Viral Life Cycles & Viruses Chapter 10 part 2 Viral Life Cycles & Viruses Lecture by Mary C. Colavito

MICROBIAL GENETICS Copyright © 2009 Pearson Education, Inc.

10.17 Viral DNA may become part of the host chromosome Viruses have two types of reproductive cycles Lytic cycle Viral particles are produced using host cell components The host cell lyses, and viruses are released Student Misconceptions and Concerns 1. Students and many parents with young children expect antibiotics to be used to treat many respiratory infections, even though such infections may result from a virus. Students will benefit from a thorough explanation of why antibiotics are inappropriate for viral infections as well as the rising numbers of antibiotic-resistant bacteria that have evolved as a result of the overprescription of antibiotics. 2. The success of modern medicine has perhaps led to overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention, by reducing the chances of contacting the virus and the use of vaccines. Teaching Tips 1. Students (and instructors) might enjoy thinking of a prophage as a smudge mark on the master copy of a class handout. The smudge is replicated every time the original is copied! Copyright © 2009 Pearson Education, Inc.

Phage attaches to bacterial cell. Phage injects DNA. Phage attaches to bacterial cell. Phage injects DNA. Phage DNA directs host cell to make more phage DNA and protein parts. New phages assemble. Cell lyses and releases new phages. Figure 10.1C A phage reproductive cycle.

10.17 Viral DNA may become part of the host chromosome Viruses have two types of reproductive cycles Lysogenic cycle Viral DNA is inserted into the host chromosome by recombination Viral DNA is duplicated along with the host chromosome during each cell division The inserted phage DNA is called a prophage Most prophage genes are inactive Environmental signals can cause a switch to the lytic cycle Student Misconceptions and Concerns 1. Students and many parents with young children expect antibiotics to be used to treat many respiratory infections, even though such infections may result from a virus. Students will benefit from a thorough explanation of why antibiotics are inappropriate for viral infections as well as the rising numbers of antibiotic-resistant bacteria that have evolved as a result of the overprescription of antibiotics. 2. The success of modern medicine has perhaps led to overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention, by reducing the chances of contacting the virus and the use of vaccines. Teaching Tips 1. Students (and instructors) might enjoy thinking of a prophage as a smudge mark on the master copy of a class handout. The smudge is replicated every time the original is copied! Animation: Phage Lambda Lysogenic and Lytic Cycles Animation: Phage T4 Lytic Cycle Copyright © 2009 Pearson Education, Inc.

Figure 10.17 Two types of phage reproductive cycles. Phage 1 Attaches to cell Bacterial chromosome Phage DNA Cell lyses, releasing phages Phage injects DNA 2 4 Lytic cycle Phages assemble Phage DNA circularizes Figure 10.17 Two types of phage reproductive cycles. The transfer of phage DNA via transduction was shown to convert a nontoxigenic strain of the botulism-causing bacterium Clostridium to a toxigenic strain. 3 New phage DNA and proteins are synthesized

Figure 10.17 Two types of phage reproductive cycles. Phage 1 Attaches to cell Bacterial chromosome Phage DNA Cell lyses, releasing phages Phage injects DNA 7 2 Many cell divisions 4 Lytic cycle Lysogenic cycle Phages assemble Lysogenic bacterium reproduces normally, replicating the prophage at each cell division Phage DNA circularizes Figure 10.17 Two types of phage reproductive cycles. The transfer of phage DNA via transduction was shown to convert a nontoxigenic strain of the botulism-causing bacterium Clostridium to a toxigenic strain. Prophage 3 5 6 OR New phage DNA and proteins are synthesized Phage DNA inserts into the bacterial chromosome by recombination

Phage DNA circularizes 1 Attaches to cell Bacterial chromosome Phage DNA Cell lyses, releasing phages Phage injects DNA 2 4 Lytic cycle Figure 10.17 Two types of phage reproductive cycles. The transfer of phage DNA via transduction was shown to convert a nontoxigenic strain of the botulism-causing bacterium Clostridium to a toxigenic strain. Phages assemble Phage DNA circularizes 3 New phage DNA and proteins are synthesized

Phage DNA circularizes 1 Attaches to cell Bacterial chromosome Phage DNA Phage injects DNA 7 2 Many cell divisions Lysogenic cycle Figure 10.17 Two types of phage reproductive cycles. The transfer of phage DNA via transduction was shown to convert a nontoxigenic strain of the botulism-causing bacterium Clostridium to a toxigenic strain. Lysogenic bacterium reproduces normally, replicating the prophage at each cell division Phage DNA circularizes Prophage 5 6 Phage DNA inserts into the bacterial chromosome by recombination

10.18 CONNECTION: Many viruses cause disease in animals and plants Both DNA viruses and RNA viruses cause disease in animals Reproductive cycle of an RNA virus Entry Glycoprotein spikes contact host cell receptors Viral envelope fuses with host plasma membrane Uncoating of viral particle to release the RNA genome mRNA synthesis using a viral enzyme Protein synthesis RNA synthesis of new viral genome Assembly of viral particles Mumps is an RNA virus that does not have a DNA phase in its reproductive cycle. The RNA genome is complementary to mRNA, so the virion particles contain an RNA-dependent RNA polymerase (from a viral gene) to produce the mRNA once the genome is inside the cell. This enzyme will also produce copies of the genome from the mRNA (step 5). Student Misconceptions and Concerns 1. Students and many parents with young children expect antibiotics to be used to treat many respiratory infections, even though such infections may result from a virus. Students will benefit from a thorough explanation of why antibiotics are inappropriate for viral infections as well as the rising numbers of antibiotic-resistant bacteria that have evolved as a result of the overprescription of antibiotics. 2. The success of modern medicine has perhaps led to overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention, by reducing the chances of contacting the virus and the use of vaccines. Teaching Tips 1. As noted in Module 10.18, viruses can spread throughout a plant by moving through plasmodesmata. This is like smoke spreading throughout a building by moving through air ducts. Copyright © 2009 Pearson Education, Inc.

10.18 CONNECTION: Many viruses cause disease in animals and plants Some animal viruses reproduce in the cell nucleus Most plant viruses are RNA viruses They breach the outer protective layer of the plant They spread from cell to cell through plasmodesmata Infection can spread to other plants by animals, humans, or farming practices While the mumps virus is produced in the cell cytoplasm, copies of the herpes virus are produced in the nucleus of a host cell. Student Misconceptions and Concerns 1. Students and many parents with young children expect antibiotics to be used to treat many respiratory infections, even though such infections may result from a virus. Students will benefit from a thorough explanation of why antibiotics are inappropriate for viral infections as well as the rising numbers of antibiotic-resistant bacteria that have evolved as a result of the overprescription of antibiotics. 2. The success of modern medicine has perhaps led to overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention, by reducing the chances of contacting the virus and the use of vaccines. Teaching Tips 1. As noted in Module 10.18, viruses can spread throughout a plant by moving through plasmodesmata. This is like smoke spreading throughout a building by moving through air ducts. Animation: Simplified Viral Reproductive Cycle Copyright © 2009 Pearson Education, Inc.

Figure 10.18 The reproductive cycle of an enveloped virus. Glycoprotein spike Protein coat Viral RNA (genome) Membranous envelope Plasma membrane of host cell 1 Entry 2 Uncoating Viral RNA (genome) 3 RNA synthesis by viral enzyme Protein synthesis RNA synthesis (other strand) 4 5 Template mRNA New viral genome New viral proteins 6 Assembly Figure 10.18 The reproductive cycle of an enveloped virus. Exit 7

VIRUS Glycoprotein spike Protein coat Viral RNA (genome) Membranous VIRUS Glycoprotein spike Protein coat Viral RNA (genome) Membranous envelope Plasma membrane of host cell 1 Entry Uncoating 2 Viral RNA (genome) Figure 10.18 The reproductive cycle of an enveloped virus. RNA synthesis by viral enzyme 3

Protein RNA synthesis synthesis (other strand) Template mRNA New viral Protein synthesis RNA synthesis (other strand) 4 5 Template mRNA New viral genome Assembly New viral proteins 6 Figure 10.18 The reproductive cycle of an enveloped virus. Exit 7

10.19 EVOLUTION CONNECTION: Emerging viruses threaten human health How do emerging viruses cause human diseases? Mutation RNA viruses mutate rapidly Contact between species Viruses from other animals spread to humans Spread from isolated populations Student Misconceptions and Concerns 1. Students and many parents with young children expect antibiotics to be used to treat many respiratory infections, even though such infections may result from a virus. Students will benefit from a thorough explanation of why antibiotics are inappropriate for viral infections as well as the rising numbers of antibiotic-resistant bacteria that have evolved as a result of the overprescription of antibiotics. 2. The success of modern medicine has perhaps led to overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention, by reducing the chances of contacting the virus and the use of vaccines. Teaching Tips 1. There is an interesting relationship between the speed at which a virus kills or debilitates a host and the extent to which it spreads from one organism to another. This is something to consider for a class discussion. Compare two viral infections. Infection A multiplies within the host, is spread by the host to other people through casual contact, but does not cause its lethal symptoms until 5–10 years after infection. Virus B kills the host within 1–2 days of infection, is easily transmitted, and causes severe symptoms within hours of contact. Which virus is likely to spread the fastest through the human population on Earth? Which might be considered the most dangerous to humans? 2. The annual mutations and variations in flu viruses require the production of a new flu vaccine every year. The Centers for Disease Control and Prevention monitors patterns of flu outbreaks, especially in Asia (where many variations of flu viruses originate). They must predict which strains are most likely to be dangerous in the coming year and then synthesize an appropriate vaccine. Copyright © 2009 Pearson Education, Inc.

10.19 EVOLUTION CONNECTION: Emerging viruses threaten human health Examples of emerging viruses HIV Ebola virus West Nile virus RNA coronavirus causing severe acute respiratory syndrome (SARS) Avian flu virus For the Discovery Video Emerging Diseases, go to Animation and Video Files. Student Misconceptions and Concerns 1. Students and many parents with young children expect antibiotics to be used to treat many respiratory infections, even though such infections may result from a virus. Students will benefit from a thorough explanation of why antibiotics are inappropriate for viral infections as well as the rising numbers of antibiotic-resistant bacteria that have evolved as a result of the overprescription of antibiotics. 2. The success of modern medicine has perhaps led to overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention, by reducing the chances of contacting the virus and the use of vaccines. Teaching Tips 1. There is an interesting relationship between the speed at which a virus kills or debilitates a host and the extent to which it spreads from one organism to another. This is something to consider for a class discussion. Compare two viral infections. Infection A multiplies within the host, is spread by the host to other people through casual contact, but does not cause its lethal symptoms until 5–10 years after infection. Virus B kills the host within 1–2 days of infection, is easily transmitted, and causes severe symptoms within hours of contact. Which virus is likely to spread the fastest through the human population on Earth? Which might be considered the most dangerous to humans? 2. The annual mutations and variations in flu viruses require the production of a new flu vaccine every year. The Centers for Disease Control and Prevention monitors patterns of flu outbreaks, especially in Asia (where many variations of flu viruses originate). They must predict which strains are most likely to be dangerous in the coming year and then synthesize an appropriate vaccine. Copyright © 2009 Pearson Education, Inc.

Figure 10.19 Ducks in Vietnam being checked for infection by the Avian flu virus.

Figure 10.19 Ducks in Vietnam being checked for infection by the Avian flu virus.

Figure 10.19 Ducks in Vietnam being checked for infection by the Avian flu virus.

10.20 The AIDS virus makes DNA on an RNA template AIDS is caused by HIV, human immunodeficiency virus HIV is a retrovirus, containing Two copies of its RNA genome Reverse transcriptase, an enzyme that produces DNA from an RNA template One of the approaches for treating HIV-positive patients involves inhibiting reverse transcriptase to prevent the formation of the DNA copy of the RNA genome. AZT (azidothymidine, zidovudine) is a thymidine analog that acts as a chain terminator, since its 3′OH group has been replaced with an azido group. When reverse transcriptase incorporates AZT into the chain, DNA synthesis stops. Since humans do not produce reverse transcriptase, AZT should affect only the viral enzyme. However, a DNA polymerase within mitochondria has a greater sensitivity to AZT than other host cell DNA polymerases, which may account for some of the side effects of the drug. Another unique aspect of HIV duplication is that the initial product of translation needs to be cleaved into individual proteins. A viral-encoded protease carries out this function. Protease inhibitors are used to prevent the formation of active viral proteins from the translated product. Therapies combining a reverse transcriptase inhibitor and a protease inhibitor have been highly effective in reducing the amount of viral production in HIV-positive patients. Student Misconceptions and Concerns 1. Students and many parents with young children expect antibiotics to be used to treat many respiratory infections, even though such infections may result from a virus. Students will benefit from a thorough explanation of why antibiotics are inappropriate for viral infections as well as the rising numbers of antibiotic-resistant bacteria that have evolved as a result of the overprescription of antibiotics. 2. The success of modern medicine has perhaps led to overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention, by reducing the chances of contacting the virus and the use of vaccines. 3. Many misconceptions about AIDS exist. A list of 18 common misconceptions is located at www.gng.org/currents/teachers/hiv101/misconceptions.html. Teaching Tips 1. The Centers for Disease Control and Prevention has extensive information about AIDS at www.cdc.gov/hiv/. 2. Students often do not understand the disproportionate distribution of HIV infections and AIDS in our world. Consider an Internet assignment, asking students to identify the regions of the world most affected by HIV-AIDS. Copyright © 2009 Pearson Education, Inc.

10.20 The AIDS virus makes DNA on an RNA template HIV duplication Reverse transcriptase uses RNA to produce one DNA strand Reverse transcriptase produces the complementary DNA strand Viral DNA enters the nucleus and integrates into the chromosome, becoming a provirus Provirus DNA is used to produce mRNA mRNA is translated to produce viral proteins Viral particles are assembled and leave the host cell For the BLAST Animation AIDS Treatment Strategies, go to Animation and Video Files. For the BLAST Animation HIV Structure, go to Animation and Video Files. Student Misconceptions and Concerns 1. Students and many parents with young children expect antibiotics to be used to treat many respiratory infections, even though such infections may result from a virus. Students will benefit from a thorough explanation of why antibiotics are inappropriate for viral infections as well as the rising numbers of antibiotic-resistant bacteria that have evolved as a result of the overprescription of antibiotics. 2. The success of modern medicine has perhaps led to overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention, by reducing the chances of contacting the virus and the use of vaccines. 3. Many misconceptions about AIDS exist. A list of 18 common misconceptions is located at www.gng.org/currents/teachers/hiv101/misconceptions.html. Teaching Tips 1. The Centers for Disease Control and Prevention has extensive information about AIDS at www.cdc.gov/hiv/. 2. Students often do not understand the disproportionate distribution of HIV infections and AIDS in our world. Consider an Internet assignment, asking students to identify the regions of the world most affected by HIV-AIDS. Animation: HIV Reproductive Cycle Copyright © 2009 Pearson Education, Inc.

Envelope Glycoprotein Protein coat RNA (two identical strands) Reverse Envelope Glycoprotein Protein coat RNA (two identical strands) Figure 10.20A A model of HIV structure. Reverse transcriptase

Viral RNA CYTOPLASM NUCLEUS DNA Chromosomal strand DNA Double- Viral RNA CYTOPLASM 1 NUCLEUS DNA strand Chromosomal DNA 2 Double- stranded DNA Provirus DNA 3 4 5 Viral RNA and proteins Figure 10.20B The behavior of HIV nucleic acid in a host cell. RNA 6

10.21 Viroids and prions are formidable pathogens in plants and animals Some infectious agents are made only of RNA or protein Viroids: circular RNA molecules that infect plants Replicate within host cells without producing proteins Interfere with plant growth Prions: infectious proteins that cause brain diseases in animals Misfolded forms of normal brain proteins Convert normal protein to misfolded form Student Misconceptions and Concerns 1. Students and many parents with young children expect antibiotics to be used to treat many respiratory infections, even though such infections may result from a virus. Students will benefit from a thorough explanation of why antibiotics are inappropriate for viral infections as well as the rising numbers of antibiotic-resistant bacteria that have evolved as a result of the overprescription of antibiotics. 2. The success of modern medicine has perhaps led to overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention, by reducing the chances of contacting the virus and the use of vaccines. Teaching Tips 1. Viroids can cause significant damage to plants. The authors note elsewhere that over 10 million coconut palms in the Philippines have been killed by viroids. Copyright © 2009 Pearson Education, Inc.

10.22 Bacteria can transfer DNA in three ways Three mechanisms allow transfer of bacterial DNA Transformation is the uptake of DNA from the surrounding environment Transduction is gene transfer through bacteriophages Conjugation is the transfer of DNA from a donor to a recipient bacterial cell through a cytoplasmic bridge Recombination of the transferred DNA with the host bacterial chromosome leads to new combinations of genes Student Misconceptions and Concerns 1. Students and many parents with young children expect antibiotics to be used to treat many respiratory infections, even though such infections may result from a virus. Students will benefit from a thorough explanation of why antibiotics are inappropriate for viral infections as well as the rising numbers of antibiotic-resistant bacteria that have evolved as a result of the overprescription of antibiotics. 2. The success of modern medicine has perhaps led to overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention, by reducing the chances of contacting the virus and the use of vaccines. Teaching Tips 1. The authors note that the figures in Module 10.22 represent the size of the bacterial chromosome as much smaller than they actually are. They note that a bacterial chromosome is hundreds of times longer than the cell. These chromosomes use extensive folding to fit inside the cell. 2. You might challenge students to explain why conjugation is sometimes called bacterial sex. Students might note that two organisms cooperate to produce a new, genetically unique bacterium. Copyright © 2009 Pearson Education, Inc.

DNA enters cell Fragment of DNA from another bacterial cell DNA enters cell Fragment of DNA from another bacterial cell Figure 10.22A Transformation. Transformation has been proposed as a method for transferring antibiotic resistance for the ulcer-causing bacteria Helicobacter pylori, both for members within this species and between species in the Helicobacter genus. This could undermine the currently successful use of antibiotics to treat ulcers. Bacterial chromosome (DNA)

Phage Fragment of DNA from another bacterial cell (former phage host) Phage Fragment of DNA from another bacterial cell (former phage host) Figure 10.22B Transduction. During phage infection, the bacterial chromosome becomes fragmented. Bacterial DNA molecules of a size similar to the phage DNA can be packaged into phage particles. These phage particles inject bacterial DNA into another cell, leading to a possible change in genotype for the host. Phage particles carrying bacterial DNA do not continue the infection.

Mating bridge Sex pili Donor cell (“male”) Recipient cell (“female”) Mating bridge Sex pili Figure 10.22C Conjugation. As described in Module 10.23, conjugation depends on a plasmid called the F factor (fertility factor) that is either separate from the chromosome in an F+ cell or integrated into the chromosome in an Hfr cell (High frequency of recombination). The F plasmid can integrate at random locations, so different Hfr cells will have the factor at a unique position on the chromosome. This figure shows conjugation for an Hfr cell. During conjugation, one strand of DNA containing a portion of the F factor and its adjacent bacterial genes is transferred to the donor. The number of bacterial genes transferred will depend on the length of time that the cytoplasmic bridge is maintained. It is unlikely that the cells would remain attached long enough to transfer the entire bacterial chromosome and all portions of the F factor. This process uses “rolling circle” replication, whereby the donor replaces the donated strand using the strand remaining in the cell as a template. Recombination is required to integrate transferred genes into the recipient cell’s chromosome. Donor cell (“male”) Recipient cell (“female”)

Donated DNA Crossovers Degraded DNA Recipient cell’s chromosome Donated DNA Crossovers Degraded DNA Figure 10.22D Integration of donated DNA into the recipient cell’s chromosome. Since the bacterial chromosome is a circle, two crossovers are needed to integrate transferred genes. If there were only one crossover event, the chromosome would be opened up into a linear structure, which would be subject to nuclease digestion within the cell. Recipient cell’s chromosome Recombinant chromosome

10.23 Bacterial plasmids can serve as carriers for gene transfer Plasmids are small circular DNA molecules that are separate from the bacterial chromosome F factor is involved in conjugation When integrated into the chromosome, transfers bacterial genes from donor to recipient When separate, transfers F-factor plasmid R plasmids transfer genes for antibiotic resistance by conjugation The R plasmid has genes for sex pilus formation along with genes for antibiotic resistance. For the BLAST Animation Plasmid, go to Animation and Video Files. Student Misconceptions and Concerns 1. Students and many parents with young children expect antibiotics to be used to treat many respiratory infections, even though such infections may result from a virus. Students will benefit from a thorough explanation of why antibiotics are inappropriate for viral infections as well as the rising numbers of antibiotic-resistant bacteria that have evolved as a result of the overprescription of antibiotics. 2. The success of modern medicine has perhaps led to overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention, by reducing the chances of contacting the virus and the use of vaccines. Teaching Tips 1. The figures in Module 10.23 provide essential imagery for a detailed discussion of bacterial conjugation. The abstract details presented in Module 10.23 are likely new to most of your students. 2. Module 10.23 notes the possible consequences of widespread use of antibiotics. Consider asking your students to consider the value of widespread use of antibacterial soaps throughout their homes. Copyright © 2009 Pearson Education, Inc.

transfer of chromosome Male (donor) cell F factor (integrated) Origin of F replication Bacterial chromosome F factor starts replication and transfer of chromosome Recipient cell Figure 10.23A Transfer of chromosomal DNA by an integrated F factor. This shows the transfer of a portion of the F factor and adjacent bacterial genes from a cell where the F factor has integrated into the bacterial chromosome. Only part of the chromosome transfers Recombination can occur

F factor (plasmid) Male (donor) cell Bacterial chromosome Male (donor) cell Bacterial chromosome F factor starts replication and transfer Figure 10.23B Transfer of an F-factor plasmid. This figure shows that the F-factor plasmid can be transferred from donor to recipient. At the end of the process the recipient is now a donor. Plasmid completes transfer and circularizes Cell now male

Plasmids Figure 10.23C Plasmids and part of a bacterial chromosome released from a ruptured E. coli cell.