Salmonella sRNAs drive the decision between active stress resistance and persister cell dormancy

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Bacterial persister cells are relatively inactive metabolically, able to cope with long-term environmental stress and are relatively tolerant of antibiotics. This project aims to study the processes that lead to persister cell formation, as a better understanding of these processes could significantly improve our ability to address societal challenges such as antibiotic resistance, foodborne illness outbreaks, and agricultural diseases. In addition, this project provides interdisciplinary student training opportunities in microbiology, molecular biology, and computational genetics/bioinformatics. Local high school students will directly benefit from this project through two separate initiatives. Notably, these efforts are intended to increase underrepresented minority student interest and enrollment in biology and other STEM fields. The sRNA profile of Salmonella subjected to short term carbon starvation is highly distinct from that seen during prolonged starvation. Similarly, highly distinct sRNA profiles are associated with initial and prolonged cellular desiccation. In contrast, significant overlaps between the sRNAs expressed in cells subjected to short durations of carbon starvation and desiccation, as well as significant overlaps between the sRNAs expressed during prolonged desiccation and long-term carbon starvation have been observed. Furthermore, several of the sRNAs commonly induced during short duration stress exposures are expressed from promoters transcribed via the RNA polymerase (RNAP) sigma subunit RpoS. Conversely, many of the sRNAs commonly induced during long term exposures are expressed from promoters targeted by the alternative sigma subunit RpoE. Together, these findings suggest the following: alternative RNAP sigma subunit selection and consequent expression of distinct sets of sRNAs drive the decision between active stress resistance and persister formation in Salmonella. Against this background, the work outlined for this project is significant, as it will employ an array of genetic manipulations and transcriptomic assays to characterize new, essential roles for alternative sigma subunits and specific sRNAs in driving the decision between active stress resistance and persister formation. Beyond characterizing the molecular switch driving the decision between active stress resistance and persister formation, the central model tested by this work-alternative sigma factors compete with one another through directing the transcription of distinct sets of sRNAs that inhibit opposing sigma factors-may well constitute a general mechanism of prokaryotic sigma molecular switch regulation with implications for an array of additional processes. As such, the work performed in this study will explore a novel, systems-level regulatory mechanism for global prokaryotic transcriptome reprogramming, which might advance our basic knowledge of the molecular mechanisms driving microbial stress responses.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.