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Nucleic Acids Research Jan 2014As the number of prescribed drugs is constantly rising, drug-drug interactions are an important issue. The simultaneous administration of several drugs can cause severe...
As the number of prescribed drugs is constantly rising, drug-drug interactions are an important issue. The simultaneous administration of several drugs can cause severe adverse effects based on interactions with the same metabolizing enzyme(s). The Transformer database (http://bioinformatics.charite.de/transformer) contains integrated information on the three phases of biotransformation (modification, conjugation and excretion) of 3000 drugs and >350 relevant food ingredients (e.g. grapefruit juice) and herbs, which are catalyzed by 400 proteins. A total of 100,000 interactions were found through text mining and manual validation. The 3D structures of 200 relevant proteins are included. The database enables users to search for drugs with a visual display of known interactions with phase I (Cytochrome P450) and phase II enzymes, transporters, food and herbs. For each interaction, PubMed references are given. To detect mutual impairments of drugs, the drug-cocktail tool displays interactions between selected drugs. By choosing the indication for a drug, the tool offers suggestions for alternative medications to avoid metabolic conflicts. Drug interactions can also be visualized in an interactive network view. Additionally, prodrugs, including their mechanisms of activation, and further information on enzymes of biotransformation, including 3D models, can be viewed.
Topics: Biotransformation; Cytochrome P-450 Enzyme System; Data Mining; Databases, Chemical; Enzymes; Humans; Internet; Membrane Transport Proteins; Pharmacokinetics; Prodrugs; Protein Conformation; Xenobiotics
PubMed: 24334957
DOI: 10.1093/nar/gkt1246 -
Microbiology (Reading, England) Jul 2015The galacto-oligosaccharide (GOS) OLIGOMATE 55N (Yakult) is a mixture of oligosaccharides, the main component of which is 4'-galactosyllactose (4'-GL). Numerous reports...
The galacto-oligosaccharide (GOS) OLIGOMATE 55N (Yakult) is a mixture of oligosaccharides, the main component of which is 4'-galactosyllactose (4'-GL). Numerous reports have shown that GOSs are non-digestible, reach the colon and selectively stimulate the growth of bifidobacteria. The product has been used as a food ingredient and its applications have expanded rapidly. However, the bifidobacterial glycoside hydrolases and transporters responsible for utilizing GOSs have not been characterized sufficiently. In this study, we aimed to identify and characterize genes responsible for metabolizing 4'-GL in Bifidobacterium breve strain Yakult. We attempted to identify B. breve Yakult genes induced by 4'-GL using transcriptional profiling during growth in basal medium containing 4'-GL with a custom microarray. We found that BbrY_0420, which encodes solute-binding protein (SBP), and BbrY_0422, which encodes β-galactosidase, were markedly upregulated relative to that during growth in basal medium containing lactose. Investigation of the substrate specificity of recombinant BbrY_0420 protein using surface plasmon resonance showed that BbrY_0420 protein bound to 4'-GL, but not to 3'-GL and 6'-GL, structural isomers of 4'-GL. Additionally, BbrY_0420 had a strong affinity for 4-galactobiose (4-GB), suggesting that this SBP recognized the non-reducing terminal structure of 4'-GL. Incubation of purified recombinant BbrY_0422 protein with 4'-GL, 3'-GL, 6'-GL and 4-GB revealed that the protein efficiently hydrolysed 4'-GL and 4-GB, but did not digest 3'-GL, 6'-GL or lactose, suggesting that BbrY_0422 digested the bond within Gal1,4-β-Gal. Thus, BbrY_0420 (SBP) and BbrY_0422 (β-galactosidase) had identical, strict substrate specificity, suggesting that they were coupled by co-induction to facilitate the transportation and hydrolysis of 4'-GL.
Topics: Bacterial Proteins; Bifidobacterium; Culture Media; Gene Expression Profiling; Metabolic Networks and Pathways; Protein Binding; Surface Plasmon Resonance; Transcription, Genetic; Trisaccharides
PubMed: 25903756
DOI: 10.1099/mic.0.000100 -
The Journal of Cell Biology Jul 2016Phosphatidylethanolamine (PE) is an essential phospholipid for mitochondrial functions and is synthesized mainly by phosphatidylserine (PS) decarboxylase at the...
Phosphatidylethanolamine (PE) is an essential phospholipid for mitochondrial functions and is synthesized mainly by phosphatidylserine (PS) decarboxylase at the mitochondrial inner membrane. In Saccharomyces cerevisiae, PS is synthesized in the endoplasmic reticulum (ER), such that mitochondrial PE synthesis requires PS transport from the ER to the mitochondrial inner membrane. Here, we provide evidence that Ups2-Mdm35, a protein complex localized at the mitochondrial intermembrane space, mediates PS transport for PE synthesis in respiration-active mitochondria. UPS2- and MDM35-null mutations greatly attenuated conversion of PS to PE in yeast cells growing logarithmically under nonfermentable conditions, but not fermentable conditions. A recombinant Ups2-Mdm35 fusion protein exhibited phospholipid-transfer activity between liposomes in vitro. Furthermore, UPS2 expression was elevated under nonfermentable conditions and at the diauxic shift, the metabolic transition from glycolysis to oxidative phosphorylation. These results demonstrate that Ups2-Mdm35 functions as a PS transfer protein and enhances mitochondrial PE synthesis in response to the cellular metabolic state.
Topics: Biological Transport; Cell Respiration; Fermentation; Gene Deletion; Mitochondria; Mitochondrial Proteins; Mutation; Phosphatidylethanolamines; Phosphatidylserines; Phospholipid Transfer Proteins; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 27354379
DOI: 10.1083/jcb.201601082 -
Frontiers in Endocrinology 2020The Carbohydrate response element binding protein, ChREBP encoded by the gene, is a transcription factor that is expressed at high levels in the liver and has a... (Review)
Review
The Carbohydrate response element binding protein, ChREBP encoded by the gene, is a transcription factor that is expressed at high levels in the liver and has a prominent function during consumption of high-carbohydrate diets. ChREBP is activated by raised cellular levels of phosphate ester intermediates of glycolysis, gluconeogenesis and the pentose phosphate pathway. Its target genes include a wide range of enzymes and regulatory proteins, including , , , and enzymes of lipogenesis. ChREBP activation cumulatively promotes increased disposal of phosphate ester intermediates to glucose, glucose 6-phosphatase or to pyruvate glycolysis with further metabolism by lipogenesis. Dietary fructose is metabolized in both the intestine and the liver and is more lipogenic than glucose. It also induces greater elevation in phosphate ester intermediates than glucose, and at high concentrations causes transient depletion of inorganic phosphate, compromised ATP homeostasis and degradation of adenine nucleotides to uric acid. ChREBP deficiency predisposes to fructose intolerance and compromised cellular phosphate ester and ATP homeostasis and thereby markedly aggravates the changes in metabolite levels caused by dietary fructose. The recent evidence that high fructose intake causes more severe hepatocyte damage in ChREBP-deficient models confirms the crucial protective role for ChREBP in maintaining intracellular phosphate homeostasis. The improved ATP homeostasis in hepatocytes isolated from mice after chronic activation of ChREBP with a glucokinase activator supports the role of ChREBP in the control of intracellular homeostasis. It is hypothesized that drugs that activate ChREBP confer a protective role in the liver particularly in compromised metabolic states.
Topics: Animals; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors; Gene Expression Regulation; Gluconeogenesis; Glycolysis; Humans; Lipogenesis; Liver; Metabolic Diseases; Protective Agents; Response Elements
PubMed: 33281747
DOI: 10.3389/fendo.2020.594041 -
Frontiers in Immunology 2023
Topics: Humans; Neoplasms; Proteins; Immunotherapy; Protein Processing, Post-Translational
PubMed: 37822939
DOI: 10.3389/fimmu.2023.1289016 -
Nature Communications Mar 2018Protein-protein interactions govern almost all cellular functions. These complex networks of stable and transient associations can be mapped by affinity purification...
Protein-protein interactions govern almost all cellular functions. These complex networks of stable and transient associations can be mapped by affinity purification mass spectrometry (AP-MS) and complementary proximity-based labeling methods such as BioID. To exploit the advantages of both strategies, we here design and optimize an integrated approach combining AP-MS and BioID in a single construct, which we term MAC-tag. We systematically apply the MAC-tag approach to 18 subcellular and 3 sub-organelle localization markers, generating a molecular context database, which can be used to define a protein's molecular location. In addition, we show that combining the AP-MS and BioID results makes it possible to obtain interaction distances within a protein complex. Taken together, our integrated strategy enables the comprehensive mapping of the physical and functional interactions of proteins, defining their molecular context and improving our understanding of the cellular interactome.
Topics: Biotinylation; Cell Line; Chromatography, Affinity; High-Throughput Screening Assays; Humans; Mass Spectrometry; Protein Binding; Protein Interaction Mapping; Protein Transport; Proteins
PubMed: 29568061
DOI: 10.1038/s41467-018-03523-2 -
Cell Cycle (Georgetown, Tex.) 2015Cell division is a metabolically demanding process, requiring the production of large amounts of energy and biomass. Not surprisingly therefore, a cell's decision to...
Cell division is a metabolically demanding process, requiring the production of large amounts of energy and biomass. Not surprisingly therefore, a cell's decision to initiate division is co-determined by its metabolic status and the availability of nutrients. Emerging evidence reveals that metabolism is not only undergoing substantial changes during the cell cycle, but it is becoming equally clear that metabolism regulates cell cycle progression. Here, we overview the emerging role of those metabolic pathways that have been best characterized to change during or influence cell cycle progression. We then studied how Notch signaling, a key angiogenic pathway that inhibits endothelial cell (EC) proliferation, controls EC metabolism (glycolysis) during the cell cycle.
Topics: Adaptor Proteins, Signal Transducing; Animals; Calcium-Binding Proteins; Cell Cycle; Cell Cycle Proteins; Cell Proliferation; Cells, Cultured; Energy Metabolism; G1 Phase Cell Cycle Checkpoints; Glycolysis; Human Umbilical Vein Endothelial Cells; Humans; Intercellular Signaling Peptides and Proteins; Phenotype; Phosphofructokinase-2; Receptors, Notch; Signal Transduction; Transfection; Ubiquitin-Protein Ligases
PubMed: 26431254
DOI: 10.1080/15384101.2015.1090068 -
The Journal of Cell Biology Feb 2022Arsenic is an environmental toxin that exists mainly as pentavalent arsenate and trivalent arsenite. Both forms activate the yeast SAPK Hog1 but with different...
Arsenic is an environmental toxin that exists mainly as pentavalent arsenate and trivalent arsenite. Both forms activate the yeast SAPK Hog1 but with different consequences. We describe a mechanism by which cells distinguish between these arsenicals through one-step metabolism to differentially regulate the bidirectional glycerol channel Fps1, an adventitious port for arsenite. Cells exposed to arsenate reduce it to thiol-reactive arsenite, which modifies a set of cysteine residues in target proteins, whereas cells exposed to arsenite metabolize it to methylarsenite, which modifies an additional set of cysteine residues. Hog1 becomes arsenylated, which prevents it from closing Fps1. However, this block is overcome in cells exposed to arsenite through methylarsenylation of Acr3, an arsenite efflux pump that we found also regulates Fps1 directly. This adaptation allows cells to restrict arsenite entry through Fps1 and also allows its exit when produced from arsenate exposure. These results have broad implications for understanding how SAPKs activated by diverse stressors can drive stress-specific outputs.
Topics: Arsenicals; Arsenites; Biological Transport; Membrane Proteins; Models, Biological; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 35139143
DOI: 10.1083/jcb.202109034 -
ACS Chemical Biology Sep 2014Metabolic chemical reporters have been largely used to study posttranslational modifications. Generally, it was assumed that these reporters entered one biosynthetic...
Metabolic chemical reporters have been largely used to study posttranslational modifications. Generally, it was assumed that these reporters entered one biosynthetic pathway, resulting in labeling of one type of modification. However, because they are metabolized by cells before their addition onto proteins, metabolic chemical reporters potentially provide a unique opportunity to read-out on both modifications of interest and cellular metabolism. We report here the development of a metabolic chemical reporter 1-deoxy-N-pentynyl glucosamine (1-deoxy-GlcNAlk). This small-molecule cannot be incorporated into glycans; however, treatment of mammalian cells results in labeling of a variety proteins and enables their visualization and identification. Competition of this labeling with sodium acetate and an acetyltransferase inhibitor suggests that 1-deoxy-GlcNAlk can enter the protein acetylation pathway. These results demonstrate that metabolic chemical reporters have the potential to isolate and potentially discover cross-talk between metabolic pathways in living cells.
Topics: Acetylation; Alkynes; Animals; Carbohydrate Metabolism; Fluorescent Dyes; Glucosamine; Glycosylation; Histones; Lysine; Metabolic Networks and Pathways; Mice; Molecular Biology; Molecular Probe Techniques; Molecular Probes; NIH 3T3 Cells; Protein Processing, Post-Translational; Proteins; Sodium Acetate; Tandem Mass Spectrometry; p300-CBP Transcription Factors
PubMed: 25062036
DOI: 10.1021/cb5005564 -
The Journal of Biological Chemistry Aug 2010Aerobic organisms are faced with a dilemma. Environmental iron is found primarily in the relatively inert Fe(III) form, whereas the more metabolically active ferrous... (Review)
Review
Aerobic organisms are faced with a dilemma. Environmental iron is found primarily in the relatively inert Fe(III) form, whereas the more metabolically active ferrous form is a strong pro-oxidant. This conundrum is solved by the redox cycling of iron between Fe(III) and Fe(II) at every step in the iron metabolic pathway. As a transition metal ion, iron can be "metabolized" only by this redox cycling, which is catalyzed in aerobes by the coupled activities of ferric iron reductases (ferrireductases) and ferrous iron oxidases (ferroxidases).
Topics: Aerobiosis; Animals; Ceruloplasmin; FMN Reductase; Humans; Ion Transport; Iron; Oxidation-Reduction
PubMed: 20522542
DOI: 10.1074/jbc.R110.113217