Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle

Bacteriophages (phages) significantly influence bacterial populations in their natural environment. However, one aspect that has not been thoroughly explored in the context of phage-bacteria interactions is the post-transcriptional regulation of gene expression, despite the growing attention it has received for bacterial physiology over the last two decades. Important players in this process are small RNAs (sRNAs) that regulate target mRNAs via base-pairing, typically using RNA chaperones like Hfq to facilitate this regulation. Here, we apply RIL-seq, to map in-vivo the sRNA-RNA network in Escherichia coli upon lambda phage infection. We highlight changes in the bacterial transcriptome and sRNA interactome while uncovering a novel phage-encoded sRNA that regulates key genes in E. coli. We decipher the molecular mechanism of the sRNA-mediated regulation and illustrate how it hijacks the host replication machinery and helps the infection cycle. Overall, we uncover an RNA-level regulatory layer that shapes the E. coli - lambda interactions. Overall design: RIL-seq and Total RNA-seq of E. coli MG1655 WT carrying a chromosomal FLAG-tagged Hfq, infected and non-infected with phage lambda, at 30 and 60 minutes after infection. As a control, libraries were similarly generated for WT cells not encoding tagged proteins. Two biological replicates were done for each sample.