Revealing the role of RNA-RNA interactions upon bacteriophage infection

Bacteriophages are viruses that infect bacteria and can lyse and kill them. Temperate phages are phages that can enter two different life cycles: lytic cycle where they instantly replicate and lyse the bacterial cells, or a lysogenic cycle in which the phage integrates into the host genome. One mechanism the bacterium has to cope with undesired conditions, such as phage infection, is by using small RNAs (sRNAs) to regulate gene expression. sRNAs are key regulators in bacteria and impact almost every pathway in the bacterial cell.

To study the involvement of sRNAs in phage infection, we applied RIL-seq (RNA Interaction by Ligation and sequencing) to E. coli infected with phage lambda, one of the most studied temperate phages. An extensive network of RNA-RNA interactions was revealed, including mixed interactions where phage-encoded RNA was found with E. coli-encoded RNA. Our work revealed a novel phage-encoded sRNA which we termed Lambda phage RNA 1 (LPR1). Intriguingly, LPR1 interacts with RNAs originating from the phage and from the bacteria. One key target of LPR1 encodes a protein essential for initiation of DNA replication in E. coli.

Translational reporter assays show that in the presence of LPR1 there is upregulation of the target, suggesting that LPR1 induces DNA replication within E. coli. Point mutations support direct base-pairing between LPR1 and its target. Overexpression of LPR1 results in increased phage activity, supporting the positive role LPR1 has on the infection cycle. Overall, this work demonstrates the importance sRNAs have during phage infection.