Bacteriophage Biology: Structure, Life Cycles, and Replication

Posted on Apr 7, 2025 in Biology

Phage Structure and Components

Most bacteriophages (phages) possess a distinct structure. Tailed phages, comprising about 95% of known phages, have double-stranded DNA (dsDNA) enclosed within a protein capsid shell. The majority feature a tail, which can be:

  • Long and flexible
  • Long and contractile
  • Short

An adsorption apparatus, including tail fibers and tail spikes, facilitates attachment to host cells.

Measuring Phage Infections: The One-Step Growth Curve

Viral infections, including those by phages, can be quantified using a one-step growth curve. This method demonstrates the timeline of infection within a host cell population, culminating in cell burst (lysis).

Key Growth Curve Periods

Eclipse Period
The period after the injection of phage DNA during which new phages are being assembled inside the host cell, but complete infectious particles are not yet detectable.
Latent Period
Includes the eclipse period plus the subsequent period of intracellular accumulation of assembled viruses and lytic proteins. This phase immediately precedes cell lysis.
Burst Size
The average number of phages released per lysed bacterium. This number varies in accordance with the specific virus and host conditions.

Bacteriophage Life Cycle Stages

Phage life cycles generally follow one of three main patterns (lytic, lysogenic, or pseudolysogenic), although all begin with the same initial steps:

Initial Steps: Adsorption and Injection

Adsorption

This process starts with a reversible phase as the virus initially associates with the cell surface. It transitions to an irreversible phase as the phage ‘walks’ across the surface to find an ideal adsorption site. Tail fibers and spikes bind specifically to receptors on the host cell surface. Proteins within the phage capsid may also aid in recognition.

Injection/Ejection

The mechanism of DNA delivery is dependent on the phage’s tail structure:

  1. Long & Contractile Tail: Once attached, the tail sheath contracts, forcefully injecting or ejecting the DNA into the host cell.
  2. Long Flexible Tail: The tail effectively ‘screws’ through the host cell envelope to eject the DNA.
  3. Short Tail: DNA ejection occurs via a needle-like action.

These injection systems may be assisted by enzymes released by the phage that locally degrade the host cell wall and/or membranes.

Following these initial steps, the phage life cycle diverges into one of three pathways: lytic, lysogenic, or pseudolysogenic.

The Lytic Cycle: Replication and Lysis

The lytic cycle is typically followed by virulent phages, especially when there is a greater concentration of host cells in the environment. The process involves several stages:

  1. Hijacking Host Machinery: First, the host cell machinery is hijacked to synthesize viral proteins for assembly, as well as lytic proteins.
  2. Phage Assembly: The virus is then assembled piece by piece.
  3. DNA Packaging: To get the DNA into the capsid, it is fed through a portal protein in the capsid shell using an ATP-driven enzyme complex called terminase. This is done in a sort of screwing motion to pack the DNA tightly inside the capsid. Once it is full, the terminase cuts the DNA strand and moves on to the next capsid.
  4. Lysis: While the phages are being assembled, lytic proteins – holins, endolysins, and spannins – accumulate in the host cell cytosol.
    • Holins form pores in the inner (cytoplasmic) membrane.
    • Endolysins then move through these pores into the periplasmic space and break down sugars in the peptidoglycan (PG) layer of the cell wall.
    • Spannins, which span both membranes, can fold in half once the PG layer is broken down. This action pulls the outer membrane inward to fuse it with the inner membrane, effectively ripping a hole in the cell envelope, leading to lysis and the release of new phages.

The Lysogenic Cycle: Integration and Survival

In the lysogenic cycle, employed by temperate phages, rather than immediately assembling and releasing new phages, the phage DNA is incorporated into the host cell’s chromosome as a prophage. It is then replicated alongside the host DNA as the cell itself replicates and divides. Temperate phages often move into the lysogenic cycle to survive harsher conditions experienced by the host cell that could potentially lower the concentration of available hosts. There is no point killing host cells to release phages if the phage population risks running out of hosts. This highlights a potential mechanism for recognizing the relative concentrations of phages and host cells, possibly triggering the lysogenic cycle when phage concentration is high compared to host cells.

Pseudolysogeny and Transduction

Pseudolysogeny is a less understood state. In this condition, viral DNA is not replicated alongside host cell DNA but is conserved separately within the host cell, with no significant viral genome degradation or replication. It appears to be triggered by unfavorable growth conditions for the host cells and typically ends with a transition to either true lysogeny or the beginning of the lytic cycle when conditions improve.

Transduction: Gene Transfer via Phages

Lysogeny and pseudolysogeny can result in the transfer of genetic material, including antimicrobial resistance genes, between bacteria via transduction:

  • Generalized Transduction: This occurs due to a mistake during the packaging of phage DNA in the lytic cycle, resulting in host cell DNA being accidentally packaged into a phage capsid instead of viral DNA. This capsid can then deliver bacterial DNA to another cell.
  • Specialized Transduction: This happens when a prophage excises imprecisely from the host chromosome during the switch from the lysogenic to the lytic cycle. Adjacent host genes are ‘stolen’ by being incorporated into the phage DNA strand that is cut from the combined host/prophage DNA. Both mechanisms can transfer traits like antimicrobial resistance from one bacterial cell to another.

Bacteriophage Isolation Technique

Bacteriophage isolation is commonly done using a double-layer agar technique. This involves cultivating a confluent bacterial lawn on an agar plate, onto which the phage-containing sample is applied. Lytic phages infect and lyse bacteria, forming clear zones called plaques on the lawn, allowing for their detection and quantification.

Key Bacteriophage Terminology

Generalist vs. Specialist Phages
Generalist phages can kill multiple bacterial strains, sometimes across multiple species. Specialist phages typically kill only one type of strain or a few related types within a single species.
Virulent vs. Temperate Phages
Virulent phages exclusively follow the lytic cycle. Temperate phages can choose between the lytic and lysogenic cycles.
Quasi-species
Describes a population of viruses where high mutation rates lead to a diverse mix of related genetic variants (e.g., flu/COVID mutations). Quasi-species often result when a virus population is under strong selective pressure or near extinction, enhancing adaptability.
Lytic / Lysogenic / Pseudolysogenic
The three primary life cycle strategies of bacteriophages, differing in how they interact with the host cell: immediate replication and lysis (lytic), integration into the host genome (lysogenic), or a temporary, non-replicative dormant state (pseudolysogenic).