The opportunistic human pathogen Klebsiella pneumoniae has recently gained attention due to the spread of hypervirulent and multidrug-resistant strains. Klebsiella's ability to acquire resistances to different antibiotics depends on the assimilation of additional genetic material and on de novo mutations. The risk of genomic mutations increases in response to DNA damage, when error-prone polymerases are expressed as part of a coordinated program termed the SOS response. While the SOS pathway is well-studied for many bacterial species, little is known about the regulon and the associated transcriptome in response to DNA damage in Klebsiella.

To fill this gap, we have combined dRNA-seq to define transcription start sites and unannotated small regulatory RNAs (sRNAs) with RNA co-immunoprecipitation (RIP-seq) to analyze interactions with the major RNA-binding protein Hfq, and RIL-seq to analyze the Hfq-mediated RNA-RNA interactome of a multidrug-resistant Klebsiella strain. In addition, we performed ChIP-seq to map the set of genes directly controlled by the key SOS regulator, LexA. Together, our datasets revealed a rich landscape of coding and non-coding transcripts induced in response to DNA damage and we present results on the identification and characterization of LexA-controlled sRNAs in K. pneumoniae.