-
The Biochemical Journal Mar 2015Pyruvate is the end-product of glycolysis, a major substrate for oxidative metabolism, and a branching point for glucose, lactate, fatty acid and amino acid synthesis.... (Review)
Review
Pyruvate is the end-product of glycolysis, a major substrate for oxidative metabolism, and a branching point for glucose, lactate, fatty acid and amino acid synthesis. The mitochondrial enzymes that metabolize pyruvate are physically separated from cytosolic pyruvate pools and rely on a membrane transport system to shuttle pyruvate across the impermeable inner mitochondrial membrane (IMM). Despite long-standing acceptance that transport of pyruvate into the mitochondrial matrix by a carrier-mediated process is required for the bulk of its metabolism, it has taken almost 40 years to determine the molecular identity of an IMM pyruvate carrier. Our current understanding is that two proteins, mitochondrial pyruvate carriers MPC1 and MPC2, form a hetero-oligomeric complex in the IMM to facilitate pyruvate transport. This step is required for mitochondrial pyruvate oxidation and carboxylation-critical reactions in intermediary metabolism that are dysregulated in several common diseases. The identification of these transporter constituents opens the door to the identification of novel compounds that modulate MPC activity, with potential utility for treating diabetes, cardiovascular disease, cancer, neurodegenerative diseases, and other common causes of morbidity and mortality. The purpose of the present review is to detail the historical, current and future research investigations concerning mitochondrial pyruvate transport, and discuss the possible consequences of altered pyruvate transport in various metabolic tissues.
Topics: Animals; Biological Transport; Forecasting; Glycolysis; Humans; Membrane Transport Proteins; Metabolic Networks and Pathways; Mitochondria; Mitochondrial Membrane Transport Proteins; Mitochondrial Membranes; Monocarboxylic Acid Transporters; Pyruvic Acid
PubMed: 25748677
DOI: 10.1042/BJ20141171 -
Pharmacotherapy Jun 2009Many physiologic differences between children and adults can result in age-related differences in pharmacokinetics. Understanding the effects of age on bioavailability,... (Review)
Review
Many physiologic differences between children and adults can result in age-related differences in pharmacokinetics. Understanding the effects of age on bioavailability, volume of distribution, protein binding, hepatic metabolic isoenzymes, and renal elimination can provide insight into optimizing doses for pediatric patients. We performed a search of English-language literature using the MEDLINE database regarding age and pharmacokinetics (1979-July 2008). We then evaluated the literature with an emphasis on drugs with one primary elimination pathway, such as renal clearance or a pathway involving a single metabolic isoenzyme. Our mechanistic-based analysis revealed that children need weight-corrected doses that are substantially higher than adult doses for drugs that are metabolically eliminated solely by the specific cytochrome P450 (CYP) isoenzymes CYP1A2, CYP2C9, and CYP3A4. In contrast, weight-corrected doses for drugs eliminated by renal excretion or metabolism involving CYP2C19, CYP2D6, N-acetyltransferase 2, or uridine diphosphate glucuronosyltransferases are similar in children and adults. In children, bioavailability of drugs with high first-pass metabolism is decreased for drugs metabolized by CYP1A2, CYP2C9, and CYP3A4. Limited data suggest that by age 5 years, bioavailability of drugs affected by efflux transporters should be equivalent to that of adults. Using a pharmacokinetics-based approach, rational predictions can be made for the effects of age on drugs that undergo similar pathways of elimination, even when specific pharmacokinetic data are limited or unavailable.
Topics: Age Factors; Arylamine N-Acetyltransferase; Biological Availability; Child; Child, Preschool; Cytochrome P-450 Enzyme System; Dose-Response Relationship, Drug; Drug Administration Schedule; Glucuronosyltransferase; Humans; Infant; Infant, Newborn; Isoenzymes; Kidney; Liver; Pediatrics; Pharmaceutical Preparations; Pharmacokinetics
PubMed: 19476420
DOI: 10.1592/phco.29.6.680 -
Nature Communications Feb 2017Eukaryotic ribosome biogenesis requires the nuclear import of ∼80 nascent ribosomal proteins and the elimination of excess amounts by the cellular degradation...
Eukaryotic ribosome biogenesis requires the nuclear import of ∼80 nascent ribosomal proteins and the elimination of excess amounts by the cellular degradation machinery. Assembly chaperones recognize nascent unassembled ribosomal proteins and transport them together with karyopherins to their nuclear destination. We report the crystal structure of ribosomal protein L4 (RpL4) bound to its dedicated assembly chaperone of L4 (Acl4), revealing extensive interactions sequestering 70 exposed residues of the extended RpL4 loop. The observed molecular recognition fundamentally differs from canonical promiscuous chaperone-substrate interactions. We demonstrate that the eukaryote-specific RpL4 extension harbours overlapping binding sites for Acl4 and the nuclear transport factor Kap104, facilitating its continuous protection from the cellular degradation machinery. Thus, Acl4 serves a dual function to facilitate nuclear import and simultaneously protect unassembled RpL4 from the cellular degradation machinery.
Topics: Active Transport, Cell Nucleus; Binding Sites; Crystallography, X-Ray; Molecular Chaperones; Protein Binding; Protein Conformation; Proteolysis; Ribosomal Proteins; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Ubiquitination; beta Karyopherins
PubMed: 28148929
DOI: 10.1038/ncomms14354 -
Journal of Proteome Research Dec 2014Many proteins, including p53, the FoxO transcription factors, RNA polymerase II, pRb, and the chaperones, have extensive post-translational modifications (PTMs). Many of...
Many proteins, including p53, the FoxO transcription factors, RNA polymerase II, pRb, and the chaperones, have extensive post-translational modifications (PTMs). Many of these modifications modulate protein-protein interactions, controlling interaction presence/absence and specificity. Here we propose the notion of the interaction code, a widespread means by which modifications are used to control interactions in the proteome. Minimal interaction codes are likely to exist on proteins that have two modifications and two or more interaction partners. By contrast, complex interaction codes are likely to be found on "date hub" proteins that have many interactions, many PTMs, or are targeted by many modifying and demodifying enzymes. Proteins with new interaction codes should be discoverable by examining protein interaction networks, annotated with PTMs and protein-modifying enzyme-substrate links. Multiple instances or combinations of phosphorylation, acetylation, methylation, O-GlcNAc, or ubiquitination will likely form interaction codes, especially when colocated on a protein's single interaction interface. A network-based example of code discovery is given, predicting the yeast protein Npl3p to have a methylation/phosphorylation-dependent interaction code.
Topics: Acetylation; Animals; Binding Sites; Fungal Proteins; Glycosylation; Humans; Methylation; Phosphorylation; Protein Binding; Protein Interaction Domains and Motifs; Protein Interaction Maps; Protein Processing, Post-Translational; Proteome; Signal Transduction; Ubiquitination
PubMed: 25337985
DOI: 10.1021/pr500585p -
Lens and Eye Toxicity Research 1989The relationship between the metabolic gradient within the ocular lens and its cellular and molecular organization is discussed. The lens shares a number of... (Review)
Review
The relationship between the metabolic gradient within the ocular lens and its cellular and molecular organization is discussed. The lens shares a number of organizational similarities with other stratified ectodermal tissues. All of these tissues were avascular and therefore, dependent upon the simple diffusion of nutrients from the surrounding medium. They contain non-metabolizing cell layers which are continually produced by an irreversible maturation process. This process is not random aging but a well orchestrated sequence of events dependent upon the physico-chemical properties of specialized proteins typical of each tissue. In the lens, these proteins are the crystallins. The signal for this maturation is decreased metabolism in conjunction with cell dehydration. Metabolism of these maturing cells is decreased by limited nutrient penetration because of barriers to nutrient diffusion and the high rate of utilization of nutrients by the more metabolically active cells near the basement membrane. Additionally, the regulation of anaerobic metabolism is dependent upon the maintenance and dissolution of an organized array of enzymes and the effects of dehydration, i.e. excluded volume effects and modified macromolecular organization. In the lens, the absence of metabolism during the maturation of the inner fiber cell layers is as important as the presence of active metabolism where differentiation and active protein synthesis occur. Therefore, any stress that disrupts tissue organization will have a detrimental effect on lens integrity.
Topics: Aging; Animals; Crystallins; Diffusion; Extracellular Space; Glycolysis; Intercellular Junctions; Lens, Crystalline
PubMed: 2487270
DOI: No ID Found -
Drug Metabolism Reviews 2005A number of therapeutic drugs with different structures and mechanisms of action have been reported to undergo metabolic activation by Phase I or Phase II... (Review)
Review
A number of therapeutic drugs with different structures and mechanisms of action have been reported to undergo metabolic activation by Phase I or Phase II drug-metabolizing enzymes. The bioactivation gives rise to reactive metabolites/intermediates, which readily confer covalent binding to various target proteins by nucleophilic substitution and/or Schiff's base mechanism. These drugs include analgesics (e.g., acetaminophen), antibacterial agents (e.g., sulfonamides and macrolide antibiotics), anticancer drugs (e.g., irinotecan), antiepileptic drugs (e.g., carbamazepine), anti-HIV agents (e.g., ritonavir), antipsychotics (e.g., clozapine), cardiovascular drugs (e.g., procainamide and hydralazine), immunosupressants (e.g., cyclosporine A), inhalational anesthetics (e.g., halothane), nonsteroidal anti-inflammatory drugs (NSAIDSs) (e.g., diclofenac), and steroids and their receptor modulators (e.g., estrogens and tamoxifen). Some herbal and dietary constituents are also bioactivated to reactive metabolites capable of binding covalently and inactivating cytochrome P450s (CYPs). A number of important target proteins of drugs have been identified by mass spectrometric techniques and proteomic approaches. The covalent binding and formation of drug-protein adducts are generally considered to be related to drug toxicity, and selective protein covalent binding by drug metabolites may lead to selective organ toxicity. However, the mechanisms involved in the protein adduct-induced toxicity are largely undefined, although it has been suggested that drug-protein adducts may cause toxicity either through impairing physiological functions of the modified proteins or through immune-mediated mechanisms. In addition, mechanism-based inhibition of CYPs may result in toxic drug-drug interactions. The clinical consequences of drug bioactivation and covalent binding to proteins are unpredictable, depending on many factors that are associated with the administered drugs and patients. Further studies using proteomic and genomic approaches with high throughput capacity are needed to identify the protein targets of reactive drug metabolites, and to elucidate the structure-activity relationships of drug's covalent binding to proteins and their clinical outcomes.
Topics: Animals; Biotransformation; Drug Interactions; Drug-Related Side Effects and Adverse Reactions; Humans; Pharmaceutical Preparations; Plant Preparations; Protein Binding; Proteins; Structure-Activity Relationship
PubMed: 15747500
DOI: 10.1081/dmr-200028812 -
Applied Microbiology and Biotechnology Aug 2010With the increasing demand for recombinant proteins and glycoproteins, research on hosts for producing these proteins is focusing increasingly on more cost-effective... (Review)
Review
With the increasing demand for recombinant proteins and glycoproteins, research on hosts for producing these proteins is focusing increasingly on more cost-effective expression systems. Yeasts and other fungi are promising alternatives because they provide easy and cheap systems that can perform eukaryotic post-translational modifications. Unfortunately, yeasts and other fungi modify their glycoproteins with heterogeneous high-mannose glycan structures, which is often detrimental to a therapeutic protein's pharmacokinetic behavior and can reduce the efficiency of downstream processing. This problem can be solved by engineering the glycosylation pathways to produce homogeneous and, if so desired, human-like glycan structures. In this review, we provide an overview of the most significant recently reported approaches for engineering the glycosylation pathways in yeasts and fungi.
Topics: Fungal Proteins; Fungi; Glycosylation; Metabolic Networks and Pathways; Protein Engineering; Recombinant Proteins
PubMed: 20585772
DOI: 10.1007/s00253-010-2721-1 -
Methods in Molecular Biology (Clifton,... 2019Phosphorylation, the process by which a phosphate group is attached to a preexisting protein, is an evolutionarily and metabolically cheap way to change the protein's...
Phosphorylation, the process by which a phosphate group is attached to a preexisting protein, is an evolutionarily and metabolically cheap way to change the protein's surface and properties. It is presumably for that reason that it is the most widespread protein modification: An estimated 10-30% of all proteins are subject to phosphorylation.MS-based methods are the methods of choice for the identification of phosphorylation sites; however biochemical pre-fractionation and enrichment protocols will be needed to produce suitable samples in the case of low-stoichiometry phosphorylation. Using emerging MS-based technology, the elucidation of the "phosphoproteome," a comprehensive inventory of phosphorylation sites, will become a realistic goal. However, validating these findings in a cellular context and defining their biological meaning remains a daunting task, which will inevitably require extensive and time-consuming additional biological research.
Topics: Alkylation; Amino Acid Sequence; Chromatography, Liquid; Phosphoproteins; Phosphorylation; Protein Processing, Post-Translational; Proteins; Proteome; Proteomics; Spectrometry, Mass, Electrospray Ionization; Tandem Mass Spectrometry
PubMed: 31256379
DOI: 10.1007/978-1-4939-9055-9_11 -
Methods in Enzymology 2005Intestinal absorption and hepatic clearance of drugs, xenobiotics, and bile acids are mediated by transporter proteins expressed at the plasma membranes of intestinal... (Review)
Review
Intestinal absorption and hepatic clearance of drugs, xenobiotics, and bile acids are mediated by transporter proteins expressed at the plasma membranes of intestinal epithelial cells and liver parenchymal cells in a polarized manner. Within enterocytes and hepatocytes, these exogenous or endogenous, potentially toxic compounds may be metabolized by phase I cytochrome P450 (CYP) and phase II conjugating enzymes. Many transporter proteins and metabolizing enzymes are subject to direct translational modification, enabling very rapid changes in their activity. However, to achieve intermediate and longer term changes in transport and enzyme activities, the genes encoding drug and bile acid transporters, as well as the CYP and conjugating enzymes, are regulated by a complex network of transcriptional cascades. These are typically mediated by specific members of the nuclear receptor family of transcription factors, particularly FXR, SHP, PXR, CAR, and HNF-4alpha. Most nuclear receptors are activated by specific ligands, including numerous xenobiotics (PXR, CAR) and bile acids (FXR). The fine-tuning of transcriptional control of drug and bile acid homeostasis depends on regulated interactions of specific nuclear receptors with their target genes.
Topics: Bile Acids and Salts; Humans; Inactivation, Metabolic; Membrane Transport Proteins; Receptors, Cytoplasmic and Nuclear; Transcriptional Activation; Xenobiotics
PubMed: 16399367
DOI: 10.1016/S0076-6879(05)00028-5 -
PLoS Genetics Jan 2023Oxidative stress is associated with cardiovascular and neurodegenerative diseases, diabetes, cancer, psychiatric disorders and aging. In order to counteract, eliminate...
Oxidative stress is associated with cardiovascular and neurodegenerative diseases, diabetes, cancer, psychiatric disorders and aging. In order to counteract, eliminate and/or adapt to the sources of stress, cells possess elaborate stress-response mechanisms, which also operate at the level of regulating transcription. Interestingly, it is becoming apparent that the metabolic state of the cell and certain metabolites can directly control the epigenetic information and gene expression. In the fission yeast Schizosaccharomyces pombe, the conserved Sty1 stress-activated protein kinase cascade is the main pathway responding to most types of stresses, and regulates the transcription of hundreds of genes via the Atf1 transcription factor. Here we report that fission yeast cells defective in fatty acid synthesis (cbf11, mga2 and ACC/cut6 mutants; FAS inhibition) show increased expression of a subset of stress-response genes. This altered gene expression depends on Sty1-Atf1, the Pap1 transcription factor, and the Gcn5 and Mst1 histone acetyltransferases, is associated with increased acetylation of histone H3 at lysine 9 in the corresponding gene promoters, and results in increased cellular resistance to oxidative stress. We propose that changes in lipid metabolism can regulate the chromatin and transcription of specific stress-response genes, which in turn might help cells to maintain redox homeostasis.
Topics: Acetyltransferases; Basic-Leucine Zipper Transcription Factors; Chromatin; Gene Expression; Gene Expression Regulation, Fungal; Lipid Metabolism; Mitogen-Activated Protein Kinases; Oxidative Stress; Phosphorylation; Schizosaccharomyces; Schizosaccharomyces pombe Proteins; Transcription Factors
PubMed: 36626368
DOI: 10.1371/journal.pgen.1010582