The σ-dependent regulatory sRNA Rli47 represses isoleucine biosynthesis in through a direct interaction with the transcript.

The facultative intracellular pathogen can persist and grow in a diverse range of environmental conditions, both outside and within its mammalian host. The alternative sigma factor Sigma B (σ) plays an important role in this adaptability and is critical for the transition into the host. While some of the functions of the σ regulon in facilitating this transition are understood the role of σ-dependent small regulatory RNAs (sRNAs) remain poorly characterized. In this study, we focused on elucidating the function of Rli47, a σ-dependent sRNA that is highly induced in the intestine and in macrophages. Using a combination of and approaches, a binding interaction was predicted with the Shine-Dalgarno region of the mRNA, which encodes threonine deaminase, an enzyme required for branched-chain amino acid biosynthesis. Both transcript levels and threonine deaminase activity were increased in a deletion mutant lacking the gene. The Δ mutant displayed a shorter growth lag in isoleucine-depleted growth media relative to the wild-type, and a similar phenotype was also observed in a mutant lacking σ. The impact of the Δ on the global transcription profile of the cell was investigated using RNA-seq, and a significant role for Rli47 in modulating amino acid metabolism was uncovered. Taken together, the data point to a model where Rli47 is responsible for specifically repressing isoleucine biosynthesis as a way to restrict growth under harsh conditions, potentially contributing to the survival of in niches both outside and within the mammalian host.