Lecture 19 In(ph)initywars: the continuous arms-race between phagesand bacteria Flashcards
Bacteriophages
*Bacteriophages (Phages) are viruses that specifically replicate in bacteria
*Phages outnumber bacteria by an estimated 10-fold in every niche
-Capsid: Contains phage genome
-Contractile sheath
-Fibers for adhesion
There is a very broad diversity of phage types in nature, many of which have not been discovered yet
Stages of bacteriophage infection
- landing
- pinning
- tail contraction and penetration
- DNA injection
Classic lytic cycle
- bacteriophage lands on host bacteria cell- Attachment- the phage attaches to the surface of the host cell
- penetration- the viral DNA enters the host cell
- Biosynthesis- phage DNA replicates and phage DNA proteins are made
- maturation- new phage particles are assembled
- lysis- the cell lyses, releasing the newly made phages
Can you summarisethe main steps of phage infection and explain what is the lytic cycle?
Main Steps of Phage Infection
Attachment (Adsorption):
The phage recognizes and binds to specific receptors on the surface of the bacterial cell. This interaction is highly specific and determines the host range of the phage.
Penetration (Entry):
The phage injects its genetic material (DNA or RNA) into the bacterial cell. This is often achieved by the contraction of the phage tail, which punctures the bacterial cell wall and membrane, allowing the phage genome to enter the host cell.
Replication (Biosynthesis):
Once inside the bacterial cell, the phage genome hijacks the host’s cellular machinery to replicate its own genetic material and produce phage proteins. The bacterial cell’s normal functions are redirected to support the production of new phage components.
Assembly (Maturation):
Newly synthesized phage genetic material and proteins are assembled into complete phage particles. This involves the formation of phage heads, tails, and the packaging of the genetic material into the phage heads.
Release (Lysis):
The bacterial cell is lysed (broken open), typically by phage-encoded enzymes such as lysozyme, releasing the newly formed phage particles into the surrounding environment. These new phages can then infect other bacterial cells, continuing the infection cycle.
The Lytic Cycle
The lytic cycle is one of the two main reproductive cycles of bacteriophages (the other being the lysogenic cycle). Here’s a detailed explanation of the lytic cycle:
Attachment: The phage attaches to a specific receptor on the surface of a susceptible bacterial cell.
Penetration: The phage injects its genetic material into the host cell, leaving the empty phage capsid outside.
Replication and Synthesis:
The phage genome takes over the host cell’s machinery.
The host’s DNA is degraded, and its resources are redirected to the synthesis of phage DNA and proteins.
The phage genome is replicated multiple times, and phage mRNA is transcribed and translated to produce phage proteins.
Assembly:
Phage components are assembled into new phage particles.
Phage heads are formed and filled with phage DNA.
Tails and other components are assembled and attached to the heads, forming complete, infective phage particles.
Release:
The bacterial cell is lysed by phage-encoded enzymes, such as lysozyme, which break down the bacterial cell wall.
The lysis releases the newly formed phage particles into the environment, where they can infect new bacterial cells.
Summary
In the lytic cycle, a phage infects a bacterial cell, hijacks its machinery to produce new phage particles, and then lyses the cell to release these particles. This cycle results in the destruction of the host cell and the propagation of the phage. The lytic cycle is characterized by rapid replication and a high burst size (number of new phage particles released per infected cell), making it a highly effective mode of viral reproduction.
The lysogenic phages
Lysogenic phages, also known as temperate phages, have the ability to integrate their genetic material into the host bacterium’s genome and enter a latent state called lysogeny. Here’s a detailed overview of the lysogenic cycle and its key features:
The Lysogenic Cycle
Attachment: The lysogenic phage attaches to a specific receptor on the surface of a susceptible bacterial cell.
Penetration: The phage injects its genetic material into the bacterial cell.
Integration:
Instead of immediately taking over the host cell’s machinery to replicate, the phage DNA integrates into the bacterial chromosome. The integrated phage DNA is called a prophage.
This integration is facilitated by specific phage enzymes that recognize and insert the phage genome into the bacterial DNA at specific sites.
Lysogeny:
Once integrated, the prophage is replicated along with the host cell’s DNA during normal bacterial cell division. This means the phage DNA is passed on to all daughter cells.
The prophage can remain dormant for an extended period, during which the bacterium is known as a lysogen.
While in this state, the prophage generally does not cause harm to the host cell and can even confer some advantages, such as immunity to superinfection by the same or related phages.
Induction:
Under certain conditions, such as stress, UV light exposure, or chemical mutagens, the prophage can be induced to excise itself from the bacterial genome.
Once excised, the phage enters the lytic cycle, where it replicates, assembles new phage particles, and lyses the host cell to release new phages.
Key Features of Lysogenic Phages
Latent State: The lysogenic cycle allows phages to maintain a latent presence within the bacterial population without killing the host cells immediately. This can be advantageous in stable environments where the host cells are not under significant stress.
Horizontal Gene Transfer: Prophages can contribute to bacterial evolution through horizontal gene transfer. The integration and subsequent excision of phage DNA can lead to the transfer of genes between different bacterial strains or species, which can include beneficial traits such as antibiotic resistance or virulence factors.
Environmental Triggers: The switch from the lysogenic to the lytic cycle (induction) can be triggered by environmental factors that signal unfavorable conditions for the host bacteria. This ability allows the phage to exit the host and find new, potentially more favorable environments.
Bacterial Immunity: Lysogenic bacteria often gain immunity to superinfection by the same type of phage due to the presence of the prophage. This is because the prophage can produce repressor proteins that inhibit the infection by additional phages of the same type.
Example of a Lysogenic Phage: Lambda Phage (λ Phage)
The lambda phage is a well-studied example of a temperate phage that infects Escherichia coli (E. coli). In the lysogenic cycle, lambda phage integrates its DNA into the host E. coli genome at a specific site. The integrated lambda DNA, or prophage, can remain dormant and be replicated along with the host genome until induced to enter the lytic cycle.
Summary
Lysogenic phages have a dual life cycle: they can integrate their genome into the host bacterium’s genome and enter a latent state (lysogeny), or they can enter the lytic cycle, leading to the production of new phage particles and the lysis of the host cell. This ability to switch between cycles allows lysogenic phages to persist in bacterial populations and contributes to genetic diversity and evolution through horizontal gene transfer.
prophage antibiotic resistance
Prophages carry antibiotic resistance genes or virulence factors that confer and advantage to the host bacterium
Food-borne disease that causes: *diarrhoea (about 50% of cases have bloody diarrhoea)
*stomach cramps
*fever
Chemical defenceRestriction modifications
Abortive infection systems
CRISPR-Cas
166 novel antiphage systems
~200differentsystemsthatbacteriacanusetoprotectthemselvesagainstphages
~400differentsubtypesintotal,whichcanactagainstabroadrangeofphages
P.aeruginosa,pathogenicE.coli and Klebsiella pneumonia all carry atleat 85-90% of the 200 known anti-phagesystems.
Their existence was only discovered 5yrs ago
These pathogens will be resistant to a big variety of phages: less likely cocktails will work against them!
Bacteria have an immunity system
- phage attachment and genome injection
- virion assembly
- virion release
No defence - Phage attachment and genome injection
- recognition of self from non-self DNA (cell realises there is foreign material)
- phage DNA degradation (cell attacks the Phage DNA)
First line of defence - phage attachment and genome injection
- sensing of assembled phage components
- cell suicide to prevent virion release
Second line of defence
Anti-phage systems examples
*Phages can encode Methyl-transferases to methylate their genome
*Phages can encode proteins that inhibit the nuclease
Anti-phage systems examples- Second line of defence
Anti-phage system component ThsB produces a signa molecule to indicate infection
ThsA mediates bacteria suicide by NAD+ depletion
ThsBproduces a small nucleotide, called cADPR, which signals the on-going phage infection and triggers ThsAto cause NAD+ depletion and growth arrest
Some phages produce Tad1, a protein that can sequester cADPRand inhibit activation of Thoeris.
The CBASS anti-phage system
*The CBASS anti-phage system produces a cyclic nucleotide, cGAMP, that activates an effector protein. The effector protein causes growth arrest during phage infection (second-line defence).
*The anti-CBASS protein Acb1 degrades cGAMP
*The anti-CBASS protein Acb2 acts like Tad1, sequestering the messenger nucleotid
Antimicrobial Resistance
Antimicrobialresistance(AMR) is a major health threat
Phage therapy represents a promising alternative to antibiotics
In Georgia and other East Europe countries, phage cocktails are sold over the counter in pharmacies to treat infections
Phage therapy example
*Phages can encode depolymerases and other enzymes to degrade biofilm matrix
*These are used to access single bacterial cells and initiate the lytic cycle
*Phage therapy has the potential to also treat infection sites with biofilms
Phage therapy example
*Bacteria can evolve changes in their envelope to prevent phage attachment
*These changes result in a fitness cost that can decrease their survival or virulence
*Sometimes these changes alter multidrug efflux pumps, reinstating sensibility to old antibiotics
Take-home message for today’s lectur
*What is bacteriophage?
oDefinition of a bacteriophage
*Steps of phage infection process.
oKnowledge of the basics of the infection process and
oDefinition and differences between lytic and lysogenic cycle.
*Phages-bacteria arms race.
*General awareness of phage defencestrategies
*General knowledge of examples of phages counter-defencestrategies (regarding the provided examples).
*Therapeutic potential of phages.
oGeneral awareness that phages are and could be used used as therapy
