Dual RNA-seq – Pilot Dual RNA-seq

Bacteria possess many small noncoding RNAs whose regulatory roles in pathogenesis are little understood due to a paucity of macroscopic phenotypes in standard virulence assays. Here, we use a novel Dual RNA-seq approach for a single-step simultaneous RNA profiling in both pathogen and host to reveal molecular phenotypes of sRNAs during infection with Salmonella Typhimurium. We identify a new PhoP/Q-activated small RNA which upon bacterial internalization acts to temporally control the expression of both, invasion-associated effectors and virulence genes required for intracellular survival. This riboregulatory activity is shown to adjust the human response to replicating Salmonella, and have a pervasive impact on host RNA expression both inside and outside protein-coding regions including infection-specific alterations of an array of long noncoding RNAs. Our study provides a paradigm for a comprehensive RNA-based analysis of intracellular bacterial pathogens without their physical purification from a host and a new discovery route for hidden functions of pathogen genes. Overall design: Pilot Dual RNA-seq: Infection of HeLa-S3 cells with wild-type Salmonella; 2 time points (4 h, 24 h p.i.; each sorted into invaded host cells [GFP+] and non-infected bystanders [GFP-]) and the respective human (4 h mock, 24 h mock) or bacterial reference controls (0 h LB, 0 h input), respectively. Three biological replicates were taken.