The Vibrio cholerae Seventh Pandemic Islands act in tandem to defend against a circulating phage

Abstract

The current circulating pandemic El Tor biotype of Vibrio cholerae has persisted for over sixty years and is characterized by its acquisition of two unique genomic islands called the Vibrio Seventh Pandemic Islands 1 and 2 (VSP-I and VSP-II). However, the functions of most of the genes on VSP-I and VSP-II are unknown and the advantages realized by El Tor through these two islands are not clear. Recent studies have broadly implicated these two mobile genetic elements with phage defense. Still, protection against phage infection through these islands has not been observed directly in any V. cholerae El Tor biotype. Here we report the isolation of a circulating phage from a cholera patient stool sample and demonstrate that propagation of this phage in its native host is inhibited by elements in both VSP-I and VSP-II, providing direct evidence for the role of these genomic islands in phage defense. Moreover, we show that these defense systems are regulated by quorum sensing and active only at certain cell densities. Finally, we have isolated a naturally occurring phage variant that is resistant to the defense conferred by the VSP islands, illustrating the countermeasures used by phages to evade these defense mechanisms. Together, this work demonstrates a functional role for the VSPs in V. cholerae and highlights the key regulatory and mechanistic insights that can be gained by studying anti-phage systems in their native contexts.

Cell density-dependent death triggered by viral palindromic DNA sequences

“…Thus, we speculated that the DdmC proteins were part of the DDC system responsible for the plasmid-induced cell death that was triggered by growth at high cell density. Other suppressor alleles independent of DdmABC and PcnB included a mutation in luxO (Table 1); the luxO mutation is consistent with the observation that the DdMABC operon is quorum-regulated 36 .…”

“…We show the Lamassu system of V. cholerae encoded by DdmABC of VSP-2 genomic island restricts some vibriophages by recognizing a signal associated with phage-encoded palindromic DNA sequences. This signal-induced cell density-dependent death (CDD) is dependent on the quorum-regulated DdmABC operon of VSP-2 36 . The signal was first identified in a laboratory plasmid vector as a coliphage T7-derived phage sequence.…”

“…The copyright holder for this preprint this version posted November 18, 2022. ; https://doi.org/10.1101/2022.11.18.517080 doi: bioRxiv preprint called SAVED 8,36,41 ; however, DdmA does not have a SAVED domain but instead a C-terminal Domain 7 motif (Pfam CDT7) belonging to ABC-three component (ABC-3C) systems. DdmB is predicted to be a small globular protein with no predicted homologs with known functions but does possess an ABC-three component system Middle Component motif (Pfam MC3).…”

“…All contemporary pathogenic V. cholerae strains have acquired two chromosomal islands termed the Vibrio 7th Pandemic Islands I (VSP-1) and II (VSP-2) 28 . Gene products encoded by both islands have recently been shown to be capable of restricting phage growth and plasmid persistence by mechanisms including programmed cell death of infected cells 7,6,8,36 . These conclusions have been largely reached based on the over-expression of VSP-1 or VSP-2 genes in the surrogate bacterial species E. coli.…”

“…These conclusions have been largely reached based on the over-expression of VSP-1 or VSP-2 genes in the surrogate bacterial species E. coli. More recently, quorum-regulated VSP-2 genes in the DdmABC operon have been demonstrated to inhibit the growth of some vibriophages by 2-3 logs but only when co-absent with specific VSP-1 putative antiphage genes 36 . Importantly, the signals that activate any anti-phage and anti-plasmid defense system in V. cholerae remain ill-defined.…”