Virus

Microbial & Plant Diversity Overview

Practical Sessions

Schedule

  • Assignments:

    • P1/P2: Bacteria

    • P3/P4: Protozoa/Fungi

Endosymbiont Theory

Background

  • Proposed By: Lynne Margulis (1966)

  • Key Concept: Origin of eukaryotic cells via the endosymbiotic relationship between bacterial cells within Archaeal cells.

  • **Organelles Origin:

    • First = Mitochondria originate from alphaproteobacterial

      • Second = chloroplasts from cyanobacteria.

Diversity of Life

Classification of Organisms

  • **Major Groups: **

    • Eukarya (contain elements of both Archaea and Bacteria)

    • Archaea: Not yet cultured, believed to be the oldest living organisms (~3 billion years old).

    • Bacteria

Phylogenetics

  • The evolutionary relationships as depicted in phylogenetic trees can change with new species studies and genome sequencing.

Phylogenomics

  • A modern approach comparing entire genomes, with a bacterial genome costing approximately £50.

Lokiarchaeota

Discoveries

  • The Lokiarchaeota are considered to be important because they provide the best evidence to date for the evolutionary link between simple single-celled organisms, prokaryotes, and organisms with complex cells, eukaryotes like multi-cellular animals and plants.

  • First Identified: 2015 in the Arctic Ocean (Nth Atlantic).

  • Key Features: Presence of cytoskeleton and unique proteins for degradation, suggesting eukaryotic characteristics.

    • Bridges the gap between Prokaryote and Eukaryotes

Asgard Archaea

Contributions to Eukaryotic Evolution

  • Possessed many properties of a Eukaryote

    • Asgard archaea have been found to encode a diverse range of eukaryotic signature proteins, including proteins involved in eukaryotic membrane trafficking machinery, eukaryotic-like structural and cytoskeleton proteins, proteins involved the ubiquitination modification system, and eukaryotic-like ribosomal proteins

  • Study by Williams et al. (2019): Investigated possible traits of the first Eukaryote Common Ancestor (FECA).

  • First Eukaryotic common ancestor

  • Model: Entangle–Engulf–Endogenize (E3).

Great Oxygenation Events Timeline

Key Historical Milestones

  • 14 BYA: Big Bang

  • 4.5 BYA: Formation of the Sun and Earth

  • 3.8 BYA: Origin of Life

  • First GOE: Development of oxygenic photosynthesis (Cyanobacteria).

  • Second GOE: Evolution of chloroplasts and colonization of land.

  • Significance of Eukaryotes: Features like mitochondria and sexual reproduction arose during elevated oxygen levels (2.1 - 1.6 BYA).

Horizontal Gene Transfer (HGT) in Bacteria

Mechanisms

  • Plasmid Transfer: Genes can be shared between bacteria via plasmids, including resistant genes.

  • Methods of Transfer:

    • Conjugation: direct transfer between bacteria.

    • Transformation: uptake of free DNA.

    • Transduction: viral delivery of genes.

Inter-Kingdom Horizontal Gene Transfer

Example: Agrobacterium tumefaciens

  • Mechanism: Transfers T-DNA into plant cells, causing crown galls.

  • Impact: Understanding gene transmission from bacteria to plants.

  • occurring between domain bacteria and domain plantae

Transposable Genetic Elements

Characteristics

  • Comprise 40% of the human genome is derived from retrotransposon DNA

    • DNA that is created by retrotransposons, which are genetic elements that move and replicate in a host genome.

    • Take RNA and makes DNA (reverse transcription)

  • Two Primary Types:

    • Transposons: Mobile genetic elements that replicate after excision.

    • Retrotransposons: Related to retroviruses; utilize reverse transcriptase for replication.

Viruses: Structure and Characteristics

Overview

  • Types: Classified by genome type (e.g., dsRNA, ssRNA).

  • Require elements of host metabolism for replication

  • Not classified as living due to lack of independent metabolism.

Diversity of Viruses

  • Examples included: HIV, Influenza, Ebola, Measles.

  • Morphological Characteristics: Large marine viruses like Mimivirus have substantial genomes.

Smallpox and Historical Impacts

On Human Populations

  • Smallpox was devastating, particularly among Amerindians, causing over 90% mortality in some cases.

  • Historical use in biological warfare (e.g., General Amherst's infected blankets).

Vaccination Development

  • Early variolation methods (Lady Montagu, 1715) and Edward Jenner’s vaccination with cowpox (1796).

Current Public Health Issues

Yellow Fever

  • A mosquito-borne virus historically significant in the Americas.

HIV Research

  • Identified in 1983; ongoing research emphasizes the importance of antiretroviral therapy for HIV management.

Small pox

  • It was caused by the variola virus and spread through coughing and sneezing. 

  • Eradicated in 1979 via vaccine

Genetic composition of viruses

Basic components of a virus

  • Structural protein = virus particle/capsule

  • Non- structural protein = enzymes needs for replication

  • Capsid proteins = shell enclosing nucleic acid

  • Nucleocapsid = Capsid + Nucleic acid

    • may be enclosed in an envelope containing host cell material and virus origin

  • Virion = Complete infective virus particle

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. 

Naked vs.  Enveloped 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.

Role of Bacteriophages in Ecosystems

Influence on Bacterial Populations

  • Bacteriophages control bacterial numbers in aquatic systems, influencing microbial loops and nutrient recycling.

    • 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. 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.

CRISPR-Cas9 in Bacterial Defense

Mechanism

  • Host samples viral genomes and stores them in CRISPR arrays, which bind to and destroy invading phage DNA with the help of Cas9 protein.

Prions

Nature and Diseases

  • Proteinaceous infectious particles leading to diseases like Scrapie and BSE in cows, and Creutzfeldt-Jakob Disease in humans.

Conclusion

  • Understanding microbial and plant diversity, along with the functioning and evolution of viruses and other pathogens, is essential for both scientific research and public health.