#FEMSmicroBlog: Arm races between bacteria and phages


All living organisms are susceptible to infections by viruses. Viruses infecting bacteria, so-called bacteriophages or phages, are amongst the most abundant and evolutionary successful forms of life on Earth. One reason is their sophisticated mechanisms to avoid the bacterial immune system. The study “T5-like phage BF23 evades host-mediated DNA restriction and methylation” in microLife helped unravel these mechanisms, as Artem Isaev explains in this #FEMSmicroBlog. #FascinatingMicrobes


Phages resisting bacterial defenses

As natural predators of bacteria, phages could be allies for humans in the fight against infectious diseases. So-called “phage therapies” aim at targeting pathogenic bacteria in human infections with high specificity. Sequencing data and modern microbiology and molecular biology tools are of great help in these efforts.

Some long-lasting mysteries about phages and their survival strategies remain. For example, a major open question is how phages avoid the immune systems of bacterial cells. To protect themselves, bacteria encode an average of 5-7 different immune systems, such as Restriction-Modification systems. These degrade the DNA of incoming mobile genetic elements to prevent their integration into the bacterial genome during the infection process.

Phages of the T5 group, in contrast to other phages, are resistant to most known bacterial immune nucleases. Yet, the molecular mechanisms by which these phages protect their nucleic acids from degradation (also called “restriction”) by bacterial immune systems are unknown.

The study “T5-like phage BF23 evades host-mediated DNA restriction and methylation” in microLife focuses on a T5-relative, the phage BF23. BF23 has been known since 1949 and has served as a model object in many studies covering the unique biology of T5-like viruses. However, the full genome sequence of this phage has never been reported. This gap was filled in this study while providing insights into how T5-like phages avoid bacterial immunity systems.


Unraveling the mysteries of T5-like phages

Using transmission electron microscopy (TEM) imaging, the study visualized the long, non-contractile tail and tail fibers of BF23, as well as its icosahedral capsid. Some phages possess capsids filled with anti-restriction proteins to protect their DNA from cleavage by bacterial nucleases.

To investigate if a similar mechanism is responsible for BF23 resistance against bacterial immune systems, the study sequenced the BF23 genome and did a proteomic analysis of its virion. Even though the study found non-structural proteins in the phage capsids, these did not show any anti-restriction functions.

Images of the BF23 virion by transmission electron microscopy (TEM), and protein composition revealed by proteome analysis.
Images of the BF23 virion by transmission electron microscopy (TEM), and protein composition revealed by proteome analysis. From Skutel et al. (2023).

Other phages modify their nucleotides to protect their genomes from restriction by bacterial nucleases. To verify this possibility for BF23, the study analysed the  DNA content of the virus. However, the DNA of neither BF23 nor that of T5 carried modified nucleotides.

Surprisingly, the study found that the DNA of BF23 and T5 lacked modification marks usually present in phage genomes. The bacterial methylases Dam and Dcm methylate DNA for regulatory purposes. As these enzymes lack the ability to discriminate bacterial and phage DNA, each phage passing a Dam/Dcm-containing cell should bear the corresponding methylation marks.

The study found that the DNA of both BF23 and T5 lacks these marks. This suggested that the phages block methylation by bacterial immune methylases, helping the phage to discriminate its own non-modified genome from the modified host DNA. One hypothesis is that this could help the phage to specifically degrade bacterial DNA during infection.


How T5-like phages evade bacterial immune systems

A last option to evade the bacterial immune system would involve BF23 to express an anti-restriction component during the early stage of infection. BF23 injects its genome in two stages and the so-called early part of the genome (that is, those parts entering the cells first) lacks Restriction-Modification recognition sites. The rest of the genome, injected after a pause, carries recognition sites. This pause might provide the time for the phage to express an anti-restriction component allowing it to protect the phage genome from cleavage.

To verify this, the study assessed the susceptibility of BF23 and other T5-like phages to a panel of Restriction-Modification systems. Indeed, only with a “match” between the Restriction-Modification system and the phage carrying corresponding recognition sites in the early part of the genome, the phage was sensitive to in vivo restriction. Similarly, the lack of restriction sites in the early part of the genome correlated with resistance.

The results thus favour the hypothesis that during the early stages of infection, BF23 and T5 produce broad-specificity anti-restriction proteins. While their molecular details are still unknown, such inhibitory proteins could be of high value for various medical and biotechnological applications.


About the author of this blog

Artem Isaev holds a PhD in molecular biology from Skoltech in Moscow (Russia) and is currently heading the Laboratory of Metagenome Analysis at the same institution. His primary research interest lies in the “arms race” between bacteria and phages and the interactions between host immunity and counter-acting viral anti-defense systems. Artem aims to understand the mechanisms of action of bacterial defense systems as well as detect viral inhibitors targeting these systems.

About this blog section

The section #FascinatingMicrobes for the #FEMSmicroBlog explains the science behind a paper and highlights the significance and broader context of a recent finding. One of the main goals is to share the fascinating spectrum of microbes across all fields of microbiology.

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