Phosphate Residues Research Articles

PPK1 and PPK2 — which polyphosphate kinase is older?

Polyphosphate kinases (PPKs) catalyse the polymerisation and degradation of polyphosphate chains. As a result of this process, PPK produces or consumes energy in the form of ATP. Polyphosphate is a linear molecule that contains tens to hundreds of phosphate residues connected by macroergic bonds, and it appears to be an easily obtainable and rich source of energy from prebiotic times to the present. Notably, polyphosphate is present in the cells of all three domains of life, but PPKs are widely distributed only in Bacteria, as Archaea and Eucarya use various unrelated or “nonhomologous” proteins for energy and metabolic balance. The present study focuses on PPK1 and PPK2 homologues, which have been described to some extent in Bacteria, and the aim was to determine which homologue group, PPK1 or PPK2, is older. Phylogenetic analyses of 109 sequence homologues of Escherichia coli PPK1 and 109 sequence homologues of Pseudomonas aeruginosa PPK2 from 109 bacterial genomes imply that polyphosphate consumption (PPK2) evolved first and that phosphate polymerisation (PPK1) evolved later. Independently, a theory of the trends in amino acid loss and gain also confirms that PPK2 is older than PPK1. According to the results of this study, we propose 68 hypothetical proteins to mark as PPK2 homologues and 3 hypothetical proteins to mark as PPK1 homologues.

Functions of inorganic polyphosphates in eukaryotic cells: a coat of many colours

PolyP (inorganic polyphosphate) is a linear polymer of tens to hundreds of orthophosphate residues linked by high-energy phosphoanhydride bonds. This polymer is present in all living organisms from bacteria to mammals. Until recently, most of the studies on polyP have focused on its function in prokaryotes. In prokaryotes, polyP has been implicated in many unrelated processes ranging from basic metabolism to structural functions. However, polyP analysis and function in higher eukaryotes has been gaining momentum recently. In the present review, we mainly aim to discuss the proposed intracellular functions of polyP in higher eukaryotes and its detection methods.

Chemical Mechanism of Glycerol 3-Phosphate Phosphatase: pH-Dependent Changes in the Rate-Limiting Step

The halo-acid dehalogenase (HAD) superfamily comprises a large number of enzymes that share a conserved core domain responsible for a diverse array of chemical transformations (e.g., phosphonatase, dehalogenase, phosphohexomutase, and phosphatase) and a cap domain that controls substrate specificity. Phosphate hydrolysis is thought to proceed via an aspartyl-phosphate intermediate, and X-ray crystallography has shown that protein active site conformational changes are required for catalytic competency. Using a combination of steady-state and pre-steady-state kinetics, pL-rate studies, solvent kinetic isotope effects, (18)O molecular isotope exchange, and partition experiments, we provide a detailed description of the chemical mechanism of a glycerol 3-phosphate phosphatase. This phosphatase has been recently recognized as a rate-limiting factor in lipid polar head recycling in Mycobacterium tuberculosis [Larrouy-Maumus, G., et al. (2013) Proc. Natl. Acad. Sci. 110 (28), 11320-11325]. Our results clearly establish the existence of an aspartyl-phosphate intermediate in this newly discovered member of the HAD superfamily. No ionizable groups are rate-limiting from pH 5.5 to 9.5, consistent with the pK values of the catalytic aspartate residues. The formation and decay of this intermediate are partially rate-limiting below pH 7.0, and a conformational change preceding catalysis is rate-limiting above pH 7.0.

Cytompatibility Assessment of the Surface of Titanium after Phosphorylation

In this study, orthophosphoric acid (H3PO4) in the treatment of porous titanium (Ti) is investigated and the ability of rat bone marrow stromal cells (BMSCs) is assessed to proliferate and differentiate on these modified surfaces in vitro. To improve the cytocompatibility of Ti surfaces, pure Ti was activated commercially by simple chemical pretreatment in H3PO4 with different densities. Next, the phosphorylated specimens were soaked in simulated body fluid (SBF) to study the effect of biomineralization. The3-[4,5-dimethylthiazol-2-y1]-2, 5-diphenytetrazolium bromide (MTT) assay and the measurement of alkaline phosphatase (ALP) activity utilized to assess proliferation and differentiation of BMSCs on exposure to modified Ti surfaces. Scanning electron microscopic (SEM) images showed that the surfaces of the pre-treated samples were characterized by a complex structure which consisted of a mesh-like morphological matrix and an uniform surface with different morphic crystals of titanium dihydrogen orthophosphate (Ti(H2PO4)3). These crystals contained hydroxyl with phosphate residues that resulted in biomineralization of cells. Therefore, BMSCs reveales a well-dispersed morphology on these modified and functionalized Ti surfaces. The viability and ALP activity of BMSCs on these altered biomimetic surfaces are found to be greater than those of the controls. It is concluded that the treatment of Ti by acid etching in orthophosphoric acid is a suitable method to enhance the in vitro proliferation and differentiation of BMSCs.

Extraction and Quantification of Poly P, Poly P Analysis by Urea-PAGE.

Inorganic polyphosphate (poly P) molecules, linear chains containing hundreds of orthophosphate (Pi) residues linked by high-energy phosphoanhydride bonds are abundant in every cell in nature. These molecules are widely distributed among bacteria, including key pathogens, and eukaryotes, poly P is present in organelles, including nuclei, mitochondria, and vesicles.

Role of Polyphosphate in Cancer Cell Proliferation

Inorganic polyphosphates (polyPs) are linear polymers of orthophosphate residues linked by phosphoanhydride bonds similar to ATP. PolyPs are ubiquitously distributed in nature from bacteria to mammalian cells where they play multiple roles. Here we investigated intracellular localization of polyP in cancer cell lines and tested the idea about the involvement of polyP in cell growth.To study PolyP localization and cellular levels we used DAPI-based method of polyP staining. Experiments were performed using the following cell lines: H1299 (lung cancer), U251 (glioma) and HEK293 as a control cell line. PolyP was also visualized by immunocytochemistry with X-press tagged PolyP-binding domain of exopolyphosphatase (PPX) and subsequent use of specific antibodies. The role of PolyP in cancer cell proliferation was studied using MTS proliferation assay. In these experiments endogenous PolyP was either blocked by spermine, a polyamine with high PolyP-binding affinity, or depleted by transient expression of PPX, an enzyme that specifically hydrolyzes PolyP into orthophosphate.PolyP levels were increased in glioma and lung cancer cells compare to HEK 293 cells. Proliferation of lung carcinoma (H1299) cells was significantly inhibited when PolyP was blocked with spermine compare to control cells. However, proliferation of glioma cells (U251) was not affected by spermine, even at high concentrations of this polyamine (60 μM), suggesting a cancer type dependent effect or, involvement of divers mechanisms of actions of PolyP in different cell types. These results suggest that PolyP plays an important role in the regulation of proliferation of cancer cells. Further investigation of PolyP contribution to cancer development and progression may provide tools to detect, prevent and/or treat cancer.

Synthesis of 11-[(2-pyridyl)amino]- and 11-[(9-anthracenylcarbonyl)amino]undecyl phosphate and investigation of their acceptor properties in the enzymic reaction catalyzed by galactosylphosphotransferases from Salmonella

11-[(2-Pyridyl)amino]undecyl phosphate and 11-[(9-anthracenylcarbonyl)amino]undecyl phosphate were chemically synthesized. The abiliy of these new fluorescent derivatives of undecyl phosphate to serve as acceptor substrate of galactosyl phosphate residue in the enzymic reaction catalyzed by galactosylphosphotransferase from Salmonella anatum or Salmonella newport membrane preparation was demonstrated.

Accumulation of Polyphosphate in Lactobacillus spp. and Its Involvement in Stress Resistance

Polyphosphate (poly-P) is a polymer of phosphate residues synthesized and in some cases accumulated by microorganisms, where it plays crucial physiological roles such as the participation in the response to nutritional stringencies and environmental stresses. Poly-P metabolism has received little attention in Lactobacillus, a genus of lactic acid bacteria of relevance for food production and health of humans and animals. We show that among 34 strains of Lactobacillus, 18 of them accumulated intracellular poly-P granules, as revealed by specific staining and electron microscopy. Poly-P accumulation was generally dependent on the presence of elevated phosphate concentrations in the culture medium, and it correlated with the presence of polyphosphate kinase (ppk) genes in the genomes. The ppk gene from Lactobacillus displayed a genetic arrangement in which it was flanked by two genes encoding exopolyphosphatases of the Ppx-GppA family. The ppk functionality was corroborated by its disruption (LCABL_27820 gene) in Lactobacillus casei BL23 strain. The constructed ppk mutant showed a lack of intracellular poly-P granules and a drastic reduction in poly-P synthesis. Resistance to several stresses was tested in the ppk-disrupted strain, showing that it presented a diminished growth under high-salt or low-pH conditions and an increased sensitivity to oxidative stress. These results show that poly-P accumulation is a characteristic of some strains of lactobacilli and may thus play important roles in the physiology of these microorganisms.

Alkaline phosphatase in boar sperm function

Alkaline phosphatase (AP) catalyses the detachment of phosphate residues from different substrates. Its activity has been demonstrated in seminal plasma and spermatozoa from porcine and other mammalian species; anyway, the role of AP in male reproduction has not been clarified yet and the aim of this study was to determine AP function in boar sperm capacitation and in vitro fertilization (IVF). AP activity was assayed in seminal plasma and in uncapacitated and in vitro capacitated (IVC) spermatozoa; in addition, capacitation was studied in presence of different doses of AP (1.2 and 2.5IU/mL). The effect of different doses of AP (1.2 and 2.5IU/mL) on several sperm parameters after IVC (viability, acrosome integrity with FITC-PSA, capacitation status with CTC staining, tyrosine phosphorylation) and on fertilizing ability during IVF were also evaluated. High AP activity was detected in seminal plasma, in particular in sperm-rich fraction; a lower activity was detected in uncapacitated spermatozoa while a significant decrease was evidenced after IVC. Viability was not changed by AP supplementation of the capacitating medium, whereas acrosome integrity and capacitation status were significantly affected by 1.2 and 2.5 doses, with a dose-dependent decrease in acrosome-reacted cells as well as in CTC B pattern displaying cells. As for sperm head protein phosphorylation, a decrease in relative fluorescence was detected in AP 2.5 group, if compared with capacitated one. After IVF, a dose-dependent decrease in penetrated oocytes was recorded, with an increase in monospermic zygote rate. In conclusion, we demonstrated that AP activity decreases under capacitating condition and that addition of AP to spermatozoa during capacitation results in a depression of the capacitating process and IVF. We can infer that AP plays a role in keeping spermatozoa quiescent until they are ejaculated and in modulating the acquisition of the fertilizing ability.

Polyphosphate-Mediated Inhibition of Tartrate-Resistant Acid Phosphatase and Suppression of Bone Resorption of Osteoclasts

Inorganic polyphosphate (poly(P)) has recently been found to play an important role in bone formation. In this study, we found that tartrate-resistant acid phosphatase (TRAP), which is abundantly expressed in osteoclasts, has polyphosphatase activity that degrades poly(P) and yields Pi as well as shorter poly(P) chains. Since the TRAP protein that coprecipitated with anti-TRAP monoclonal antibodies exhibited both polyphosphatase and the original phosphatase activity, poly(P) degradation activity is dependent on TRAP and not on other contaminating enzymes. The ferrous chelator α, α’-bipyridyl, which inhibits the TRAP-mediated production of reactive oxygen species (ROS), had no effect on such poly(P) degradation, suggesting that the degradation is not dependent on ROS. In addition, shorter chain length poly(P) molecules were better substrates than longer chains for TRAP, and poly(P) inhibited the phosphatase activity of TRAP depending on its chain length. The IC50 of poly(P) against the original phosphatase activity of TRAP was 9.8 µM with an average chain length more than 300 phosphate residues, whereas the IC50 of poly(P) with a shorter average chain length of 15 phosphate residues was 8.3 mM. Finally, the pit formation activity of cultured rat osteoclasts differentiated by RANKL and M-CSF were markedly inhibited by poly(P), while no obvious decrease in cell number or differentiation efficiency was observed for poly(P). In particular, the inhibition of pit formation by long chain poly(P) with 300 phosphate residues was stronger than that of shorter chain poly(P). Thus, poly(P) may play an important regulatory role in osteoclastic bone resorption by inhibiting TRAP activity, which is dependent on its chain length.

Yolk hydrolases in the eggs of Anticarsia gemmatalis hubner (Lepidoptera: Noctuidae): A role for inorganic polyphosphate towards yolk mobilization

Despite being the main insect pest on soybean crops in the Americas, very few studies have approached the general biology of the lepidopteran Anticarsia gemmatalis and there is a paucity of studies with embryo formation and yolk mobilization in this species. In the present work, we identified an acid phosphatase activity in the eggs of A. gemmatalis (agAP) that we further characterized by means of biochemistry and cell biology experiments. By testing several candidate substrates, this enzyme proved chiefly active with phosphotyrosine; in vitro assays suggested a link between agAP activity and dephosphorylation of egg yolk phosphotyrosine. We also detected strong activity with endogenous and exogenous short chain polyphosphates (PolyP), which are polymers of phosphate residues involved in a number of physiological processes. Both agAP activity and PolyP were shown to initially concentrate in small vesicles clearly distinct from typically larger yolk granules, suggesting subcellular compartmentalization. As PolyP has been implicated in inhibition of yolk proteases, we performed in vitro enzymatic assays with a cysteine protease to test whether it would be inhibited by PolyP. This cysteine protease is prominent in Anticarsia egg homogenates. Accordingly, short chain PolyP was a potent inhibitor of cysteine protease. We thereby suggest that PolyP hydrolysis by agAP is a triggering mechanism of yolk mobilization in A. gemmatalis.

DNA Damage Processing by Human 8-Oxoguanine-DNA Glycosylase Mutants with the Occluded Active Site

8-Oxoguanine-DNA glycosylase (OGG1) removes premutagenic lesion 8-oxoguanine (8-oxo-G) from DNA and then nicks the nascent abasic (apurinic/apyrimidinic) site by β-elimination. Although the structure of OGG1 bound to damaged DNA is known, the dynamic aspects of 8-oxo-G recognition are not well understood. To comprehend the mechanisms of substrate recognition and processing, we have constructed OGG1 mutants with the active site occluded by replacement of Cys-253, which forms a wall of the base-binding pocket, with bulky leucine or isoleucine. The conformational dynamics of OGG1 mutants were characterized by single-turnover kinetics and stopped-flow kinetics with fluorescent detection. Additionally, the conformational mobility of wild type and the mutant OGG1 substrate complex was assessed using molecular dynamics simulations. Although pocket occlusion distorted the active site and greatly decreased the catalytic activity of OGG1, it did not fully prevent processing of 8-oxo-G and apurinic/apyrimidinic sites. Both mutants were notably stimulated in the presence of free 8-bromoguanine, indicating that this base can bind to the distorted OGG1 and facilitate β-elimination. The results agree with the concept of enzyme plasticity, suggesting that the active site of OGG1 is flexible enough to compensate partially for distortions caused by mutation.

The Role of Soluble 5'.-Nucleotidases in the Conversion of Nucleotide Analogs: Metabolic and Therapeutic Aspects

A variety of anti-proliferative drugs is based on the structure of purine or pyrimidine nucleosides. These compounds, after phosphorylation, act as analogs of natural nucleotides. In vivo they are recognized by enzymes that transform them either into anti-metabolites targeted to the synthesis of DNA or RNA, or to inactive products of detoxification. 5'-Nucleotidases of different specificity and cellular localization can either remove the phosphate residue from the 5'- position of (deoxy) nucleotide or transfer it from nucleoside monophosphate onto other nucleosides. Such a nucleoside phosphotransferase activity also works with analogs of canonical nucleotides and nucleosides. The majority of nucleoside analogs is metabolized by intracellular cytoplasmic or mitochondrial 5'-nucleotidases and only few reactions proceed on the cell surface. This review summarizes our knowledge of cytoplasmic and mitochondrial forms of 5'-nucleotidases and focuses on their ability to dephosphorylate different analogs of canonical nucleoside 5'-monophosphates. The involvement of 5'-nucleotidases in the phosphotransfer reaction with some nucleoside analogs has been also presented. The importance of the reactions catalyzed by 5'-nucleotidases in clinical resistance to nucleoside-based drugs used in the treatment of cancer or viral diseases, as well as in activation of pro-drugs has been highlighted.

Unique Structural Modifications Are Present in the Lipopolysaccharide from Colistin-Resistant Strains of Acinetobacter baumannii

Acinetobacter baumannii is a nosocomial opportunistic pathogen that can cause severe infections, including hospital-acquired pneumonia, wound infections, and sepsis. Multidrug-resistant (MDR) strains are prevalent, further complicating patient treatment. Due to the increase in MDR strains, the cationic antimicrobial peptide colistin has been used to treat A. baumannii infections. Colistin-resistant strains of A. baumannii with alterations to the lipid A component of lipopolysaccharide (LPS) have been reported; specifically, the lipid A structure was shown to be hepta-acylated with a phosphoethanolamine (pEtN) modification present on one of the terminal phosphate residues. Using a tandem mass spectrometry platform, we provide definitive evidence that the lipid A isolated from colistin-resistant A. baumannii MAC204 LPS contains a novel structure corresponding to a diphosphoryl hepta-acylated lipid A structure with both pEtN and galactosamine (GalN) modifications. To correlate our structural studies with clinically relevant samples, we characterized colistin-susceptible and -resistant isolates obtained from patients. These results demonstrated that the clinical colistin-resistant isolate had the same pEtN and GalN modifications as those seen in the laboratory-adapted A. baumannii strain MAC204. In summary, this work has shown complete structure characterization including the accurate assignment of acylation, phosphorylation, and glycosylation of lipid A from A. baumannii, which are important for resistance to colistin.

Dephosphorylation of D-peptide derivatives to form biofunctional, supramolecular nanofibers/hydrogels and their potential applications for intracellular imaging and intratumoral chemotherapy.

D-Peptides, as the enantiomers of the naturally occurring L-peptides, usually resist endogenous proteases and are presumably insensitive to most enzymes. But, it is unclear whether or how a phosphatase catalyzes the dephosphorylation from D-peptides. In this work, we examine the formation of the nanofibers of D-peptides via enzymatic dephosphorylation. By comparing the enzymatic hydrogelation of L-peptide and D-peptide based hydrogelators, we find that the chirality of the precursors of the hydrogelators affects little on the enzymatic hydrogelation resulted from the removal of the phosphate group from a tyrosine phosphate residue. The attachment of a therapeutic agent (e.g., taxol) or a fluorophore (e.g., 4-nitro-2,1,3-benzoxadiazole) to the D-peptide based hydrogelators affords a new type of biostable or biocompatible hydrogelators, which may find applications in intratumoral chemotherapy or intracellular imaging, respectively. This work, as the first comprehensive and systematic study of the unexpected enzymatic dephosphorylation of D-peptides, illustrates a useful approach to generate supramolecular hydrogels that have both biostability and other desired functions.

Adaptation ofSaccharomyces cerevisiaeto toxic manganese concentration triggers changes in inorganic polyphosphates

The ability of Saccharomyces cerevisiae to adapt to toxic Mn(2+) concentration (4 mM) after an unusually long lag phase has been demonstrated for the first time. The mutants lacking exopolyphosphatase PPX1 did not change the adaptation time, whereas the mutants lacking exopolyphosphatase PPN1 reduced the lag period compared with the wild-type strains. The cell populations of WT and ΔPPN1 in the stationary phase at cultivation with Mn(2+) contained a substantial number of enlarged cells with a giant vacuole. The adaptation correlated with the triggering of polyphosphate metabolism: the drastic increase in the rate and chain length of acid-soluble polyphosphate. The share of this fraction, which is believed to be localized in the cytoplasm, increased to 76%. Its average chain length increased to 200 phosphate residues compared with 15 at the cultivation in the absence of manganese. DAPI-stained inclusions in the cytoplasm were accumulated in the lag phase during the cultivation with Mn(2+).

A fluorescence-based assay for the apurinic/apyrimidinic-site cleavage activity of human tyrosyl-DNA phosphodiesterase 1

Tyrosyl-DNA phosphodiesterase 1 (Tdp1) catalyzes the hydrolysis of phosphodiester bonds between the DNA 3′-phosphate and tyrosine residues and plays a major role in the repair of stalled topoisomerase I-DNA covalent complexes. Given this role, Tdp1 is of interest as a potential target for anticancer therapy. Inhibiting Tdp1 in combination with clinically used Top1 inhibitors may potentiate the effects of the latter and help to overcome some of the chemoresistance issues currently observed. In addition, Tdp1 can function during DNA repair to remove a variety of other 3′ adducts from DNA such as phosphoglycolates and abasic or apurinic/apyrimidinic (AP) sites. Here we describe a new mix-and-read homogeneous fluorogenic assay for the measurement of the AP-site cleavage activity of Tdp1 that is compatible with high-throughput screening. The application of such an assay will open up further avenues for the discovery of novel Tdp1 inhibitors.

Polyphosphate and Its Diverse Functions in Host Cells and Pathogens

Polyphosphate (polyP) is a linear polymer of a few to many hundreds of phosphate (Pi) residues linked by high-energy phosphoanhydride bonds (Figure 1A). This ubiquitous polymer is found in bacteria, protists, and mammalian cells, and it was likely present prebiotically [1]. In bacteria, polyP accumulates in volutin or metachromatic granules, which are equivalent to acidocalcisomes [2]. In eukaryotic cells, polyP is present in different compartments, including the cytosol, nucleus, lysosomes, and mitochondria, but is preferentially accumulated in acidic vacuoles such as the yeast vacuole and acidocalcisomes [1], [3]. In these organelles, polyP, which is negatively charged, is in close association of inorganic (Ca2+, Mg2+, Zn2+, Fe2+, Na+, K+) and organic (basic amino acids, polyamines) cations. PolyP also combines with calcium and polyhydroxybutyrate forming channels in bacterial membranes, which make them competent for DNA entry; in mitochondria, as part of the mitochondrial permeability transition pore; and in the plasma membrane, as part of the potassium channel and the calcium pump (reviewed in [1], [4]). PolyP is arbitrarily divided into two forms: short-chain (from 3 to ∼300 Pi) and long-chain (from 300 to ∼1000 Pi) polyP, based on the method used for its extraction. For the detection of polyP, several methods have been described and a few examples are shown in Figure 1B–F. Figure 1 Methods used to detect polyP in cells.

Metabolism and Biological Function of Cardiolipin

Cardiolipin (CL) is a phospholipid, which is exclusively located in mitochondria, and has a unique structure that consists of 2 phosphate residues and 4 kinds of fatty acyl chains. Cardiolipin plays an important role in regulating various kinds of mitochondrial proteins such as electron transport complexes, carrier proteins and phosphate kinases, and is also essential for the organization of particular mitochondrial structures such as cristae and contact sites. Mitochondrial phospholipase D hydrolyzes CL to produce phosphatidic acid, which is required for mitochondrial fusion. Oxidative stress-induced peroxidation of CL occurs because CL is rich in polyunsaturated fatty acids, especially linoleic acid. Accumulation of CL hydroperoxide (CLOOH) triggers the initiation of apoptosis. Formation of CLOOH causes the release of proapoptotic factors such as cytochrome c from the inner mitochondrial membrane and triggers opening of the permeability transition pore. Levels of CL decrease in the heart following ischemia or disease. Apoptosis is enhanced in temperature-dependent mutant cells whose amounts of CL reduce to half when compared to that of wild type cells. Low levels of CL cause the accumulation of CLOOH and enhance sensitivity to apoptosis. Accumulation of CLOOH in mitochondria causes instability of the membrane, because swelling of mitochondria is induced by the presence of CLOOH in the membrane and is significantly enhanced in CLOOH-loaded mitochondria by the addition of inducer of swelling.

Polyphosphate Deficiency in Mycobacterium tuberculosis Is Associated with Enhanced Drug Susceptibility and Impaired Growth in Guinea Pigs

Inorganic polyphosphate (polyP), a linear polymer of hundreds of phosphate residues linked by ATP-like phosphoanhydride bonds, is found in all organisms and performs a wide variety of functions. This study shows that polyP accumulation occurs in Mycobacterium tuberculosis upon exposure to various stress conditions. M. tuberculosis possesses a single homolog of ppk-1, and we have disrupted ppk-1 in the M. tuberculosis genome by allelic replacement. The mutant strain exhibited negligible levels of intracellular polyP, decreased expression of sigF and phoP, and reduced growth in the stationary phase and displayed a survival defect in response to nitrosative stress and in THP-1 macrophages compared to the wild-type strain. We report that reduction in polyP levels is associated with increased susceptibility of M. tuberculosis to certain TB drugs and impairs its ability to cause disease in guinea pigs. These results suggest that polyP contributes to persistence of M. tuberculosis in vitro and plays an important role in the physiology of bacteria residing within guinea pigs.