1. I. The Nature of Viruses 8.1 What Is a Virus? Plus 9.1, 9.2 (parts)
8.2 Structure of the Virion
8.3 Overview of the Virus Life Cycle
8.8 Temperate Bacteriophages and Lysogeny
8.10, 9.6, 9.7 Overview of Animal Viruses

2. 8.1 What Is a Virus?
Virus: subcellular genetic element that cannot replicate independently of a living (host) cell
Virus particle (virion): extracellular form of a virus
Exists outside host and facilitates transmission from one host cell to another
Contains nucleic acid genome surrounded by a protein coat and, in some cases, other layers of material (Figure 8.1)

3. Viral genomes (Figure 8.2) a variety of forms
Either DNA or RNA genomes
Some are circular, but most are linear
Viruses
Genome:
DNA
RNA
RNA
DNA
Types:
ssDNA
dsDNA
ssRNA
dsRNA
ssRNA
(Retroviruses)
dsDNA
(Hepadnaviruses)
Single or double-stranded
Some have ability to reverse flow of information
Figure 8.2 Viral genomes.

4. 9.1 Size and Structure of Viral Genomes-Range
Viral genome size (Figure 9.1)
Smallest circovirus: 1.75-kilobase single strand
Largest megavirus: 1.25-megabase pairs (Pandoravirus)

5. Figure 9.1 Comparative genomics.

6. 9.1 Size and Structure of Viral Genomes
Taxonomy
Based mainly on idea proposed by David Baltimore (Baltimore Scheme)
Depends on relationship of genome to mRNA
Genome structure is the key feature

7. Class I & VII
Class II
Class III
Class IV
Class V
Class VI
dsDNA (±) virus
ssDNA (+) virus
dsRNA (±) virus
ssRNA (+) virus
ssRNA (–) virus
ssRNA (+) retrovirus
Transcription of
the minus strand
Synthesis of the
minus strand
Transcription of
the minus strand
Used directly
as mRNA
Transcription of
the minus strand
Reverse
transcription
dsDNA intermediate
(replicative form)
dsDNA intermediate
Transcription
mRNA (+)
Transcription of
the minus strand
DNA Viruses
RNA Viruses
Class I classical semiconservative
Class II classical semiconservative,
discard (–) strand
Class VII transcription followed by
reverse transcription
Class III make ssRNA (+) and transcribe from this to give ssRNA (–) complementary strand
Class IV make ssRNA (–) and transcribe from this to give ssRNA (+) genome
Class V make ssRNA (+) and transcribe from this to give ssRNA (–) genome
Class VI make ssRNA (+) genome by transcription of (–) strand of dsDNA
Genome
replication
Figure 9.2 The Baltimore classification of viral genomes.
Figure 9.2

8. 9.2 Viral Evolution No one knows where viruses came from
Viruses may date from before the evolution of
cells or
Viruses may have evolved after cells
Or both
Do some viruses represent a 4th domain?

9. 8.2 Structure of the Virion
Viral structure
Genome: nucleic acid of the virus
Capsid: the protein shell that surrounds the genome of a virus particle (Figure 8.3)
Composed of a number of protein molecules arranged in a precise and highly repetitive pattern around the nucleic acid
Capsid protein: individual protein molecule building block
Capsomere: subunit of the capsid that can be observed microscopically
Smallest morphological unit visible with an electron microscope

10. 8.2 Structure of the Virion
Viral structure (cont'd)
Nucleocapsid: nucleic acid and protein packaged in the virion-different in different viruses
Enveloped virus: virus that contains additional layers around the nucleocapsid-lipids derived from host

11. Naked virus Enveloped virus (Unenveloped) Figure 8.1 Nucleocapsid
Nucleic
acid
Nucleic
acid
Capsid
(composed of
capsid proteins)
Figure 8.1 Comparison of naked and enveloped virus particles.
Naked virus
(Unenveloped)
Enveloped virus
Figure 8.1

12. 8.2 Structure of the Virion
Nucleocapsids are constructed in highly symmetric ways
Helical symmetry: rod-shaped viruses (e.g., tobacco mosaic virus)
Length of virus determined by length of nucleic acid
Width of virus determined by size and packaging of protein subunits
May or may not be surrounded by an envelope
Icosahedral symmetry: near-spherical viruses (e.g., human papillomavirus; Figure 8.4)
Most efficient arrangement of subunits in a closed shell

13. Figure 8.3 18 nm Structural subunits (capsid proteins) Virus RNA
Figure 8.3 The arrangement of RNA and protein coat in a simple virus, tobacco mosaic virus.
Figure 8.3

14. Figure 8.4 5-Fold 3-Fold 2-Fold Cluster of 5 units “pentamer” Symmetry
Figure 8.4 Icosahedral symmetry.
Figure 8.4

16. Enveloped viruses (Figure 8.5)
Have membrane surrounding nucleocapsid (aka core)
Lipid bilayer with embedded proteins
Envelope makes initial contact with host cell
Figure 8.5 Enveloped viruses.
Figure 8.5

17. 8.2 Structure of the Virion
Some virions contain enzymes critical to infection
Lysozyme
Makes hole in cell wall
Lyses bacterial cell
Nucleic acid polymerases (reverse transcriptase)
Neuraminidases
Enzymes that cleave glycosidic bonds
Allows liberation of viruses from cell

18. 8.3 Overview of the Virus Life Cycle
Phases or steps of viral replication (Figure 8.6)
Attachment (adsorption) of the virus to a susceptible host cell via a receptor
Entry (penetration) of the virion or its nucleic acid
Synthesis of virus nucleic acid and protein by cell metabolism as redirected by virus
Assembly of capsids and packaging of viral genomes into new virions (maturation)
Release of mature virions from host cell

19. 8.3 Overview of the Virus Life Cycle (Bacteriophage = bacterial virus)
Head
Protein coat
remains outside
Virions
Virion
DNA
Viral DNA enters
Cell (host) 1.
Attachment (adsorption of phage virion) 2.
Penetration
of viral
nucleic acid 3.
Synthesis of
viral nucleic acid
and protein 4.
Assembly and
packaging of
new viruses 5.
Cell lysis and
release of
new virions
Virus replication is typically characterized by a one-step growth curve (Figure 8.7)
Figure 8.6 The replication cycle of a bacterial virus.
Figure 8.6

20. Maturation Figure 8.7 Nucleic acid Protein coats Early enzymes Virus
Eclipse
Maturation
Early enzymes
Nucleic acid
Protein coats
Virus
added
Assembly and release
Figure 8.7 One-step growth curve of virus replication.
Latent period
Figure 8.7

21. 8.4 Culturing, Detecting, and Counting Viruses
Viruses replicate only in certain types of cells or in whole organisms
Bacterial viruses are easiest to grow; model systems
Animal viruses (and some plant viruses) can be cultivated in tissue or cell cultures

22. 8.8 Temperate Bacteriophages and Lysogeny
Viral life cycles
Virulent mode: viruses lyse host cells after infection-T4 is an example (aka lytic pathway or cycle)
Temperate mode: viruses replicate their genomes in tandem with host genome and without killing host. Phage lambda is an example (aka lysogenic pathway or cycle)

23. Temperate viruses: can undergo a stable genetic relationship within the host (Figure 8.15)
Lysogeny: state where most virus genes are not expressed and virus genome (prophage) is replicated in synchrony with host chromosome
Lysogen: a bacterium containing a prophage
Under certain conditions, lysogenic viruses may revert to the lytic pathway and begin to produce virions

24. Temperate virus
Host DNA
Viral DNA
Attachment of the virus to the host cell
Cell (host)
Injection of viral DNA
Lytic pathway
Lysogenic pathway
Lytic events are initiated.
Induction
Phage components are synthesized and virions are assembled.
Viral DNA is integrated
into host DNA.
Lysogenized
cell
Figure 8.15 Consequences of infection by a temperate bacteriophage.
Prophage
Lysis of the host cell and release of new phage virions
Viral DNA is replicated with host DNA at cell division.
Figure 8.15

25. Lambda DNA forms a circle
Attaches to host DNA and integrates itself into DNA
Lambda “att” site
Lambda repressor protein keeps lambda genes shut off
Unfavorable cell growth conditions tend to favor lysogenic pathway
Lysogeny stable until cell is injured or damaged

26. Lambda can cause specialized transduction

27. Unusual mode of replication for lambda DNA When it enters lytic pathway, lambda synthesizes long, linear concatemers of DNA by rolling circle replication (Figure 8.17b) Starts with ss break = “nick” Not standard replication fork as used for host DNA Complementary strands synthesized at different times

28. Rolling Circle Replication

29. II. Viruses with DNA Genomes
8.10 An Overview of Animal Viruses
9.6 Uniquely Replicating DNA Animal Viruses
9.7 DNA Tumor Viruses

30. 8.10 An Overview of Animal Viruses
Often, entire virion enters the animal cell, unlike in prokaryotes
Nucleus is the site of replication for many animal viruses
Animal viruses contain all known modes of viral genome replication (Figure 8.21)
There are many more kinds of enveloped animal viruses than enveloped bacterial viruses

31. Figure 8.21 Diversity of animal viruses.

32. 8.10 An Overview of Animal Viruses
Consequences of virus infection in animal cells (Figure 8.22)
Lytic infections: the infected cell dies quickly (acute)
Persistent infections: release of virions from host cell does not result in cell lysis (chronic)
Infected cell remains alive and continues to produce virus
Latent infections: delay between infection by the virus and lytic events or disease symptoms
Cell Transformation: conversion of normal cell into tumor cell

33. 9.6 Uniquely Replicating DNA Animal Viruses
Double-stranded DNA animal viruses that have unusual replication strategies
Pox viruses
Adenoviruses

34. Pox viruses are ds DNA viruses that replicate in the cytoplasm
What do they need to do this?
Figure 9.11 Smallpox virus.

35. 9.6 Uniquely Replicating DNA Animal Viruses
Adenoviruses
Major group of icosahedral, linear, double-stranded DNA viruses, no envelope
Cause mild respiratory infections in humans
DNA replicates in the nucleus
Replication requires protein primers and avoids synthesis of a lagging strand (Figure 9.12)
Two unusual characteristics

36. Covalently linked protein TP
pTP is primer
Strand displacement replication
Viral proteins

37. 9.7 DNA Tumor Viruses
Some DNA viruses can induce cancer (“tumor viruses or “oncoviruses”
Human Papilloma Viruses (HPV)
Herpesviruses

38. 9.7 DNA Tumor Viruses
HPV
Nonenveloped icosahedral virion-no enzymes in the virion; replicates in host nucleus
Basal skin cells
8 kbp DNA is circular (Figure 9.13a)
Small genome, has overlapping genes

39. 9.7 DNA Tumor Viruses Some papilloma viruses cause cancer
In most infected host cells, virus infection results in the formation of new virions and the release from host cell
In a few infected host cells, part or all of the virus DNA becomes integrated into host DNA (analogous to a prophage), genetically altering cells in the process (Figure 9.13b)
Integrated virus DNA can interfere with normal cell division

40. Interfere with regulation
Infection
Papilloma virus DNA +
Host DNA
Accidental
Viral DNA integrates
into host DNA.
All or part
Viral DNA
Transcription of
tumor-inducing genes
Interfere with regulation
mRNA
Transport of mRNA to
cytoplasm and translation
Figure 9.13b Polyomaviruses and tumor induction.
tumor-induction
proteins
Transformation of
cell to tumor state
Cell transformation
Figure 9.13b

41. 9.7 DNA Tumor Viruses Genes involved in cancer are oncogenes
C-oncogenes are plain old cellular genes that somehow lead to transformation and cancer: tumor suppressor or tumor activator genes-sometimes called proto-oncogenes before they start trouble
V-oncogenes are viral versions of c-oncogenes

42. 9.7 DNA Tumor Viruses Herpesviruses
dsDNA, enveloped, nuclear replication
Invertebrates, fish, reptiles, birds, mammals
At least 8 types infect humans: HHV’s
HHV-3 = VZV, HHV-4 = EBV
Very widespread
Cause latent infections

43. 9.7 DNA Tumor Viruses Some Herpesviruses cause cancer
Diverse mechanisms lead to cancer
HHV-8 (Kaposi’s Sarcoma)
Epstein-Barr Virus HHV-4
EBV causes Burkitt’s Lymphoma by disrupting regulation of the c-myc oncogene

44. III. Viruses with RNA Genomes
9.8 Positive-Strand RNA Viruses
9.9 Negative-Strand RNA Animal Viruses
9.11 Viruses That Use Reverse Transcriptase

45. 9.8 Positive-Strand RNA Viruses
Poliovirus (Figure 9.16a and b)
Small virus
Viral RNA is translated directly, producing a single long, giant protein (polyprotein) that undergoes self-cleavage to generate ~20 smaller proteins necessary for nucleic acid replication and virus assembly (Figure 9.16c)

46. Figure 9.16a Poliovirus.
Figure 9.16a

47. Figure 9.16b Poliovirus.
Figure 9.16b

48. Figure 9.16c AAAA 5′ + 3′ Replicase-mediated 3′ – 5′ 5′ + AAAA 3′ VPg
Synthesis of the new plus strand
Replicase-mediated 3′ – 5′
Synthesis of the minus strand
Poliovirus genome 5′ +
AAAA 3′
VPg
Poly(A)
Translation
Polyprotein
Proteases
cleave the
polyprotein.
Figure 9.16c Poliovirus.
Structural coat
proteins
Proteases
RNA replicase
Figure 9.16c

49. Replication of positive-strand RNA viruses requires a negative-strand RNA intermediate from which new positive strands are synthesized
RNA replicase makes the viral RNAs

50. 9.9 Negative-Strand RNA Animal Viruses
Negative-strand RNA viruses
Negative-strand RNAs are complementary to the mRNA
They are copied into mRNA by an enzyme present in the virion
Only those that infect Eukarya are known

51. 9.9 Negative-Strand RNA Animal Viruses
Influenza A
Enveloped, pleomorphic virus (Figure 9.19)
Segmented genome-8 pieces ss - RNA
Surface proteins interact with host cell surface, elicit immune response

52. 9.9 Negative-Strand RNA Animal Viruses
Influenza
Nuclear replication
Genome segments transcribed and transcripts processed
Cap-stealing ensures preferential treatment for influenza mRNAs
Antigenic shift-new pandemic strains
Antigenic drift-seasonal strains

53. Reassortment
mechanism,
New combinations
of genes
Produces new
pandemic strains
2009 strain was a shift strain

54. 9.11 Viruses That Use Reverse Transcriptase
Retroviruses (RNA viruses) and hepadnaviruses (DNA viruses) use reverse transcriptase for replication
Key step in virus replication cycle
Reverse Transcriptase
Enzyme activity that converts ss RNA into ds DNA

55. 9.11 Viruses That Use Reverse Transcriptase
Hepadnaviruses
Virions small, irregular-shaped particles (Figure 9.23a)
Unusual genomes
partially double-stranded (Figure 9.23b)
Include hepatitis B virus HBV
Complex symptoms, may progress to chronic phase with liver cancer
Viral replication occurs through an RNA intermediate
Transmission through exposure to body fluids

56. 9.11 Viruses That Use Reverse Transcriptase
Retroviruses
Genome RNA reverse transcribed to dsDNA
Aka “cDNA” inserts into chromosome
Provirus
Gene expression and protein processing are complex (Figure 9.22)
Gag, pol, env gene regions common to all retroviruses
Retroviruses that cause cancer often have an extra gene region “src”

58. 9.11 Viruses That Use Reverse Transcriptase
Gag, pol, env regions common to all retroviruses
Retroviruses that cause cancer often have an extra gene region “src”
Rous sarcoma virus (chickens) has acquired a src gene
Host cell gene acquired by defective excision
“v-src” is the name given to the gene

64. IV. Subviral Agents
9.12 Viroids
9.13 Prions

65. 9.12 Viroids
Viroids: infectious RNA molecules that lack a protein coat
Smallest known pathogens (246–399 bp)
Cause a number of important plant diseases (Figure 9.24)
Small, circular, ssRNA molecules (Figure 9.25)
Do not encode proteins; completely dependent on host-encoded enzymes

66. Figure 9.24 Viroids and plant diseases.

67. 9.13 Prions
Prions: infectious proteins whose extracellular form contains no nucleic acid
Known to cause disease in animals (transmissible spongiform encephalopathies)
Host cell contains gene (PrnP) that encodes native form of prion protein that is found in healthy animals (Figure 9.27)
Prion misfolding results in neurological symptoms of disease (e.g., resistance to proteases, insolubility, and aggregation)

68. Figure 9.27 Figure 9.27 Prions. Neuronal cell Prnp Nucleus DNA
Transcription
Translation
Normal
function
Figure 9.27 Prions.
PrPc
(normal
prion)
PrPSc-induced
misfolding of PrPC
Abnormal
function
PrPSc
(misfolded prion)
Figure 9.27

69. Chronic Wasting Disease in deer and elk
Mad Cow Disease
Kuru, KJD in humans

70. 10.12 Preserving Genome Integrity: CRISPR Interference
CRISPR: Clustered Regulatory Interspaced Short Palindromic Repeats
Type of prokaryotic "immune system"
Region of bacterial chromosome containing DNA sequences similar to foreign DNA (spacers) alternating with identical repeated sequences (Figure 10.28)
CRISPR-associated proteins (Cas proteins)
Obtain and store segments of foreign DNA as spacers
Recognize and destroy foreign DNA

71. Figure 10.28 Figure 10.28 Operation of the CRISPR system.
Unique spacer
sequences
Bacterial chromosome
DNA
cas genes
Repeat
Repeat
Cas proteins
Transcription and translation
Transcription
CRISPR RNA
Cutting of RNA by Cas proteins
Foreign sequence is recognized by CRISPR RNA.
Figure Operation of the CRISPR system.
Viral
infection or
conjugation
Viral or plasmid DNA
Cas proteins cut and destroy foreign nucleic acid.
Figure 10.28