# A prophage-encoded sRNA limits phage infection of adherent-invasive E. coli

## TL;DR

A prophage-encoded small RNA in E. coli limits phage infection by repressing genes involved in maltodextrin transport, reducing phage spread and promoting bacterial persistence in the gut.

## Contribution

Discovery of a prophage-encoded sRNA (svsR) that limits phage infection by reprogramming host metabolism in adherent-invasive E. coli.

## Key findings

- svsR represses maltodextrin transport genes, including lamB, a phage receptor, reducing phage adsorption and replication.
- Mice colonized with NC101 had lower phage burdens and increased extraintestinal dissemination of E. coli compared to those without the prophage.
- Maltodextrin and glucose availability influence phage plaque expansion and adsorption, linking nutrient conditions to phage resistance.

## Abstract

Prophages are prevalent features of bacterial genomes that can reduce susceptibility to infection by competing phages, yet the mechanisms involved are often elusive. Here, we identify a small RNA (svsR) encoded by the lambdoid prophage NC-SV in adherent-invasive Escherichia coli strain NC101 that limits infection by virulent coliphages. Comparative genomics revealed that NC-SV–like prophages and svsR homologs are broadly conserved across Enterobacteriaceae. Transcriptomic analyses show that svsR represses maltodextrin transport genes, including lamB, which encodes the outer membrane maltoporin LamB, a known receptor for numerous coliphages. Deletion of the lamB gene reveals that while LamB is not required for replication of the virulent phages tested, it contributes to plaque expansion, indicating a role in phage spread but not as an essential receptor. Nutrient supplementation experiments further linked maltodextrin and glucose availability to changes in plaque expansion and phage adsorption. In vivo, we compared wild-type NC101 and a prophage-deletion strain (NC101∆NC-SV) in mice to assess the impact of NC-SV on lytic phage susceptibility. Although intestinal E. coli densities remained stable across groups, animals colonized with NC101 exhibited markedly reduced phage burdens in both the intestinal lumen and mucosa compared to mice colonized with NC101∆NC-SV. This reduced phage pressure was associated with increased dissemination of E. coli to extraintestinal tissues, including the spleen and liver. Together, these findings highlight a nutrient-responsive, prophage-encoded mechanism that protects E. coli from phage predation and may promote bacterial persistence in and dissemination from the mammalian gut.

Prophages—viral genomes integrated into bacterial chromosomes—are common in enteric bacteria and can profoundly influence bacterial physiology and ecological fitness. Here we show that a lambdoid prophage, NC-SV, in the adherent-invasive Escherichia coli strain NC101 modulates host metabolism to limit infection by virulent coliphages. NC-SV encodes a small regulatory RNA, svsR, that represses maltodextrin transport genes, including lamB, which encodes a maltoporin frequently used as a phage receptor. Through this transcriptional reprogramming, NC-SV reduces phage adsorption and replication both in vitro and in the mouse intestine. Consequently, mice colonized with NC101 exhibited markedly lower phage loads in the gut compared with those colonized by NC101 cured of the NC-SV prophage, and this reduction in intestinal phage burden was associated with greater dissemination of NC101 to extraintestinal sites such as the liver and spleen. These findings reveal a nutrient-responsive mechanism of phage resistance mediated by a prophage-encoded sRNA and illustrate how prophages can rewire bacterial regulatory networks in ways that alter phage–host dynamics in the gut.