Prophage-encoded phage defense proteins with cognate self-immunity

Abstract

SummaryTemperate phages are pervasive in bacterial genomes, existing as vertically-inherited islands called prophages. Prophages are vulnerable to the predation of their host bacterium by exogenous phages. Here we identify BstA, a novel family of prophage-encoded phage defence proteins found in diverse Gram-negative bacteria. BstA drives potent suppression of phage epidemics through abortive infection. The bstA-encoding prophage itself is not inhibited by BstA during lytic replication due to a self-immunity mechanism driven by the anti-BstA (aba) element, a short stretch of DNA within the bstA locus. Phage-targeting by distinct BstA proteins from Salmonella, Klebsiella and Escherichia prophages is functionally interchangeable, but each possesses a cognate aba element. The specificity of the aba element ensures that immunity is exclusive to the replicating prophage, and cannot be exploited by heterologous BstA-encoding phages. BstA allows prophages to defend their host cells against exogenous phage attack, without sacrificing their own lytic autonomy.

Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa

“…4a). The P22-like prophage had almost identical replication, lysis and capsid genes to BTP1, differing only in the Ea, immunity, tail and gtr regions, and lacking the bstA 34 gene. The ST313 L3 P22-like prophage carried the sieB gene, which encodes a superinfection exclusion phage immunity protein 35 .…”

“…The SieB proteins of ST313 L3 and P22 were 92% identical, with the two proteins sharing 177 out of 192 amino acids. Carriage of a gene that mediates abortive phage infection could confer a selective advantage to ST313 L3, reflecting the functional role of the BTP1 prophage-encoded BstA virus defence protein in ST313 L2 34 . BstA defends bacterial cells that carry BTP1 against exogenous attack by a variety of lytic phages, conferring a beneficial trait to ST313 L2 without sacrificing lytic autonomy 34 .…”

“…Carriage of a gene that mediates abortive phage infection could confer a selective advantage to ST313 L3, reflecting the functional role of the BTP1 prophage-encoded BstA virus defence protein in ST313 L2 34 . BstA defends bacterial cells that carry BTP1 against exogenous attack by a variety of lytic phages, conferring a beneficial trait to ST313 L2 without sacrificing lytic autonomy 34 . Although BTP1 is absent from the UK reference strain U2, two UK-isolated ST313 strains (U15 and U8 7 ) carried a P22-like prophage with 99.96% sequence identity to the one found in ST313 L3 (Extended Data Fig.…”

Prophage-encoded hotspots of bacterial immune systems

“…coli K-12 MG1655 strains carrying each of the systems or the control plasmid pFR66 were grown overnight in LB + Kan. Bacterial lawns were prepared by mixing 250 µL of a stationary culture with 62.5 µL of CaCl2 1M and 12.5 mL of LB + 0.5% agar and the mixture was poured onto large square plates (12x12 cm) of LB + Kan. Serial dilutions of high-titer (>10 8 pfu/mL) stocks of phages λ, T4, P1vir (a lytic-only variant of P1), 186cIts (a thermosensitive variant of 186), CLB_P2 (7), LF82_P8 (8), AL505_P2 (9) and AL505_P3 (9) were spotted on each plate and incubated overnight at 37°C. For phage T7, plates were incubated overnight at room temperature.…”

Isolation and characterisation of bacteriophages with activity against invasive non-typhoidalSalmonellacausing bloodstream infection in Malawi

“…Enteritidis [3]. Prophages play an important role in Salmonella virulence, increasing fitness and preventing infection by other phages [6,10,11]. Indeed, a novel phage exclusion system was identified encoded in S .…”