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Purinergic Signalling Jun 2023Conventionally, ATP is considered to be the principal energy source in cells. However, over the last few years, a novel role for ATP as a potent extracellular signaling... (Review)
Review
Conventionally, ATP is considered to be the principal energy source in cells. However, over the last few years, a novel role for ATP as a potent extracellular signaling molecule and the principal source of extracellular pyrophosphate, the main endogenous inhibitor of vascular calcification, has emerged. A large body of evidence suggests that two principal mechanisms are involved in the initiation and progression of ectopic calcification: high phosphate concentration and pyrophosphate deficiency. Pathologic calcification of cardiovascular structures, or vascular calcification, is a feature of several genetic diseases and a common complication of chronic kidney disease, diabetes, and aging. Previous studies have shown that the loss of function of several enzymes and transporters involved in extracellular ATP/pyrophosphate metabolism is associated with vascular calcification. Therefore, pyrophosphate homeostasis should be further studied to facilitate the design of novel therapeutic approaches for ectopic calcification of cardiovascular structures, including strategies to increase pyrophosphate concentrations by targeting the ATP/pyrophosphate metabolism cycle.
Topics: Humans; Diphosphates; Vascular Calcification; Homeostasis; Adenosine Triphosphate
PubMed: 35511317
DOI: 10.1007/s11302-022-09867-1 -
Scientific Reports Apr 2022The solid-state reaction was employed to synthesize CaCuPO by varying the mole ratio between Ca and Cu. The structure and crystallography of the pyrophosphate compounds...
The solid-state reaction was employed to synthesize CaCuPO by varying the mole ratio between Ca and Cu. The structure and crystallography of the pyrophosphate compounds were identified and confirmed by using X-ray diffraction (XRD). The Rietveld refinement method and the extended X-ray absorption fine structure (EXAFS) least-squares fitting technique were also applied to refine the sample crystal structure. The single phases of the obtained CaPO, CaCuPO, and CuPO samples and the mixing phases of the obtained CaCuPO and CaCuPO samples were identified, and then only a single phase of the samples was subjected to structural and dielectrical analyses. The structural results exhibit the tetragonal crystal system with the P4 space group for β-CaPO, the monoclinic crystal system with the P2/c space group for CaCuPO, and the C2/c space group for α-CuPO. The dielectric constant (ε) of the single metal pyrophosphates (CaPO and CuPO) was higher than that of binary metal pyrophosphates (CaCuPO). The image sensor result of the CuPO sample (x = 2.00) illustrated a yellowish-green color, while other compounds (x = 0.50-1.50) presented color tones that changed from blue-green to bluish-green. Raman and Fourier transform infrared (FTIR) spectrophotometers were employed to characterize and confirm the vibrational characteristics of the PO group, which contains the O-P-O radical ([PO]) and the P-O-P bride ([OPO]) and approximate M-O stretching modes. Furthermore, this work reports for the first time that the change in the crystal structure of CaCuPO (i.e., bond angle of P-O-P in PO and distortion phenomena in the M-O octahedral site) are cause the correlation between the structure, chromaticity, and dielectric properties of calcium copper pyrophosphates, CaCuPO.
Topics: Calcium; Calcium Pyrophosphate; Copper; Diphosphates; X-Ray Diffraction
PubMed: 35477985
DOI: 10.1038/s41598-022-11056-4 -
Advances in Biological Regulation Jan 2022Inositol poly- and pyrophosphates (InsPs and PP-InsPs) are a group of central eukaryotic metabolites and signaling molecules. Due to the diverse cellular functions and... (Review)
Review
Inositol poly- and pyrophosphates (InsPs and PP-InsPs) are a group of central eukaryotic metabolites and signaling molecules. Due to the diverse cellular functions and widespread diseases InsPs and PP-InsPs are associated with, pharmacological targeting of the kinases involved in their biosynthesis has become a significant research interest in the last decade. In particular, the development of inhibitors for inositol hexakisphosphate kinases (IP6Ks) has leaped forward, while other inositol phosphate kinases have received scant attention. This review summarizes the efforts undertaken so far for discovering potent and selective inhibitors for this diverse group of small molecule kinases. The benefits of pharmacological inhibition are highlighted, given the multiple kinase-independent functions of inositol phosphate kinases. The distinct structural families of InsP and PP-InsP kinases are presented, and we discuss how compound availability for different inositol phosphate kinase families varies drastically. Lead compound discovery and optimization for the inositol kinases would benefit from detailed structural information on the ATP-binding sites of these kinases, as well as reliable biochemical and cellular read-outs to monitor inositol phosphate kinase activity in complex settings. Efforts to further tune well-established inhibitors, while simultaneously reviving tool compound development for the more neglected kinases from this family are indisputably worthwhile, considering the large potential therapeutic benefits.
Topics: Diphosphates; Eukaryotic Cells; Humans; Inositol Phosphates; Phosphorylation; Phosphotransferases (Phosphate Group Acceptor); Signal Transduction
PubMed: 34802993
DOI: 10.1016/j.jbior.2021.100836 -
Biochemistry Jun 2022Inositol pyrophosphates are signaling molecules containing at least one phosphoanhydride bond that regulate a wide range of cellular processes in eukaryotes. With a...
Inositol pyrophosphates are signaling molecules containing at least one phosphoanhydride bond that regulate a wide range of cellular processes in eukaryotes. With a cyclic array of phosphate esters and diphosphate groups around -inositol, these molecular messengers possess the highest charge density found in nature. Recent work deciphering inositol pyrophosphate biosynthesis in revealed important functions of these messengers in nutrient sensing, hormone signaling, and plant immunity. However, despite the rapid hydrolysis of these molecules in plant extracts, very little is known about the molecular identity of the phosphohydrolases that convert these messengers back to their inositol polyphosphate precursors. Here, we investigate whether Plant and Fungi Atypical Dual Specificity Phosphatases (PFA-DSP1-5) catalyze inositol pyrophosphate phosphohydrolase activity. We find that recombinant proteins of all five PFA-DSP homologues display phosphohydrolase activity with a high specificity for the 5-β-phosphate of inositol pyrophosphates and only minor activity against the β-phosphates of 4-InsP and 6-InsP. We further show that heterologous expression of PFA-DSP1-5 rescues wortmannin sensitivity and deranged inositol pyrophosphate homeostasis caused by the deficiency of the PFA-DSP-type inositol pyrophosphate phosphohydrolase Siw14 in yeast. Heterologous expression in leaves provided evidence that PFA-DSP1 also displays 5-β-phosphate-specific inositol pyrophosphate phosphohydrolase activity . Our findings lay the biochemical basis and provide the genetic tools to uncover the roles of inositol pyrophosphates in plant physiology and plant development.
Topics: Arabidopsis; Diphosphates; Dual-Specificity Phosphatases; Inositol Phosphates; Saccharomyces cerevisiae
PubMed: 35640071
DOI: 10.1021/acs.biochem.2c00145 -
Frontiers in Endocrinology 2023Serum alkaline phosphatase (ALP) and its isoenzymes reflect bone metabolism: ALP increases the ratio of inorganic phosphate to pyrophosphate systemically and facilitates... (Review)
Review
Serum alkaline phosphatase (ALP) and its isoenzymes reflect bone metabolism: ALP increases the ratio of inorganic phosphate to pyrophosphate systemically and facilitates mineralization as well as reduces extracellular pyrophosphate concentration, an inhibitor of mineral formation. On the contrary, low ALP activity is associated with reduction of bone turnover. ALP includes four isoenzymes depending on the site of tissue expression: intestinal ALP, placental ALP, germ cell ALP and tissue nonspecific ALP or liver/bone/kidney ALP. The bone isoenzyme (B-ALP) is involved in bone calcification and is a marker of bone turnover as a result of osteoblastic activity. ALP and its isoenzymes are crucial in the diagnostic process of all the forms of rickets.The most common cause of rickets is vitamin D nutritional deficiency. The aim of this review is to update on the role played by ALP serum concentrations as a relevant marker in thediagnosis and treatment of rickets. Indeed, the diagnosis of rickets is based on its clinical, radiological and laboratory characteristics. An elevated ALP level is one of the markers for the diagnosis of rickets in children, though it is also associated with bone formation process. ALP is also useful for the differentiation between rickets and other disorders that can mimic rickets because of their clinical and laboratory characteristics, and, together with other biochemical markers, is crucial for the differential diagnosis of the different forms of rickets. Age, severity and duration of rickets may also modulate ALP elevation. Finally, ALP measurements are useful in clinical and therapeutic follow-up.
Topics: Pregnancy; Child; Humans; Female; Alkaline Phosphatase; Isoenzymes; Diphosphates; Placenta; Rickets; Vitamin D Deficiency
PubMed: 36817604
DOI: 10.3389/fendo.2023.1111445 -
International Journal of Molecular... Aug 2022Membrane pyrophosphatases (mPPases) found in plant vacuoles and some prokaryotes and protists are ancient cation pumps that couple pyrophosphate hydrolysis with the H... (Review)
Review
Membrane pyrophosphatases (mPPases) found in plant vacuoles and some prokaryotes and protists are ancient cation pumps that couple pyrophosphate hydrolysis with the H and/or Na transport out of the cytoplasm. Because this function is reversible, mPPases play a role in maintaining the level of cytoplasmic pyrophosphate, a known regulator of numerous metabolic reactions. mPPases arouse interest because they are among the simplest membrane transporters and have no homologs among known ion pumps. Detailed phylogenetic studies have revealed various subtypes of mPPases and suggested their roles in the evolution of the "sodium" and "proton" bioenergetics. This treatise focuses on the mechanistic aspects of the transport reaction, namely, the coupling step, the role of the chemically produced proton, subunit cooperation, and the relationship between the proton and sodium ion transport. The available data identify H-PPases as the first non-oxidoreductase pump with a "direct-coupling" mechanism, i.e., the transported proton is produced in the coupled chemical reaction. They also support a "billiard" hypothesis, which unifies the H and Na transport mechanisms in mPPase and, probably, other transporters.
Topics: Diphosphates; Inorganic Pyrophosphatase; Phylogeny; Probability; Protons; Pyrophosphatases; Sodium
PubMed: 36012762
DOI: 10.3390/ijms23169504 -
Advances in Biological Regulation Jan 2020Inositol pyrophosphates (PP-IPs) are a class of energy rich metabolites present in all eukaryotic cells. The hydroxyl groups on these water soluble derivatives of... (Review)
Review
Inositol pyrophosphates (PP-IPs) are a class of energy rich metabolites present in all eukaryotic cells. The hydroxyl groups on these water soluble derivatives of inositol are substituted with diphosphate and monophosphate moieties. Since the discovery of PP-IPs in the early 1990s, enormous progress has been made in uncovering pleiotropic roles for these small molecules in cellular physiology. PP-IPs exert their effect on proteins in two ways - allosteric regulation by direct binding, or post-translational regulation by serine pyrophosphorylation, a modification unique to PP-IPs. Serine pyrophosphorylation is achieved by Mg-dependent, but enzyme independent transfer of a β-phosphate from a PP-IP to a pre-phosphorylated serine residue located in an acidic motif, within an intrinsically disordered protein sequence. This distinctive post-translational modification has been shown to regulate diverse cellular processes, including rRNA synthesis, glycolysis, and vesicle transport. However, our understanding of the molecular details of this phosphotransfer from pyrophospho-inositol to generate pyrophospho-serine, is still nascent. This review discusses our current knowledge of protein pyrophosphorylation, and recent advances in understanding the mechanism of this important yet overlooked post-translational modification.
Topics: Biological Transport; Diphosphates; Energy Metabolism; Eukaryotic Cells; Inositol Phosphates; Phosphorylation; Protein Processing, Post-Translational; Serine; Signal Transduction
PubMed: 31668836
DOI: 10.1016/j.jbior.2019.100662 -
Protein Science : a Publication of the... Aug 2019The Nudix hydrolase superfamily is identified by a conserved cassette of 23 amino acids, and it is characterized by its pyrophosphorylytic activity on a wide variety of...
The Nudix hydrolase superfamily is identified by a conserved cassette of 23 amino acids, and it is characterized by its pyrophosphorylytic activity on a wide variety of nucleoside diphosphate derivatives. Of the 13 members of the family in Escherichia coli, only one, Orf180, has not been identified with a substrate, although a host of nucleoside diphosphate compounds has been tested. Several reports have noted a strong similarity in the three-dimensional structure of the unrelated enzyme, isopentenyl diphosphate isomerase (IDI) to the Nudix structure, and the report that a Nudix enzyme was involved in the synthesis of geraniol, a product of the two substrates of IDI, prompted an investigation of whether the IDI substrates, isopentenyl diphosphate (IPP), and dimethylallyl diphosphate (DAPP) could be substrates of Orf180. This article demonstrates that Orf180 does have a very low activity on IPP, DAPP, and geranyl pyrophosphate (GPP). However, several of the other Nudix enzymes with established nucleoside diphosphate substrates hydrolyze these compounds at substantial rates. In fact, some Nudix hydrolases have higher activities on IPP, DAPP, and GPP than on their signature nucleoside diphosphate derivatives.
Topics: Diphosphates; Escherichia coli; Hemiterpenes; Models, Molecular; Molecular Structure; Organophosphorus Compounds; Pyrophosphatases; Nudix Hydrolases
PubMed: 31173659
DOI: 10.1002/pro.3666 -
Brazilian Journal of Microbiology :... Sep 2021Guanosine 5'-diphosphate-3'-diphosphate (ppGpp) is a small molecule nucleotide alarmone that can accumulate under the amino acid starvation state and trigger the...
Guanosine 5'-diphosphate-3'-diphosphate (ppGpp) is a small molecule nucleotide alarmone that can accumulate under the amino acid starvation state and trigger the stringent response. This study reported the extraction of ppGpp from the Gram-positive bacteria Clavibacter michiganensis through methods using formic acid, lysozyme, or methanol. Following extraction, ppGpp was detected through ultra-high-performance liquid chromatography (UHPLC) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). The methanol method showed the highest extraction efficiency for ppGpp among the three methods tested. C. michiganensis cells in exponential growth phase was induced in amino acid starvation by serine hydroxamate (SHX) and used for ppGpp extraction and detection. When using the methanol extraction method, the results showed that ppGpp concentrations in SHX-treated samples were 15.645 nM, 17.656 nM, 20.372 nM, and 19.280 nM at 0 min, 15 min, 30 min and 1 h, respectively, when detected using LC-MS/MS. This is the first report on ppGpp extraction and detection in Clavibacter providing a new idea and approach for nucleotide detection and extraction in bacteria.
Topics: Amino Acids; Chromatography, Liquid; Clavibacter; Diphosphates; Guanosine Tetraphosphate; Methanol; Tandem Mass Spectrometry
PubMed: 33837930
DOI: 10.1007/s42770-021-00488-1 -
Journal of Medicinal Chemistry Jun 2023We tested a series of SQ109 analogues against and , in addition to determining their uncoupling activity. We then investigated potential protein targets, involved in...
We tested a series of SQ109 analogues against and , in addition to determining their uncoupling activity. We then investigated potential protein targets, involved in quinone and cell wall biosynthesis, using "rescue" experiments. There was little effect of menaquinone on growth inhibition by SQ109, but there were large increases in the IC of SQ109 and its analogues (up to 20×) on addition of undecaprenyl phosphate (Up), a homologue of the mycobacterial decaprenyl (C) diphosphate. Inhibition of an undecaprenyl diphosphate phosphatase, an ortholog of the mycobacterial phosphatase, correlated with cell growth inhibition, and we found that cell growth inhibition could be well predicted by using uncoupler and Up-rescue results. We also investigated whether SQ109 was metabolized inside , finding only a single metabolite, previously shown to be inactive. The results are of general interest since they help explain the mechanism of SQ109 in mycobacteria.
Topics: Humans; Antitubercular Agents; Diphosphates; Tuberculosis; Mycobacterium tuberculosis; Mycobacterium smegmatis
PubMed: 37235809
DOI: 10.1021/acs.jmedchem.3c00398