The Escherichia coli two-component signal sensor BarA binds protonated acetate via a conserved hydrophobic-binding pocket

Abstract

The BarA/UvrY two-component signal transduction system is widely conserved in γ-proteobacteria and provides a link between the metabolic state of the cells and the Csr posttranscriptional regulatory system. In Escherichia coli , the BarA/UvrY system responds to the presence of acetate and other short-chain carboxylic acids by activating transcription of the noncoding RNAs, CsrB and CsrC, which sequester the RNA-binding protein CsrA, a global regulator of gene expression. However, the state of the carboxyl group in the acetate molecule, which serves as the BarA stimulus, and the signal reception site of BarA remain unknown. In this study, we show that the deletion or replacement of the periplasmic domain of BarA and also the substitution of certain hydroxylated and hydrophobic amino acid residues in this region, result in a sensor kinase that remains unresponsive to its physiological stimulus, demonstrating that the periplasmic region of BarA constitutes a functional detector domain. Moreover, we provide evidence that the protonated state of acetate or formate serves as the physiological stimulus of BarA. In addition, modeling of the BarA sensor domain and prediction of the signal-binding site, by blind molecular docking, revealed a calcium channels and chemotaxis receptors domain with a conserved binding pocket, which comprised uncharged polar and hydrophobic amino acid residues. Based on the comparative sequence and phylogenetic analyses, we propose that, at least, two types of BarA orthologues diverged and evolved separately to acquire distinct signal-binding properties, illustrating the wide adaptability of the bacterial sensor kinase proteins.

Synergistic application of atmospheric and room temperature plasma mutagenesis and adaptive laboratory evolution improves the tolerance of Escherichia coli to L‐cysteine

“…In the mutations observed in the high‐performance strain 40AP02, BarA is an endosomal sensor histidine kinase that is involved in the regulation of central carbon metabolism by sensing short‐chain carboxylic acids. [ 36 ] It was found that deletion of barA leads to sensitization of E. coli to hydrogen peroxide. [ 37 ] Interestingly, L‐cysteine, a strong oxidant, is actively involved in responding to intracellular oxidative stress induced by hydrogen peroxide in the periplasm.…”

Current understandings of colibactin regulation

“…Research has shown that promoter activity of the ClbR transcriptional regulator varies during E. coli growth, with the highest activity seen at the transition from late exponential phase to early stationary phase in all tested medias, excepting brain heart infusion (BHI) and epithelial cell culture medium, where promoter activity instead peaked at mid-exponential phase [32, 33]. Discussed in greater depth later in this review, this may be orchestrated through the BarA-UvrY system which senses the presence of protonated short-chain carboxylic acids that are produced at the late exponential phase of E. coli growth, leading to alterations in colibactin expression [62–64]. Interestingly, it has also been observed that expression of clb genes clbA – clbH is higher in shaking cultures than in static cultures, but that, conversely, genes clbJ – clbQ show significantly lower expression [32].…”

Battle for Metals: Regulatory RNAs at the Front Line

“…CsrA also seems to lower RyhB sRNA level via an unknown mechanism ( Potts et al., 2017 ). The activity of CsrA is modulated by two sRNAs, named CsrB and CsrC ( Liu et al., 1997 ; Weilbacher et al., 2003 ), in response to short-chain carboxylic acids and carbon nutritional status ( Pannuri et al., 2016 ; Alvarez et al., 2021 ). In stark contrast with above-mentioned mechanisms of action, CsrB/C sRNAs bind the CsrA protein via recognition motif mimicry, preventing it from interacting with its ‘true’ targets.…”