What Does the Talking?: Quorum Sensing Signalling Genes Discovered in a Bacteriophage Genome

Abstract

The transfer of novel genetic material into the genomes of bacterial viruses (phages) has been widely documented in several host-phage systems. Bacterial genes are incorporated into the phage genome and, if retained, subsequently evolve within them. The expression of these phage genes can subvert or bolster bacterial processes, including altering bacterial pathogenicity. The phage phiCDHM1 infects Clostridium difficile, a pathogenic bacterium that causes nosocomial infections and is associated with antibiotic treatment. Genome sequencing and annotation of phiCDHM1 shows that despite being closely related to other C. difficile myoviruses, it has several genes that have not been previously reported in any phage genomes. Notably, these include three homologs of bacterial genes from the accessory gene regulator (agr) quorum sensing (QS) system. These are; a pre-peptide (AgrD) of an autoinducing peptide (AIP), an enzyme which processes the pre-peptide (AgrB) and a histidine kinase (AgrC) that detects the AIP to activate a response regulator. Phylogenetic analysis of the phage and C. difficile agr genes revealed that there are three types of agr loci in this species. We propose that the phage genes belonging to a third type, agr3, and have been horizontally transferred from the host. AgrB and AgrC are transcribed during the infection of two different strains. In addition, the phage agrC appears not to be confined to the phiCDHM1 genome as it was detected in genetically distinct C. difficile strains. The discovery of QS gene homologs in a phage genome presents a novel way in which phages could influence their bacterial hosts, or neighbouring bacterial populations. This is the first time that these QS genes have been reported in a phage genome and their distribution both in C. difficile and phage genomes suggests that the agr3 locus undergoes horizontal gene transfer within this species.

Diversity and Evolution in the Genome of Clostridium difficile

“…Furthermore, the in vitro induction of these phages was increased significantly in the presence of fluoroquinolone antimicrobials, demonstrating how the established CDI risk factor of antimicrobial exposure may influence phage biology and may ultimately promote phage-mediated HGT (113). Notably, Hargreaves et al (134) describe the presence of agr homologues in the genome of phage CDHM1. In C. difficile, the agr locus is responsible for modulating the expression of 75 genes associated with various cellular functions, such as flagellum assembly and toxin synthesis, particularly during late exponential growth (113).…”

“…In C. difficile, the agr locus is responsible for modulating the expression of 75 genes associated with various cellular functions, such as flagellum assembly and toxin synthesis, particularly during late exponential growth (113). It is hypothesized that the expression of these agr-like genes during phage lysogeny may influence gene expression in the host bacterium through a quorum-signaling mechanism (113,134). Moreover, phages CD119, CD38-2, and CD27 have been shown to modulate toxin production in C. difficile; however, the genetic basis of these interactions is not yet understood (113,134).…”

“…It is hypothesized that the expression of these agr-like genes during phage lysogeny may influence gene expression in the host bacterium through a quorum-signaling mechanism (113,134). Moreover, phages CD119, CD38-2, and CD27 have been shown to modulate toxin production in C. difficile; however, the genetic basis of these interactions is not yet understood (113,134).…”

Clostridium difficile infection: Evolution, phylogeny and molecular epidemiology

“…Interestingly, alternative agr loci have also been detected in C. difficile bacteriophages, although the significance of these is unknown (Hargreaves et al, 2014b).…”

Global Transcriptional Response of Clostridium difficile Carrying the ϕCD38-2 Prophage

“…Toxigenic strains produce two main exotoxins, TcdA and TcdB, encoded on an ϳ19.6-kb pathogenicity locus (PaLoc) (30). Most strains of C. difficile analyzed to date carry one or more integrated prophages (31)(32)(33)(34)(35)(36), and a limited number of genome sequences from characterized temperate phages are available in public databases (37)(38)(39)(40)(41)(42)(43)(44). Of note, none of them seem to encode virulence factors or toxins, although recent studies suggest that some of them might influence the lifestyle and virulence of C. difficile.…”