Superoxide, Neuroleptics and the Ubiquinone and Cytochrome B5
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Characterization of a Microsomal Retinol Dehydrogenase Gene from Amphioxus: Retinoid Metabolism Before Vertebrates
Chemico-Biological Interactions 130–132 (2001) 359–370 www.elsevier.com/locate/chembiont Characterization of a microsomal retinol dehydrogenase gene from amphioxus: retinoid metabolism before vertebrates Diana Dalfo´, Cristian Can˜estro, Ricard Albalat, Roser Gonza`lez-Duarte * Departament de Gene`tica, Facultat de Biologia, Uni6ersitat de Barcelona, A6. Diagonal, 645, E-08028, Barcelona, Spain Abstract Amphioxus, a member of the subphylum Cephalochordata, is thought to be the closest living relative to vertebrates. Although these animals have a vertebrate-like response to retinoic acid, the pathway of retinoid metabolism remains unknown. Two different enzyme systems — the short chain dehydrogenase/reductases and the cytosolic medium-chain alcohol dehydrogenases (ADHs) — have been postulated in vertebrates. Nevertheless, recent data show that the vertebrate-ADH1 and ADH4 retinol-active forms originated after the divergence of cephalochordates and vertebrates. Moreover, no data has been gathered in support of medium-chain retinol active forms in amphioxus. Then, if the cytosolic ADH system is absent and these animals use retinol, the microsomal retinol dehydrogenases could be involved in retinol oxidation. We have identified the genomic region and cDNA of an amphioxus Rdh gene as a preliminary step for functional characterization. Besides, phyloge- netic analysis supports the ancestral position of amphioxus Rdh in relation to the vertebrate forms. © 2001 Elsevier Science Ireland Ltd. All rights reserved. Keywords: Retinol dehydrogenase; Retinoid metabolism; Amphioxus * Corresponding author. Fax: +34-93-4110969. E-mail address: [email protected] (R. Gonza`lez-Duarte). 0009-2797/01/$ - see front matter © 2001 Elsevier Science Ireland Ltd. All rights reserved. PII: S0009-2797(00)00261-1 360 D. -
Methionine Sulfoxide Reductase a Is a Stereospecific Methionine Oxidase
Methionine sulfoxide reductase A is a stereospecific methionine oxidase Jung Chae Lim, Zheng You, Geumsoo Kim, and Rodney L. Levine1 Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, Bethesda, MD 20892-8012 Edited by Irwin Fridovich, Duke University Medical Center, Durham, NC, and approved May 10, 2011 (received for review February 10, 2011) Methionine sulfoxide reductase A (MsrA) catalyzes the reduction Results of methionine sulfoxide to methionine and is specific for the S epi- Stoichiometry. Branlant and coworkers have studied in careful mer of methionine sulfoxide. The enzyme participates in defense detail the mechanism of the MsrA reaction in bacteria (17, 18). against oxidative stresses by reducing methionine sulfoxide resi- In the absence of reducing agents, each molecule of MsrA dues in proteins back to methionine. Because oxidation of methio- reduces two molecules of MetO. Reduction of the first MetO nine residues is reversible, this covalent modification could also generates a sulfenic acid at the active site cysteine, and it is function as a mechanism for cellular regulation, provided there reduced back to the thiol by a fast reaction, which generates a exists a stereospecific methionine oxidase. We show that MsrA disulfide bond in the resolving domain of the protein. The second itself is a stereospecific methionine oxidase, producing S-methio- MetO is then reduced and again generates a sulfenic acid at the nine sulfoxide as its product. MsrA catalyzes its own autooxidation active site. Because the resolving domain cysteines have already as well as oxidation of free methionine and methionine residues formed a disulfide, no further reaction forms. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
And Detoxification (Benzola]Pyrene Quinones/Oxygen Radicals/NADPH-Cytochrome P-450 Reductase) PAUL L
Proc. Nati. Acad. Sci. USA Vol. 81, pp. 1696-1700, March 1984 Biochemistry Mutagenicity of quinones: Pathways of metabolic activation and detoxification (benzola]pyrene quinones/oxygen radicals/NADPH-cytochrome P-450 reductase) PAUL L. CHESIS*, DAVID E. LEVIN*, MARTYN T. SMITHt, LARS ERNSTERt, AND BRUCE N. AMES* Departments of *Biochemistry and tBiomedical and Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA 94720; and tDepartment of Biochemistry, Arrhenius Laboratory, University of Stockholm, S-10691 Stockholm, Sweden Contributed by Bruce N. Ames, December 12, 1983 ABSTRACT The mutagenicity of various quinones, a class nones might also be mutagenic, and we have tested this pos- of compounds widely distributed in nature, is demonstrated in sibility using the TA104 strain, which is sensitive to a wide the Salmonella TA104 tester strain. The metabolic pathways variety of oxidative mutagens (17). We have also attempted by which four quinones, menadione, benzo[alpyrene 3,6-qui- to characterize the pathways by which several different qui- none, 9,10-phenanthrenequinone, and danthron, caused mu- nones are metabolized and to study the potential mutagenic- tagenicity in this test system were investigated in detail as were ity of the metabolites and side products formed. We there- the detoxification pathways. The two-electron reduction of fore decided to investigate only those quinones that required these quinones by NAD(P)H-quinone oxidoreductase (DT-di- metabolic activation to exhibit mutagenicity. To limit the aphorase) was not mutagenic, whereas the one-electron reduc- scope of this project we also chose not to study quinones tion, catalyzed by NADPH-cytochrome P-450 reductase, was that possess reactive leaving groups. -
A Brief Guide to Enzyme Classification and Nomenclature Rev AM
A Brief Guide to Enzyme Nomenclature and Classification Keith Tipton and Andrew McDonald 1) Introduction NC-IUBMB Enzyme List, or, to give it its full title, “Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes by the Reactions they Catalyse,1 is a functional system, based solely on the substrates transformed and products formed by an enzyme. The basic layout of the classification for each enzyme is described below with some indication of the guidelines followed. More detailed rules for enzyme nomenclature and classification are available online.2 Further details of the principles governing the nomenclature of individual enzyme classes are given in the following sections. 2. Basic Concepts 2.1. EC numbers Enzymes are identified by EC (Enzyme Commission) numbers. These are also valuable for relating the information to other databases. They were divided into 6 major classes according to the type of reaction catalysed and a seventh, the translocases, was added in 2018.3 These are shown in Table 1. Table 1. Enzyme classes Name Reaction catalysed 1 Oxidoreductases *AH2 + B = A +BH2 2 Transferases AX + B = BX + A 3 Hydrolases A-B + H2O = AH + BOH 4 Lyases A=B + X-Y = A-B ç ç X Y 5 Isomerases A = B 6 LiGases †A + B + NTP = A-B + NDP + P (or NMP + PP) 7 Translocases AX + B çç = A + X + ççB (side 1) (side 2) *Where nicotinamide-adenine dinucleotides are the acceptors, NAD+ and NADH + H+ are used, by convention. †NTP = nucleoside triphosphate. The EC number is made up of four components separated by full stops. -
Expression in Escherichia Coli of Cytochrome C Reductase Activity from a Maize NADH:Nitrate Reductase Complementary DNA'
Plant Physiol. (1992) 99, 693-699 Received for publication September 20, 1991 0032-0889/92/99/0693/07/$01 .00/0 Accepted December 11, 1991 Expression in Escherichia coli of Cytochrome c Reductase Activity from a Maize NADH:Nitrate Reductase Complementary DNA' Wilbur H. Campbell Phytotechnology Research Center and Department of Biological Sciences, Michigan Technological University, Houghton, Michigan 49931-1295 ABSTRACT the deduced amino acid sequences of NR to related mam- A cDNA clone was isolated from a maize (Zea mays L. cv malian protein sequences because of its similarity to the Mo- W64AxW183E) scutellum Xgtl 1 library using maize leaf pterin domain of sulfite oxidase, and the C-terminal region NADH:nitrate reductase Zmnrl cDNA clone as a hybridization of NR has sequence homology to NADH:Cyt b5 reductase, probe; it was designated Zmnr1S. ZmnrlS was shown to be an which is a FAD-containing enzyme (3, 22). In between the NADH:nitrate reductase clone by nucleotide sequencing and com- Mo-pterin and FAD domains, NR has similarity to mam- parison of its deduced amino acid sequence to Zmnrl. Zmnr1S, malian Cyt b5. This central Cyt b domain of NR is bridged to which is 1.8 kilobases in length and contains the code for both the other two domains on either side of it by highly variable the cytochrome b and flavin adenine dinucleotide domains of sequence regions that appear to be hinges (3). These hinge nitrate reductase, was cloned into the EcoRI site of the Esche- regions are probably exposed in native NR and susceptible to richia coli expression vector pET5b and expressed. -
Cytochrome C, Cytochrome B5 and Electron Transfer
Cytochrome c, cytochrome b5: electron transfer and new functions 1 Iron Protoporphyrin IX, heme b Heme a Prosthetic group Heme a is a form of heme found A flat and planar structure. In cytochromes a and a3. -. Itself Toxic O2 , H2O2 are formed. Insoluble 2 Covalent bonds Cytochrome c is a major player in membrane associated electron transport systems in bacteria and mitochondria. 3 Myoglobin, Hemoglobin His E7 Distal side Heme iron His F8 Proximal side Myoglobin has a strong affinity for oxygen Heme is located in the hydrophobic site. when it is in the lungs, and where the pressure is around 100 torr. When it reaches Heme Fe interacts with His. the tissues, where it's around 20 torr, the Coordination bond affinity for oxygen is still quite high. This makes myoglobin less efficient of an oxygen Propionates of heme interact with Arg. transporter than hemoglobin, which loses it's Ionic bond affinity for oxygen as the pressure goes down and releases the oxygen into the tissues. Heme is easily dissociated from the protein. Myoglobin's strong affinity for oxygen means that it keeps the oxygen binded to itself His (E7) is the oxygen binding site. instead of releasing it into the tissues. 4 Sickle cell anemia & malaria resistance In sickle cell hemoglobin (HbS) glutamic acid in position 6 (in beta chain) is mutated to valine. This change allows the deoxygenated form of the hemoglobin to stick to itself. 5 Figure 1. HO-1 Protects against Severe Malaria Using a mouse model for cerebral malaria, Ferreira et al. (2011) suggest a biochemical basis for the link between sickle cell disease and severe malaria. -
Supplementary Material
Supplementary material: Figure S1. Protein-Protein Interactions of the 127 Dysregulated proteins in brain tissues following IONP exposure. The graph was generated from STRING database. 125 nodes, 183 edges, 2.93 Average node degree, 0.411 Avg. local clustering coefficient, 122 Expected number of edges, PPI enrichment p-value 1.83e-07. 1 Figure S2. Protein-Protein Interactions of the 66 Dysregulated proteins in liver tissues following IONP exposure. The graph was generated from STRING database. 61 nodes, 103 edges, 3.38 Average node degree, 0.412 Avg. local clustering coefficient, 22 Expected number of edges, PPI enrichment p-value < 1.0e-16. 2 Figure S3. Protein-Protein Interactions of the 84 Dysregulated proteins in lung tissues following IONP exposure. The graph was generated from STRING database. 82 nodes, 125 edges, 3.05 Average node degree, 0.422 Avg. local clustering coefficient, 64 Expected number of edges, PPI enrichment p-value 1.07e-11. 3 Table S1. List of all dysregulated proteins in brain tissues following IONP exposure. A) Down regulated proteins and B) Upregulated proteins. Statistically significant iTRAQ ratios (p-value ratio and p-value sample≤0.05) for the 127 proteins that are dysregulated. A) Sequence Peptide Spectral P-Value P-Value Log 10 Accession Name Description Gene Coverage Ratio Count Count Ratio Sample Ratio % P00762 TRY1_RAT Anionic trypsin-1 Prss1 1 8 8.13 0.526 0.001 0.004 -0.279 P08592 A4_RAT Amyloid beta A4 protein App 1 2 1.17 0.546 0.010 0.004 -0.263 Q62696 DLG1_RAT Disks large homolog 1 Dlg1 1 1 1.32 -
SELENOF) with Retinol Dehydrogenase 11 (RDH11
Tian et al. Nutrition & Metabolism (2018) 15:7 DOI 10.1186/s12986-017-0235-x RESEARCH Open Access The interaction of selenoprotein F (SELENOF) with retinol dehydrogenase 11 (RDH11) implied a role of SELENOF in vitamin A metabolism Jing Tian1* , Jiapan Liu1, Jieqiong Li2, Jingxin Zheng3, Lifang Chen4, Yujuan Wang1, Qiong Liu1 and Jiazuan Ni1 Abstract Background: Selenoprotein F (SELENOF, was named as 15-kDa selenoprotein) has been reported to play important roles in oxidative stress, endoplasmic reticulum (ER) stress and carcinogenesis. However, the biological function of SELENOF is still unclear. Methods: A yeast two-hybrid system was used to screen the interactive protein of SELENOF in a human fetal brain cDNA library. The interaction between SELENOF and interactive protein was validated by fluorescence resonance energy transfer (FRET), co-immunoprecipitation (co-IP) and pull-down assays. The production of retinol was detected by high performance liquid chromatograph (HPLC). Results: Retinol dehydrogenase 11 (RDH11) was found to interact with SELENOF. RDH11 is an enzyme for the reduction of all-trans-retinaldehyde to all-trans-retinol (vitamin A). The production of retinol was decreased by SELENOF overexpression, resulting in more retinaldehyde. Conclusions: SELENOF interacts with RDH11 and blocks its enzyme activity to reduce all-trans-retinaldehyde. Keywords: SELENOF (Seleonoprotein F) , Yeast two hybrid system, Protein-protein interaction, Retinol dehydrogenase 11 (RDH11), Fluorescence resonance energy transfer (FRET), Co-immunoprecipitation (co-IP), Pull- down, Retinol (vitamin a), Retinaldehyde Background SELENOF shows that the protein contains a Selenium (Se) is a necessary trace element for human thioredoxin-like motif. The redox potential of this motif health. -
Ferroptosis-Related Flavoproteins: Their Function and Stability
International Journal of Molecular Sciences Review Ferroptosis-Related Flavoproteins: Their Function and Stability R. Martin Vabulas Charité-Universitätsmedizin, Institute of Biochemistry, Charitéplatz 1, 10117 Berlin, Germany; [email protected]; Tel.: +49-30-4505-28176 Abstract: Ferroptosis has been described recently as an iron-dependent cell death driven by peroxida- tion of membrane lipids. It is involved in the pathogenesis of a number of diverse diseases. From the other side, the induction of ferroptosis can be used to kill tumor cells as a novel therapeutic approach. Because of the broad clinical relevance, a comprehensive understanding of the ferroptosis-controlling protein network is necessary. Noteworthy, several proteins from this network are flavoenzymes. This review is an attempt to present the ferroptosis-related flavoproteins in light of their involvement in anti-ferroptotic and pro-ferroptotic roles. When available, the data on the structural stability of mutants and cofactor-free apoenzymes are discussed. The stability of the flavoproteins could be an important component of the cellular death processes. Keywords: flavoproteins; riboflavin; ferroptosis; lipid peroxidation; protein quality control 1. Introduction Human flavoproteome encompasses slightly more than one hundred enzymes that par- ticipate in a number of key metabolic pathways. The chemical versatility of flavoproteins relies on the associated cofactors, flavin mononucleotide (FMN) and flavin adenine dinu- cleotide (FAD). In humans, flavin cofactors are biosynthesized from a precursor riboflavin that has to be supplied with food. To underline its nutritional essentiality, riboflavin is called vitamin B2. In compliance with manifold cellular demands, flavoproteins have been accommo- Citation: Vabulas, R.M. dated to operate at different subcellular locations [1]. -
Trans-Plasma Membrane Electron Transport System in the Myelin Membrane
Wilfrid Laurier University Scholars Commons @ Laurier Theses and Dissertations (Comprehensive) 2015 Characterization of the Trans-plasma Membrane Electron Transport System in the Myelin Membrane Afshan Sohail Wilfrid Laurier University, [email protected] Follow this and additional works at: https://scholars.wlu.ca/etd Part of the Biochemistry Commons, Molecular and Cellular Neuroscience Commons, and the Molecular Biology Commons Recommended Citation Sohail, Afshan, "Characterization of the Trans-plasma Membrane Electron Transport System in the Myelin Membrane" (2015). Theses and Dissertations (Comprehensive). 1694. https://scholars.wlu.ca/etd/1694 This Thesis is brought to you for free and open access by Scholars Commons @ Laurier. It has been accepted for inclusion in Theses and Dissertations (Comprehensive) by an authorized administrator of Scholars Commons @ Laurier. For more information, please contact [email protected]. Characterization of the Trans-plasma Membrane Electron Transport System in the Myelin Membrane By Afshan Sohail THESIS Submitted to the Department of Chemistry Faculty of Science In partial fulfillment of the requirements for Master of Science in Chemistry Wilfrid Laurier University 2014 © Afshan Sohail 2014 Abstract Myelination is the key feature of evolution in the nervous system of vertebrates. Myelin is the protrusion of glial cells. More specifically, "oligodendrocytes" in the central nervous system (CNS), and "Schwann" cells in the peripheral nervous system (PNS) form myelin membranes. Myelin remarkably, enhances the propagation of nerve impulses. However, myelin restricts the access of extracellular metabolites to the axons. A pathology called "demyelination" is associated with myelin. The myelin sheath is not only an insulator, but it is itself metabolically active. In this study it is hypothesized that the ratio of NAD(P)+/NAD(P)H and the glycolytic pathway of the myelin sheath is maintained via trans-plasma membrane electron transport system (t-PMET). -
Genomic Evidence of Reactive Oxygen Species Elevation in Papillary Thyroid Carcinoma with Hashimoto Thyroiditis
Endocrine Journal 2015, 62 (10), 857-877 Original Genomic evidence of reactive oxygen species elevation in papillary thyroid carcinoma with Hashimoto thyroiditis Jin Wook Yi1), 2), Ji Yeon Park1), Ji-Youn Sung1), 3), Sang Hyuk Kwak1), 4), Jihan Yu1), 5), Ji Hyun Chang1), 6), Jo-Heon Kim1), 7), Sang Yun Ha1), 8), Eun Kyung Paik1), 9), Woo Seung Lee1), Su-Jin Kim2), Kyu Eun Lee2)* and Ju Han Kim1)* 1) Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul, Korea 2) Department of Surgery, Seoul National University Hospital and College of Medicine, Seoul, Korea 3) Department of Pathology, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Korea 4) Kwak Clinic, Okcheon-gun, Chungbuk, Korea 5) Department of Internal Medicine, Uijeongbu St. Mary’s Hospital, Uijeongbu, Korea 6) Department of Radiation Oncology, Seoul St. Mary’s Hospital, Seoul, Korea 7) Department of Pathology, Chonnam National University Hospital, Kwang-Ju, Korea 8) Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea 9) Department of Radiation Oncology, Korea Cancer Center Hospital, Korea Institute of Radiological and Medical Sciences, Seoul, Korea Abstract. Elevated levels of reactive oxygen species (ROS) have been proposed as a risk factor for the development of papillary thyroid carcinoma (PTC) in patients with Hashimoto thyroiditis (HT). However, it has yet to be proven that the total levels of ROS are sufficiently increased to contribute to carcinogenesis. We hypothesized that if the ROS levels were increased in HT, ROS-related genes would also be differently expressed in PTC with HT. To find differentially expressed genes (DEGs) we analyzed data from the Cancer Genomic Atlas, gene expression data from RNA sequencing: 33 from normal thyroid tissue, 232 from PTC without HT, and 60 from PTC with HT.