DNA tumor viruses When infecting a permissive cell (supports viral replication), the virus replicates, lyses and destroys the cell. When infecting a non permissive cell (does not support viral replication), occasionally the viral DNA becomes integrated or replicates as an extrachromosomal element under host control. Some of the viral encoded proteins produced under these conditions force the cell from Go into S phase and the result is uncontrolled cellular replication. Some examples of possible transforming proteins are: 1. Surface receptor for growth factor. 2. Inhibitor of a regulatory factor (also called a tumor suppressor). For example, RB protein (a tumor suppressor) normally binds transcription E2F which activates cell proliferation genes. So, RB E2F complex is an inactive transcription activator. Papilloma virus encoded E7 protein binds RB, which sets E2F free to carry out its activation of proliferation genes. B. RNA tumor viruses (Retroviruses) These viruses carry single strand RNA and the gene for reverse transcriptase (copies RNA to produce a DNA strand). The resulting cdna can be integrated into the host genome. The genomes retroviruses contain genes, called oncogenes, which alter the control of host cell proliferation. The cancer causing retroviral oncogenes are modified versions of normal host cell genes (proto oncogenes) that are picked up accidentally, modified by rampant mutation during successive infections, then returned to an unsuspecting host cell as a tumor causing gene. These mutations are gain of function mutations. These genes are not required for the life of the virus per se. HIV is a relevant example of a retrovirus. This would be a great time to view the Lehninger CD movie A

6 VII. Conversion of regulatory gene to a viral oncogene