Small RNA-seq of carbon starved Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium). Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Small RNAs (sRNAs) are short sequences (~50-200 nucleotides) of RNA that regulate organismal activities across a wide-array of bacterial species. Salmonella enterica starved of a carbon-energy source (C) experience a host of genetic and physiological changes broadly referred to as the starvation-stress response (SSR). In this study, we grew log-phase, 5-h C-starved and 24-h C-starved cultures of the mouse virulent Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium) strain SL1344 bacterium. The total RNA from the three cultures was isolated and submitted for commercial small RNA sequencing. Sequencing results were bioinformatically analyzed, and 63 unique sequences were identified as novel, candidate sRNAs (candidate sRNAs). In our analysis, we focused exclusively on sequences that mapped to gene-empty regions of the SL1344 chromosome. 30 of our 63 candidate sRNAs aligned to known sRNAs and/or RNA elements of other bacterial species. All 63 formed hairpin secondary structures as predicted by Mfold, and all 63 were within 300 base pairs (bps) of known SL1344 genes. Twelve aligned to known mRNAs in SL1344. Taken together, these results suggest a real, functional role for our candidate sRNAs in either modulating the SSR or regulating other cellular activity.