Characterization of acetic acid-detoxifying Escherichia coli evolved under phosphate starvation conditions

An intracellular phosphorus-starvation signal activates the PhoB/PhoR two-component system in Salmonella enterica

Bacteria acquire P primarily as inorganic orthophosphate (Pi, PO43-). Once internalized, Pi is rapidly assimilated into biomass during the synthesis of ATP. Because Pi is essential, but excessive ATP is toxic, the acquisition of environmental Pi is tightly regulated. In the bacterium Salmonella enterica (Salmonella), growth in Pi-limiting environments activates the membrane sensor histidine kinase PhoR, leading to the phosphorylation of its cognate transcriptional regulator PhoB and subsequent transcription of genes involved in adaptations to low Pi. Pi limitation promotes PhoR kinase activity by altering the conformation of a membrane signaling complex comprised of PhoR, the multicomponent Pi transporter system PstSACB and the regulatory protein PhoU. However, the identity of the Pi-starvation signal and how it controls PhoR activity remain unknown. Here, we identify conditions where the PhoB and PhoR signal transduction proteins can be maintained in an inactive state when Salmonella is grown in media lacking Pi. Our results demonstrate that PhoB/PhoR is activated by an intracellular P-insufficiency signal.IMPORTANCEIn enteric bacteria, the transcriptional response to phosphorus (P) starvation is controlled by a specialized signal transduction system comprised of a membrane-bound, multicomponent signal sensor, and a cytoplasmic transcriptional factor. Whereas this system has been primarily studied in the context of phosphate (Pi) starvation, it is currently unknown how this stress initiates signal transduction. In the current study, we establish that this signaling system is regulated by a cytoplasmic signal arising from insufficient P. We demonstrate that rather than responding to extracellular conditions, cells couple the activation of their P starvation response to the availability of cytoplasmic P. This regulatory logic may enable cells to prevent toxicity resulting from excessive Pi acquisition and hinder the onset of a P starvation response when their metabolic demands are being met through the consumption of P sources other than Pi.

RpoS and the bacterial general stress response

SUMMARYThe general stress response (GSR) is a widespread strategy developed by bacteria to adapt and respond to their changing environments. The GSR is induced by one or multiple simultaneous stresses, as well as during entry into stationary phase and leads to a global response that protects cells against multiple stresses. The alternative sigma factor RpoS is the central GSR regulator in E. coli and conserved in most γ-proteobacteria. In E. coli, RpoS is induced under conditions of nutrient deprivation and other stresses, primarily via the activation of RpoS translation and inhibition of RpoS proteolysis. This review includes recent advances in our understanding of how stresses lead to RpoS induction and a summary of the recent studies attempting to define RpoS-dependent genes and pathways.

Regulation of phosphate starvation-specific responses in Escherichia coli

Toxic agents added into the medium of rapidly growing Escherichia coli induce specific stress responses through the activation of specialized transcription factors. Each transcription factor and downstream regulon (e.g. SoxR) are linked to a unique stress (e.g. superoxide stress). Cells starved of phosphate induce several specific stress regulons during the transition to stationary phase when the growth rate is steadily declining. Whereas the regulatory cascades leading to the expression of specific stress regulons are well known in rapidly growing cells stressed by toxic products, they are poorly understood in cells starved of phosphate. The intent of this review is to both describe the unique mechanisms of activation of specialized transcription factors and discuss signalling cascades leading to the induction of specific stress regulons in phosphate-starved cells. Finally, I discuss unique defence mechanisms that could be induced in cells starved of ammonium and glucose.

Experimental evolution of extremophile resistance to ionizing radiation

A growing number of known species possess a remarkable characteristic - extreme resistance to the effects of ionizing radiation (IR). This review examines our current understanding of how organisms can adapt to and survive exposure to IR, one of the most toxic stressors known. The study of natural extremophiles such as Deinococcus radiodurans has revealed much. However, the evolution of Deinococcus was not driven by IR. Another approach, pioneered by Evelyn Witkin in 1946, is to utilize experimental evolution. Contributions to the IR-resistance phenotype affect multiple aspects of cell physiology, including DNA repair, removal of reactive oxygen species, the structure and packaging of DNA and the cell itself, and repair of iron-sulfur centers. Based on progress to date, we overview the diversity of mechanisms that can contribute to biological IR resistance arising as a result of either natural or experimental evolution.

Escherichia Coli Increases its ATP Concentration in Weakly Acidic Environments Principally through the Glycolytic Pathway

Acid resistance is an intrinsic characteristic of intestinal bacteria in order to survive passage through the stomach. Adenosine triphosphate (ATP), the ubiquitous chemical used to power metabolic reactions, activate signaling cascades, and form precursors of nucleic acids, was also found to be associated with the survival of Escherichia coli (E. coli) in acidic environments. The metabolic pathway responsible for elevating the level of ATP inside these bacteria during acid adaptation has been unclear. E. coli uses several mechanisms of ATP production, including oxidative phosphorylation, glycolysis and the oxidation of organic compounds. To uncover which is primarily used during adaptation to acidic conditions, we broadly analyzed the levels of gene transcription of multiple E. coli metabolic pathway components. Our findings confirmed that the primary producers of ATP in E. coli undergoing mild acidic stress are the glycolytic enzymes Glk, PykF and Pgk, which are also essential for survival under markedly acidic conditions. By contrast, the transcription of genes related to oxidative phosphorylation was downregulated, despite it being the major producer of ATP in neutral pH environments.

Regulated Assembly of LPS, Its Structural Alterations and Cellular Response to LPS Defects

Distinguishing feature of the outer membrane (OM) of Gram-negative bacteria is its asymmetry due to the presence of lipopolysaccharide (LPS) in the outer leaflet of the OM and phospholipids in the inner leaflet. Recent studies have revealed the existence of regulatory controls that ensure a balanced biosynthesis of LPS and phospholipids, both of which are essential for bacterial viability. LPS provides the essential permeability barrier function and act as a major virulence determinant. In Escherichia coli, more than 100 genes are required for LPS synthesis, its assembly at inner leaflet of the inner membrane (IM), extraction from the IM, translocation to the OM, and in its structural alterations in response to various environmental and stress signals. Although LPS are highly heterogeneous, they share common structural elements defining their most conserved hydrophobic lipid A part to which a core polysaccharide is attached, which is further extended in smooth bacteria by O-antigen. Defects or any imbalance in LPS biosynthesis cause major cellular defects, which elicit envelope responsive signal transduction controlled by RpoE sigma factor and two-component systems (TCS). RpoE regulon members and specific TCSs, including their non-coding arm, regulate incorporation of non-stoichiometric modifications of LPS, contributing to LPS heterogeneity and impacting antibiotic resistance.

Rapid evolution of acetic acid-detoxifying Escherichia coli under phosphate starvation conditions requires activation of the cryptic PhnE permease and induction of translesion synthesis DNA polymerases

Escherichia coli incubated in phosphate-limiting minimal medium dies during prolonged incubation as a result of the production of acetic acid. Variants that consume acetic acid generally sweep through the population after three serial cultures. Evolvability may primarily result from induction of the potentially mutagenic LexA DNA damage response or from growth of preexisting mutants. Cells starved of phosphate induce the LexA regulon through a unique mechanism based on an increase in the internal pH at the approach of the stationary phase. Evolved cells resume growth on phosphorylated products as a result of the activation of the cryptic PhnE permease. Here, it is shown that first PhnE-expressing revertants swept through starved populations independently of the expression of the LexA regulon. Induction of the LexA regulon and especially of the translesion synthesis DNA polymerases Pol IV and Pol V was, however, absolutely required for the ultimate evolution of acetic acid-detoxifying mutant strains. Both growth under selection and induction of translesion synthesis DNA polymerases are therefore required for adaptive evolution under phosphate starvation conditions.

Revisiting regulation of potassium homeostasis in Escherichia coli: the connection to phosphate limitation

Two-component signal transduction constitutes the predominant strategy used by bacteria to adapt to fluctuating environments. The KdpD/KdpE system is one of the most widespread, and is crucial for K⁺ homeostasis. In Escherichia coli, the histidine kinase KdpD senses K⁺ availability, whereas the response regulator KdpE activates synthesis of the high-affinity K⁺ uptake system KdpFABC. Here we show that, in the absence of KdpD, kdpFABC expression can be activated via phosphorylation of KdpE by the histidine kinase PhoR. PhoR and its cognate response regulator PhoB comprise a phosphate-responsive two-component system, which senses phosphate limitation indirectly through the phosphate transporter PstCAB and its accessory protein PhoU. In vivo two-hybrid interaction studies based on the bacterial adenylate cyclase reveal pairwise interactions between KdpD, PhoR, and PhoU. Finally, we demonstrate that cross-regulation between the kdpFABC and pstSCAB operons occurs in both directions under simultaneous K⁺ and phosphate limitation, both in vitro and in vivo. This study for the first time demonstrates direct coupling between intracellular K⁺ and phosphate homeostasis and provides a mechanism for fine-tuning of the balance between positively and negatively charged ions in the bacterial cell.