Identification of Z nucleotides as an ancient signal for two-component system activation in bacteria

Abstract

Two-component systems (TCSs) in bacteria are molecular circuits that allow the perception of and response to diverse stimuli. These signaling circuits rely on phosphoryl-group transfers between transmitter and receiver domains of sensor kinase and response regulator proteins, and regulate several cellular processes in response to internal or external cues. Phosphorylation, and thereby activation, of response regulators has been demonstrated to occur by their cognate histidine kinases but also by low molecular weight phosphodonors such as acetyl phosphate and carbamoyl phosphate. Here, we present data indicating that the intermediates of the de novo syntheses of purines and histidine, 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5′-monophosphate (ZMP) and/or 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5′-triphosphate (ZTP), activate the response regulator UvrY, by promoting its autophosphorylation at the conserved aspartate at position 54. Moreover, these Z nucleotides are shown to also activate the nonrelated response regulators ArcA, CpxR, RcsB, and PhoQ. We propose that ZMP and/or ZTP act as alarmones for a wide range of response regulators in vivo, providing a novel mechanism by which they could impact gene expression in response to metabolic cues.

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

“…Also, addition of acetate, but not formate, resulted in the activation of reporter expression in the ΔbarA mutant strain (Fig. 1C), due to acetyl-P−dependent UvrY phosphorylation, in agreement with previous reports (15,34). On the other hand, no activation of csrB-lacZ expression was observed in the strains expressing the BarA Δ1-197 or the BarA PDArcB proteins, indicating that these BarA variants fail to respond to acetate and formate, but retain their phosphatase activity, and are therefore functional proteins that remain locked in their phosphatase state.…”

Regulation of constant cell elongation and Sfm pili synthesis in Escherichia coli via two active forms of FimZ orphan response regulator

“…Although FimZ also stimulated constant cell elongation in hisH‐ and purC‐ deficient strains (e and f in Figure 5a), as the defective purA gene suppressed cell elongation (g in Figure 5a). Addition of AMP, which prevents ZMP/ZTP accumulation in purA null mutants (Vázquez‐Ciros et al, 2020; Watanabe et al, 2011), recovered cell elongation suppression in purA null mutants (h in Figure 5a). The D56A mutant also recovered cell elongation suppression in purA null mutants (i in Figure 5a).…”

“…The reporter assay showed that the sfmA promoter was significantly induced in all mutants (Figure S7A). A response regulator is usually phosphorylated by low‐molecular‐weight phosphorylated compounds, acetyl phosphate, and Z‐nucleotides (Vázquez‐Ciros et al, 2020; Wolfe, 2005). The sfmA promoter was induced in cobB, ackA, pta , and yfiQ mutants, similar to that in the parent strain, and purA deficiency slightly enhanced the sfmA promoter activity (Figure S7B).…”

“…Unfortunately, this study did not identify the known factors involved in FimZ phosphorylation and acetylation. A recent report has showed that 5‐aminoimidazole‐4‐carboxamide‐1‐beta‐D‐ribofuranosyl 5‐monophosphate (ZMP) and 5‐aminoimdazole‐4‐carboxamide‐1‐beta‐D‐ribofuranosyl 5′‐triphosphate (ZTP), intermediates of purine and histidine metabolism catalyzed by PurA adenylosuccinate synthetase, activate response regulators without cognate sensor kinases (Vázquez‐Ciros et al, 2020). The E. coli K‐12 purA mutant accumulates ZMP and/or ZTP, which phosphorylate the response regulators (Vázquez‐Ciros et al, 2020).…”

Phosphorylation chemistry of the Bordetella PlrSR TCS and its contribution to bacterial persistence in the lower respiratory tract

“…Many response regulators can catalyze their own phosphorylation using small molecule phosphodonors (Lukat et al ., 1992; Silversmith et al ., 1997; Vazquez-Ciros et al ., 2020; Wolfe, 2010). Changes in fluorescence intensity of a Trp residue upon phosphorylation at a neighboring residue was used to demonstrate autophosphorylation of the Brucellus abortis NtrX receiver domain with acetyl phosphate (Fernandez et al ., 2015).…”