🦠Virology Unit 5 – Bacteriophages and Bacterial Viruses

What Are Bacteriophages?

• Bacteriophages, or phages, are viruses that specifically infect and replicate within bacterial cells
• Phages are the most abundant biological entities on Earth, with an estimated 10^31 particles globally
• Consist of genetic material (DNA or RNA) encapsulated within a protein capsid
• Phages are obligate intracellular parasites, requiring bacterial hosts for replication and survival
• Exhibit high host specificity, typically infecting only specific bacterial strains or species
• Play crucial roles in shaping bacterial populations and evolution through selective pressure and horizontal gene transfer
• Serve as important tools in molecular biology, biotechnology, and phage therapy applications

Phage Structure and Classification

• Phages are classified based on their morphology, genetic material, and host range
• Tailed phages (Caudovirales) are the most common, with an icosahedral head, tail, and tail fibers
  • Divided into three families: Myoviridae (long contractile tails), Siphoviridae (long non-contractile tails), and Podoviridae (short tails)
• Polyhedral, filamentous, and pleomorphic phages lack tails and have diverse capsid structures
• Genetic material can be double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), double-stranded RNA (dsRNA), or single-stranded RNA (ssRNA)
• Phage genomes range in size from a few kilobases to over 500 kilobases
• Capsids protect the genetic material and facilitate attachment to bacterial host cells
• Tail fibers and other surface proteins mediate host recognition and specificity

Lytic vs Lysogenic Cycles

• Phages can undergo two distinct life cycles: lytic and lysogenic
• In the lytic cycle, phages immediately replicate and lyse the host cell, releasing new phage particles
  1. Adsorption: Phage attaches to specific receptors on the bacterial cell surface
  2. Injection: Phage injects its genetic material into the host cell
  3. Replication: Phage hijacks host machinery to replicate its genome and synthesize new phage components
  4. Assembly: New phage particles are assembled within the host cell
  5. Lysis: Phage-encoded enzymes (holins and lysins) disrupt the cell membrane and wall, releasing new phages
• Lysogenic cycle involves the integration of the phage genome into the host chromosome as a prophage
  • Prophage replicates along with the host genome, allowing vertical transmission to daughter cells
  • Prophage can remain dormant until induced by environmental stressors (UV radiation, chemicals) to enter the lytic cycle
• Temperate phages can undergo both lytic and lysogenic cycles, while virulent phages only undergo the lytic cycle

Phage Replication Process

• Phage replication involves a series of coordinated events to produce new phage particles
• Adsorption is mediated by specific interactions between phage tail fibers or capsid proteins and bacterial surface receptors (lipopolysaccharides, teichoic acids, outer membrane proteins)
• Injection of phage genetic material occurs through the tail or specialized structures (e.g., T4 phage contractile tail sheath)
• Phage early genes are expressed to redirect host metabolism and initiate replication
  • Phage-encoded proteins inhibit host DNA replication and transcription
  • Nucleases degrade host DNA to provide nucleotides for phage genome synthesis
• Phage DNA replication occurs using host machinery and phage-encoded proteins (DNA polymerases, helicases, primases)
  • Rolling circle replication is common for ssDNA phages
  • Theta replication and recombination-dependent replication for dsDNA phages
• Late genes are expressed to produce structural proteins for phage assembly
• Phage particles are assembled in a highly organized process, with the capsid, tail, and fibers forming separately before joining
• Lysis is triggered by phage-encoded holins (form pores in the cell membrane) and lysins (degrade peptidoglycan)

Genetic Diversity and Evolution

• Phages exhibit immense genetic diversity, with a wide range of genome sizes, compositions, and organizations
• Rapid replication rates and large population sizes contribute to high mutation rates and genetic variability
• Phages evolve through various mechanisms, including point mutations, recombination, and horizontal gene transfer
  • Recombination occurs between related phages during co-infection of the same host cell
  • Transduction allows the transfer of bacterial genes between cells via phage particles
• Phage-host coevolution drives the development of new phage strategies to overcome bacterial defenses (restriction-modification systems, CRISPR-Cas)
• Phages can acquire new genes from their hosts (morons) that provide selective advantages (antibiotic resistance, virulence factors)
• Metagenomic studies have revealed the vast diversity of phages in various environments (oceans, soil, human gut)
• Phage diversity plays a crucial role in shaping bacterial communities and maintaining ecological balance

Applications in Biotechnology and Medicine

• Phages have been used as tools in molecular biology and biotechnology for decades
• Phage display is a powerful technique for identifying peptides or proteins with specific binding affinities
  • Peptides or proteins are fused to phage coat proteins and displayed on the phage surface
  • Libraries of phage-displayed peptides/proteins are screened against targets to identify high-affinity binders
• Phage therapy involves the use of phages to treat bacterial infections, particularly those caused by antibiotic-resistant strains
  • Phages can be used alone or in combination with antibiotics to target specific bacterial pathogens
  • Advantages include specificity, self-amplification, and the ability to evolve alongside their bacterial hosts
• Phages can be engineered as delivery vehicles for gene therapy or as biosensors for pathogen detection
• Phage-derived enzymes (lysins) have potential as novel antimicrobial agents
  • Lysins can be applied exogenously to rapidly lyse bacterial cells
  • Engineered lysins with expanded host ranges and increased stability are being developed

Environmental Impact and Ecology

• Phages play critical roles in shaping microbial communities and biogeochemical cycles
• Phages are major drivers of bacterial mortality, influencing population dynamics and diversity
  • Kill the winner hypothesis suggests that phages target the most abundant bacterial strains, preventing their dominance
  • Phage-mediated lysis releases nutrients and organic matter, stimulating microbial growth and nutrient cycling
• Phages contribute to horizontal gene transfer in natural environments, facilitating the spread of genes (antibiotic resistance, metabolic functions)
• Phage-encoded toxins and virulence factors can alter bacterial pathogenicity and impact host health
• Phages can influence the structure and function of microbial communities in various ecosystems (marine, soil, human microbiome)
  • Phage predation can alter community composition and metabolic activities
  • Phages may provide a protective effect to their bacterial hosts in certain environments (biofilms, soil)
• Understanding phage ecology is crucial for predicting and manipulating microbial communities for biotechnological and environmental applications

Key Experiments and Discoveries

• 1915: Frederick Twort discovers bacteriophages as agents that lyse bacterial cultures
• 1917: Félix d'Herelle independently isolates phages and coins the term "bacteriophage"
• 1952: Alfred Hershey and Martha Chase demonstrate that phage DNA, not protein, is injected into the host cell (Hershey-Chase experiment)
• 1961: François Jacob and Jacques Monod propose the operon model of gene regulation based on studies of the lambda phage
• 1977: Frederick Sanger and colleagues sequence the first complete genome of a bacteriophage (ΦX174)
• 1985: George Smith develops phage display, revolutionizing the field of antibody engineering and drug discovery
• 2002: Rohwer and Edwards estimate the global phage population to be 10^31 particles, highlighting their abundance and ecological significance
• 2005: Merril and colleagues demonstrate the efficacy of phage therapy in treating antibiotic-resistant infections in mice
• 2010s: Advances in metagenomics and high-throughput sequencing reveal the vast diversity of phages in various environments (human gut, oceans, soil)
• Ongoing research continues to explore the potential applications of phages in medicine, biotechnology, and environmental management