The σ^B-dependent regulatory sRNA Rli47 represses isoleucine biosynthesis in<i>Listeria monocytogenes</i>through a direct interaction with the<i>ilvA</i>transcript

Abstract

The facultative intracellular pathogen <i>Listeria monocytogenes</i> 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^B) plays an important role in this adaptability and is critical for the transition into the host. While some of the functions of the σ^B regulon in facilitating this transition are understood the role of σ^B-dependent small regulatory RNAs (sRNAs) remain poorly characterized. In this study, we focused on elucidating the function of Rli47, a σ^B-dependent sRNA that is highly induced in the intestine and in macrophages. Using a combination of <i>in silico</i> and <i>in vivo</i> approaches, a binding interaction was predicted with the Shine-Dalgarno region of the <i>ilvA</i> mRNA, which encodes threonine deaminase, an enzyme required for branched-chain amino acid biosynthesis. Both <i>ilvA</i> transcript levels and threonine deaminase activity were increased in a deletion mutant lacking the <i>rli47</i> gene. The Δ<i>rli47</i> 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^B. The impact of the Δ<i>rli47</i> 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 <i>L. monocytogenes</i> in niches both outside and within the mammalian host.