Chapter 19: Viruses and Prions

# The Discovery and Nature of Viruses

Conceptual Overview of Viruses: * A virus is an infectious particle consisting of nucleic acid (genes) packaged in a protein coat. * Structure: Most viruses are significantly smaller and simpler than eukaryotic or even prokaryotic cells. They lack metabolic machinery and structures found in living cells. * Biological Status: Viruses exist in a "shady area" between chemicals and life-forms. They are often described as leading "a kind of borrowed life" because they cannot reproduce or carry out metabolic activities outside a host cell.
Timeline of Scientific Discovery: * 1883 (Adolf Mayer): Studied tobacco mosaic disease (stunting growth and creating mottled/mosaic coloration in tobacco leaves). He demonstrated that the disease could be transmitted by rubbing sap from diseased leaves onto healthy plants. He hypothesized the cause was unusually small bacteria invisible under a microscope. * 1893 (Dmitri Ivanowsky): Passed diseased tobacco sap through a porcelain filter designed to remove bacteria. The filtered sap still caused the disease. Ivanowsky reasoned the bacteria were small enough to pass the filter or produced a toxin that passed through it. * Martinus Beijerinck: Conducted experiments showing the infectious agent in filtered sap could replicate. He observed that the pathogen only replicated within the host and could not be cultivated on nutrient media (petri dishes or test tubes). He is credited with voicing the concept of a virus. * 1935 (Wendell Stanley): Successfully crystallized the infectious particle, now known as tobacco mosaic virus (TMV). This was highly unusual as even simple cells cannot aggregate into regular crystals.

Structure of Viruses

General Dimensions: * The smallest viruses are approximately $20\,nm$ in diameter (smaller than a ribosome). * The largest known virus is $1,500\,nm$ ( $1.5\,\mu m$ ) in diameter, which is barely visible under a light microscope.
Viral Genomes: * Genomes can consist of: double-stranded DNA ( $dsDNA$ ), single-stranded DNA ( $ssDNA$ ), double-stranded RNA ( $dsRNA$ ), or single-stranded RNA ( $ssRNA$ ). * Organization: Usually a single linear or circular molecule, though some viruses have multiple molecules. * Gene Count: Smallest viruses have only $3$ genes; the largest have between several hundred and $2,000$ genes (comparing to bacterial genomes which have $200$ to a few thousand genes).
Capsids and Envelopes: * Capsid: The protein shell enclosing the genome, built from protein subunits called capsomeres. Shapes include: * Helical Viruses: Rod-shaped (e.g., TMV with over $1,000$ molecules of a single protein type in a helix). * Icosahedral Viruses: Polyhedral with $20$ triangular facets (e.g., Adenoviruses with $252$ identical protein molecules). * Viral Envelopes: Membranous layers surrounding capsids of influenza and many animal viruses. Derived from host cell membranes, they contain host phospholipids and proteins, plus viral-origin proteins and glycoproteins (proteins with covalently attached carbohydrates). * Viral Enzymes: Some viruses carry enzymes like viral polymerase within their capsids.
Bacteriophages (Phages): * Viruses that infect bacteria. E. coli phages T1 through T7 were the first studied. * T-even Phages (T2, T4, T6): Feature complex capsids with an elongated icosahedral head (enclosing DNA) and a protein tail piece with fibers for attachment.

Viral Replicative Cycles

General Replicative Process: 1. Binding: Virus identifies host cells by a "handshake" fit between viral surface proteins and specific host receptor molecules. 2. Entry: The genome enters the cell via injection (T-even phages), endocytosis, or fusion of the viral envelope with the plasma membrane. 3. Reprogramming: The virus uses host nucleotides, enzymes, ribosomes, tRNAs, amino acids, and ATP to replicate the viral genome and manufacture proteins. 4. Self-Assembly: Nucleic acids and capsomeres spontaneously assemble into new viruses. 5. Exit: Hundreds or thousands of viruses exit, often damaging or destroying the host cell.
Host Range: * The limited number of species a virus can infect. * Broad range: West Nile virus and equine encephalitis virus (mosquitoes, birds, horses, humans). * Narrow range: Measles virus (humans only). * Tissue Specificity: Human cold viruses (upper respiratory tract lining); HIV (specific immune cells).

Replicative Cycles of Phages

The Lytic Cycle: * Culminates in host cell death. The bacterium lyses (bursts) to release phages. * Virulent Phages: Phages that replicate only via the lytic cycle. * T4 Example: The entire cycle takes $20-30$ minutes at $37^\circ\text{C}$ . One early phage gene codes for an enzyme that degrades host DNA (the phage DNA is protected by a modified cytosine).
The Lysogenic Cycle: * Allows replication of the phage genome without destroying the host. * Temperate Phages: Capable of both lytic and lysogenic modes (e.g., Phage $\lambda$ ). * Prophage: The viral DNA when integrated into the bacterial chromosome. Viral proteins break both circular DNA molecules and join them. One prophage gene produces a protein to prevent transcription of other viral genes, keeping it silent. * Induction: An environmental signal (chemical or radiation) triggers the prophage to exit the chromosome and initiate a lytic cycle. * Phenotypic Alteration: Prophage genes can cause host bacteria to produce toxins (e.g., diphtheria, botulism, scarlet fever, and E. coli O157:H7).

Bacterial Defenses Against Phages

Natural Selection: Favors mutants with receptors no longer recognized by phages.
Restriction Enzymes: Cellular enzymes that identify and cut up foreign (phage) DNA. Host DNA is protected by methylation.
CRISPR-Cas System: * CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats. * Spacer DNA: Stretches between repeats that correspond to DNA from phages that previously infected the cell. * Cas (CRISPR-associated) Proteins: Nucleases that interact with CRISPR regions. * Mechanism: If re-infected, the CRISPR region is transcribed to RNA. RNA is cut into pieces and bound by Cas proteins (like Cas9). The RNA acts as a homing device for the Cas protein to identify and cut the invading phage DNA for degradation.

Replicative Cycles of Animal Viruses

Table 19.1: Classes of Animal Viruses: * Class I: $dsDNA$ (Adenovirus, Herpesvirus, Poxvirus). * Class II: $ssDNA$ (Parvovirus). * Class III: $dsRNA$ (Reovirus). * Class IV: $ssRNA$ ; serves as mRNA (Picornavirus, Coronavirus, Flavivirus, Togavirus). * Class V: $ssRNA$ ; serves as template for mRNA synthesis (Filovirus like Ebola, Orthomyxovirus like Influenza). * Class VI: $ssRNA$ ; serves as template for DNA synthesis (Retroviruses like HIV).
Enveloped Animal Viruses: * Use viral glycoproteins on the envelope to bind to receptors. * Envelopes are typically derived from the host plasma membrane during budding (exocytosis). * Herpesviruses: Cloaked in membrane derived from the nuclear envelope, then shed it and acquire a new envelope from the Golgi apparatus. They can remain latent as mini-chromosomes in nerve cell nuclei.
RNA as Genetic Material: * Class V viruses use virally encoded RNA polymerase to transcribe complementary RNA strands from the RNA genome to serve as mRNA.
Retroviruses (Class VI): * Use Reverse Transcriptase to transcribe RNA into DNA. * Example: HIV (Human Immunodeficiency Virus) causes AIDS (Acquired Immunodeficiency Syndrome). * Provirus: The integrated viral DNA in a retrovirus cycle. Unlike a prophage, it never leaves the host's genome.

Evolution of Viruses

Abundance: Seawater contains between $1 \times 10^0$ and $1 \times 10^2$ million viruses per milliliter.
Origin Hypotheses: Most biologists believe viruses originated from naked bits of cellular nucleic acids (mobile genetic elements) like plasmids (circular bacterial/yeast DNA) or transposons (DNA segments that move within a genome).
Giant Viruses: * Mimivirus: $dsDNA$ , $400\,nm$ diameter. Genome of $1.2\,Mb$ (million bases) and $1,000$ genes. Includes genes for translation and DNA repair. * Pandoravirus: $1\,\mu m$ diameter. Genome of $2-2.5\,Mb$ and $1,500-2,500$ genes. $90\%$ of genes are unrelated to cellular genes. * Pithovirus sibericum: $1.5\,\mu m$ diameter with $500$ genes. Discovered in Siberian permafrost; remained infectious after $30,000$ years.

Viral Diseases in Animals and Plants

Animal Symptoms: Result from lysosome rupture (releasing hydrolytic enzymes), viral toxins (envelope proteins), or the body's immune response (fever, aches).
Regeneration: Colds are recoverable because respiratory epithelium repairs itself; Poliovirus damage is permanent in non-dividing nerve cells.
Medical Tools: * Vaccines: Harmless derivatives of pathogens that stimulate immune defenses (e.g., Smallpox eradicated by WHO in $1980$ ). * Antiviral Drugs: Nucleoside mimics (e.g., Acyclovir for herpes, AZT for HIV). * Treatments: "Cocktails" (combination of nucleoside mimics and protease inhibitors). Maraviroc blocks the protein on human immune cells that HIV binds to.
Emerging Viruses: * Causes: Mutation of existing viruses (RNA viruses have high mutation rates due to lack of proofreading), spread from isolated populations, or spread from animals (natural reservoirs). * Ebola: Hemorrhagic fever. $2014$ epidemic killed over $11,000$ people. * Zika: Mosquito-borne; linked to microcephaly in infants. * Chikungunya: Expansion aided by mutation allowing it to infect Aedes albopictus mosquitoes.
Influenza A: * Standard naming: HA (hemagglutinin - $18$ types) and NA (neuraminidase - $11$ types). * H5N1 (Avian Flu): High mortality rate (over $50\%$ ). * H1N1 (2009 Pandemic): Unique reassortment of swine, avian, and human genes. * Reassortment: Influenza genomes consist of $9$ RNA segments, allowing "mix and match" during assembly in hosts like pigs.
Plant Viruses: * Causes over $\$30$ billion in annual crop loss. * Horizontal Transmission: Infection from external sources (insects, injury, tools). * Vertical Transmission: Inheritance from parent (asexual cuttings or infected seeds). * Spread: Viral proteins enlarge plasmodesmata to allow passage of viral macromolecules between cells.

Prions: Infectious Proteins

Characteristics: Proteins that cause degenerative brain diseases (Scrapie in sheep, Mad Cow disease/BSE, Creutzfeldt-Jakob, Kuru).
Alarming Traits: 1. Very slow acting (incubation periods of at least $10$ years). 2. Virtually indestructible (not deactivated by normal cooking temperatures).
Propagation Model (Stanley Prusiner): A misfolded protein contacts a normally folded version of the same protein and induces it to assume the abnormal shape. This chain reaction leads to prion aggregation and cellular malfunction.

Questions & Discussion

Tobacco Mosaic Disease Experiment (Figure 19.2): * Question: What if Beijerinck observed the infection getting weaker with each group until it stopped? * Answer: He might have concluded the agent was a toxin rather than a replicating particle.
Visual Skills (Concept 19.1): * Question: Describe one similarity and two differences between TMV and influenza virus. * Comparison: Both have RNA genomes. TMV is helical and non-enveloped, while influenza is enveloped and has a segmented genome with multiple RNA-protein complexes.
Concept Check 19.2: * Question 1: Compare effect on host cell of lytic vs. lysogenic phages. * Response: Lytic phages kill the host cell; lysogenic phages integrate into the genome and replicate with it without destruction. * Question 3: Compare viral vs. cellular RNA polymerase template/function. * Response: Viral RNA polymerase (Class V) uses RNA as a template to make mRNA; cellular RNA polymerase uses DNA as a template.
Concept Check 19.3: * Question 3: Why is TMV infection in commercial tobacco not a hazard for smokers? * Response: TMV (a plant virus) cannot infect animal cells because it doesn't recognize human cell receptors.