Bacterial Polyphosphate Kinases Revisited: Role in Pathogenesis and Therapeutic Potential

C-terminal Poly-histidine Tags Alter Escherichia coli Polyphosphate Kinase Activity and Susceptibility to Inhibition

In Escherichia coli, many environmental stressors trigger polyphosphate (polyP) synthesis by polyphosphate kinase (PPK1), including heat, nutrient restriction, toxic compounds, and osmotic imbalances. PPK1 is essential for virulence in many pathogens and has been the target of multiple screens for small molecule inhibitors that might serve as new anti-virulence drugs. However, the mechanisms by which PPK1 activity and polyP synthesis are regulated are poorly understood. Our previous attempts to uncover PPK1 regulatory elements resulted in the discovery of PPK1* mutants, which accumulate more polyP in vivo, but do not produce more in vitro. In attempting to further characterize these mutant enzymes, we discovered that the most commonly-used PPK1 purification method - Ni-affinity chromatography using a C-terminal poly-histidine tag - altered intrinsic aspects of the PPK1 enzyme, including specific activity, oligomeric state, and kinetic values. We developed an alternative purification strategy using a C-terminal C-tag which did not have these effects. Using this strategy, we were able to demonstrate major differences in the in vitro response of PPK1 to 5-aminosalicylic acid, a known PPK1 inhibitor, and observed several key differences between the wild-type and PPK1* enzymes, including changes in oligomeric distribution, increased enzymatic activity, and increased resistance to both product (ADP) and substrate (ATP) inhibition, that help to explain their in vivo effects. Importantly, our results indicate that the C-terminal poly-histidine tag is inappropriate for purification of PPK1, and that any in vitro studies or inhibitor screens performed with such tags need to be reconsidered in that light.

Polyphosphate uses mTOR, pyrophosphate, and Rho GTPase components to potentiate bacterial survival in Dictyostelium

IMPORTANCE

Although most bacteria are quickly killed after phagocytosis by a eukaryotic cell, some pathogenic bacteria escape death after phagocytosis. Pathogenic Mycobacterium species secrete polyP, and the polyP is necessary for the bacteria to prevent their killing after phagocytosis. Conversely, exogenous polyP prevents the killing of ingested bacteria that are normally killed after phagocytosis by human macrophages and the eukaryotic microbe Dictyostelium discoideum. This suggests the possibility that in these cells, a signal transduction pathway is used to sense polyP and prevent killing of ingested bacteria. In this report, we identify key components of the polyP signal transduction pathway in D. discoideum. In cells lacking these components, polyP is unable to inhibit killing of ingested bacteria. The pathway components have orthologs in human cells, and an exciting possibility is that pharmacologically blocking this pathway in human macrophages would cause them to kill ingested pathogens such as Mycobacterium tuberculosis.

Structural insight into substrate binding of Acinetobacter baumannii polyphosphate-AMP phosphotransferase (PPK2), a novel drug target

Acinetobacter baumannii is an opportunistic pathogen known for high morbidity and mortality. It causes life-threatening infections, such as ventilator-associated pneumonia (VAP), bacteremia, meningitis, wound and urinary tract infections (UTI). Increase in carbapenem resistance exhibited by A. baumannii has accentuated the need for novel targets for effective treatment. Despite the pronounced relevance of PPK2 as a pathogenicity determinant in several pathogens, it has not been explored as a drug target in A. baumannii. The present study was piloted to investigate the substrate binding by A. baumannii PPK2 (AbPPK2), a two-domain Class II polyphosphate kinase 2. A homology model of AbPPK2 was developed and validated for molecular docking of ATP and ADP in the predicted binding pocket. Further analysis of AbPPK2 revealed a set of common residues in the catalytic cleft interacting with ATP and ADP which would be useful for the screening of inhibitors against A. baumannii.

Polyphosphate Kinase Is Required for the Processes of Virulence and Persistence in Acinetobacter baumannii

Acinetobacter baumannii, one of the most successful bacteria causing severe nosocomial infection, was identified as a top-priority pathogen by the WHO. Thus, genetic manipulations to clarify the potential targets for fighting A. baumannii resistance and virulence are vital. Polyphosphate (polyP) kinase (PPK) is conserved in nearly all bacteria and is responsible for polyP formation, which is associated with bacterial pathogenicity and antibiotic resistance. In this study, ppk1-deficient (Δppk1::Apr), ppk1-complemented (Δppk1::Apr/PJL02-ppk1), and wild-type strains of A. baumannii ATCC 17978 were used to determine the influence of PPK1 on A. baumannii virulence and persistence mainly by polyP quantification, surface motility, biofilm formation, and bacterial persistence assays. Our work found that PPK1 is indispensable for polyP formation in vivo and that the motility of the PPK1-deficient strain was significantly impaired due to the lack of a pilus-like structure typically present compared with the complemented and wild-type strains. The deficiency of PPK1 also inhibited the biofilm formation of A. baumannii and decreased bacterial persistence under stimuli of high-concentration ampicillin (Amp) treatment, H₂O₂ stress, heat shock, and starvation stress. Furthermore, ppk1-deficient bacterium-infected mice showed a significantly reduced bacterial load and a decreased inflammatory response. However, complementation with PPK1 effectively rescued the impaired virulence and persistence of ppk1-deficient A. baumannii. In addition, metabonomic analysis revealed that PPK1 was associated with glycerophospholipid metabolism and fatty acid biosynthesis. Taken together, our results suggest that targeting PPK1 to control A. baumannii pathogenicity and persistence is a feasible strategy to fight this pathogen.

IMPORTANCEA. baumannii was identified as a top-priority pathogen by the WHO due to its antibiotic resistance. Meanwhile, the pathogenicity of A. baumannii mediated by several vital virulence factors also cannot be ignored. Here, the role of PPK1 in A. baumannii was also explored. We found that the motility ability and biofilm formation of a PPK1-deficient strain were significantly impaired. Furthermore, PPK1 was essential for its persistence maintenance to resist stimuli of high-concentration Amp treatment, H₂O₂ stress, heat shock, and starvation stress. Metabonomic analysis revealed that PPK1 was associated with glycerophospholipid metabolism and fatty acid biosynthesis. In addition, ppk1-deficient bacterium-infected mice showed significantly reduced bacterial loads and a decreased inflammatory responses in vivo. Together, our results suggest that PPK1 is vital for A. baumannii pathogenicity and persistence.

The role of nitrogen-responsive regulators in controlling inorganic polyphosphate synthesis in Escherichia coli

Inorganic polyphosphate (polyP) is synthesized by bacteria under stressful environmental conditions and acts by a variety of mechanisms to promote cell survival. While the kinase that synthesizes polyP (PPK, encoded by the ppk gene) is well known, ppk transcription is not activated by environmental stress and little is understood about how environmental stress signals lead to polyP accumulation. Previous work has shown that the transcriptional regulators DksA, RpoN (σ54) and RpoE (σ24) positively regulate polyP production, but not ppk transcription, in Escherichia coli. In this work, we examine the role of the alternative sigma factor RpoN and nitrogen starvation stress response pathways in controlling polyP synthesis. We show that the RpoN enhancer binding proteins GlnG and GlrR impact polyP production, and uncover a new role for the nitrogen phosphotransferase regulator PtsN (EIIANtr) as a positive regulator of polyP production, acting upstream of DksA, downstream of RpoN and apparently independently of RpoE. However, neither these regulatory proteins nor common nitrogen metabolites appear to act directly on PPK, and the precise mechanism(s) by which polyP production is modulated after stress remain(s) unclear. Unexpectedly, we also found that the genes that impact polyP production vary depending on the composition of the rich media in which the cells were grown before exposure to polyP-inducing stress. These results constitute progress towards deciphering the regulatory networks driving polyP production under stress, and highlight the remarkable complexity of this regulation and its connections to a broad range of stress-sensing pathways.

Inorganic Polyphosphate in Host and Microbe Biology

Inorganic polyphosphate (polyP) is produced by both bacteria and their eukaryotic hosts, and it appears to play multiple important roles in the interactions between those organisms. However, the detailed mechanisms of how polyP synthesis is regulated in bacteria, and how it influences both bacterial and host biology, remain largely unexplored. In this review, we examine recent developments in the understanding of how bacteria regulate the synthesis of polyP, what roles polyP plays in controlling virulence in pathogenic bacteria, and the effects of polyP on the mammalian immune system, as well as progress on developing drugs that may be able to target bacterial polyP synthesis as novel means of treating infectious disease.

Attenuation of Acinetobacter baumannii virulence by inhibition of polyphosphate kinase 1 with repurposed drugs

Acinetobacter baumannii is clinically one of the most significant pathogens, especially in intensive care settings, because of its multidrug-resistance (MDR). Repurposing of high-affinity drugs is a faster and more plausible approach for combating the emergence of MDR and to tackle bacterial infections. This study was aimed to evaluate the approved drugs potentially inhibiting A. baumannii PPK1 (AbPPK1) mediated synthesis of polyphosphates (polyP). Based on virtual screening, molecular dynamic simulation, and CD spectroscopy for thermal stability, two stable ligands, etoposide and genistein, were found with promising contours for further investigation. Following in vitro inhibition of AbPPK1, the efficacy of selected drugs was further tested against virulence traits of A. baumannii. These drugs significantly reduced the biofilm formation, surface motility in A. baumannii and led to decreased survival under desiccation. In addition to inhibition of PPK1, both drugs increased the expression of polyP degrading enzyme, exopolyphosphatase (PPX), that might be responsible for the decrease in the total cellular polyP. Since polyP modulates the virulence factors in bacteria, destabilization of the polyP pool by these drugs seems particularly striking for their therapeutic applications against A. baumannii.

Effect of Fe on inorganic polyphosphate level in autotrophic and heterotrophic cells of Rhodospirillum rubrum

Inorganic polyphosphate is involved in metal homeostasis in microorganisms. The aim of the study was to reveal differences in polyphosphate metabolism of Rhodospirillum rubrum under autotrophic and heterotrophic cultivation in the presence of Fe (2.3 mg Fe³⁺ L^-1) and without Fe (traces). Heterotrophic conditions without Fe resulted in cell lysis and low biomass yield. High polyphosphate content and low exopolyphosphatase activity were observed in the cells cultivated autotrophically in the presence of Fe. The cells grown heterotrophically in the presence of Fe contained more phosphate and low-molecular polyphosphate; on the contrary, the content of the high molecular polyphosphate decreased in parallel with the increase in exopolyphosphatase activity. The possible involvement of Pi and polyphosphate to the formation of Fe-containing inclusions is discussed.

Polyphosphate as a Target for Interference With Inflammation and Thrombosis

Activated platelets and mast cells expose the inorganic polymer, polyphosphate (polyP) on their surfaces. PolyP initiates procoagulant and proinflammatory reactions and the polymer has been recognized as a therapeutic target for interference with blood coagulation and vascular hyperpermeability. PolyP content and chain length depend on the specific cell type and energy status, which may affect cellular functions. PolyP metabolism has mainly been studied in bacteria and yeast, but its roles in eukaryotic cells and mammalian systems have remained enigmatic. In this review, we will present an overview of polyP functions, focusing on intra- and extracellular roles of the polymer and discuss open questions that emerge from the current knowledge on polyP regulation.