Modulation of purinergic signaling by NPP-type ectophosphodiesterases

Extracellular nucleotides can elicit a wide array of cellular responses by binding to specific purinergic receptors. The level of ectonucleotides is dynamically controlled by their release from cells, synthesis by ectonucleoside diphosphokinases and ectoadenylate kinases, and hydrolysis by ectonucleotidases. One of the four structurally unrelated families of ectonucleotidases is represented by the NPP-type ectophosphodiesterases. Three of the seven members of the NPP family, namely NPP1–3, are known to hydrolyze nucleotides. The enzymatic action of NPP1–3 (in)directly results in the termination of nucleotide signaling, the salvage of nucleotides and/or the generation of new messengers like ADP, adenosine or pyrophosphate. NPP2 is unique in that it hydrolyzes both nucleotides and lysophospholipids and, thereby, generates products that could synergistically promote cell motility. We review here the enzymatic properties of NPPs and analyze current evidence that links their nucleotide-hydrolyzing capability to epithelial and neural functions, the immune response and cell motility.     

The evolution of the new permeability pathways in Plasmodium falciparum--infected erythrocytes--a kinetic analysis

Malaria parasites demonstrably increase the permeability of the membrane of the erythrocyte in which they develop and propagate. New permeability pathways (NPPs) generated by parasite activity and identified in the erythrocyte membrane are held responsible for these changes. Here, we present a novel analysis of hemolysis curves of infected cells in iso-osmotic solutions of solutes that penetrate selectively into infected cells, as a function of parasite development. The analysis yields three parameters: the t(1/2) of lysis (reciprocally related to permeability), the maximal lysis, and a parameter that expresses the variation of the cell population. Different developmental stages of the parasite were obtained either by sampling synchronized cultures with time or by the fractionation of asynchronous cultures on a Percoll-sorbitol density gradient. While the results confirm previous reports on the stage-dependent evolution of NPPs, they also reveal that the evolution of NPPs is not synchronous: NPPs evolve differentially throughout the ring stage and only at the mid-trophozoite stage they are fully deployed in the majority of the infected cells, but not in all. This leads to desynchronization in the culture and to less than the maximal possible rate of multiplication.     

Does nanosized plastic affect aquatic fungal litter decomposition?

Nanosized plastics are an emerging concern in freshwater ecosystems, raising the question whether they put freshwater ecological processes at risk. Litter decomposition is a major ecological function in forested streams which is mainly driven by aquatic hyphomycetes. Here we investigated whether increasing concentrations (up to 102.4 mg/L) of nanosized polystyrene plastics (NPPs; 100nm) affect litter decomposition by five widely distributed species of aquatic hyphomycetes. Results showed that average litter decomposition decreased by 8% relative to the control when exposed to 102.4 mg/L NPPs. Aquatic hyphomycete species differed in their sensitivity to NPPs. The greatest inhibition of litter decomposition was found with Tetracladium marchalianum, where it dropped from 37 (control) to 16% (102.4 mg/L of NPP). Overall our study highlights the emerging risks and potential dangers of NPPs to freshwater ecosystem functioning. It also indicates that the impact of NPPs may be species specific.     

Structural and catalytic similarities between nucleotide pyrophosphatases/phosphodiesterases and alkaline phosphatases

Nucleotide pyrophosphatases/phosphodiesterases (NPPs) generate nucleoside 5'-monophosphates from a variety of nucleotides and their derivatives. Here we show by data base analysis that these enzymes are conserved from eubacteria to higher eukaryotes. We also provide evidence for the existence of two additional members of the mammalian family of ecto-NPPs. Homology searches and alignment-assisted mutagenesis revealed that the catalytic core of NPPs assumes a fold similar to that of a superfamily of phospho-/sulfo-coordinating metalloenzymes comprising alkaline phosphatases, phosphoglycerate mutases, and arysulfatases. Mutation of mouse NPP1 in some of its predicted metal-coordinating residues (D358N or H362Q) or in the catalytic site threonine (T238S) resulted in an enzyme that could still form the nucleotidylated catalytic intermediate but was hampered in the second step of catalysis. We also obtained data indicating that the ability of some mammalian NPPs to auto(de)phosphorylate is due to an intrinsic phosphatase activity, whereby the enzyme phosphorylated on Thr-238 represents the covalent intermediate of the phosphatase reaction. The results of site-directed mutagenesis suggested that the nucleotide pyrophosphatase/phosphodiesterase and the phosphatase activities of NPPs are mediated by a single catalytic site.     

Nucleotide pyrophosphatases/phosphodiesterases on the move

Nucleotide pyrophosphatases/phosphodiesterases (NPPs) release nucleoside 5'-monophosphates from nucleotides and their derivatives. They exist both as membrane proteins, with an extracellular active site, and as soluble proteins in body fluids. The only well-characterized NPPs are the mammalian ecto-enzymes NPP1 (PC-1), NPP2 (autotaxin) and NPP3 (B10; gp130(RB13-6)). These are modular proteins consisting of a short N-terminal intracellular domain, a single transmembrane domain, two somatomedin-B-like domains, a catalytic domain, and a C-terminal nuclease-like domain. The catalytic domain of NPPs is conserved from prokaryotes to mammals and shows remarkable structural and catalytic similarities with the catalytic domain of other phospho-/sulfo-coordinating enzymes such as alkaline phosphatases. Hydrolysis of pyrophosphate/phosphodiester bonds by NPPs occurs via a nucleotidylated threonine. NPPs are also known to auto(de)phosphorylate this active-site threonine, a process accounted for by an intrinsic phosphatase activity, with the phosphorylated enzyme representing the catalytic intermediate of the phosphatase reaction. NPP1-3 have been implicated in various processes, including bone mineralization, signaling by insulin and by nucleotides, and the differentiation and motility of cells. While it has been established that most of these biological effects of NPPs require a functional catalytic site, their physiological substrates remain to be identified.     

自分泌运动因子-溶血磷脂酸轴的生物学功能与调控

自分泌运动因子(autotaxin,ATX)也称作磷酸二酯酶Iα,是核苷酸焦磷酸酶/磷酸二酯酶家族(nucleotide pyrophosphatases,NPPs)中的一员,因而也称作NPP2.ATX是NPPs中唯一具有溶血磷脂酶D(lysophospholipase D,lysoPLD)活性的成员,它可以将溶血磷脂...     

Nucleotide Pyrophosphatases/Phosphodiesterases on the Move

Nucleotide pyrophosphatases/phosphodiesterases (NPPs) release nucleoside 5′-monophosphates from nucleotides and their derivatives. They exist both as membrane proteins, with an extracellular active site, and as soluble proteins in body fluids. The only well-characterized NPPs are the mammalian ecto-enzymes NPP1 (PC-1), NPP2 (autotaxin) and NPP3 (B10; gp130^RB13-6). These are modular proteins consisting of a short N-terminal intracellular domain, a single transmembrane domain, two somatomedin-B-like domains, a catalytic domain, and a C-terminal nuclease-like domain. The catalytic domain of NPPs is conserved from prokaryotes to mammals and shows remarkable structural and catalytic similarities with the catalytic domain of other phospho-/sulfo-coordinating enzymes such as alkaline phosphatases. Hydrolysis of pyrophosphate/phosphodiester bonds by NPPs occurs via a nucleotidylated threonine. NPPs are also known to auto(de)phosphorylate this active-site threonine, a process accounted for by an intrinsic phosphatase activity, with the phosphorylated enzyme representing the catalytic intermediate of the phosphatase reaction. NPP1-3 have been implicated in various processes, including bone mineralization, signaling by insulin and by nucleotides, and the differentiation and motility of cells. While it has been established that most of these biological effects of NPPs require a functional catalytic site, their physiological substrates remain to be identified.     

Identification of 18 genes encoding necrosis-inducing proteins from the plant pathogen Phytophthora capsici (Pythiaceae: Oomycetes)

Phytophthora capsici is an aggressive plant pathogen that affects solanaceous and cucurbitaceous hosts. Necrosis-inducing Phytophthora proteins (NPPs) are a group of secreted toxins found particularly in oomycetes. Several NPPs from Phytophthora species trigger plant cell death and activate host defense gene expression. We isolated 18 P. capsici NPP genes, of which 12 were active during hypha growth from a Phytophthora stain isolated from pepper (Capsicum annuum) plants in China. The 18 predicted proteins had a sequence homology of 46.26%. The 18 Pcnpp sequences had a conserved GHRHDWE motif and fell into two groups. Eleven sequences in group 1 had two conserved cysteine residues, whereas the other seven sequences in group 2 lacked these two cysteine residues. A phylogenetic tree was constructed on the basis of the alignment of the predicted protein sequences of 52 selected NPP genes from oomycetes, fungi and bacteria from Genbank. The tree did not rigorously follow the taxonomic classification of the species; all the NPPs from oomycetes formed their own clusters, while fungal sequences were grouped into two separate clades, indicating that based on NPPs, we can separate oomycetes from fungi and bacteria, and that expansion of the NPP family was a feature of Phytophthora evolution.     

Nucleotide ester-forming alcoholytic activities of nucleotide pyrophosphatases: implications for practical biotransformation, enzyme mechanisms and biological function

Nucleotide pyrophosphatases (NPP) hydrolyze phosphoanhydride and phosphodiester derivatives of nucleoside 5′-monophosphates (NMP) yielding NMP as a product. In a water–alcohol mixture, the alcohol (R–OH) competes and substitutes for water as the splitting agent, so a mixture of NMP and NMP-O-alkyl ester (NMP-O-R) is formed. NPPs from snake venom, potato tuber and mammalian tissues have been studied in this regard. Snake and potato NPPs were considered as possible practical biocatalysts to synthesize NMP-O-Rs from various nucleotidic substrates and alcohols. Mammalian NPPs, mainly from human blood and rat liver, were studied considering the possibility that the alcoholytic reactions catalyzed by them could be biologically relevant. Valuable information on the active centers and catalytic mechanisms of NPPs was also obtained.     

Identification of human intestinal alkaline sphingomyelinase as a novel ecto-enzyme related to the nucleotide phosphodiesterase family

Alkaline sphingomyelinase (alk-SMase) hydrolyzes dietary sphingomyelin and generates sphingolipid messengers in the gut. In the present study, we purified the enzyme, identified a part of the amino acid sequence, and found a cDNA in the GenBank coding for the protein. The cDNA contains 1841 bp, and the open reading frame encodes 458 amino acids. Transient expression of the cDNA linked to a Myc tag in COS-7 cells increased alk-SMase activity in the cell extract by 689-fold and in the medium by 27-fold. High activity was also identified in the anti-Myc immunoprecipitated proteins and the proteins cross-reacted with anti-human alk-SMase. Northern blotting of human intestinal tissues found high levels of alk-SMase mRNA in the intestine and liver. The amino acid sequence shared no similarity with acid and neutral SMases but was related to the ecto-nucleotide phosphodiesterase (NPP) family with 30-36% identity to human NPPs. Alk-SMase has a predicted signal peptide domain at the N terminus and a signal anchor domain at the C terminus. The ion-binding sites and the catalytic residue of NPPs were conserved, but the substrate specificity domain was modified. Alk-SMase had no detectable nucleotidase activity, but its activity against sphingomyelin could be inhibited by orthovanadate, imidazole, and ATP. In contrast to NPPs, alk-SMase activity was not stimulated by divalent metal ions but inhibited by Zn2+. Differing from NPP2, the alk-SMase cleaved phosphocholine but not choline from lysophosphatidylcholine. Phylogenetic tree indicated that the enzyme is a new branch derived from the NPP family. Two cDNA sequences of mouse and rat that shared 83% identity to human alk-SMase were identified in the GenBank. In conclusion, we identified the amino acid and cDNA sequences of human intestinal alk-SMase, and found that it is a novel ecto-enzyme related to the NPP family with specific features essential for its SMase activity.     

Nucleotide pyrophosphatase/phosphodiesterase 1 is responsible for degradation of antisense phosphorothioate oligonucleotides

The rapid degradation of unmodified phosphodiester oligodeoxynucleotides (PO-oligos) by exo -and endonucleases limits their application as antisense constructs and requires the synthesis and use of modified oligonucleotides. Phosphorothioate analogs of oligonucleotides (PS-oligos) are much more stable against nucleolytic degradation than their unmodified counterparts, and this is one of the reasons for which they are a promising class of antisense oligonucleotides. However, PS-oligos also undergo slow hydrolysis by enzymes present in plasma. The oligonucleotide degradation proceeds mainly from the 3' -end, resulting in the formation of a typical ladder of shorter products and the release of the mononucleoside 5' -phosphorothioates. So far, little has been known concerning the molecular identity of the enzymes involved in the degradation of PS-oligos. We now identify the human plasma 3' -exonuclease responsible for their degradation as a soluble form of nucleotide pyrophosphatase/phosphodiesterase 1 (NPP1) (EC 3.1.4.1/EC 3.6.1.9), also known as the plasma cell differentiation antigen PC-1. We also show that adenosine or deoxyadenosine (alpha-thio)triphosphates can act as potent inhibitors of NPPs.     

Nutrient availability and climate as the main determinants of the ratio of biomass to NPP in woody and non-woody forest compartments

Key message

Once the effect of stand age has been taken into account, nutrient availability and climate play a crucial role in determining the B:NPPs of woody and non-woody tissues.

Abstract

Forest ecosystems accumulate large amounts of carbon in living tissues. The residence time of this carbon in the ecosystem depends largely on the turnover time of these tissues, which can be estimated as a surrogate of the ratio of biomass to net primary production (B:NPP). We used a global forest database of 310 sites containing data for biomass stocks and NPP to investigate the differences of B:NPPs among species and forest compartments and to determine B:NPPs main exogenous (mainly climate and nutrient availability) and endogenous (leaf habit and stand age) drivers. We used asymptotic exponential functions to adjust the B:NPPs of woody compartments to a theoretical stationary state to allow comparisons between forests of different ages. The B:NPPs of woody tissues (branches, stems, and coarse roots) were positively influenced by stand age, conversely to fine roots and leaves, which were weakly dependent on the age of the forest. The B:NPPs of woody tissues were positively correlated with nutrient availability, whereas fine-root B:NPPs decreased with increasing nutrient availability. The foliar B:NPP of evergreen forests was positively correlated with water deficit, and the fine-root B:NPP was correlated positively with the seasonality of precipitation and with annual thermal amplitude but negatively with water deficit. Our results support the influence of climate on the B:NPPs of non-woody compartments and identify nutrient availability as the main influence on the B:NPPs of woody tissues.

     

Ectonucleotidases in the kidney

Members of all four families of ectonucleotidases, namely ectonucleoside triphosphate diphosphohydrolases (NTPDases), ectonucleotide pyrophosphatase/phosphodiesterases (NPPs), ecto-5′-nucleotidase and alkaline phosphatases, have been identified in the renal vasculature and/or tubular structures. In rats and mice, NTPDase1, which hydrolyses ATP through to AMP, is prominent throughout most of the renal vasculature and is also present in the thin ascending limb of Henle and medullary collecting duct. NTPDase2 and NTPDase3, which both prefer ATP over ADP as a substrate, are found in most nephron segments beyond the proximal tubule. NPPs catalyse not only the hydrolysis of ATP and ADP, but also of diadenosine polyphosphates. NPP1 has been identified in proximal and distal tubules of the mouse, while NPP3 is expressed in the rat glomerulus and pars recta, but not in more distal segments. Ecto-5′-nucleotidase, which catalyses the conversion of AMP to adenosine, is found in apical membranes of rat proximal convoluted tubule and intercalated cells of the distal nephron, as well as in the peritubular space. Finally, an alkaline phosphatase, which can theoretically catalyse the entire hydrolysis chain from nucleoside triphosphate to nucleoside, has been identified in apical membranes of rat proximal tubules; however, this enzyme exhibits relatively high K _m values for adenine nucleotides. Although information on renal ectonucleotidases is still incomplete, the enzymes’ varied distribution in the vasculature and along the nephron suggests that they can profoundly influence purinoceptor activity through the hydrolysis, and generation, of agonists of the various purinoceptor subtypes. This review provides an update on renal ectonucleotidases and speculates on the functional significance of these enzymes in terms of glomerular and tubular physiology and pathophysiology.     

Are grammatical representations useful for learning from biological sequence data?--a case study.

This paper investigates whether Chomsky-like grammar representations are useful for learning cost-effective, comprehensible predictors of members of biological sequence families. The Inductive Logic Programming (ILP) Bayesian approach to learning from positive examples is used to generate a grammar for recognising a class of proteins known as human neuropeptide precursors (NPPs). Collectively, five of the co-authors of this paper, have extensive expertise on NPPs and general bioinformatics methods. Their motivation for generating a NPP grammar was that none of the existing bioinformatics methods could provide sufficient cost-savings during the search for new NPPs. Prior to this project experienced specialists at SmithKline Beecham had tried for many months to hand-code such a grammar but without success. Our best predictor makes the search for novel NPPs more than 100 times more efficient than randomly selecting proteins for synthesis and testing them for biological activity. As far as these authors are aware, this is both the first biological grammar learnt using ILP and the first real-world scientific application of the ILP Bayesian approach to learning from positive examples. A group of features is derived from this grammar. Other groups of features of NPPs are derived using other learning strategies. Amalgams of these groups are formed. A recognition model is generated for each amalgam using C4.5 and C4.5rules and its performance is measured using both predictive accuracy and a new cost function, Relative Advantage (RA). The highest RA was achieved by a model which includes grammar-derived features. This RA is significantly higher than the best RA achieved without the use of the grammar-derived features. Predictive accuracy is not a good measure of performance for this domain because it does not discriminate well between NPP recognition models: despite covering varying numbers of (the rare) positives, all the models are awarded a similar (high) score by predictive accuracy because they all exclude most of the abundant negatives.     

Regulation and biological activities of the autotaxin-LPA axis

Autotaxin (ATX), or nucleotide pyrophosphatase/phosphodiesterase 2 (NPP2), is an exo-enzyme originally identified as a tumor cell autocrine motility factor. ATX is unique among the NPPs in that it primarily functions as a lysophospholipase D, converting lysophosphatidylcholine into the lipid mediator lysophosphatidic acid (LPA). LPA acts on specific G protein-coupled receptors to elicit a wide range of cellular responses, ranging from cell proliferation and migration to neurite remodeling and cytokine production. While LPA signaling has been studied extensively over the last decade, we are only now beginning to explore the properties and biological importance of ATX as the major LPA-producing phospholipase. In this review, we highlight recent advances in our understanding of the ATX-LPA axis, giving first an update on LPA action and then focusing on ATX, in particular its regulation, its link to cancer and its vital role in vascular development.     

阔叶红松林净初级生产力模型参数的敏感性

PnET-Ⅱ(photosynthesis and evapotranspiration)模型是生态系统过程模型,运行过程中所需的参数较多, 包括植被、土壤和气候参数等.本文估计了丰林自然保护区阔叶红松林中红松和阔叶树的总净初级生产力（NPP）和枝干NPP对PnET-Ⅱ模型参数变化的敏感程度.结果表明: PnET-Ⅱ模型的植被参数中,林冠参数变化对模拟结果影响较大,且红松总NPP对植被参数的敏感性大于阔叶树;红松和阔叶树NPP对土壤持水量变化敏感性较小,且红松NPP对土壤持水量的敏感性略小于阔叶树;在气候情景范围内,气温变化对红松和阔叶树NPP的影响最大,降水和光合有效辐射次之.不同气候情景对NPP模拟结果的影响不同.红松和阔叶树的总NPP和枝干NPP对各输入参数的敏感程度并不完全一致.     

Convergence of forelimb and hindlimb Natural Pendular Period in baboons (Papio cynocephalus) and its implication for the evolution of primate quadrupedalism

The patterns of muscle mass distribution along the lengths of limbs may have important effects on the mechanics and energetics of quadrupedalism. Specifically, Myers and Steudel (J. Morphol. 234 (1997) 183) have shown that fore- and hindlimb Natural Pendular Periods (NPPs) may affect quadrupedal kinematics and must converge to reduce locomotor energetic costs. This study quantifies patterns of limb mass distribution in a live sample of Papio cynocephalus using limb inertial properties (mass, center of mass, mass moment of inertia, and radius of gyration). These inertial properties are calculated using a geometric modeling technique similar to that of Crompton et al. (Am. J. phys. Anthrop. 99 (1996) 547). The inertial properties in Papio are compared to those of Canis from Myers and Steudel (J. Morphol. 234 (1997) 183). The Papio sample has convergent fore- and hindlimb NPPs. Additionally, these limb NPPs are relatively large compared to those of Canis due to the relatively distally distributed limb mass in the Papio sample (relatively large limb masses, relatively distal centers of mass and radii of gyration, and relatively large limb mass moments of inertia). This relatively distal limb mass appears related to the grasping abilities of their hands and feet. Causal links are explored between limb shape adaptations for grasping hands and feet and the kinematics of primate quadrupedalism. In particular, if primates in general follow Papio's limb mass distribution pattern, then relatively large limb NPPs may lead to the relatively low stride frequencies already documented for primates. The kinematics of primate quadrupedalism appears to have been strongly influenced by both selection for grasping hands and feet and selection for reduced locomotor energetic costs.     

Mutational analysis of wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.) nucleotide pyrophosphatase/phosphodiesterase shows the role of six amino acids in the catalytic mechanism

Nucleotide pyrophosphatases/phosphodiesterases (NPPs, PF01663) release nucleoside 5′-monophosphates from a wide range of nucleotide substrates. Only very recently, the first plant members of the NPP family were characterised (Joye et al. J Cereal Sci 51: 326–336, 2010), and little is known about their substrate-specifying residues. We elucidated the role of six amino acid residues of the recently identified and characterised Triticum aestivum L. NPP (Joye et al. J Cereal Sci 51: 326–336, 2010). Substitution of the highly conserved catalytic Thr132 into Ser or Ala completely abolished enzyme activity. Mutation of a highly conserved His255 residue into an apolar Ala suprisingly increased enzyme activity against most phosphodiester substrates. Four other residues moderately to highly conserved over NPPs of different organisms were studied as well. Mutation of the Asn153, Asn165 and Glu199 into an Arg, Ser and Asp residue, respectively, increased the relative enzyme activity against p-nitrophenyl phosphate. Furthermore, mutation of Phe194 into Ser increased the relative enzyme activity against adenosine 5′-monophosphate-containing substrates, although the overall enzyme activity of this mutant enzyme decreased. We conclude that the structural requirements and the conservation of the amino acids of the catalytic site of TaNPPr and, by extension, probably of all NPPs, are very stringent.     

Characterization of nucleotide pyrophosphatase-5 as an oligomannosidic glycoprotein in rat brain

Membrane glycoproteins of neural cells play crucial roles in axon guidance, synaptogenesis, and neuronal transmission. We have here characterized membrane glycoproteins containing terminal alpha-mannose residues in rat brain membranes. Affinity purification using Galanthus nivalis agglutinin, that is highly specific for terminal alpha-mannose residues, revealed a 50-kDa protein as well as 80-kDa SHPS-1 and 45-kDa beta2 subunit of Na,K-ATPase in rat brain membranes. Combination of N-terminal peptide sequencing and mass spectrometry indicated that the 50-kDa protein was rat nucleotide pyrophosphatase-5 (NPP-5). In contrast to other NPPs, NPP-5 was a type-I transmembrane protein. Northern blot analysis showed that NPP-5 was highly expressed in brain, but also expressed in other peripheral tissues. However, we could not detect either the NPP activity or the lysophospholipase D activity in the immunoprecipitates with antibodies to NPP-5 from rat brain membranes. These data, therefore, suggest that NPP-5 is a neural oligomannosidic glycoprotein that may participate in neural cell communications.