A RAD Search: Identification of antiphage defense systems using a conserved serine recombinase

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Presenter Information(s)

Navtej Singh

Abstract or Description

The emergence of multidrug-resistant (MDR) infections has sparked interest in bacteriophage (phage) therapy. However, bacteria have also developed defense mechanisms against phages that allow them to evade infection, hence threatening the success of phage therapy. The research effort herein is intended to discover and describe new antiphage systems by means of a bioinformatics platform called Recombinase Associated Defense Search (RADS). RADS employs a conserved serine recombinase as a genetic "bait" that searches for bacterial antiphage defense systems linked with these recombinases. RADS was run on genomes from the Bacillota phylum. Using co-transcription prediction combined with statistical methods, genes that are likely co-transcribed with the serine recombinase and contain domains that are enriched in the RADS contigs were selected to test for antiphage activity. Using this method, we discovered a KAP P-loop NTPase domain-containing protein that is a potent antiphage defense system. This protein contains an N-terminal KAP P-loop NTPase, followed by a putative effector region with no known domains or characterized homologues. Using reverse genetic experiments including gene deletion, truncations, and phage infection assays, we aim to determine the mechanism by which this protein suppresses phage replication. In addition, we will investigate whether inactivation of this ORF its native context of the Enterococcus faecalis 661 plasmid p661b, restores phage sensitivity. This study will show phage defense strategies in bacteria. Using computational prediction followed by experimental validation, the project bridges microbiology with bioinformatics, providing insights that can be utilized to drive more effective development of phage therapies targeting multidrug-resistant infections.

Mentor

Shelby E. Andersen