Prescott’s Microbiology, 9th Edition

27 Viruses

CHAPTER OVERVIEW

This chapter describes the life cycles of viruses of all types and specificities.Viruses are grouped by the type of genome they possess and the details of replication for each type is given.Important examples from each group are used for illustration and to introduce broader concepts such as latency and virulence.

LEARNING OUTCOMES

After reading this chapter you should be able to:

  • distinguish between the Baltimore system of grouping viruses and the official taxonomy of viruses proposed by the International Committee on Taxonomy of Viruses
  • determine if a virus has a positive- or negative-strand genome
  • differentiate the Baltimore group of viruses
  • describe in general terms the strategy used by double-stranded (ds) DNA viruses to synthesize their nucleic acids and proteins
  • describe in general terms how bacteriophage lambda regulates the switch between the lytic and lysogenic cycles
  • choose one specific bacterial, archaeal, and eukaryal dsDNA virus and outline the major events in their life cycles, noting, when possible, the specific mechanisms used to accomplish each step
  • describe in general terms the strategy used by single-stranded(ss) DNA viruses to synthesize their nucleic acids and proteins
  • choose one specific bacterial and eukaryal ssDNA virus and illustrate the major events in their life cycles, noting, when possible, the specific mechanisms used to accomplish each step
  • identify which RNA viruses use RNA-dependent RNA polymerases and which use DNA-dependent RNA polymerases to complete their life cycles
  • describe the different approaches used by RNA viruses to synthesize the proteins they need to complete their life cycles
  • propose how a virus with a single RNA molecule as its genome might generate multiple proteins from that molecule
  • describe in general terms the strategy used by dsRNA viruses to synthesize their nucleic acids and proteins
  • describe the major events in the life cycles of and rotaviruses, noting, when possible, the specific mechanisms used to accomplish each step
  • describe in general terms the strategy used by plus-strand RNA viruses to synthesize their nucleic acids and proteins
  • outline the major events in the life cycles of poliovirus and tobacco mosaic virus, noting, when possible, the specific mechanisms used to accomplish each step
  • describe in general terms the strategy used by minus-strand RNA viruses to synthesize their nucleic acids and proteins
  • explain how having a segmented genome impacts synthesis of viral mRNA and proteins and the generation of new strains of a virus
  • create a flow chart that summarizes the life cycle of influenza virus, noting the specific mechanisms it uses to accomplish each step of its life cycle
  • describe in general terms the strategy used by retroviruses to synthesize their nucleic acids and proteins
  • differentiate a segmented genome from the genome of a retrovirus
  • describe in general terms the strategy used by reverse transcribing DNA viruses to synthesize their nucleic acids and proteins
  • compare the role of reverse transcriptase in the life cycle of a retrovirus to that in the life cycle of a hepadnavirus

CHAPTER OUTLINE

  1. Virus Taxonomy and Phylogeny

A.Almost 2,000 viral species have been placed in 3 orders, 73 families, and 287 genera; genome type, capsid structure, and envelope are used for classification

B.Some viruses are known to possess positive- or negative-strand RNA or DNA genomes, while others have double-stranded DNA or RNA genomes; seven groups of viruses are defined by life cycle, and this system is used here

C.While some evolutionary relationships are emerging through comparative genomics, it remains difficult to follow viral phylogenies

  1. Double-Stranded DNA Viruses

A.Largest group of known viruses; mainly bacteriophages with dsDNA genomes; includes herpesviruses and poxviruses; rely on host DNA and RNA polymerases

B.Bacteriophage T4: A virulent bacteriophage

  1. Virulent phages can only undergo the lytic cycle in several stages
  2. Attachment (adsorption) and penetration

1)Viruses attach to specific receptor sites on the host cell using tail fibers and baseplate settles on surface

2)Tail sheath contracts, injecting DNA into the host cell, leaving an empty capsid outside

  1. Synthesis of phage nucleic acids and proteins

1)mRNA molecules transcribed early in the infection (early mRNA) are synthesized using host RNA polymerase; early proteins, made at the direction of early mRNA molecules, direct the synthesis of protein factors and enzymes required to take over the host cell

2)Transcription of viral genes then follows an orderly sequence due to the modification of the host RNA polymerase and changes in sigma factors

3)Later in the infection viral DNA is replicated using a virus-encoded DNA polymerase

(i)Synthesis of viral DNA requires the initial synthesis of alternate bases; these are used to protect the phage DNA from host enzymes (restriction endonucleases) that would otherwise degrade the viral DNA and thereby protect the host

(ii)T4 can form concatemers (long chains) of the DNA genome are formed; these are later cleaved during assembly

  1. Assembly of phage particles

1)Late mRNA molecules (those made after viral nucleic acid replication) direct the synthesis of capsid proteins and other proteins involved in assembly (e.g., scaffolding proteins) and release of the virus

2)Assembly proceeds sequentially by subassembly lines, which assemble different structural units (e.g., baseplate, tail tube); these are then put together to make the complete virion

3)DNA packaging is accomplished with a protein complex called the packasome, which includes the terminase complex that fills in gaps at the end of concatemers

  1. Release of phage particles—host is lysed by damaging the cell wall or the cytoplasmic membrane with T4 lysozyme and holin enzyme

C.Bacteriophage lambda: A temperate bacteriophage

  1. Temperate phages are capable of lysogeny, a nonlytic relationship with their hosts (virulent phages lyse their hosts)
  2. In lysogeny, the viral genome (called a prophage) remains in the host (usually integrated into the host chromosome) but does not kill (lyse) the host cell; the cells are said to be lysogenic (or are called lysogens)
  3. It may switch to the lytic cycle at some later time; this process is called induction
  4. Most bacteriophages are temperate; it is thought that being able to lysogenize bacteria is advantageous; supporting this is the observation that certain conditions favor the establishment of lysogeny
  5. Lysogenic conversion is a change that is induced in the host phenotype by the presence of a prophage, and that is not directly related to the completion of the viral life cycle; examples include:
  6. Modification of lipopolysaccharide structure in infected Salmonella
  7. Production of diphtheria toxin only by lysogenized strains of Corynebacterium diphtheriae
  8. Establishment of lysogeny
  9. Two sets of viral promoters are available to host RNA polymerase
  10. A repressor protein (lambda repressor) may be made from genes adjacent to one of these promoters
  11. If the lambda repressor binds to its target operator before the other promoter is used, that promoter is blocked and lysogeny is established
  12. If genes associated with that second promoter (Cro protein) are expressed before the lambda repressor can bind to the operator, the lytic cycle is established
  13. Induction (the termination of lysogeny and entry into the lytic cycle) will occur if the level of lambda repressor protein decreases; this is usually in response to environmental damage to host DNA
  14. For lambda and most temperate phages, if lysogeny is established, the viral genome integrates into the host chromosome; however, some temperate phages can establish lysogeny without integration

D.Archaeal viruses

  1. All known archaeal viruses have dsDNA genomes; some have unusual morphologies
  2. Some archaeal viruses are virulent, while others are temperate
  3. Many Archeae and eubacteria have developed a mechansim to defend against viruses known as the CRISPR/Cas system

a. Clustered regularly interspaced short palindromic repeats (CRISPR)

b. Regions between repeats have homology to viral genes and may act similar to RNA silencers to future infections

E.Herpesviruses

  1. Family of human pathogens with dsDNA genome; cause chicken pox, shingles, genital herpes, cold sores; include cytomegalovirus and Epstein-Barr virus
  2. Enveloped pleomorphic virus with spikes; genome contains 50 to 100 genes in an icosahedral capsid
  3. First exposure leads to productive herpes infections that generate many new virions leading to host cell death; infected neurons develop latent infections that can be reactivated
  4. Receptor-mediated viral binding to host cell herpesvirus entry mediators (HVEMs) leads to capsid penetration and movement of the viral particle to the nucleus; the viral genome is expressed using host cell machinery and produce early gene products required for replication; late gene expression directs production of viral proteins
  5. Exit from the cell starts with viral budding through the inner nuclear membrane; the virus moves to the plasma membrane for exocytosis in an vesicle derived from the Golgi

F.Nucleo-cytoplasmic large DNA (NCLD) viruses

  1. A group of large enveloped icosahedral virions with a large dsDNA genome that includes members from several virus families (e.g., Poxviridae and Phycodnaviridae); some are the size of small bacteria
  2. Large genome houses many genes needed for viral replication and assembly
  3. Poxviruses are large brick-shaped virions with a dumbbell-shaped core; enter through receptor-mediated endocytosis; early and late genes are expressed during the life cycle
  1. Single-Stranded DNA Viruses

A.Bacteriophages X174 and fd

  1. X174 is plus-strand DNA virus—virus genome that has the same sequence as the viral mRNA
  2. The single-stranded genome is converted to a double-stranded replicative form (RF) by the host DNA polymerase
  3. The RF directs synthesis of more RF, RNA, and +strand DNA genome
  4. Phages are released by lysis of host cell
  5. Filamentous phage fd—plus-strand DNA virus
  6. Phage DNA enters via the host cell’s sex pilus and an RF is synthesized
  7. The RF directs mRNA synthesis and DNA replication via the rolling-circle method
  8. Phages are released without lysing the host cell; instead they are released by a secretory process

B.Parvoviruses

  1. Group of viruses of eukaryotic cells, including Human parvovirus B19
  2. Naked icosahedral virions with mainly negative-strand DNA genomes; among simplest DNA viruses, codes for no enzymatic proteins
  3. Enter by receptor-mediated endocytosis and move to the nucleus; viral genomes have palindromic ends that act as sites for DNA polymerase binding and rolling-circle replication
  1. RNA Viruses: Unity Amidst Diversity

A.Many viruses with RNA genomes carry RNA-dependent RNA polymerase (replicase), an enzyme not found in host cells

  1. Double-Stranded RNA Viruses

A.Bacteriophage 6

  1. Enveloped dsRNA virus with segmented genome; uses pilus for entry through fusion with the outer membrane, viral enzymes degrade peptidoglycan allowing entry
  2. Inside host, viral RNA polymerase generates mRNA and viral genomes; host cells are lysed to release mature virions

B.Rotaviruses

  1. Human pathogens causing severe diarrhea; survive in the environment
  2. Naked dsRNA viruses with a segmented genome and a wheel-like capsid with three-layers of proteins
  3. Outer protein layer lost during penetration releasing double-layered particle (DLP); viral genes expressed and viral proteins accumulate in cytoplasmic inclusions called viroplasm; viral envelope arises from endoplasmic reticulum
  1. Plus-Strand RNA Viruses

A.Replicate in host cell cytoplasm using viral RNA-dependent RNA polymerase to generate replicative form; progeny viruses assembled in replication complexes; includes most plant viruses and some human pathogens

B.Bacteriophages MS2 and Q—small, tailless, icosahedral virions with very simple genomes; use pili to reach cell membrane and then insert genome; uses viral RNA polymerase to generative replicative form and produce new virions that are released by host cell lysis

C.Poliovirus

  1. Naked plus-strand RNA virus causes polio in humans
  2. Enters host cell by ingestion; genome acts as mRNA but without a 5' cap an internal ribosome binding site mediates recognition
  3. A polyprotein is produced that self-cleaves into capsid proteins, RNA polymerase, and others; mature virions are released through host cell lysis

D.Tobacco mosaic virus (TMV)

  1. Plant viruses are mainly plus-strand RNA viruses
  2. TMV is a helical filamentous virion that resembles animal viruses and bacteriophages
  3. Penetration through the plant cuticle through wounds or by the action of biting insects
  4. The virus uses either a cellular or a virus-specific RNA-dependent RNA polymerase
  5. The virus produces proteins, which then spontaneously assemble
  6. Viral spread is through the plant vascular system or to adjacent cells through plasmodesmata
  7. The virus causes many cytological changes, such as the formation of inclusion bodies and the degeneration of chloroplasts
  1. Minus-Strand RNA Viruses

A.Spherical or pleomorphic, enveloped virions having segmented or unsegmented genomes; includes Rabies virus, Ebola virus, influenza viruses, and Measles virus

B.Must carry RNA-dependent RNA polymerase to generate mRNA from minus-strand RNA genome

C.Influenza

  1. Causes three major types of flu; has segmented genome
  2. Uses surface neuraminidase and hemagglutinin spikes to enter cells through receptor-mediated endocytosis; membrane fusion with endosome releases capsid to cytoplasm; mature virions released through cell lysis
  1. Retroviruses

A.Contain positive-strand RNA genomes that do not act as mRNA;ssRNA genome converted to dsDNA using reverse transcriptase; dsDNA genome can then integrate into the host cell chromosome

B.Human immunodeficiency virus (HIV)

  1. Causative agent of AIDS; enveloped virion with two RNA genomes and enzymes including reverse transcriptase and integrase
  2. Surface GP120 protein binds to host CD4+ T-helper cells and other immune cells; entrance is by receptor-mediated endocytosis
  3. Reverse transcriptase copies the RNA genome into dsDNA that integrates as a provirus into the host cell chromosome; mature viruses bud from host cell surface; eventually the host cell is killed
  1. Reverse Transcribing DNA Viruses

A.Hepadnaviruses include Hepatitis B virus, a spherical virion with a circular genome

B.One strand of the dsDNA genome is nicked, while the complementary strand has a large gap which is repaired by host cell enzymes; viral replication involves reverse transcription of progenome RNA formed from the minus-strand DNA

CRITICAL THINKING

1.Describe the life cycle of the HIV viruses being sure to include the replication process. Why do you think that a retrovirus like HIV might be difficult to treat? What features of the viral replication cycle are unique to the virus and hence could make good targets to anti-HIV drugs?

2.Describe the differences between temperate and virulent phages. What survival advantages are offered by each life cycle? How might you expect human disease caused by each class of virus to differ from each other?

3.Why might an RNA virus like influenza be such a prevalent viral infection in humans?

4. Would it be advantageous for a virus to damage host cells? if not, then why isn’t damage to the host avoided? Is it possible that a virus might become less pathogenic when it has been associated with the host population for a longer time?

CONCEPT MAPPING CHALLENGE

Construct a concept map that illustrates which enzymes are involved in the life cycles of each of the Baltimore groups of viruses and how those enzymes are used. Use the concepts that follow or any other concepts or terms needed to link the concepts in your map. Provide examples of the viruses that utilize each of these enzymes.

DNA-dependent DNA polymerase Transcriptase DNA-dependent RNA polymerase Replicase RNA dependent RNA polymerase

Integrase RNA-dependent DNA polymerase Protease Excisionase Reverse transcriptase RNAseH Recombinase Lysozyme

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