TattleTail: A Pyocin Prediction Tool

Abstract

Tailocins are phage tail-like bacteriocins (PTLBs) thought to be remnants of prophages that have lost the ability to package viral genomes while retaining the ability to kill closely-related bacterial strains, thereby mediating bacterial competition. Tailocins produced by Pseudomonas aeruginosa are referred to as pyocins. Apart from their contribution to ecological fitness, they also have the potential to be harnessed as highly-specific antimicrobials to treat antibiotic resistant bacterial infections. Although pyocins lack the genetic components to package viral genomes, pyocin-encoding gene clusters share a high degree of genetic homology to phage tail genes, attributed to their shared ancestry. This poses a significant annotation-based challenge, as current prophage prediction tools, which rely on phage homology for prediction, can misclassify pyocins or tailocins as prophages. Pyocins unknowingly being misannotated as prophages is not only a bioinformatic issue, but can certainly confound experiments examining bacterial competition and prophage induction, if the experimental setup is based on this unintentional misannotation. In this study, we present "TattleTail", the first version of a bioinformatic tool designed to accurately identify tailocins in genome sequences, with a focus on identifying phage tail-derived pyocin-encoding gene clusters in P. aeruginosa in its first iteration. The tool leverages conserved pyocin gene cluster markers and accounts for the absence of canonical phage features, such as capsid, terminase and integrase genes, thereby distinguishing pyocins from intact and cryptic prophages. Validation in P. aeruginosa and non-P. aeruginosa genomes confirmed the presence of pyocin regions in all P. aeruginosa genomes, while none were detected in any non-P. aeruginosa genomes. Notably, TattleTail enabled the identification of representative pyocin-encoding gene clusters in clinical P. aeruginosa isolates. The identified pyocins in the clinical isolates were induced using mitomycin C, visualized via transmission electron microscopy, processed via tangential flow filtration and demonstrated bactericidal activity, thereby confirming TattleTail predictions. TattleTail aims to complement existing prophage prediction tools during genomic analyses involving phage-derived elements in bacterial genomes, allowing more accurate identification of these elements facilitated by robust discrimination between prophages and tailocins.