Unit 9. Viruses

What is a virus?

• Infectious, obligate intracellular parasite comprising genetic material (either DNA or RNA) surrounded by a protein coat, and sometimes a membrane

• non-living entities that must hijack a host cell’s machinery to replicate and reproduce

When did the study of plant viruses begin?

Late 19th century with investigations into Tobacco Mosaic Disease

Dimitrii Ivanowski (Early 1890s)

Showed that the causal agent of tobacco mosaic disease could pass through a fine-pored Chamberland filter, which retained bacteria. Despite this, he still concluded that bacteria were the causal agents.

Martinus Beijerinck (Late 1890s)

Confirmed that the agent was filterable and could diffuse through agar, still retaining infectivity after drying. He correctly concluded that the agent was not a known living organism. He coined the term contagium vivum fluidum (contagious living fluid), which eventually led to the modern term virus

Why is the study of plant viruses important?

They cause significant economic damage to crops worldwide, and their study has historically been foundational to the entire field of virology

General Symptoms and Structure

• Mosaic or Mottle: Irregular patterns of light (chlorotic) and dark green tissue on leaves.

• Stunting: Reduced overall plant growth and size.

• Ringspot: Localized death of tissue.

• Other less common symptoms: Wilt, abnormal growth, systemic necrosis, and blight.

What does the virus particle (virion) consist of?

a core of nucleic acid (genome) surrounded by a protective layer of coat protein (CP)

What two shapes do plant viruses most commonly exhibit?

• Helical: Rod-shaped or filamentous (e.g., Tobacco Mosaic Virus).

• Icosahedral (Isometric): Spherical or polyhedral.

Segmented (multipartite) genomes

Genetic material is divided across more than one piece of RNA or DNA.

Unlike segmented animal viruses (such as influenza), which typically package all segments together inside a single particle, plant viruses with multipartite genomes commonly package each segment into its own separate virion.

This arrangement may make the genome as a whole more resilient to damage to any one particle, but it also means a cell must be infected by enough different particles to assemble a complete set of segments before replication can proceed, so an infection can fail if a segment is missing.

What is the Tobacco Mosaic Virus (TMV)

Belongs to the family Virgaviridae, is one of the most studied viruses in history. Its primary host is Tobacco (Nicotiana tabacum), a plant native to the Americas that became a major cash crop for colonial powers, but now widely recognized as a major risk factor for human disease

TMV is a classic example of a rod-shaped virus with a single-stranded, positive-sense RNA (+ssRNA) genome. This positive-sense genome can be immediately translated by the houst cell’s ribosomes upon infection

What is the TMV life cycle?

1. Entry and Uncoating: The virus is released into the cytoplasm of the host cell and the coat protein is shed (enters host cell through wound or a vector)

2. Replication and Genome Expression: The +ssRNA genome acts as mRNA and is translated into an RNA-dependent RNA polymerase (replicase). This replicase then creates negative-sense RNA (-ssRNA) strands, which serve as a template for new +ssRNA genomes and subgenomic RNAs

3. Synthesis of Viral Proteins: The subgenomic RNAs are translated to produce proteins, notably the Movement Protein (MP) and the Coat Protein (CP)

4. Movement and Assembly: The MP facilitates the cell-to-cell spread of the virus by modifying the plant's plasmodesmata (channels between adjacent cells). Once a critical concentration of genome and CP is reached, new virions are assembled.

5. Systemic Spread: The virus moves from the initially infected cell, through adjacent cells (local lesion), into the vascular tissue (phloem), allowing it to spread systemically throughout the entire plant.

What’s a key defense response that plants use against viruses?

Hypersensitive Response (HR) - involves the rapid, localized death of a small group of cells around the initial infection site to restrict the virus

What is the most effective long-term defense?

RNA-induced gene silencing pathway —> often called RNA interference (RNAi)

The viRNA Pathway (RNAi)

1. Recognition: During viral replication, double-stranded RNA (dsRNA) is produced.

2. Processing: This dsRNA is recognized by a host enzyme called Dicer (or Dicer-like 2 in the diagram) and is cut into short, double-stranded fragments known as viral small interfering RNAs (viRNAs).

3. Complex Loading: These viRNAs are loaded into the RNA-induced silencing complex (RISC), which contains the enzyme Argonaute (Ago-2 in the diagram). One strand of the viRNA is degraded, leaving a single-stranded guide.

4. Cleavage: The active Argonaute-containing complex then uses the viRNA guide to locate and cleave (degrade) any viral RNA with a complementary sequence, effectively blocking viral gene expression and replication

Management Strategies - Cultural Practices

Sanitation (removing and destroying infected plants), weed control (to eliminate alternate hosts), and vector control.

Management Strategies - Cross-Protection (Inoculation)

A mild strain of a virus is intentionally introduced to a host plant. This mild infection can induce host defenses that protect the plant from subsequent, more severe strains of the same virus. This strategy is currently in commercial use for certain viruses.

Management Strategies - Biotechnology

Transgenic plants can be engineered to express viral components, such as the TMV Coat Protein (CP). The free CP in the cell can inhibit the disassembly process of the invading virus, providing protection

Management Strategies - RNAi Technology

Modern genetic engineering can introduce DNA that stably expresses dsRNA corresponding to pest genes (e.g., insect or nematode genes). When the pest ingests this dsRNA while feeding on the plant, it triggers the RNAi pathway in the pest, silencing essential genes and causing resistance in the plant. This demonstrates the broad applicability of the RNAi mechanism beyond just viral defense

Baltimore Classification

• Why is mRNA placed at the center of Baltimore scheme?

• Why are there viruses with both RNA and DNA genomes?

• Which came first?

• Does viral genome size matter?

• What limits the size of viral genomes?

• What information is encoded in a viral genome?

• What information is not encoded in a viral genome?

Plant Virus Transmission

• Generally, viruses must enter plant through healable wounds - they do not enter through natural openings (no receptors)

• Insect vectors are important means of natural spread

• Type of transmission or vector relationship determines epidemiology

• Seed transmission is relatively common, but specific for virus and plant

Vector Transmission

Many organisms can act as vectors and spread plant viruses such as:

• Bacteria

• Fungi

• Nematodes

• Parasitic plants

• Insects

Tobamovirus Multiplication (Replication Cycle)

1. Virus enters injured cells.

2. Ribosomes strip off coat and begin to translate the RdRp.

3. RdRp binds to the tRNA-like 3′ end & initiates synthesis of minus strands to form RI RNA.

4. Plus-strand genomic RNAs & the movement protein (MP) & coat protein (CP) sgRNAs are synthesized from the minus strand RNA.

5. MP & CP are translated.

6. MP forms complexes with newly synthesized viral RNA & membranes. The complex moves through plasmodesmata to adjacent cells.

7. CP & genomic RNAs accumulate to very high levels and virus crystals accumulate in the cytoplasm. Double-strand replicative form (RF) RNA accumulates in the cell and elicits host gene silencing responses.

8. Replication is very highly regulated but many details are not yet known