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Avaritia is a prophage-encoded PIN-domain anti-phage defence system in E. coli

Raspanti, Alessandro (2026) MOBN03 20252
Degree Projects in Molecular Biology
Popular Abstract
Bacteria can use viral genes to protect themselves from other phages

Bacteriophages are viruses that specifically infect bacteria. To survive, bacteria use many different defence mechanisms. Some of these defence systems come from a peculiar source: inside bacteriophage genomes.

Phages can undergo two different life cycles: they can multiply within the bacterial cell, which is then lysed, releasing progeny into the environment, or they can integrate their genetic material into the host cell genome. Temperate phages integrate their genomes, which are then called prophages. This remains dormant and replicates along with the host cell. Prophages can bring to the host cell genes that confer survival advantages, including defence systems... (More)
Bacteria can use viral genes to protect themselves from other phages

Bacteriophages are viruses that specifically infect bacteria. To survive, bacteria use many different defence mechanisms. Some of these defence systems come from a peculiar source: inside bacteriophage genomes.

Phages can undergo two different life cycles: they can multiply within the bacterial cell, which is then lysed, releasing progeny into the environment, or they can integrate their genetic material into the host cell genome. Temperate phages integrate their genomes, which are then called prophages. This remains dormant and replicates along with the host cell. Prophages can bring to the host cell genes that confer survival advantages, including defence systems that protect bacteria from phage infections. During my thesis, I characterised Avaritia, a novel defence system encoded in a prophage found in Escherichia coli.

Avaritia is a 500-amino-acid protein that contains a PIN domain (140 amino acids), a “scissor” that cuts RNA. To prove that this protein confers protection, it was tested against more than 70 phages. The results show that Avaritia confers protection on more than 20 phages that share a long, flexible tail. Infecting bacteria with phages at different doses (0.01 to 10 times the number of bacteria) resulted in strong protection at low doses and low to no protection at high doses. The infected cells’ growth rate was also noticeably slower, suggesting that Avaritia’s protection comes at a high cost for the cells.

The PIN Domain is widely conserved across all forms of life, but in bacteria, it is usually associated with an antitoxin partner that keeps the PIN domain inactive and prevents nonspecific RNA degradation. In Avaritia, this partner is absent, and the PIN domain of the remainder of the protein is not annotated. The lack of an antitoxin partner suggests that Avaritia can be autoinhibited and activated from an external source.

Next, I identified the trigger that activates Avaritia. To do so, I isolated phage mutants capable of infecting cells carrying Avaritia, and I sequenced their genomes. These mutants carry mutations in the TMP chaperone genes. TMP chaperones are proteins that form a spiral along the Tape Measure Proteins (TMPs) chains to keep them soluble while they are being produced. When Avaritia was expressed in cells alongside TMP and its chaperones, the resulting colonies were small and translucent, suggesting mild toxicity. This suggests that both are needed to trigger Avaritia. My proposed model states that Avaritia can mimic the TMPs chains and incorporate TMP chaperones that are recognised by the sensor domain and activate the ribonuclease domain, which then degrades RNA, protecting the cell from phage infection.


Master’s Degree Project in Molecular Biology 60 credits 2026
Department of Biology, Lund University

Advisor: Marcus Johansson
Department of Experimental Medical Science, Lund University (Less)
Please use this url to cite or link to this publication:
author
Raspanti, Alessandro
supervisor
organization
course
MOBN03 20252
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
9228716
date added to LUP
2026-05-27 14:06:40
date last changed
2026-05-27 14:06:40
@misc{9228716,
  author       = {{Raspanti, Alessandro}},
  language     = {{eng}},
  note         = {{Student Paper}},
  title        = {{Avaritia is a prophage-encoded PIN-domain anti-phage defence system in E. coli}},
  year         = {{2026}},
}