The σ^B-dependent regulatory sRNA Rli47 represses isoleucine biosynthesis inListeria monocytogenesthrough a direct interaction with theilvAtranscript

Abstract

The facultative intracellular pathogen Listeria monocytogenes 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 Bdependent 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 in silico and in vivo approaches, a binding interaction was predicted with the Shine-Dalgarno region of the ilvA mRNA, which encodes threonine deaminase, an enzyme required for branched-chain amino acid biosynthesis. Both ilvA transcript levels and threonine deaminase activity were increased in a deletion mutant lacking the rli47 gene. The Δrli47 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 Δrli47 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 L. monocytogenes in niches both outside and within the mammalian host.

The transcriptome of Listeria monocytogenes during co-cultivation with cheese rind bacteria suggests adaptation by induction of ethanolamine and 1,2-propanediol catabolism pathway genes

“…In line with this, Rli47 is expressed during various stress conditions, including acidic [24], oxidative [65], stationary-phase [65][66][67], in the gastrointestinal tract [66], and during intracellular replication in macrophages [68]. Marinho et al [64] discovered that Rli47 hinders L. monocytogenes growth during harsh conditions by the suppression of branched-chained amino acid biosynthesis. Additionally, in the same study, it was revealed that Rli47 influences the expression of over 150 genes that are involved in amino acid metabolism and transport, electron transport, fermentation, chorismate biosynthesis (aro pathway), and purine biosynthesis.…”

“…The gene expression of frdA, pflABC, pplA, and the putative formate/nitrite transporter significantly altered in a Rli47 deletion mutant study mentioned previously, suggesting that Rli47 may have a broad role in modulating energy metabolism [64]. Perhaps most notably, Rli47 influences the transcription of four key aro pathway genes.…”

“…Inferences from the currently presented data and from previous research that revealed lap is upregulated during nutrient limitation [82] leads us to suggest that the upregulation of lap in this study may be due to nutrient acquisition stress as a consequence of co-culture. Notably, lap was found to be the most impacted Rli47-dependent gene in the Rli47 deletion mutant study mentioned above [64], and Cortes et al [24] highlight a putative consistent regulatory relationship of Rli47 with LAP among transcriptional studies. These data suggest that Rli47 may directly or indirectly regulate LAP-among others-under various stress conditions, including co-cultivation with other bacteria.…”

Transcriptome Sequencing of Listeria monocytogenes Reveals Major Gene Expression Changes in Response to Lactic Acid Stress Exposure but a Less Pronounced Response to Oxidative Stress

“…This pattern is present during stationary phase (Oliver et al, 2009;Toledo-Arana et al, 2009;Mujahid et al, 2012), the overexpression of σ B (Liu et al, 2017), multiplication in the gut (Toledo-Arana et al, 2009), and in macrophages (Chatterjee et al, 2006;Mraheil et al, 2011). Furthermore, lap was the highest upregulated gene (29.9fold) in an rli47 deletion mutant (Marinho et al, 2019), suggesting that Rli47 is somehow involved in lap expression. The aforementioned evidence seems to implicate a relationship between LAP and Rli47 in L. monocytogenes, specifically that FIGURE 4 | Average mean of normalized transcriptome sequencing reads mapped to the non-coding RNA Rli47 in L. monocytogenes strains 6179 and R479a exposed to control conditions, acid (1% lactic acid, pH 3.4), and oxidative stress (0.01% H 2 O 2 ).…”

“…Expression of rli47 significantly increased during exposure to lactic acid, with a log2fold change of 8.47 in 6179 and 9.97 in R479a. Recently, Marinho et al (2019) determined that rli47 transcripts hinder cell growth under stress conditions by suppressing translation of ilvA, an enzyme involved in isoleucine biosynthesis. Other studies also support the notion that rli47 is important for response to various stressors including stationary phase (Oliver et al, 2009;Toledo-Arana et al, 2009;Mujahid et al, 2012), intracellar survival in macrophages (Mraheil et al, 2011), and oxidative stress (Mujahid et al, 2012).…”