Identification of novel small RNAs contributing to the Salmonella enterica serovar Typhimurium desiccation stress response

Salmonella enterica has proven extremely difficult to eliminate and persists as a major human pathogen primarily due to its ability to adapt to a variety of environmental stresses. Salmonella adaptation relies on an array of poorly understood, mechanistically complex genetic regulations that allow Salmonella to remain virulent for weeks or even months under various adverse conditions. Mounting evidence now suggests that a class of short non-coding RNAs known as small RNAs (sRNAs) may be primarily responsible for orchestrating the dynamic changes in gene expression driving Salmonella adaptation. Approximately 50-500 nucleotides in length, sRNAs are known to regulate gene expression through complementary base pairing in bacteria. In this work, we have undertaken a comprehensive analysis of sRNA involvement in the Salmonella response to desiccation. To achieve this, we sequenced the small RNA transcriptomes of water suspended, 24 hour desiccated, and 72 hour desiccated Salmonella enterica subspecies enterica serovar Typhimurium strain SL1344 cultures in order to identify sRNAs differentially expressed in response to desiccation. Utilizing this strategy, we identified 102 previously annotated sRNAs significantly differentially expressed (>2x fold change) during desiccation, and excitingly, also identified 71 novel sRNAs similarly differentially expressed. Likely endogenous sRNA targets included several proteins known to be necessary for desiccation survival and this, in part, suggested a direct role for desiccation-induced sRNAs in the dehydration response. Furthermore, we find individual deletions of at least two of the novel sRNAs identified, either sRNA1320429 or sRNA3981754, significantly impairs the ability of Salmonella to survive desiccation confirming their involvements (and suggesting the potential involvements of other sRNAs identified in this work) in the Salmonella response to desiccation.