2: Viruses

Microbial & Plant Diversity - Lecture 2: Viruses

Practicals 2025

• Four practical sessions starting February 3rd/4th.
• P1/P2: Bacteria.
• P3/P4: Protozoa/FLO’s/Fungi.
• Students must adhere to assigned pairs and practical split groups.
• Contact the instructor if absence is unavoidable.

Endosymbiont Theory

• Proposed by Lynne Margulis (1966).
• Explains the origin of Eukaryotes:
  • Endosymbiosis of bacterial cell within an Archaeal cell.
  • Mitochondria originated from alphaproteobacteria.
  • Chloroplasts originated from cyanobacteria.

Eukarya, Archaea, and Bacteria

• Archaea/Bacteria are the oldest living organisms (approximately 3 billion years old).
• Most Archaea are obligate anaerobes from inaccessible habitats such as deep sea environments.
• Phylogenomics: Comparison of whole genomes (costing around £50 for a bacterial genome).
• Eukaryotic genomes contain elements from both Archaea and Bacteria.

Lokiarchaeota

• Discovered in 2015 in the Arctic Ocean.
• Metagenomes show eukaryote features (DNA only, not cultured).
• Exhibit:
  • Cytoskeleton.
  • Protein degradation.
  • ER proteins

Asgard Archaea

• Williams et al., 2019.
• FECA (First Eukaryote Common Ancestor?).
• 10-year quest to culture.
• Nature, Dec 2019, Dec 2022.
• Includes:
  • Lokiarchaeum.
  • Heimdallarchaeota LC2.
  • Heimdallarchaeota LC3.
• E3 model: Entangle–Engulf–Endogenize.
• Lokiactin cytoskeleton (Hiroyuki Imachi).

Timeline: Great Oxygenation Events

• Big Bang: 14 {BYA}
• Sun/Earth formed: 4.5 {BYA}
• Origin of Life: 3.8 {BYA} - (4.2 {BYA}?)
• 1st GOE: Evolution of oxygenic photosynthesis (Cyanobacteria).
• 2nd GOE: Evolution of chloroplasts in marine Eukaryotes.
• Colonisation of Land.
• 'Boring' billion.
• Eukaryote evolution – mitochondria/meiosis are core features.
• LECA (Last Euk CA) was aerobic and reproduced sexually (driven by elevated oxygen levels), 2.1 - 1.6 {BYA}.

Horizontal Gene Transfer (HGT) in Bacteria

• Transformation: Transfer of free DNA.
• Conjugation: Plasmid transfer.
• Transduction: Transfer by viral delivery.

Agrobacterium tumefaciens

• Inter-Kingdom HGT.
• Crown galls in plants.
• Transfers Ti plasmid into host nucleus.
• Involves:
  • Ti-plasmid.
  • T-DNA.
  • Virulence proteins.

Transposable Genetic Elements

• 40% of the human genome (50-80% in maize) is derived from retrotransposon DNA.
• Transposons: Mobile genetic elements that replicate after excision from the genome.
• Retrotransposons: Closely related to retroviruses and copied via RNA to DNA using reverse transcriptase.
• LTR: Long terminal repeats encoding genes for transposition.

Virus Examples

• HIV (Lentivirus): ss(+)RNA.
• Influenza (Orthomyxovirus): ss(-)RNA.
• Lambda (Siphoviridae): dsDNA.
• Ebola (Filoviridae): ss(-)RNA.
• Mimivirus: >1Mbp dsDNA genome (bigger than many bacteria).

Viruses

• Require elements of host metabolism for replication.
• Lack independent metabolism.
• Are they alive?

Virus examples and eradication

• Smallpox: Eradicated in 1979.
• Rinderpest: Eradicated in 2011.
• Yellow Fever.
• Tomato Spotted Wilt Virus.
• Plaques on lawn of E. coli cells.

Molecular Clock

• Measles is caused by MeV (-ve strand ssRNA virus, Paramyxoviridae).
• Measles Rinderpest.
• Jumped to humans as global human population and local population density increased (R_0 = 12-18!).
• Molecular clock: 2600 years ago Peste des Petits Ruminants Virus.
• Critical Community Size.

Causes of Death

• Shift from infectious diseases to cancer and heart disease from 1911-2013 in England and Wales.

London General Bill of Christenings and Burials (1763-1764)

• Statistics on deaths from various diseases and casualties.

Smallpox and the Columbian Exchange

• Smallpox (Variola): Airborne dsDNA virus with 30% mortality in most human populations.
• Mortality was >90% in Amerindians (55/60 million died).
• 8 million Hispaniola Amerindians died by 1550.
• Downfall of Inca/Aztec Empires.
• Biological Warfare (General Amherst, 1763) - infected blankets.

Smallpox Outbreaks and Eradication

• Variolation, Turkey (Lady Montagu, 1715) - Insertion of scab into cut on the back
• Edward Jenner (1796) and cowpox vaccination
• 1st virus to be eradicated (1979).

Yellow Fever

• Named by Griffith Hughes, Tywyn Nat. Hist. Barbados (1750).
• Mosquito-borne (Aedes spp. from Africa).
• 200K cases/year, 15% mortality (now mostly in Africa).
• Spread by slave trade, Europeans very susceptible (Philadelphia 1793 outbreak: 5000 dead, 10% of population).
• Max Theiler developed vaccine (1937).
• Dengue fever and Zika fever both from Africa and closely related to YFV.
• Dengvaxia vaccine (2015) but no vaccine yet for Zika.

HIV

• Identified in 1983 but still no vaccine.
• Effective therapy via antiretroviral drugs (reduce transmission and halt progression to AIDS).

Virus Classification

• I – double-stranded DNA: Smallpox, vaccinia, Herpes simplex
• II – single-stranded DNA: Parvovirus
• III – double-stranded RNA: Human rotaviruses, Colorado tick fever
• IV – single-stranded RNA (+): Yellow fever, Hepatitis A/C, Rubella, SARS-CoV2
• V – single-stranded RNA (-): Measles, mumps, rabies, Ebola, Influenza
• VI – single-stranded RNA (DNA interm.): HIV, HTLV (retrovirus)
• VII – double-stranded DNA (RNA interm.): Hepatitis B
• Genetic composition of viruses RNA (+) = coding strand

Virus Expression and Replication

• Expression and Replication of virus genes inside host cell
• By convention, the mRNA is always considered to be of the plus (+) complementarity.
• ssRNA viruses mutate more rapidly (eg. Flu virus evolution).

Virus Structure

• STRUCTURAL PROTEINS: Make up the virus particle.
• NON-STRUCTURAL PROTEINS (NS PROTEINS): Enzymes needed for replication (not incorporated in the VIRION).
• CAPSID: Protein shell enclosing nucleic acid (made up of numerous CAPSOMERS).
• NUCLEOCAPSID: Capsid plus the enclosed NUCLEIC ACID.
• ENVELOPE: May enclose the nucleocapsid, containing material of host cell as well as viral origin.
• VIRION: The complete infective virus particle.
• The outer shell of a virus particle protects nucleic acid from physical, chemical, or enzymatic damage outside the host cell (e.g. UV etc).

Helical Capsids

• Simplest way to arrange multiple, identical protein subunits (rotational symmetry) - arranged around the circumference (spiral staircase).
• Multiple disks stacked on top of one another to form a cylinder.
• Virus genome is coated by the protein shell or contained in hollow cylinder.
• Example: Tobacco mosaic virus (TMV).

Naked vs. Enveloped Virus

• Naked virus: Has capsid and nucleic acid, composed of capsomers
• Enveloped virus: Has envelope, nucleocapsid, capsid, and nucleic acid

Virus Penetration and Uncoating in Animal Cells

• Penetration of an Enveloped Virus by Fusion of Its Envelope with the Host Cell Membrane: Viral envelope fuses with host cell membrane and nucleocapsid enters the host cell.
• Penetration of an Enveloped Virus by Endocytosis: The host cell membrane invaginates forming an endocytic vesicle and the entire virus is placed in an endocytic vesicle.

Virus Penetration in Bacteria

• Example: T4 phage in E. coli.

Bacteriophage Replication Cycle

• Typical bacteriophage replication cycle (eg. Phage lambda in E. coli):
  1. ATTACHMENT
  2. PENETRATION AND UNCOATING
  3. EXPRESSION AND REPLICATION
  4. ASSEMBLY
  5. MATURATION
  6. RELEASE

Lysis vs Lysogeny in Bacteriophages

• Lytic (or virulent) phages can only multiply on bacteria and kill the cell by lysis at the end of the life cycle.
• Lysogenic (or temperate) phages can either multiply via the lytic cycle or enter a dormant state in the cell.
• Prophage: In this dormant state most phage genes are in a repressed state (not transcribed) - called a prophage because it is not a phage but it has the potential to produce phage.

Bacteriophages Control Bacterial Numbers

• In marine and freshwater habitats, per litre of water:
  • 1,000,000,000 bacteria
  • 10,000,000,000 bacteriophages
• Bacteriophages (viruses which attack bacteria) are abundant in nature
• Viruses control bacterial numbers in aquatic systems

CRISPR-Cas9

• Bacterial defence against phages
• Clustered Regularly Interspaced Short Palindromic Repeats
• Acr: Anti-CRISPR gene
• Phage/plasmid genomes ’sampled’ by host, stored in CRISPR array and expressed as crRNA.
• crRNA bind to later invading phages/plasmids and Cas9 protein destroys invading DNA
• Nobel Prize Chem2020: Charpentier/Doudna
• Acr Phage defence

Prions

• Prions – a proteinaceous infectious particle
• Believed to be responsible for diseases such as:
  • Scrapie: sheep and
  • BSE (bovine spongiform encephalopathy): cows
• Humans are also susceptible to several prion diseases:
  • CJD: Creutzfeld- Jacob Disease
  • FFI: Fatal familial Insomnia

Viral Exit Strategies

• 'Naked' virus particles (capsid proteins exposed to the external environment), are produced from infected cells at the end of the replicative cycle when the cell dies, breaks down & lyses, releasing the virions.
• Many viruses have devised strategies to exit from the infected cell without its total destruction (avoids host cell bursting).
• This is achieved by extrusion (budding) of the particle through the membrane, during which process the particle becomes coated in a lipid envelope derived from the host cell membrane & with a similar composition.

2019 Novel Coronavirus, Wuhan, China

• CDC is closely monitoring an outbreak of respiratory illness caused by a novel (new) coronavirus (named "2019-nCoV") that was first detected in Wuhan City, Hubei Province, China and which continues to expand.
• Coronaviruses are a large family of viruses that are common in many different species of animals, including camels, cattle, cats, and bats.

The Microbial Loop in Marine Ecosystems

• Viruses control bacterial numbers in aquatic systems.
• Includes: flagellates, ciliates, bacteria, phytoplankton, zooplankton, fish, and viruses.
• Nutrients Dissolved organic matter

Endosymbiont theory for the origin of Eukaryotes

• Lynne Margulis
• Eukaryotes are more closely related to Archaea than Bacteria.
• BUT the organelles of Eukaryotes originated by endosymbiosis of Bacteria
  • Non-phototrophic - mitochondria
  • Phototrophic - chloroplasts (+mitochondria)