Specificity of bacterial defense systems against bacteriophages

  • Emile Dantzer

Student thesis: Master typesMaster in molecular microbiology, research focus

Abstract

Phages utilize the machinery of bacterial hosts for replication, often leading to bacterial death. In response, bacteria employ defense systems to counteract phage multiplication and propagation. Genome context methods have recently identified over a hundred new defense systems, clustered in bacterial genomes. Moreover, functional selection of phage-resistant bacteria has led to the discovery of other defense systems. Most defense systems fall into one of three categories: restriction-modification (RM) systems, CRISPR-Cas systems, and abortive infection (Abi). RM and CRISPR/Cas systems degrade invading nucleic acids, while Abi triggers cell death. RM and CRISPR function by distinguishing between self and non-self-genetic material, whereas Abi relies on differentiating between infected and non-infected cells. Despite the rapid progress in this field, the comprehension of the molecular mechanisms from defense triggering to phage defeat is still limited. To address the latter issue, here I leverage AlphaFold multimer, an extension of the protein structure prediction program AlphaFold2, specifically built to predict protein-protein complexes, to discover phage-encoded defense system triggers. This involves predicting the structure of potential protein complexes between phage proteins and cognate defense system proteins. A screening of 4988 potential interactions resulted in the selection of 62 top-scoring candidate pairs. I tested three of these pairs, all involving the Aditi system, by co-expression of phage and the Aditi defense genes in Escherichia coli. The co-expression of the bacteriophage SPP1 holin and the Aditi defense system suggests that this holin could trigger Aditi, but further experiments are needed to confirm these preliminary results.
Date of Award25 Jan 2024
Original languageEnglish
Awarding Institution
  • University of Namur
SupervisorRemy DUGAUQUIER (Supervisor) & Diana Bittremieux (Co-Supervisor)

Keywords

  • Defense system
  • phage
  • AlphaFold
  • DALI
  • Bacterial antiphage defense system
  • Aditi
  • Azaca
  • Phage infection profile assay
  • Co-expression assay
  • Abortive infection
  • phage trigger

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