# A method for discovery of transcription factors controlling Brucella sRNAs

## TL;DR

This paper introduces a method to identify transcription factors that control sRNA levels in Brucella, helping to understand bacterial virulence.

## Contribution

A novel method for rapidly discovering transcription factors and conditions regulating sRNA levels in Brucella from transcriptomic data.

## Key findings

- VjbR controls the MavR sRNA, and RpoE1 is essential for bsr6 and Bsr8 production.
- RNase E affects Bsr7 transcript levels, and PhyK modulates two Brucella sRNAs.
- The method can be applied to other bacteria to study sRNA-mediated virulence factors.

## Abstract

In the genus Brucella, approximately 40 small regulatory RNAs (sRNAs) have been identified and validated via northern blot analysis, but the transcription factors controlling sRNA transcript levels are largely unknown. Here, we present a method for more rapidly discovering conditions and transcription factors controlling sRNA levels from transcriptomic data sets. Using this approach, we reanalyzed publicly available RNA-seq data sets and generated a large list of predicted regulatory relationships. Northern blot analyses confirmed several of these predictions, covering a wide range of potential transcription factors. Specific findings include that VjbR, a major quorum-sensing regulator of virulence in Brucella, controls levels of the MavR sRNA, and the alternative sigma factor RpoE1 is absolutely required for the expression of bsr6 while also contributing to Bsr8 production during oxidative stress. We also found that RNase E is linked to transcript levels of Bsr7, and the transcriptional regulator PhyK modulates the expression of two Brucella sRNAs. Overall, the methods described here can be used in future transcriptomic studies to predict and validate transcriptional regulators and conditions that influence sRNA levels in bacteria.

Regulatory small RNAs control translation for numerous proteins linked to virulence in pathogenic bacteria, but have proven difficult to fully characterize. We developed a new method to discover transcription factors and conditions controlling small regulatory RNAs (sRNA) expression. This method can be applied to other bacteria and future Brucella transcriptomic studies to aid in understanding pathogenesis and virulence factors mediated by sRNAs.