Polyphosphate kinase from Escherichia coli. Purification and demonstration of a phosphoenzyme intermediate

Pharmacological inhibition of host pathways enhances macrophage killing of intracellular bacterial pathogens

After ingestion into macrophage phagosomes, some bacterial pathogens such as Mycobacterium tuberculosis ( Mtb ) evade killing by preventing phagosome acidification and fusion of the phagosome with a lysosome. Mtb accumulates extracellular polyphosphate (polyP), and polyP inhibits macrophage phagosome acidification and bacterial killing. In Dictyostelium discoideum , polyP also inhibits bacterial killing, and we identified some proteins in D. discoideum that polyP requires to suppress the killing of ingested bacteria. Here, we find that pharmacological inhibition of human orthologues of the D. discoideum proteins, including P2Y1 receptors, mammalian Target of Rapamycin (mTOR), and inositol hexakisphosphate kinase, enhances the killing of Mtb , Legionella pneumophila , and Listeria monocytogenes by human macrophages. Mtb inhibits phagosome acidification, expression of the proinflammatory marker CD54, and autophagy, and increases expression of the anti-inflammatory marker CD206. In Mtb -infected macrophages, the polyP-degrading enzyme polyphosphatase (ScPPX) and inhibitors reversed these effects, with ScPPX increasing CD54 expression more in female macrophages compared to male macrophages. In addition, Mtb inhibits proteasome activity, and some, but not all, inhibitors reversed these effects. While the existence of a dedicated polyP signaling pathway remains uncertain, our findings suggest that pharmacological inhibition of select host proteins can restore macrophage function and enhances the killing of intracellular pathogens.

Importance

Human macrophages engulf bacteria into phagosomes, which then fuse with lysosomes to kill the bacteria. However, after engulfment, pathogenic bacteria such as Mycobacterium tuberculosis , Legionella pneumophila , and Listeria monocytogenes can block phagosome-lysosome fusion, allowing their survival. Here, we show that pharmacological inhibition of specific macrophage proteins reverses these effects and enhances bacterial killing. These findings suggest that targeting host factors involved in these processes may provide a therapeutic strategy to improve macrophage function against infections such as tuberculosis, Legionnaires' disease, and listeriosis.

Isolation and cultivation of a novel freshwater magnetotactic coccus FCR-1 containing unchained magnetosomes

Magnetotactic bacteria are ubiquitous aquatic prokaryotes that have the ability to biomineralize magnetite (Fe3O4) and/or greigite (Fe3S4) nanoparticles called magnetosomes. Magnetotactic cocci belonging to the class "Ca. Magnetococcia" are most frequently identified in freshwater habitats, but remain uncultivated. Here, we report for the first time axenic cultivation of freshwater magnetotactic coccus FCR-1 isolated from Chichijima, Japan. Strain FCR-1 grows microaerophilically in a semi-solid gellan gum medium. We find that strain FCR-1 biomineralizes Fe3O4 nanoparticles, which are not chained, into a cell. Based on phylogenomic analysis, compared with strains of the class "Ca. Magnetococcia", strain FCR-1 represents a novel genus of candidate family "Ca. Magnetaquicoccaceae" within the class "Ca. Magnetococcia" and we tentatively name this novel genus "Ca. Magnetaquiglobus chichijimensis". Our isolate provides a promising tool for elucidating the functions of unchained magnetosomes, the global distribution of magnetotactic bacteria and the origin of magnetotaxis.

A Novel Silver-Ruthenium-Based Antimicrobial Kills Gram-Negative Bacteria Through Oxidative Stress-Induced Macromolecular Damage

Amplified by the decline in antibiotic discovery, the rise of antibiotic resistance has become a significant global challenge in infectious disease control. Extraintestinal Escherichia coli (ExPEC), known to be the most common instigators of urinary tract infections (UTIs), represent such global threat. Novel strategies for more efficient treatments are therefore desperately needed. These include silver nanoparticles, which have been used as antimicrobial surface-coatings on catheters to eliminate biofilm-forming uropathogens and reduce the risk of nosocomial infections. AGXX® is a promising silver coating that presumably kills bacteria through the generation of reactive oxygen species (ROS) but is more potent than silver. However, neither is AGXX®'s mode of action fully understood, nor have its effects on Gram-negative bacteria or bacterial response and defense mechanisms towards AGXX® been studied in detail. Here, we report that the bactericidal effects of AGXX® are primarily based on ROS formation, as supplementation of the media with a ROS scavenger completely abolished AGXX®-induced killing. We further show that AGXX® impairs the integrity of the bacterial cell envelope and causes substantial protein aggregation and DNA damage already at sublethal concentrations. ExPEC strains appear to be more resistant to the proteotoxic effects of AGXX® compared to non-pathogenic E. coli, indicating improved defense capabilities of the uropathogen. Global transcriptomic studies of AGXX®-stressed ExPEC revealed a strong oxidative stress response, perturbations in metal homeostasis, as well as the activation of heat shock and DNA damage responses. Finally, we present evidence that ExPEC counter AGXX® damage through the production of the chaperone polyphosphate.

Mammalian mitochondrial inorganic polyphosphate (polyP) and cell signaling: Crosstalk between polyP and the activity of AMPK

Inorganic polyphosphate (polyP) is an evolutionary and ancient polymer composed by orthophosphate units linked by phosphoanhydride bonds. In mammalian cells, polyP shows a high localization in mammalian mitochondria, and its regulatory role in various aspects of bioenergetics has already been demonstrated, via molecular mechanism(s) yet to be fully elucidated. In recent years, a role for polyP in signal transduction, from brain physiology to the bloodstream, has also emerged.

OBJECTIVE

In this manuscript, we explored the intriguing possibility that the effects of polyP on signal transduction could be mechanistically linked to those exerted on bioenergetics.

METHODS

To conduct our studies, we used a combination of cellular and animal models.

RESULTS

Our findings demonstrate for the first time the intimate crosstalk between the levels of polyP and the activation status of the AMPK signaling pathway, via a mechanism involving free phosphate homeostasis. AMPK is a key player in mammalian cell signaling, and a crucial regulator of cellular and mitochondrial homeostasis. Our results show that the depletion of mitochondrial polyP in mammalian cells downregulates the activity of AMPK. Moreover, increased levels of polyP activate AMPK. Accordingly, the genetic downregulation of AMPKF0611 impairs polyP levels in both SH-SY5Y cells and in the brains of female mice.

CONCLUSIONS

This manuscript sheds new light on the regulation of AMPK and positions polyP as a potent regulator of mammalian cell physiology beyond mere bioenergetics, paving the road for using its metabolism as an innovative pharmacological target in pathologies characterized by dysregulated bioenergetics.

Diversity and physiology of abundant Rhodoferax species in global wastewater treatment systems

Wastewater treatment plants rely on complex microbial communities for bioconversion and removal of pollutants, but many process-critical species are still poorly investigated. One of these genera is Rhodoferax, an abundant core genus in wastewater treatment plants across the world. The genus has been associated with many metabolic traits such as iron reduction and oxidation and denitrification. We used 16S rRNA gene amplicon data to uncover the diversity and abundance of Rhodoferax species in Danish and global treatment plants. Publicly available metagenome-assembled genomes were analyzed based on phylogenomics to delineate species and assign taxonomies based on the SeqCode. The phylogenetic analysis of "Rhodoferax" revealed that species previously assigned to Rhodoferax in wastewater treatment plants should be considered as at least eight different genera, with five representing previously undescribed genera. Genome annotation showed potential for several key-bioconversions in wastewater treatment, such as nitrate reduction, carbohydrate degradation, and accumulations of various storage compounds. Iron oxidation and reduction capabilities were not predicted for abundant species. Species-resolved FISH-Raman was performed to gain an overview of the morphology and ecophysiology of selected taxa to clarify their potential role in global wastewater treatment systems. Our study provides a first insight into the functional and ecological characteristics of several novel genera abundant in global wastewater treatment plants, previously assigned to the Rhodoferax genus.

A fusion protein of polyphosphate kinase 1 (PPK1) and a Nudix hydrolase is involved in inorganic polyphosphate accumulation in the unicellular red alga Cyanidioschyzon merolae

Inorganic polyphosphate (polyP) is a linear polymer of phosphate that plays various roles in cells, including in phosphate and metal homeostasis. Homologs of the vacuolar transporter chaperone 4 (VTC4), catalyzing polyP synthesis in many eukaryotes, are absent in red algae, which are among the earliest divergent plant lineages. We identified homologs of polyphosphate kinase 1 (PPK1), a conserved polyP synthase in bacteria, in 42 eukaryotic genomes, including 31 species detected in this study and 12 species of red algae. Phylogenetic analysis suggested that most eukaryotic PPK1 homologs originated from horizontal gene transfer from a prokaryote to a plant before the divergence of red algae and Viridiplantae. In red algae, the homologs were fused to a nucleoside diphosphate-linked moiety X (Nudix) hydrolase of the diphosphoinositol polyphosphate phosphohydrolase (DIPP) family. We characterized the fusion protein CmPPK1 in the unicellular red alga Cyanidioschyzon merolae, which has been used in studies on basic features of eukaryotes. In the knockout strain ∆CmPPK1, polyP was undetectable, suggesting a primary role for CmPPK1 in polyP synthesis. In addition, ∆CmPPK1 showed altered metal balance. Mutations in the catalytically important residues of the Nudix hydrolase domain (NHD) either increased or decreased polyP contents. Both high and low polyP NHD mutants were susceptible to phosphate deprivation, indicating that adequate NHD function is necessary for normal phosphate starvation responses. The results reveal the unique features of PPK1 in red algae and promote further investigation of polyP metabolism and functions in red algae and eukaryotic evolution.

Differential inhibition of tire wear particles on sludge dewatering by aging modes

The study assessed the acute toxicities of tire wear particles (TWPs) on activated sludge, comparing cryogenically ground TWPs (C-TWPs) with photo-aged (PA-TWPs), ozone-aged (OA-TWPs), and Fenton-aged (FA-TWPs) variants over 96 h. At 0.1 mg/L, TWPs showed no significant effects on sludge respiration or purification. However, at 50 mg/L, significant impacts on respiration, decontamination capacity, and microbial community structure were observed, particularly in aged TWPs. Specifically, aged TWPs, especially FA-TWPs, are prone to inducing necrosis by generating non-cellular reactive oxygen species (ROS) catalyzed by persistent free radicals, leading to an increase in lactate dehydrogenase release ranging from 215 % to 284 %. Conversely, C-TWPs tend to trigger apoptosis via intracellular ROS accumulation, leading to a 358 % increase in intracellular ROS. Aged TWPs exhibited higher affinities for proteins and polysaccharides, while C-TWPs preferred phospholipids. All TWPs adversely affected sludge dewatering, with strong correlations found between specific resistance to filtration (SRF) and total protein (r = 0.981, p < 0.001) and between bound water and early cell apoptosis (r = 0.961, p < 0.01). Additionally, a correlation between SRF and cellular necrosis (r = 0.956, p < 0.01) was noted, linked to increased protein and extracellular polymeric substance levels. These results emphasize substantial influence of aged TWPs on sludge dewatering efficiency via diverse bacterial cell death mechanisms.

Acute inhibitory effects of tire wear particles on the removal of biological phosphorus：The critical role of aging in improving environmentally persistent free radicals

A comparative study explored how photoaging, ozonation aging, and Fenton aging affect tire wear particles (TWPs) and their phosphorus (P) removal in activated sludge. Aging altered TWPs' properties, increasing surface roughness, porosity, and generating more small particles, especially environmental persistent free radicals (EPFRs) in ozonation and Fenton aging. Post-aging TWPs (50 mg/L) inhibited sludge P removal significantly (p < 0.05), with rates of 44.3% and 59.6% for ozonation and Fenton aging, respectively. In addition, the metabolites involved in P cycling (poly-β-hydroxyalkanoates: PHA and glycogen) and essential enzymes (Exopolyphosphatase: PPX and Polyphosphate kinase: PPK) were significantly inhibited (p < 0.05). Moreover, TWPs led to a decrease in microbial cells within the sludge and altered the community structure, a situation exacerbated by the aging of TWPs. P-removing bacteria decreased (e.g., Burkholderia, Candidatus), while extracellular polymeric substance-secreting bacteria increased (e.g., Pseudomonas, Novosphingobium). Pearson correlation analysis highlighted EPFRs' role in TWPs' acute toxicity to microbial cells, yet, emphasizing particle size's impact on the sludge system's purification and community structure.

Pseudomonas aeruginosa kills Staphylococcus aureus in a polyphosphate-dependent manner

Due to their frequent coexistence in many polymicrobial infections, including in patients with cystic fibrosis or burn/chronic wounds, many studies have investigated the mechanistic details of the interaction between the opportunistic pathogens Pseudomonas aeruginosa and Staphylococcus aureus. P. aeruginosa rapidly outcompetes S. aureus under in vitro cocultivation conditions, which is mediated by several of P. aeruginosa's virulence factors. Here, we report that polyphosphate (polyP), an efficient stress defense system and virulence factor in P. aeruginosa, plays a role in the pathogen's ability to inhibit and kill S. aureus in a contact-independent manner. We show that P. aeruginosa cells characterized by low polyP levels are less detrimental to S. aureus growth and survival while the Gram-positive pathogen is significantly more compromised by the presence of P. aeruginosa cells that produce high levels of polyP. The polyP-dependent phenotype of P. aeruginosa-mediated killing of S. aureus could at least in part be direct, as polyP was detected in the spent media and causes significant damage to the S. aureus cell envelope. However, more likely is that polyP's effects are indirect through modulating the production of one of P. aeruginosa's virulence factors, pyocyanin. We show that pyocyanin production in P. aeruginosa occurs polyP-dependently and harms S. aureus through membrane damage and potentially the generation of reactive oxygen species, resulting in the increased expression of antioxidant enzymes. In summary, our study adds a new component to the list of biomolecules that the Gram-negative pathogen P. aeruginosa generates to compete with S. aureus for resources.IMPORTANCEHow do interactions between microorganisms shape the course of polymicrobial infections? Previous studies have provided evidence that the two opportunistic pathogens Pseudomonas aeruginosa and Staphylococcus aureus generate molecules that modulate their interaction with potentially significant impact on disease outcomes. Our study identified the biopolymer polyphosphate (polyP) as a new effector molecule that impacts P. aeruginosa's interaction with S. aureus. We show that P. aeruginosa kills S. aureus in a polyP-dependent manner, which occurs primarily through the polyP-dependent production of the P. aeruginosa virulence factor pyocyanin. Our findings add a new role for polyP to an already extensive list of functions. A more in-depth understanding of how polyP influences interspecies interactions is critical, as targeting polyP synthesis in bacteria such as P. aeruginosa may have a significant impact on other microorganisms and potentially result in dynamic changes in the microbial composition.

Inorganic Polyphosphate Promotes Colorectal Cancer Growth via TRPM8 Receptor Signaling Pathway

BACKGROUND

Colorectal cancer (CRC) is characterized by a pro-inflammatory microenvironment and features high-energy-supply molecules that assure tumor growth. A still less studied macromolecule is inorganic polyphosphate (iPolyP), a high-energy linear polymer that is ubiquitous in all forms of life. Made up of hundreds of repeated orthophosphate units, iPolyP is essential for a wide variety of functions in mammalian cells, including the regulation of proliferative signaling pathways. Some evidence has suggested its involvement in carcinogenesis, although more studies need to be pursued. Moreover, iPolyP regulates several homeostatic processes in animals, spanning from energy metabolism to blood coagulation and tissue regeneration.

RESULTS

In this study, we tested the role of iPolyP on CRC proliferation, using in vitro and ex vivo approaches, in order to evaluate its effect on tumor growth. We found that iPolyP is significantly increased in tumor tissues, derived from affected individuals enrolled in this study, compared to the corresponding peritumoral counterparts. In addition, iPolyP signaling occurs through the TRPM8 receptor, a well-characterized Na+ and Ca2+ ion channel often overexpressed in CRC and linked with poor prognosis, thus promoting CRC cell proliferation. The pharmacological inhibition of TRPM8 or RNA interference experiments performed in established CRC cell lines, such as Caco-2 and SW620, showed that the involvement of TRPM8 is essential, greater than that of the other two known iPolyP receptors, P2Y1 and RAGE. The presence of iPolyP drives cancer cells towards the mitotic phase of the cell cycle by enhancing the expression of ccnb1, which encodes the Cyclin B protein. In vitro 2D and 3D data reflected the ex vivo results, obtained by the generation of CRC-derived organoids, which increased in size.

CONCLUSIONS

These results indicate that iPolyP may be considered a novel and unexpected early biomarker supporting colorectal cancer cell proliferation.

Enhancing L-Asparagine Bioproduction Efficiency Through L-Asparagine Synthetase and Polyphosphate Kinase-Coupled Conversion and ATP Regeneration

L-Asparagine, a crucial amino acid widely used in both food and medicine, presents pollution-related and side reaction challenges when prepared using chemical synthesis method. Although biotransformation methods offer significant advantages such as high efficiency and mild reaction conditions, they also entail increased costs due to the need for ATP supplementation. This study aimed to address the challenges associated with biopreparation of L-asparagine. Firstly, the functionality and characteristics of recombinant L-asparagine synthetase enzymes derived from Escherichia coli and Lactobacillus salivarius were evaluated to determine their practical applicability. Subsequently, recombinant expression of polyphosphate kinase from Erysipelotrichaceae bacterium was conducted. A reaction system for L-asparagine synthesis was established using a dual enzyme-coupled conversion approach. Under the optimal reaction conditions, a maximum yield of 11.67 g/L of L-asparagine was achieved, with an 88.43% conversion rate, representing a 5.03-fold increase compared to the initial conversion conditions. Notably, the initial addition of ATP was reduced to only 5.66% of the theoretical demand, indicating the effectiveness of our ATP regeneration system. These findings highlight the potential of our approach in enhancing the efficiency of L-asparagine preparation, offering promising prospects for the food and medical industries.

The archaeal family 3 polyphosphate kinase reveals a function of polyphosphate as energy buffer under low energy charge

Inorganic polyphosphate, a linear polymer of orthophosphate residues linked by phosphoanhydride bonds, occurs in all three domains of life and plays a diverse and prominent role in metabolism and cellular regulation. While the polyphosphate metabolism and its physiological significance have been well studied in bacteria and eukaryotes including human, there are only few studies in archaea available so far. In Crenarchaeota including members of Sulfolobaceae , the presence of polyphosphate and degradation via exopolyphosphatase has been reported and there is some evidence for a functional role in metal ion chelation, biofilm formation, adhesion and motility, however, the nature of the crenarchaeal polyphosphate kinase is still unknown. Here we used the crenarchaeal model organism Sulfolobus acidocaldarius to study the enzymes involved in polyphosphate synthesis. The two genes annotated as thymidylate kinase ( saci_2019 and saci_2020 ), localized downstream of the exopolyphosphatase, were identified as the missing polyphosphate kinase in S. acidocaldarius ( Sa PPK3). Thymidylate kinase activity was confirmed for Saci_0893. Notably Saci_2020 showed no polyphosphate kinase activity on its own but served as regulatory subunit (rPPK3) and was able to enhance polyphosphate kinase activity of the catalytically active subunit Saci_2019 (cPPK3). Heteromeric polyphosphate kinase activity is reversible and shows a clear preference for polyP-dependent nucleotide kinase activity, i.e. polyP-dependent formation of ATP from ADP (12.4 U/mg) and to a lower extent of GDP to GTP whereas AMP does not serve as substrate. PPK activity in the direction of ATP-dependent polyP synthesis is rather low (0.25 U/mg); GTP was not used as phosphoryl donor. A combined experimental modelling approach using quantitative 31 P NMR allowed to follow the reversible enzyme reaction for both ATP and polyP synthesis. PolyP synthesis was only observed when the ATP/ADP ratio was kept high, using an ATP recycling system. In absence of such a recycling system, all incubations with polyP and PPK would reach an equilibrium state with an ATP/ADP ratio between 3 and 4, independent of the initial conditions. Structural and sequence comparisons as well as phylogenetic analysis reveal that the S. acidocaldarius PPK is a member of a new PPK family, named PPK3, within the thymidylate kinase family of the P-loop kinase superfamily, clearly separated from PPK2. Our studies show that polyP, in addition to its function as phosphate storage, has a special importance for the energy homeostasis of S. acidocaldarius and due to its reversibility serves as energy buffer under low energy charge enabling a quick response to changes in cellular demand.

Wastewater Treatment with Bacterial Representatives of the Thiothrix Morphotype

Bacteria of the Thiothrix morphotype, comprising the genera Thiothrix, Thiolinea and Thiofilum, are frequently encountered in domestic and industrial wastewater treatment systems, but they are usually not clearly differentiated due to the marked similarity in their morphologies. Methods ranging from light microscopy, FISH and PCR to modern high-throughput sequencing are used to identify them. The development of these bacteria in wastewater treatment systems has both advantages and disadvantages. On the one hand, the explosive growth of these bacteria can lead to activated sludge bulking or clogging of the treatment system's membranes, with a consequent decrease in the water treatment efficiency. On the other hand, members of the Thiothrix morphotype can improve the quality of granular sludge and increase the water treatment efficiency. This may be due to their capacity for sulfide oxidation, denitrification combined with the oxidation of reduced sulfur compounds, enhanced biological phosphate removal and possibly denitrifying phosphate removal. The recently obtained pangenome of the genus Thiothrix allows the explanation, at the genomic level, of the experimental results of various studies. Moreover, this review summarizes the data on the factors affecting the proliferation of representatives of the Thiothrix morphotype.

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.

Quantitative Analysis of Rhodobacter sphaeroides Storage Organelles via Cryo-Electron Tomography and Light Microscopy

Bacterial cytoplasmic organelles are diverse and serve many varied purposes. Here, we employed Rhodobacter sphaeroides to investigate the accumulation of carbon and inorganic phosphate in the storage organelles, polyhydroxybutyrate (PHB) and polyphosphate (PP), respectively. Using cryo-electron tomography (cryo-ET), these organelles were observed to increase in size and abundance when growth was arrested by chloramphenicol treatment. The accumulation of PHB and PP was quantified from three-dimensional (3D) segmentations in cryo-tomograms and the analysis of these 3D models. The quantification of PHB using both segmentation analysis and liquid chromatography and mass spectrometry (LCMS) each demonstrated an over 10- to 20-fold accumulation of PHB. The cytoplasmic location of PHB in cells was assessed with fluorescence light microscopy using a PhaP-mNeonGreen fusion-protein construct. The subcellular location and enumeration of these organelles were correlated by comparing the cryo-ET and fluorescence microscopy data. A potential link between PHB and PP localization and possible explanations for co-localization are discussed. Finally, the study of PHB and PP granules, and their accumulation, is discussed in the context of advancing fundamental knowledge about bacterial stress response, the study of renewable sources of bioplastics, and highly energetic compounds.

An Update on Polyphosphate In Vivo Activities

Polyphosphate (polyP) is an evolutionary ancient inorganic molecule widespread in biology, exerting a broad range of biological activities. The intracellular polymer serves as an energy storage pool and phosphate/calcium ion reservoir with implications for basal cellular functions. Metabolisms of the polymer are well understood in procaryotes and unicellular eukaryotic cells. However, functions, regulation, and association with disease states of the polymer in higher eukaryotic species such as mammalians are just beginning to emerge. The review summarises our current understanding of polyP metabolism, the polymer's functions, and methods for polyP analysis. In-depth knowledge of the pathways that control polyP turnover will open future perspectives for selective targeting of the polymer.

Polyphosphate Nanoparticles: Balancing Energy Requirements in Tissue Regeneration Processes

Nanoparticles of a particular, evolutionarily old inorganic polymer found across the biological kingdoms have attracted increasing interest in recent years not only because of their crucial role in metabolism but also their potential medical applicability: it is inorganic polyphosphate (polyP). This ubiquitous linear polymer is composed of 10-1000 phosphate residues linked by high-energy anhydride bonds. PolyP causes induction of gene activity, provides phosphate for bone mineralization, and serves as an energy supplier through enzymatic cleavage of its acid anhydride bonds and subsequent ATP formation. The biomedical breakthrough of polyP came with the development of a successful fabrication process, in depot form, as Ca- or Mg-polyP nanoparticles, or as the directly effective polymer, as soluble Na-polyP, for regenerative repair and healing processes, especially in tissue areas with insufficient blood supply. Physiologically, the platelets are the main vehicles for polyP nanoparticles in the circulating blood. To be biomedically active, these particles undergo coacervation. This review provides an overview of the properties of polyP and polyP nanoparticles for applications in the regeneration and repair of bone, cartilage, and skin. In addition to studies on animal models, the first successful proof-of-concept studies on humans for the healing of chronic wounds are outlined.

Control of a chemical chaperone by a universally conserved ATPase

The universally conserved YchF/Ola1 ATPases regulate stress response pathways in prokaryotes and eukaryotes. Deletion of YchF/Ola1 leads to increased resistance against environmental stressors, such as reactive oxygen species, while their upregulation is associated with tumorigenesis in humans. The current study shows that in E. coli, the absence of YchF stimulates the synthesis of the alternative sigma factor RpoS by a transcription-independent mechanism. Elevated levels of RpoS then enhance the transcription of major stress-responsive genes. In addition, the deletion of ychF increases the levels of polyphosphate kinase, which in turn boosts the production of the evolutionary conserved and ancient chemical chaperone polyphosphate. This potentially provides a unifying concept for the increased stress resistance in bacteria and eukaryotes upon YchF/Ola1 deletion. Intriguingly, the simultaneous deletion of ychF and the polyphosphate-degrading enzyme exopolyphosphatase causes synthetic lethality in E. coli, demonstrating that polyphosphate production needs to be fine-tuned to prevent toxicity.

The Protein Scaffolding Functions of Polyphosphate

Inorganic polyphosphate (polyP), one of the first high-energy compound on earth, defies its extreme compositional and structural simplicity with an astoundingly wide array of biological activities across all domains of life. However, the underlying mechanism of such functional pleiotropy remains largely elusive. In this review, we will summarize recent studies demonstrating that this simple polyanion stabilizes protein folding intermediates and scaffolds select native proteins. These functions allow polyP to act as molecular chaperone that protects cells against protein aggregation, as pro-amyloidogenic factor that accelerates both physiological and disease-associated amyloid formation, and as a modulator of liquid-liquid phase separation processes. These activities help to explain polyP's known roles in bacterial stress responses and pathogenicity, provide the mechanistic foundation for its potential role in human neurodegenerative diseases, and open a new direction regarding its influence on gene expression through condensate formation. We will highlight critical unanswered questions and point out potential directions that will help to further understand the pleiotropic functions of this ancient and ubiquitous biopolymer.

Structure of the exopolyphosphatase (PPX) from Zymomonas mobilis reveals a two-magnesium-ions PPX

Rapid adaptation of metabolic capabilities is crucial for bacterial survival in habitats with fluctuating nutrient availability. In such conditions, the bacterial stringent response is a central regulatory mechanism activated by nutrient starvation or other stressors. This response is primarily controlled by exopolyphosphatase/guanosine pentaphosphate phosphohydrolase (PPX/GPPA) enzymes. To gain further insight into these enzymes, the high-resolution crystal structure of PPX from Zymomonas mobilis (ZmPPX) was determined at 1.8 Å. The phosphatase activity of PPX was strictly dependent on the presence of divalent metal cations. Notably, the structure of ZmPPX revealed the presence of two magnesium ions in the active site center, which is atypical compared to other PPX structures where only one divalent ion is observed. ZmPPX exists as a dimer in solution and belongs to the "long" PPX group consisting of four domains. Remarkably, the dimer configuration exhibits a substantial and deep aqueduct with positive potential along its interface. This aqueduct appears to extend towards the active site region, suggesting that this positively charged aqueduct could potentially serve as a binding site for polyP.

Possible Role of CHAD Proteins in Copper Resistance

Conserved Histidine Alpha-helical Domain (CHAD) proteins attached to the surface of polyphosphate (PolyP) have been studied in some bacteria and one archaeon. However, the activity of CHAD proteins is unknown beyond their interaction with PolyP granules. By using bioinformatic analysis, we report that several species of the biomining acidophilic bacteria contain orthologs of CHAD proteins with high sequence identity. Furthermore, the gene coding for the CHAD protein is in the same genetic context of the enzyme polyphosphate kinase (PPK), which is in charge of PolyP synthesis. Particularly, the group of ppk and CHAD genes is highly conserved. Metallosphaera sedula and other acidophilic archaea used in biomining also contain CHAD proteins. These archaea show high levels of identity in genes coding for a cluster having the same organization. Amongst these genes are chad and ppx. In general, both biomining bacteria and archaea contain high PolyP levels and are highly resistant to heavy metals. Therefore, the presence of this conserved genetic organization suggests a high relevance for their metabolism. It has been formerly reported that a crystallized CHAD protein contains a copper-binding site. Based on this previous knowledge, in the present report, it was determined that all analyzed CHAD proteins are very conserved at their structural level. In addition, it was found that the lack of YgiF, an Escherichia coli CHAD-containing protein, decreases copper resistance in this bacterium. This phenotype was not only complemented by transforming E. coli with YgiF but also by expressing CHAD from Acidithiobacillus ferrooxidans in it. Interestingly, the strains in which the possible copper-binding sites were mutated were also more metal sensitive. Based on these results, we propose that CHAD proteins are involved in copper resistance in microorganisms. These findings are very interesting and may eventually improve biomining operations in the future.

Polyphosphate kinase-1 regulates bacterial and host metabolic pathways involved in pathogenesis of Mycobacterium tuberculosis

Inorganic polyphosphate (polyP) is primarily synthesized by Polyphosphate Kinase-1 (PPK-1) and regulates numerous cellular processes, including energy metabolism, stress adaptation, drug tolerance, and microbial pathogenesis. Here, we report that polyP interacts with acyl CoA carboxylases, enzymes involved in lipid biosynthesis in Mycobacterium tuberculosis. We show that deletion of ppk-1 in M. tuberculosis results in transcriptional and metabolic reprogramming. In comparison to the parental strain, the Δppk-1 mutant strain had reduced levels of virulence-associated lipids such as PDIMs and TDM. We also observed that polyP deficiency in M. tuberculosis is associated with enhanced phagosome-lysosome fusion in infected macrophages and attenuated growth in mice. Host RNA-seq analysis revealed decreased levels of transcripts encoding for proteins involved in either type I interferon signaling or formation of foamy macrophages in the lungs of Δppk-1 mutant-infected mice relative to parental strain-infected animals. Using target-based screening and molecular docking, we have identified raloxifene hydrochloride as a broad-spectrum PPK-1 inhibitor. We show that raloxifene hydrochloride significantly enhanced the activity of isoniazid, bedaquiline, and pretomanid against M. tuberculosis in macrophages. Additionally, raloxifene inhibited the growth of M. tuberculosis in mice. This is an in-depth study that provides mechanistic insights into the regulation of mycobacterial pathogenesis by polyP deficiency.

Unraveling microbial characteristics of simultaneous nitrification, denitrification and phosphorus removal in a membrane-aerated biofilm reactor

This study describes the simultaneous removal of carbon, ammonium, and phosphate from domestic wastewater by a membrane-aerated biofilm reactor (MABR) which was operated for 360 days. During the operation, the maximum removal efficiencies of chemical oxygen demand (COD), total nitrogen (TN) and total phosphorus (TP) reached 93.1%, 83.98%, and 96.41%, respectively. Statistical analysis showed that the MABR could potentially treat wastewater with a high ammonium concentration and a relatively low C/N ratio. Dissolved oxygen and multiple pollutants, including ammonium, carbon, phosphate, and sulfate, shaped the structure of the microbial community in the MABR. High throughput sequencing uncovered the crucial microbiome in ammonium transformation in MABR. Phylogenetic analysis of the ammonia monooxygenase (amoA) genes revealed an important role for comammox Nitrospira in the nitrification process. Diverse novel phosphate-accumulating organisms (Thauera, Bacillus, and Pseudomonas) and sulfur-oxidizing bacteria (Thiobacillus, Thiothrix and Sulfurimonas) were potentially involved in denitrification in MABR. The results from this study suggested that MABR could be a feasible system for the simultaneous removal of nitrogen, carbon, phosphorus, and sulfur from sewage water.

Pseudomonas aeruginosa kills Staphylococcus aureus in a polyphosphate-dependent manner

Due to their frequent coexistence in many polymicrobial infections, including in patients with burn or chronic wounds or cystic fibrosis, recent studies have started to investigate the mechanistic details of the interaction between the opportunistic pathogens Pseudomonas aeruginosa and Staphylococcus aureus. P. aeruginosa rapidly outcompetes S. aureus under in vitro co-cultivation conditions, which is mediated by several of P. aeruginosa's virulence factors. Here, we report that polyphosphate (polyP), an efficient stress defense system and virulence factor in P. aeruginosa, plays a role for the pathogen's ability to inhibit and kill S. aureus in a contact-independent manner. We show that P. aeruginosa cells characterized by low polyP level are less detrimental to S. aureus growth and survival while the gram-positive pathogen is significantly more compromised by the presence of P. aeruginosa cells that produce high level of polyP. We show that the polyP-dependent phenotype could be a direct effect by the biopolymer, as polyP is present in the spent media and causes significant damage to the S. aureus cell envelope. However, more likely is that polyP's effects are indirect through the regulation of one of P. aeruginosa's virulence factors, pyocyanin. We show that pyocyanin production in P. aeruginosa occurs polyP-dependent and harms S. aureus through membrane damage and the generation of reactive oxygen species, resulting in increased expression of antioxidant enzymes. In summary, our study adds a new component to the list of biomolecules that the gram-negative pathogen P. aeruginosa generates to compete with S. aureus for resources.

A Cell-Free Multi-enzyme Cascade Reaction for the Synthesis of CDP-Glycerol

CDP-glycerol is a nucleotide-diphosphate-activated version of glycerol. In nature, it is required for the biosynthesis of teichoic acid in Gram-positive bacteria, which is an appealing target epitope for the development of new vaccines. Here, a cell-free multi-enzyme cascade was developed to synthetize nucleotide-activated glycerol from the inexpensive and readily available substrates cytidine and glycerol. The cascade comprises five recombinant enzymes expressed in Escherichia coli that were purified by immobilized metal affinity chromatography. As part of the cascade, ATP is regenerated in situ from polyphosphate to reduce synthesis costs. The enzymatic cascade was characterized at the laboratory scale, and the products were analyzed by high-performance anion-exchange chromatography (HPAEC)-UV and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). After the successful synthesis had been confirmed, a design-of-experiments approach was used to screen for optimal operation conditions (temperature, pH value and MgCl2 concentration). Overall, a substrate conversion of 89 % was achieved with respect to the substrate cytidine.

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.

Model-based optimization of cell-free enzyme cascades exemplified for the production of GDP-fucose

Cell-free production systems are increasingly used for the synthesis of industrially relevant chemicals and biopharmaceuticals. Cell-free systems often utilize cell lysates, but biocatalytic cascades based on recombinant enzymes have emerged as a promising alternative strategy. However, implementing efficient enzyme cascades is a non-trivial task and mathematical modeling and optimization has become a key tool to improve their performance. In this work, we introduce a generic framework for the model-based optimization of cell-free enzyme cascades based on a given kinetic model of the system. We first formulate and systematize seven optimization problems relevant in the context of cell-free production processes including, for example, the maximization of productivity or product yield and the minimization of overall costs. We then present an approach that accounts for parameter uncertainties, not only during model calibration and model analysis but also when performing the actual optimization. After constructing a kinetic model of the enzyme cascade, experimental data are used to generate an ensemble of kinetic parameter sets reflecting their variabilities. For every parameter set, systems optimization is then performed and the resulting solution subsequently cross-validated for all other parameterizations to identify the solution with the highest overall performance under parameter uncertainty. We exemplify our approach for the cell-free synthesis of GDP-fucose, an important sugar nucleotide with various applications. We selected and solved three optimization problems based on a constructed dynamic model and validated two of them experimentally leading to significant improvements of the process (e.g., 50% increase of titer under identical total enzyme load). Overall, our results demonstrate the potential of model-driven optimization for the rational design and improvement of cell-free production systems. The developed approach for systems optimization under parameter uncertainty could also be relevant for the metabolic design of cell factories.

Human Prune Regulates the Metabolism of Mammalian Inorganic Polyphosphate and Bioenergetics

Inorganic polyphosphate (polyP) is an evolutionarily conserved and ubiquitous polymer that is present in all studied organisms. PolyP consists of orthophosphates (Pi) linked together by phosphoanhydride bonds. The metabolism of polyP still remains poorly understood in higher eukaryotes. Currently, only F0F1-ATP synthase, Nudt3, and Prune have been proposed to be involved in this metabolism, although their exact roles and regulation in the context of polyP biology have not been fully elucidated. In the case of Prune, in vitro studies have shown that it exhibits exopolyphosphatase activity on very short-chain polyP (up to four units of Pi), in addition to its known cAMP phosphodiesterase (PDE) activity. Here, we expand upon studies regarding the effects of human Prune (h-Prune) on polyP metabolism. Our data show that recombinant h-Prune is unable to hydrolyze short (13-33 Pi) and medium (45-160 Pi) chains of polyP, which are the most common chain lengths of the polymer in mammalian cells. Moreover, we found that the knockdown of h-Prune (h-Prune KD) results in significantly decreased levels of polyP in HEK293 cells. Likewise, a reduction in the levels of polyP is also observed in Drosophila melanogaster loss-of-function mutants of the h-Prune ortholog. Furthermore, while the activity of ATP synthase, and the levels of ATP, are decreased in h-Prune KD HEK293 cells, the expression of ATP5A, which is a main component of the catalytic subunit of ATP synthase, is upregulated in the same cells, likely as a compensatory mechanism. Our results also show that the effects of h-Prune on mitochondrial bioenergetics are not a result of a loss of mitochondrial membrane potential or of significant changes in mitochondrial biomass. Overall, our work corroborates the role of polyP in mitochondrial bioenergetics. It also demonstrates a conserved effect of h-Prune on the metabolism of short- and medium-chain polyP (which are the predominant chain lengths found in mammalian cells). The effects of Prune in polyP are most likely exerted via the regulation of the activity of ATP synthase. Our findings pave the way for modifying the levels of polyP in mammalian cells, which could have pharmacological implications in many diseases where dysregulated bioenergetics has been demonstrated.

The ppk-expressing transgenic rice floating bed improves P removal in slightly polluted water

With significant economic advantages, the plant floating bed has been widely utilized in the ecological remediation of eutrophic water because of the excessive phosphorus (P) and nitrogen discharge in China. Previous research has demonstrated that polyphosphate kinase (ppk)-expressing transgenic rice (Oryza sativa L. ssp. japonica) (ETR) can increase the P absorption capacity to support rice growth and boost rice yield. In this study, the floating beds of ETR with single copy line (ETRS) and double copy line (ETRD) are built to investigate their capacity to remove aqueous P in slightly polluted water. Compared with the wild type Nipponbare (WT) floating bed, the ETR floating beds greatly reduce the total P concentration in slightly polluted water though the ETR floating beds have the same removal rates of chlorophyll-a, NO3--N, and total nitrogen in slightly polluted water. The P uptake rate of ETRD on the floating bed is 72.37% in slightly polluted water, which is higher than that of ETRS and WT on the floating beds. Polyphosphate (polyP) synthesis is a critical factor for the excessive phosphate uptake of ETR on the floating beds. The synthesis of polyP decreases the level of free intracellular phosphate (Pi) in ETR on the floating beds, simulating the phosphate starvation signaling. The OsPHR2 expression in the shoot and root of ETR on the floating bed increased, and the corresponding P metabolism gene expression in ETR was changed, which promoted Pi uptake by ETR in slightly polluted water. The Pi accumulation further promoted the growth of ETR on the floating beds. These findings highlight that the ETR floating beds, especially ETRD floating bed, have significant potential for P removal and can be exploited as a novel method for phytoremediation in slightly polluted water.

Functional characterization of the gonococcal polyphosphate pseudo-capsule

Neisseria gonorrhoeae is an exclusively human pathogen able to evade the host immune system through multiple mechanisms. Gonococci accumulate a large portion of phosphate moieties as polyphosphate (polyP) on the exterior of the cell. Although its polyanionic nature has suggested that it may form a protective shield on the cell surface, its role remains controversial. Taking advantage of a recombinant His-tagged polyP-binding protein, the presence of a polyP pseudo-capsule in gonococcus was demonstrated. Interestingly, the polyP pseudo-capsule was found to be present in specific strains only. To investigate its putative role in host immune evasion mechanisms, such as resistance to serum bactericidal activity, antimicrobial peptides and phagocytosis, the enzymes involved in polyP metabolism were genetically deleted, generating mutants with altered polyP external content. The mutants with lower polyP content on their surface compared to the wild-type strains, became sensitive to complement-mediated killing in presence of normal human serum. Conversely, naturally serum sensitive strains that did not display a significant polyP pseudo-capsule became resistant to complement in the presence of exogenous polyP. The presence of polyP pseudo-capsule was also critical in the protection from antibacterial activity of cationic antimicrobial peptide, such as cathelicidin LL-37. Results showed that the minimum bactericidal concentration was lower in strains lacking polyP than in those harboring the pseudo-capsule. Data referring to phagocytic killing resistance, assessed by using neutrophil-like cells, showed a significant decrease in viability of mutants lacking polyP on their cell surface in comparison to the wild-type strain. The addition of exogenous polyP overturned the killing phenotype of sensitive strains suggesting that gonococcus could exploit environmental polyP to survive to complement-mediated, cathelicidin and intracellular killing. Taken together, data presented here indicate an essential role of the polyP pseudo-capsule in the gonococcal pathogenesis, opening new perspective on gonococcal biology and more effective treatments.

Polyphosphate kinase 1 is involved in formation, the morphology and ultramicrostructure of biofilm of Mycobacterium smegmatis and its survivability in macrophage

The most unique characteristic of Mycobacterium tuberculosis is persistence in the human host, and the biofilm formation is related to the persistance. Polyphosphate (polyP) kinase 1 (PPK1) is conserved in Mycobacteria and is responsible for polyP synthesis. polyP is a chain molecule linked by high-energy phosphate bonds, which is considered to play a very important role in bacterial persistence. However, the relationship of PPK1 and mycobacterial biofilm formation is still adequately unclear. In current study, ppk1-deficient mutant (MT), ppk1-complemented (CT) and wild-type strains of M. smegmatis mc² 155 were used to investigate the formation, morphology and ultramicrostructure of the biofilm and to analyze the lipid levels and susceptibility to vancomycin antibiotic. And then WT, MT and CT strains were used to infect macrophages and to analyze the expression levels of various inflammatory factors, respectively. We found that PPK1 was required for M. smegmatis polyP production in vivo and polyP deficiency not only attenuated the biofilm formation, but also altered the phenotype and ultramicrostructure of the biofilm and reduced the cell lipid composition (except for C16.1 and C17.1, most of the fatty acid components from C8-C24). Moreover, the ppk1-deficient mutant was also significantly more sensitive to vancomycin which targets the cell wall, and its ability to survive in macrophages was decreased, which was related to the change of the expression level of inflammatory factors in macrophage. This study demonstrates that the PPK1 can affect the biofilm structure through affecting the content of short chain fatty acid and promote intracellular survival of M. smegmatis by altering the expression of inflammatory factors. These findings establish a basis for investigating the role of PPK1 in the persistence of M. tuberculosis, and provide clues for treating latent infection of M. tuberculosis with PPK1 as a potential drug target.

Nutrients removal by Olivibacter jilunii immobilized on activated carbon for aquaculture wastewater treatment: ppk1 gene and bacterial community structure

In this study, immobilized biological activated carbon (IBAC) mediated with Olivibacter jilunii (strain PAO-9) was utilized to treat aquaculture wastewater for nutrients removal. IBAC with strain PAO-9 could load the greatest ppk1 gene copy numbers (129524.6) per gram on activated carbon at 28 °C for 2 d in 120 rpm of stirring speed and 2 d in stationary condition. Moreover, the results about the nutrients removal and microbiology community structure showed that strain PAO-9 on IBAC could alter the structure and diversity of microbial communities and then promoted to remove the total phosphorus and total nitrogen of eel aquaculture wastewater. The highest total phosphorus, chemical oxygen demand, ammonia and total nitrogen of the wastewater treated by strain PAO-9 on IBAC were 96.1 %, 98.0 %, 100.0 % and 97.4 %, respectively. In all, O. jilunii PAO-9 immobilized activated carbon was a potential and effective approach to remove the nutrients of eel aquaculture wastewater.

Inorganic Polyphosphate: Coacervate Formation and Functional Significance in Nanomedical Applications

Inorganic polyphosphates (polyP) are long-chain polymers of orthophosphate residues, which, depending on the external conditions, can be present both physiologically and synthetically in either soluble, nanoparticulate or coacervate form. In recent years, these polymers have received increasing attention due to their unprecedented ability to exhibit both morphogenetic and metabolic energy delivering properties. There are no other physiological molecules that contain as many metabolically utilizable, high-energy bonds as polyP, making these polymers of particular medical interest as components of advanced hydrogel scaffold materials for potential applications in ATP-dependent tissue regeneration and repair. However, these polymers show physiological activity only in soluble form and in the coacervate phase, but not as stable metal-polyP nanoparticles. Therefore, understanding the mechanisms of formation of polyP coacervates and nanoparticles as well as their transformations is important for the design of novel materials for tissue implants, wound healing, and drug delivery and is discussed here.

Hierarchical Assembly of Flexible Biopolymer Polyphosphate-Manganese into Nanosheets

Polyphosphate (polyP) is one of the most compact inorganic polyanionic biopolymers that participates in various physiological processes. However, the development of polyP-based nanomaterials is still in its infancy. Here, biocompatible polyphosphate-manganese nanosheets are designed and synthesized by a hierarchical assembly strategy. The thickness and the lateral size of the resulting polyP-Mn nanosheets (PMNSs) are 5 nm and 120-130 nm, respectively. Molecular dynamics simulations suggested that the polyP-hexadecyl trimethyl ammonium bromide flat structure possesses a strong aggregating capacity and serves as the template for the 2D assembly of polyP-Mn. The PMNSs can activate the inflammatory response of macrophages resulting in the recovery of innate immunological functions to inhibit tumor proliferation. This work has initiated a new direction in constructing layered polyP-based nanomaterials and provides guidance for biocompatible and biodegradable biopolymer-based materials in the regulation of innate responses.

Make or break: the thermodynamic equilibrium of polyphosphate kinase-catalysed reactions

Polyphosphate kinases (PPKs) have become popular biocatalysts for nucleotide 5'-triphosphate (NTP) synthesis and regeneration. Two unrelated families are described: PPK1 and PPK2. They are structurally unrelated and use different catalytic mechanisms. PPK1 enzymes prefer the usage of adenosine 5'-triphosphate (ATP) for polyphosphate (polyP) synthesis while PPK2 enzymes favour the reverse reaction. With the emerging use of PPK enzymes in biosynthesis, a deeper understanding of the enzymes and their thermodynamic reaction course is of need, especially in comparison to other kinases. Here, we tested four PPKs from different organisms under the same conditions without any coupling reactions. In comparison to other kinases using phosphate donors with comparably higher phosphate transfer potentials that are characterised by reaction yields close to full conversion, the PPK-catalysed reaction reaches an equilibrium in which about 30% ADP is left. These results were obtained for PPK1 and PPK2 enzymes, and are supported by theoretical data on the basic reaction. At high concentrations of substrate, the different kinetic preferences of PPK1 and PPK2 can be observed. The implications of these results for the application of PPKs in chemical synthesis and as enzymes for ATP regeneration systems are discussed.

Polyphosphate Kinases Phosphorylate Thiamine Phosphates

Polyphosphate kinases (PPKs) catalyze the reversible transfer of the γ-phosphate moiety of ATP (or of another nucleoside triphosphate) to a growing chain of polyphosphate (polyP). In this study, we describe that PPKs of various sources are additionally able to phosphorylate thiamine diphosphate (ThP2) to produce thiamine triphosphate (ThP3) and even thiamine tetraphosphate in vitro using polyP as phosphate donor. Furthermore, all tested PPK2s, but not PPK1s, were able to phosphorylate thiamine monophosphate (ThP1) to ThP2 and ThP3 although at low efficiency. The predicted masses and identities of the mono- and oligo-phosphorylated thiamine metabolites were identified by high-performance liquid chromatography tandem mass spectrometry. Moreover, the biological activity of ThP2, that was synthesized by phosphorylation of ThP1 with polyP and PPK, as a cofactor of ThP2-dependent enzymes (here transketolase TktA from Escherichia coli) was confirmed in a coupled enzyme assay. Our study shows that PPKs are promiscuous enzymes in vitro that could be involved in the formation of a variety of phosphorylated metabolites in vivo.

Dictyostelium discoideum cells retain nutrients when the cells are about to overgrow their food source

Dictyostelium discoideum is a unicellular eukaryote that eats bacteria, and eventually outgrows the bacteria. D. discoideum cells accumulate extracellular polyphosphate (polyP), and the polyP concentration increases as the local cell density increases. At high cell densities, the correspondingly high extracellular polyP concentrations allow cells to sense that they are about to outgrow their food supply and starve, causing the D. discoideum cells to inhibit their proliferation. In this report, we show that high extracellular polyP inhibits exocytosis of undigested or partially digested nutrients. PolyP decreases plasma membrane recycling and apparent cell membrane fluidity, and this requires the G protein-coupled polyP receptor GrlD, the polyphosphate kinase Ppk1 and the inositol hexakisphosphate kinase I6kA. PolyP alters protein contents in detergent-insoluble crude cytoskeletons, but does not significantly affect random cell motility, cell speed or F-actin levels. Together, these data suggest that D. discoideum cells use polyP as a signal to sense their local cell density and reduce cell membrane fluidity and membrane recycling, perhaps as a mechanism to retain ingested food when the cells are about to starve.

This article has an associated First Person interview with the first author of the paper.

Enzymatic Depletion of Mitochondrial Inorganic Polyphosphate (polyP) Increases the Generation of Reactive Oxygen Species (ROS) and the Activity of the Pentose Phosphate Pathway (PPP) in Mammalian Cells

Inorganic polyphosphate (polyP) is an ancient biopolymer that is well preserved throughout evolution and present in all studied organisms. In mammals, it shows a high co-localization with mitochondria, and it has been demonstrated to be involved in the homeostasis of key processes within the organelle, including mitochondrial bioenergetics. However, the exact extent of the effects of polyP on the regulation of cellular bioenergetics, as well as the mechanisms explaining these effects, still remain poorly understood. Here, using HEK293 mammalian cells under Wild-type (Wt) and MitoPPX (cells enzymatically depleted of mitochondrial polyP) conditions, we show that depletion of polyP within mitochondria increased oxidative stress conditions. This is characterized by enhanced mitochondrial O2- and intracellular H2O2 levels, which may be a consequence of the dysregulation of oxidative phosphorylation (OXPHOS) that we have demonstrated in MitoPPX cells in our previous work. These findings were associated with an increase in basal peroxiredoxin-1 (Prx1), superoxide dismutase-2 (SOD2), and thioredoxin (Trx) antioxidant protein levels. Using 13C-NMR and immunoblotting, we assayed the status of glycolysis and the pentose phosphate pathway (PPP) in Wt and MitoPPX cells. Our results show that MitoPPX cells display a significant increase in the activity of the PPP and an increase in the protein levels of transaldolase (TAL), which is a crucial component of the non-oxidative phase of the PPP and is involved in the regulation of oxidative stress. In addition, we observed a trend towards increased glycolysis in MitoPPX cells, which corroborates our prior work. Here, for the first time, we show the crucial role played by mitochondrial polyP in the regulation of mammalian redox homeostasis. Moreover, we demonstrate a significant effect of mitochondrial polyP on the regulation of global cellular bioenergetics in these cells.

Polyphosphate Kinase 2 (PPK2) Enzymes: Structure, Function, and Roles in Bacterial Physiology and Virulence

Inorganic polyphosphate (polyP) has been implicated in an astonishing array of biological functions, ranging from phosphorus storage to molecular chaperone activity to bacterial virulence. In bacteria, polyP is synthesized by polyphosphate kinase (PPK) enzymes, which are broadly subdivided into two families: PPK1 and PPK2. While both enzyme families are capable of catalyzing polyP synthesis, PPK1s preferentially synthesize polyP from nucleoside triphosphates, and PPK2s preferentially consume polyP to phosphorylate nucleoside mono- or diphosphates. Importantly, many pathogenic bacteria such as Pseudomonas aeruginosa and Acinetobacter baumannii encode at least one of each PPK1 and PPK2, suggesting these enzymes may be attractive targets for antibacterial drugs. Although the majority of bacterial polyP studies to date have focused on PPK1s, PPK2 enzymes have also begun to emerge as important regulators of bacterial physiology and downstream virulence. In this review, we specifically examine the contributions of PPK2s to bacterial polyP homeostasis. Beginning with a survey of the structures and functions of biochemically characterized PPK2s, we summarize the roles of PPK2s in the bacterial cell, with a particular emphasis on virulence phenotypes. Furthermore, we outline recent progress on developing drugs that inhibit PPK2 enzymes and discuss this strategy as a novel means of combatting bacterial infections.

Inorganic Polyphosphate and F0F1-ATP Synthase of Mammalian Mitochondria

Inorganic polyphosphate is a polymer which plays multiple important roles in yeast and bacteria. In higher organisms the role of polyP has been intensively studied in last decades and involvements of this polymer in signal transduction, cell death mechanisms, energy production, and many other processes were demonstrated. In contrast to yeast and bacteria, where enzymes responsible for synthesis and hydrolysis of polyP were identified, in mammalian cells polyP clearly plays important role in physiology and pathology but enzymes responsible for synthesis of polyP or consumption of this polymer are still not identified. Here, we discuss the role of mitochondrial F₀F₁-ATP synthase in polyP synthesis with results, which confirm this proposal. We also discuss the role of other enzymes which may play important roles in polyP metabolism.

Inorganic Polyphosphate in Mitochondrial Energy Metabolism and Pathology

In this chapter, the current understanding of the potential roles played by polyphosphate in mitochondrial function with a specific focus on energy metabolism and mitochondrial pathologies caused by stress is summarized. Here we will discuss details of the possible ion transporting mechanisms of mitochondria that might involve polyP and their role in mitochondrial physiology and pathology are discussed.

Inorganic Polyphosphate, Mitochondria, and Neurodegeneration

With an aging population, the presence of aging-associated pathologies is expected to increase within the next decades. Regrettably, we still do not have any valid pharmacological or non-pharmacological tools to prevent, revert, or cure these pathologies. The absence of therapeutical approaches against aging-associated pathologies can be at least partially explained by the relatively lack of knowledge that we still have regarding the molecular mechanisms underlying them, as well as by the complexity of their etiopathology. In fact, a complex number of changes in the physiological function of the cell has been described in all these aging-associated pathologies, including neurodegenerative disorders. Based on multiple scientific manuscripts produced by us and others, it seems clear that mitochondria are dysfunctional in many of these aging-associated pathologies. For example, mitochondrial dysfunction is an early event in the etiopathology of all the main neurodegenerative disorders, and it could be a trigger of many of the other deleterious changes which are present at the cellular level in these pathologies. While mitochondria are complex organelles and their regulation is still not yet entirely understood, inorganic polyphosphate (polyP) could play a crucial role in the regulation of some mitochondrial processes, which are dysfunctional in neurodegeneration. PolyP is a well-preserved biopolymer; it has been identified in every organism that has been studied. It is constituted by a series of orthophosphates connected by highly energetic phosphoanhydride bonds, comparable to those found in ATP. The literature suggests that the role of polyP in maintaining mitochondrial physiology might be related, at least partially, to its effects as a key regulator of cellular bioenergetics. However, further research needs to be conducted to fully elucidate the molecular mechanisms underlying the effects of polyP in the regulation of mitochondrial physiology in aging-associated pathologies, including neurodegenerative disorders. With a significant lack of therapeutic options for the prevention and/or treatment of neurodegeneration, the search for new pharmacological tools against these conditions has been continuous in past decades, even though very few therapeutic approaches have shown potential in treating these pathologies. Therefore, increasing our knowledge about the molecular mechanisms underlying the effects of polyP in mitochondrial physiology as well as its metabolism could place this polymer as a promising and innovative pharmacological target not only in neurodegeneration, but also in a wide range of aging-associated pathologies and conditions where mitochondrial dysfunction has been described as a crucial component of its etiopathology, such as diabetes, musculoskeletal disorders, and cardiovascular disorders.

Production of Glucose 6-Phosphate From a Cellulosic Feedstock in a One Pot Multi-Enzyme Synthesis

Glucose 6-phosphate is the phosphorylated form of glucose and is used as a reagent in enzymatic assays. Current production occurs via a multi-step chemical synthesis. In this study we established a fully enzymatic route for the synthesis of glucose 6-phosphate from cellulose. As the enzymatic phosphorylation requires ATP as phosphoryl donor, the use of a cofactor regeneration system is required. We evaluated Escherichia coli glucokinase and Saccharomyces cerevisiae hexokinase (HK) for the phosphorylation reaction and Pseudomonas aeruginosa polyphosphate kinase 2 (PPK2) for ATP regeneration. All three enzymes were characterized in terms of temperature and pH optimum and the effects of substrates and products concentrations on enzymatic activities. After optimization of the conditions, we achieved a 85% conversion of glucose into glucose 6-phosphate using the HK/PPK2 activities within a 24 h reaction resulting in 12.56 g/l of glucose 6-phosphate. Finally, we demonstrated the glucose 6-phosphate formation from microcrystalline cellulose in a one-pot reaction comprising Aspergillus niger cellulase for glucose release and HK/PPK2 activities. We achieved a 77% conversion of released glucose into glucose 6-phosphate, however at the expense of a lower glucose 6-phosphate yield of 1.17 g/l. Overall, our study shows an alternative approach for synthesis of glucose 6-phosphate that can be used to valorize biomass derived cellulose.

Probiotic Aspergillus oryzae produces anti-tumor mediator and exerts anti-tumor effects in pancreatic cancer through the p38 MAPK signaling pathway

Intake of probiotics or fermented food produced by some probiotic bacteria is believed to exert anti-tumor functions in various cancers, including pancreatic cancer, because several studies have demonstrated the anti-tumor effects of probiotic bacteria in vitro and in vivo in animal carcinogenesis models. However, the mechanisms underlying the anticancer effects of probiotics on pancreatic cancer have not been clarified. In this study, we assessed the anti-tumor effects of probiotic bacteria against pancreatic cancer cells. Among the known probiotic bacteria, Aspergillus oryzae exhibited a strong pancreatic tumor suppression effect. The culture supernatant of A. oryzae was separated by HPLC. Heptelidic acid was identified as an anti-tumor molecule derived from A. oryzae by LC–MS and NMR analysis. The anti-tumor effect of heptelidic acid was exhibited in vitro and in vivo in a xenograft model of pancreatic cancer cells. The anti-tumor effect of heptelidic acid was exerted by the p38 MAPK signaling pathway. Heptelidic acid traverses the intestinal mucosa and exerts anti-tumor effects on pancreatic cancer cells. This is a novel anti-tumor mechanism induced by beneficial bacteria against pancreatic cancer in which bacterial molecules pass through the intestinal tract, reach the extra-intestinal organs, and then induce apoptosis via an inducible signaling pathway.

The Multiple Roles of Polyphosphate in Ralstonia eutropha and Other Bacteria

An astonishing variety of functions has been attributed to polyphosphate (polyP) in prokaryotes. Besides being a reservoir of phosphorus, functions in exopolysaccharide formation, motility, virulence and in surviving various forms of stresses such as exposure to heat, extreme pH, oxidative agents, high osmolarity, heavy metals and others have been ascribed to polyP. In this contribution, we will provide a historical overview on polyP, will then describe the key proteins of polyP synthesis, the polyP kinases, before we will critically assess of the underlying data on the multiple functions of polyP and provide evidence that - with the exception of a P-storage-function - most other functions of polyP are not relevant for survival of Ralstonia eutropha, a biotechnologically important beta-proteobacterial species.

Enzymatic properties of Myxococcus xanthus exopolyphosphatases mxPpx1 and mxPpx2

Myxococcus xanthus possesses two exopolyphosphatases, mxPpx1 and mxPpx2, which belong to the family of Ppx/GppA phosphatases; however, their catalytic properties have not been described. mxPpx1 and mxPpx2 contain 311 and 505 amino acid residues, respectively; mxPpx2 has an additional C-terminal region, which corresponds to the metal-dependent HDc phosphohydrolase domain. mxPpx1 mainly hydrolyzed short-chain polyPs (polyP₃ and polyP₄), whereas mxPpx2 preferred long-chain polyP_60-70 and polyP_700-1000. mxPpx2 was activated by 25-50 mM KCl, but mxPpx1 did not significantly depend on K⁺. In addition, mxPpx1 and mxPpx2 showed weak hydrolysis of ATP and GTP in the absence of K⁺, and mxPpx2 could also hydrolyze guanosine pentaphosphate (pppGpp) in the presence of K⁺. The exopolyphosphatase activity of mxPpx1 toward polyP₃ was inhibited by polyP_700-1000 and that of mxPpx2 toward polyP_60-70 and polyP_700-1000, by pyrophosphate. To clarify the function of the mxPpx2 C-terminal domain, it was fused to mxPpx1 (mxPpx1-2C) and deleted from mxPpx2 (mxPpx2∆C). Compared to wild-type mxPpx2, mxPpx2∆C had significantly reduced exopolyphosphatase activity toward long-chain polyPs (by 90%), whereas that toward polyP₃ and polyP₄ was much less affected; furthermore, the phosphohydrolase activity toward pppGpp, ATP, and GTP was also decreased (by 30-75%). In contrast, mxPpx1-2C had increased hydrolytic activity compared to mxPpx1. Furthermore, mxPpx2∆C lost the requirement for K⁺ characteristic for the wild-type enzyme, whereas mxPpx1-2C acquired it. These results suggest that the C-terminal domain of mxPpx2 is necessary for its maximum hydrolytic activity, especially toward long-chain polyPs, and defines mxPpx2 dependency on K⁺ for activation.

Biomedical Applications of Bacteria-Derived Polymers

Plastics have found widespread use in the fields of cosmetic, engineering, and medical sciences due to their wide-ranging mechanical and physical properties, as well as suitability in biomedical applications. However, in the light of the environmental cost of further upscaling current methods of synthesizing many plastics, work has recently focused on the manufacture of these polymers using biological methods (often bacterial fermentation), which brings with them the advantages of both low temperature synthesis and a reduced reliance on potentially toxic and non-eco-friendly compounds. This can be seen as a boon in the biomaterials industry, where there is a need for highly bespoke, biocompatible, processable polymers with unique biological properties, for the regeneration and replacement of a large number of tissue types, following disease. However, barriers still remain to the mass-production of some of these polymers, necessitating new research. This review attempts a critical analysis of the contemporary literature concerning the use of a number of bacteria-derived polymers in the context of biomedical applications, including the biosynthetic pathways and organisms involved, as well as the challenges surrounding their mass production. This review will also consider the unique properties of these bacteria-derived polymers, contributing to bioactivity, including antibacterial properties, oxygen permittivity, and properties pertaining to cell adhesion, proliferation, and differentiation. Finally, the review will select notable examples in literature to indicate future directions, should the aforementioned barriers be addressed, as well as improvements to current bacterial fermentation methods that could help to address these barriers.

Did Cyclic Metaphosphates Have a Role in the Origin of Life?

How life began still eludes science life, the initial progenote in the context presented herein, being a chemical aggregate of primordial inorganic and organic molecules capable of self-replication and evolution into ever increasingly complex forms and functions.Presented is a hypothesis that a mineral scaffold generated by geological processes and containing polymerized phosphate units was present in primordial seas that provided the initiating factor responsible for the sequestration and organization of primordial life's constituents. Unlike previous hypotheses proposing phosphates as the essential initiating factor, the key phosphate described here is not a polynucleotide or just any condensed phosphate but a large (in the range of at least 1 kilo-phosphate subunits), water soluble, cyclic metaphosphate, which is a closed loop chain of polymerized inorganic phosphate residues containing only phosphate middle groups. The chain forms an intrinsic 4-phosphate helix analogous to its structure in Na Kurrol's salt, and as with DNA, very large metaphosphates may fold into hairpin structures. Using a Holliday-junction-like scrambling mechanism, also analogous to DNA, rings may be manipulated (increased, decreased, exchanged) easily with little to no need for additional energy, the reaction being essentially an isomerization.A literature review is presented describing findings that support the above hypothesis. Reviewed is condensed phosphate inorganic chemistry including its geological origins, biological occurrence, enzymes and their genetics through eukaryotes, polyphosphate functions, circular polynucleotides and the role of the Holliday junction, previous biogenesis hypotheses, and an Eoarchean Era timeline.