-
Scientific Reports Jul 2019The aims of this study were to establish the role of MC4Rrs17782313 and ENPP1rs1044498 gene polymorphisms on pre-pregnancy BMI and the newborn's status. We performed a...
The aims of this study were to establish the role of MC4Rrs17782313 and ENPP1rs1044498 gene polymorphisms on pre-pregnancy BMI and the newborn's status. We performed a cross-sectional study on 185 mothers and their offspring. The groups were divided into: control group- underweight or normal mothers with BMI < 25 kg/m (n = 134) and study group-overweight/obese mothers with BMI ≥ 25 kg/m (n = 51). All subjects underwent demographic, anthropometric, paraclinical, bioimpedance and genetic parameters. We found association between initial BMI and gestational weight gain (GWG), and a higher frequency of excessive GWG in overweight/obese women (p = 0.037). Higher values of anthropometric and bioimpedance parameters were observed in overweight/obese versus underweight/normal women. The MC4R rs17782313 and ENPP1 rs1044498 variant genotypes had an increased risk of pre-pregnancy overweight (OR = 1.41; 95% CI:[0.72; 2.78]; OR = 1.34; 95% CI:[0.65; 2.75]). The newborns from mothers with excessive GWG had a higher birth weight (BW) (p = 0.001). Higher MUAC values were noticed in newborns with MC4R rs17782313 wild-type genotype. Also, BW was correlated with GWG status smoking in pregnancy, gestational age and neonatal ENPP1rs1044498 variant genotype (p = 0.026). Our study pointed out the role of MC4R rs17782313 and ENPP1 rs1044498 genotypes in obesity determinisms in mothers and their newborns in correlation with BMI, MUAC, TST and bioimpedance parameters.
Topics: Adult; Arm; Birth Weight; Body Mass Index; Body Size; Cross-Sectional Studies; Female; Genotype; Gestational Weight Gain; Humans; Infant, Newborn; Obesity, Maternal; Phosphoric Diester Hydrolases; Polymorphism, Single Nucleotide; Pregnancy; Pyrophosphatases; Receptor, Melanocortin, Type 4; Risk Factors; Skinfold Thickness; Young Adult
PubMed: 31350533
DOI: 10.1038/s41598-019-47402-2 -
Scientific Reports Sep 2020Identifying stabilising variants of membrane protein targets is often required for structure determination. Our new computational pipeline, the Integral Membrane Protein...
Identifying stabilising variants of membrane protein targets is often required for structure determination. Our new computational pipeline, the Integral Membrane Protein Stability Selector (IMPROvER) provides a rational approach to variant selection by employing three independent approaches: deep-sequence, model-based and data-driven. In silico tests using known stability data, and in vitro tests using three membrane protein targets with 7, 11 and 16 transmembrane helices provided measures of success. In vitro, individual approaches alone all identified stabilising variants at a rate better than expected by random selection. Low numbers of overlapping predictions between approaches meant a greater success rate was achieved (fourfold better than random) when approaches were combined and selections restricted to the highest ranked sites. The mix of information IMPROvER uses can be extracted for any helical membrane protein. We have developed the first general-purpose tool for selecting stabilising variants of [Formula: see text]-helical membrane proteins, increasing efficiency and reducing workload. IMPROvER can be accessed at http://improver.ddns.net/IMPROvER/ .
Topics: Bacterial Proteins; Clostridium; Computer Simulation; Equilibrative Nucleoside Transporter 1; Genetic Variation; High-Throughput Nucleotide Sequencing; Humans; Membrane Proteins; Models, Molecular; Protein Conformation, alpha-Helical; Protein Denaturation; Protein Engineering; Protein Stability; Pyrophosphatases; Receptor, Parathyroid Hormone, Type 1; Receptors, G-Protein-Coupled; Sequence Alignment; Sequence Analysis, Protein; Software; Structural Homology, Protein
PubMed: 32938971
DOI: 10.1038/s41598-020-71744-x -
Cells Oct 2019Many facets of ribosome biogenesis and function, including ribosomal RNA (rRNA) transcription, 70S assembly and protein translation, are negatively impacted upon... (Review)
Review
Many facets of ribosome biogenesis and function, including ribosomal RNA (rRNA) transcription, 70S assembly and protein translation, are negatively impacted upon induction of a nutrient stress-sensing signalling pathway termed the stringent response. This stress response is mediated by the alarmones guanosine tetra- and penta-phosphate ((p)ppGpp), the accumulation of which leads to a massive cellular response that slows growth and aids survival. The 70S bacterial ribosome is an intricate structure, with assembly both complex and highly modular. Presiding over the assembly process is a group of P-loop GTPases within the TRAFAC (Translation Factor Association) superclass that are crucial for correct positioning of both early and late stage ribosomal proteins (r-proteins) onto the rRNA. Often described as 'molecular switches', members of this GTPase superfamily readily bind and hydrolyse GTP to GDP in a cyclic manner that alters the propensity of the GTPase to carry out a function. TRAFAC GTPases are considered to act as checkpoints to ribosome assembly, involved in binding to immature sections in the GTP-bound state, preventing further r-protein association until maturation is complete. Here we review our current understanding of the impact of the stringent response and (p)ppGpp production on ribosome maturation in prokaryotic cells, focusing on the inhibition of (p)ppGpp on GTPase-mediated subunit assembly, but also touching upon the inhibition of rRNA transcription and protein translation.
Topics: Amino Acid Sequence; Bacterial Proteins; GTP Phosphohydrolases; Guanosine Pentaphosphate; Guanosine Tetraphosphate; Guanosine Triphosphate; Models, Molecular; Prokaryotic Cells; Protein Binding; Protein Biosynthesis; Pyrophosphatases; Ribosomal Proteins; Ribosomes
PubMed: 31653044
DOI: 10.3390/cells8111313 -
Pharmacogenomics Aug 2022To investigate whether genotypes of , and were associated with azathioprine-induced adverse drug reaction (ADR) and had the gene-gene interactions with rs116855232...
To investigate whether genotypes of , and were associated with azathioprine-induced adverse drug reaction (ADR) and had the gene-gene interactions with rs116855232 to induce leukopenia. Patients who had taken azathioprine were recruited. Genotyping of those gene was performed. Risk factor to ADR was analyzed by logistic regression. The generalized multifactor dimensionality reduction (GMDR) was assessed based on gene-gene interactions with ADR. A total of 111 patients were included in this study, all of whom were Han Chinese. rs2295475 was a risk factor of myelotoxicity (p = 0.022). rs116855232 was a risk factor of myelotoxicity, grade ≥2 leukopenia and drug treatment termination (p-values were <0.05). Rs2295475 and rs116855232 had a gene-gene interaction. The model was associated with grade ≥2 leukopenia (OR: 17.99; 95% CI: 4.11-78.81). Combined testing genotype for rs2295475 and rs116855232 could improve the prediction of azathioprine-induced leukopenia.
Topics: Azathioprine; China; Genotype; Humans; Leukopenia; Pyrophosphatases; Sulfurtransferases; Xanthine Dehydrogenase
PubMed: 35916133
DOI: 10.2217/pgs-2022-0063 -
Scientific Reports Apr 2021Proton-translocating inorganic pyrophosphatases (H-PPases) are an ancient family of membrane bound enzymes that couple pyrophosphate (PPi) hydrolysis to H translocation...
Proton-translocating inorganic pyrophosphatases (H-PPases) are an ancient family of membrane bound enzymes that couple pyrophosphate (PPi) hydrolysis to H translocation across membranes. In this study, we conducted a molecular characterization of two isoenzymes (PdVP1 and PdVP2) located in respectively the alveolar sacs and in the membranes of the intracellular vacuoles of a scuticociliate parasite (Philasterides dicentrarchi) of farmed turbot. We analyzed the genetic expression of the isoenzymes after administration of antiparasitic drugs and after infection in the host. PdVP1 and PdVP2 are encoded by two genes of 2485 and 3069 bp, which respectively contain 3 and 11 exons and express proteins of 746 and 810 aa of molecular mass 78.9 and 87.6 kDa. Topological predictions from isoenzyme sequences indicate the formation of thirteen transmembrane regions (TMRs) for PdVP1 and seventeen TMRs for PdVP2. Protein structure modelling indicated that both isoenzymes are homodimeric, with three Mg binding sites and an additional K binding site in PdVP2. The levels of identity and similarity between the isoenzyme sequences are respectively 33.5 and 51.2%. The molecular weights of the native proteins are 158 kDa (PdVP1) and 178 kDa (PdVP2). The isoenzyme sequences are derived from paralogous genes that form a monophyletic grouping with other ciliate species. Genetic expression of the isoenzymes is closely related to the acidification of alveolar sacs (PdVP1) and intracellular vacuoles (PdVP2): antiparasitic drugs inhibit transcription, while infection increases transcription of both isoenzymes. The study findings show that P. dicentrarchi possesses two isoenzymes with H-PPase activity which are located in acidophilic cell compartment membranes and which are activated during infection in the host and are sensitive to antiparasitic drugs. The findings open the way to using molecular modelling to design drugs for the treatment of scuticociliatosis.
Topics: Amino Acid Sequence; Animals; Exons; Fish Diseases; Flatfishes; Gene Expression Regulation; Inorganic Pyrophosphatase; Isoenzymes; Parasites; Transcription, Genetic; Vacuoles
PubMed: 33875762
DOI: 10.1038/s41598-021-88102-0 -
Journal of Bone and Mineral Research :... Sep 2022Biallelic ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) deficiency induces vascular/soft tissue calcifications in generalized arterial calcification of...
Biallelic ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) deficiency induces vascular/soft tissue calcifications in generalized arterial calcification of infancy (GACI), and low bone mass with phosphate-wasting rickets in GACI survivors (autosomal hypophosphatemic rickets type-2). ENPP1 haploinsufficiency induces early-onset osteoporosis and mild phosphate wasting in adults. Both conditions demonstrate the unusual combination of reduced accrual of skeletal mineral, yet excess and progressive heterotopic mineralization. ENPP1 is the only enzyme that generates extracellular pyrophosphate (PPi), a potent inhibitor of both bone and heterotopic mineralization. Life-threatening vascular calcification in ENPP1 deficiency is due to decreased plasma PPi; however, the mechanism by which osteopenia results is not apparent from an understanding of the enzyme's catalytic activity. To probe for catalysis-independent ENPP1 pathways regulating bone, we developed a murine model uncoupling ENPP1 protein signaling from ENPP1 catalysis, Enpp1 mice. In contrast to Enpp1 mice, which lack ENPP1, Enpp1 mice have normal trabecular bone microarchitecture and favorable biomechanical properties. However, both models demonstrate low plasma Pi and PPi, increased fibroblast growth factor 23 (FGF23), and by 23 weeks, osteomalacia demonstrating equivalent phosphate wasting in both models. Reflecting findings in whole bone, calvarial cell cultures from Enpp1 mice demonstrated markedly decreased calcification, elevated transcription of Sfrp1, and decreased nuclear β-catenin signaling compared to wild-type (WT) and Enpp1 cultures. Finally, the decreased calcification and nuclear β-catenin signaling observed in Enpp1 cultures was restored to WT levels by knockout of Sfrp1. Collectively, our findings demonstrate that catalysis-independent ENPP1 signaling pathways regulate bone mass via the expression of soluble Wnt inhibitors such as secreted frizzled-related protein 1 (SFRP1), whereas catalysis dependent pathways regulate phosphate homeostasis through the regulation of plasma FGF23. © 2022 American Society for Bone and Mineral Research (ASBMR).
Topics: Animals; Bone and Bones; Catalysis; Familial Hypophosphatemic Rickets; Fibroblast Growth Factors; Mammals; Mice; Phosphates; Phosphoric Diester Hydrolases; Pyrophosphatases; Vascular Calcification; beta Catenin
PubMed: 35773783
DOI: 10.1002/jbmr.4640 -
European Journal of Medicinal Chemistry May 2021Ecto-nucleotide pyrophosphatases/phosphodiesterases (NPPs) together with nucleoside triphosphate diphosphohydrolases (NTPDases) and alkaline phosphatases (APs) are...
Synthesis, biological evaluation, and docking studies of novel pyrrolo[2,3-b]pyridine derivatives as both ectonucleotide pyrophosphatase/phosphodiesterase inhibitors and antiproliferative agents.
Ecto-nucleotide pyrophosphatases/phosphodiesterases (NPPs) together with nucleoside triphosphate diphosphohydrolases (NTPDases) and alkaline phosphatases (APs) are nucleotidases located at the surface of the cells. NPP1 and NPP3 are important members of NPP family that are known as druggable targets for a number of disorders such as impaired calcification, type 2 diabetes, and cancer. Sulfonylurea derivatives have been reported as antidiabetic and anticancer agents, therefore, we synthesized and investigated series of sulfonylurea derivatives 1a-m possessing pyrrolo[2,3-b]pyridine core as inhibitors of NPP1 and NPP3 isozymes that are over-expressed in cancer and diabetes. The enzymatic evaluation highlighted compound 1a as selective NPP1 inhibitor, however, 1c was observed as the most potent inhibitor of NPP1 with an IC value of 0.80 ± 0.04 μM. Compound 1l was found to be the most potent and moderately selective inhibitor of NPP3 (IC = 0.55 ± 0.01 μM). Furthermore, in vitro cytotoxicity assays of compounds 1a-m against MCF-7 and HT-29 cancer cell lines exhibited compound 1c (IC = 4.70 ± 0.67 μM), and 1h (IC = 1.58 ± 0.20 μM) as the most cytotoxic compounds against MCF-7 and HT-29 cancer cell lines, respectively. Both of the investigated compounds showed high degree of selectivity towards cancer cells than normal cells (WI-38). Molecular docking studies of selective and potent enzyme inhibitors revealed promising mode of interactions with important binding sites residues of both isozymes i.e., Thr256, His380, Lys255, Asn277 residues of NPP1 and His329, Thr205, and Leu239 residues of NPP3. In addition, the most potent antiproliferative agent, compound 1h, doesn't produce hypoglycemia as a side effect when injected to mice. This is an additional merit of the promising compound 1h.
Topics: Antineoplastic Agents; Cell Proliferation; Cells, Cultured; Dose-Response Relationship, Drug; Drug Screening Assays, Antitumor; Enzyme Inhibitors; Humans; Molecular Docking Simulation; Molecular Structure; Phosphoric Diester Hydrolases; Pyridines; Pyrophosphatases; Pyrroles; Structure-Activity Relationship
PubMed: 33744686
DOI: 10.1016/j.ejmech.2021.113339 -
MBio Feb 2022Inositol pyrophosphate (IPP) dynamics govern expression of the fission yeast phosphate homeostasis regulon via their effects on lncRNA-mediated transcription...
Inositol pyrophosphate (IPP) dynamics govern expression of the fission yeast phosphate homeostasis regulon via their effects on lncRNA-mediated transcription interference. The growth defects (ranging from sickness to lethality) elicited by fission yeast mutations that inactivate IPP pyrophosphatase enzymes are exerted via the agonistic effects of too much 1,5-IP8 on RNA 3'-processing and transcription termination. To illuminate determinants of IPP toxicosis, we conducted a genetic screen for spontaneous mutations that suppressed the sickness of Asp1 pyrophosphatase mutants. We identified a missense mutation, C823R, in the essential Cft1 subunit of the cleavage and polyadenylation factor complex that suppresses even lethal Asp1 IPP pyrophosphatase mutations, thereby fortifying the case for 3'-processing/termination as the target of IPP toxicity. The suppressor screen also identified Gde1 and Spx1 (SPAC6B12.07c), both of which have an IPP-binding SPX domain and both of which are required for lethality elicited by Asp1 mutations. A survey of other SPX proteins in the proteome identified the Vtc4 and Vtc2 subunits of the vacuolar polyphosphate polymerase as additional agents of IPP toxicosis. Gde1, Spx1, and Vtc4 contain enzymatic modules (glycerophosphodiesterase, RING finger ubiquitin ligase, and polyphosphate polymerase, respectively) fused to their IPP-sensing SPX domains. Structure-guided mutagenesis of the IPP-binding sites and the catalytic domains of Gde1 and Spx1 indicated that both modules are necessary to elicit IPP toxicity. Whereas Vtc4 polymerase catalytic activity is required for IPP toxicity, its IPP-binding site is not. Epistasis analysis, transcriptome profiling, and assays of Pho1 expression implicate Spx1 as a transducer of IP8 signaling to the 3'-processing/transcription termination machinery. Impeding the catabolism of the inositol pyrophosphate (IPP) signaling molecule IP8 is cytotoxic to fission yeast. Here, by performing a genetic suppressor screen, we identified several cellular proteins required for IPP toxicosis. Alleviation of IPP lethality by a missense mutation in the essential Cft1 subunit of the cleavage and polyadenylation factor consolidates previous evidence that toxicity results from IP8 action as an agonist of RNA 3'-processing and transcription termination. Novel findings are that IP8 toxicity depends on IPP-sensing SPX domain proteins with associated enzymatic functions: Gde1 (glycerophosphodiesterase), Spx1 (ubiquitin ligase), and Vtc2/4 (polyphosphate polymerase). The effects of Spx1 deletion on phosphate homeostasis imply a role for Spx1 in communicating an IP8-driven signal to the transcription and RNA processing apparatus.
Topics: Diphosphates; Fungal Proteins; Inositol Phosphates; Ligases; mRNA Cleavage and Polyadenylation Factors; Polyphosphates; Pyrophosphatases; RNA; Schizosaccharomyces; Ubiquitins
PubMed: 35012333
DOI: 10.1128/mbio.03476-21 -
The Journal of Molecular Diagnostics :... Oct 2022The goals of the Association for Molecular Pathology Clinical Practice Committee's Pharmacogenomics (PGx) Working Group are to define the key attributes of... (Review)
Review
TPMT and NUDT15 Genotyping Recommendations: A Joint Consensus Recommendation of the Association for Molecular Pathology, Clinical Pharmacogenetics Implementation Consortium, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, European...
The goals of the Association for Molecular Pathology Clinical Practice Committee's Pharmacogenomics (PGx) Working Group are to define the key attributes of pharmacogenetic alleles recommended for clinical testing and a minimum set of variants that should be included in clinical PGx genotyping assays. This article provides recommendations for a minimum panel of variant alleles (Tier 1) and an extended panel of variant alleles (Tier 2) that will aid clinical laboratories when designing assays for PGx testing. The Association for Molecular Pathology PGx Working Group considered the functional impact of the variant alleles, allele frequencies in multiethnic populations, the availability of reference materials, as well as other technical considerations for PGx testing when developing these recommendations. The ultimate goal of this Working Group is to promote standardization of PGx gene/allele testing across clinical laboratories. This article focuses on clinical TPMT and NUDT15 PGx testing, which may be applied to all thiopurine S-methyltransferase (TPMT) and nudix hydrolase 15 (NUDT15)-related medications. These recommendations are not to be interpreted as prescriptive, but to provide a reference guide.
Topics: Consensus; Genotype; Humans; Knowledge Bases; Methyltransferases; Pathologists; Pathology, Molecular; Pharmacists; Pharmacogenetics; Pyrophosphatases
PubMed: 35931343
DOI: 10.1016/j.jmoldx.2022.06.007 -
PeerJ 2024Pyrophosphatases (PPases) are enzymes that catalyze the hydrolysis of pyrophosphate (PPi), a byproduct of the synthesis and degradation of diverse biomolecules. The... (Review)
Review
Pyrophosphatases (PPases) are enzymes that catalyze the hydrolysis of pyrophosphate (PPi), a byproduct of the synthesis and degradation of diverse biomolecules. The accumulation of PPi in the cell can result in cell death. Although the substrate is the same, there are variations in the catalysis and features of these enzymes. Two enzyme forms have been identified in bacteria: cytoplasmic or soluble pyrophosphatases and membrane-bound pyrophosphatases, which play major roles in cell bioenergetics. In eukaryotic cells, cytoplasmic enzymes are the predominant form of PPases (c-PPases), while membrane enzymes (m-PPases) are found only in protists and plants. The study of bacterial cytoplasmic and membrane-bound pyrophosphatases has slowed in recent years. These enzymes are central to cell metabolism and physiology since phospholipid and nucleic acid synthesis release important amounts of PPi that must be removed to allow biosynthesis to continue. In this review, two aims were pursued: first, to provide insight into the structural features of PPases known to date and that are well characterized, and to provide examples of enzymes with novel features. Second, the scientific community should continue studying these enzymes because they have many biotechnological applications. Additionally, in this review, we provide evidence that there are m-PPases present in fungi; to date, no examples have been characterized. Therefore, the diversity of PPase enzymes is still a fruitful field of research. Additionally, we focused on the roles of H/Na pumps and m-PPases in cell bioenergetics. Finally, we provide some examples of the applications of these enzymes in molecular biology and biotechnology, especially in plants. This review is valuable for professionals in the biochemistry field of protein structure-function relationships and experts in other fields, such as chemistry, nanotechnology, and plant sciences.
Topics: Inorganic Pyrophosphatase; Bacteria; Fungi; Diphosphates
PubMed: 38938619
DOI: 10.7717/peerj.17496