Springer Handbook of Enzymes

Total Page:16

File Type:pdf, Size:1020Kb

Springer Handbook of Enzymes Dietmar Schomburg and Ida Schomburg (Eds.) Springer Handbook of Enzymes Volume 25 Class 1 • Oxidoreductases X EC 1.9-1.13 co edited by Antje Chang Second Edition 4y Springer Index of Recommended Enzyme Names EC-No. Recommended Name Page 1.13.11.50 acetylacetone-cleaving enzyme 673 1.10.3.4 o-aminophenol oxidase 149 1.13.12.12 apo-/?-carotenoid-14',13'-dioxygenase 732 1.13.11.34 arachidonate 5-lipoxygenase 591 1.13.11.40 arachidonate 8-lipoxygenase 627 1.13.11.31 arachidonate 12-lipoxygenase 568 1.13.11.33 arachidonate 15-lipoxygenase 585 1.13.12.1 arginine 2-monooxygenase 675 1.13.11.13 ascorbate 2,3-dioxygenase 491 1.10.2.1 L-ascorbate-cytochrome-b5 reductase 79 1.10.3.3 L-ascorbate oxidase 134 1.11.1.11 L-ascorbate peroxidase 257 1.13.99.2 benzoate 1,2-dioxygenase (transferred to EC 1.14.12.10) 740 1.13.11.39 biphenyl-2,3-diol 1,2-dioxygenase 618 1.13.11.22 caffeate 3,4-dioxygenase 531 1.13.11.16 3-carboxyethylcatechol 2,3-dioxygenase 505 1.13.11.21 p-carotene 15,15'-dioxygenase (transferred to EC 1.14.99.36) 530 1.11.1.6 catalase 194 1.13.11.1 catechol 1,2-dioxygenase 382 1.13.11.2 catechol 2,3-dioxygenase 395 1.10.3.1 catechol oxidase 105 1.13.11.36 chloridazon-catechol dioxygenase 607 1.11.1.10 chloride peroxidase 245 1.13.11.49 chlorite O2-lyase 670 1.13.99.4 4-chlorophenylacetate 3,4-dioxygenase (transferred to EC 1.14.12.9) . 748 1.12.99.1 coenzyme F42o hydrogenase (transferred to EC 1.12.98.1) 368 1.12.98.1 coenzyme F42o hydrogenase 351 1.12.99.2 coenzyme-M-7-mercaptoheptanoylthreonine-phosphate-heterodisulfide 369 hydrogenase (deleted, this was a system comprising two enzymes and not a single enzyme, as was thought) 1.13.12.6 Cypridina-luciferin 2-monooxygenase 708 1.13.11.19 cysteamine dioxygenase 517 1.13.11.20 cysteine dioxygenase 522 1.9.3.1 cytochrome-c oxidase 1 1.11.1.5 cytochrome-c peroxidase 186 1.12.2.1 cytochrome-C3 hydrogenase 328 1.11.1.14 diarylpropane peroxidase 309 1.13.11.25 3,4-dihydroxy-9,10-secoandrosta-l,3,5(10)-triene-9,17-dione 4,5-dioxy- 539 genase 1.13.11.41 2,4'-dihydroxyacetophenone dioxygenase 631 1.13.11.28 2,3-dihydroxybenzoate 2,3-dioxygenase 559 1.13.11.14 2,3-dihydroxybenzoate 3,4-dioxygenase 493 1.13.11.23 2,3-dihydroxyindole 2,3-dioxygenase 533 1.13.11.10 7,8-dihydroxykynurenate 8,8a-dioxygenase 455 1.13.11.15 3,4-dihydroxyphenylacetate 2,3-dioxygenase 496 XV Index of Recommended Enzyme Names, 1.13.11.7 3,4-dihydroxyphenylacetate 3,4-dioxygenase (deleted) 446 1.13.11.9 2,5-dihydroxypyridine 5,6-dioxygenase 451 1.12.99.5 3,4-dihydroxyquinoline 2,4-dioxygenase 372 (deleted, identical to EC 1.13.11.47) 1.13.99.5 3,4-dihydroxyquinoline 2,4-dioxygenase (transferred to EC 1.13.11.47) 749 1.11.1.3 fatty-acid peroxidase 182 1.12.7.1 ferredoxin hydrogenase (transferred to EC 1.18.99.1) 337 1.12.7.2 ferredoxin hydrogenase 338 1.13.11.4 gentisate 1,2-dioxygenase 422 1.11.1.9 glutathione peroxidase 233 1.13.11.5 homogentisate 1,2-dioxygenase 430 1.12.1.2 hydrogen dehydrogenase 316 1.12.1.3 hydrogen dehydrogenase (NADP+) 325 1.12.5.1 hydrogen:quinone oxidoreductase 335 1.12.99.3 hydrogen-.quinone oxidoreductase (transferred to EC 1.12.5.1) .... 370 1.12.99.6 hydrogenase (acceptor) 373 1.13.11.48 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase 667 1.13.11.38 l-hydroxy-2-naphthoate 1,2-dioxygenase 616 1.13.11.47 3-hydroxy-4-oxoquinoline 2,4-dioxygenase 663 1.13.11.6 3-hydroxyanthranilate 3,4-dioxygenase 439 1.10.3.5 3-hydroxyanthranilate oxidase 153 1.13.11.46 4-hydroxymandelate synthase 661 1.13.11.27 4-hydroxyphenylpyruvate dioxygenase 546 1.13.11.37 hydroxyquinol 1,2-dioxygenase 610 1.13.11.17 indole 2,3-dioxygenase 509 1.13.11.42 indoleamine-pyrrole 2,3-dioxygenase 633 1.13.99.1 inositol oxygenase 734 1.11.1.8 iodide peroxidase 227 1.9.99.1 iron-cytochrome-c reductase 73 1.10.3.2 laccase 115 1.13.12.4 lactate 2-monooxygenase 692 1.13.11.43 lignostilbene a/3-dioxygenase 649 1.13.11.45 linoleate 11-lipoxygenase 658 1.13.11.44 linoleate diol synthase 653 1.13.11.12 lipoxygenase 473 1.13.12.2 lysine 2-monooxygenase 679 1.13.12.10 lysine 6-monooxygenase (deleted, reaction covered by EC 1.14.13.59) . 729 1.11.1.13 manganese peroxidase 283 1.12.98.3 Methanosarcina-phenazine hydrogenase 365 1.12.99.4 ^^"-methenyltetrahydromethanopterin hydrogenase 371 (transferred to EC 1.12.98.2) 1.12.98.2 N5,N10-methenyltetrahydromethanopterin hydrogenase 361 1.13.12.11 methylphenyltetrahydropyridine N-monooxygenase 730 1.11.1.1 NADH peroxidase 172 1.11.1.2 NADPH peroxidase 180 1.9.6.1 nitrate reductase (cytochrome) 49 1.13.11.32 2-nitropropane dioxygenase 581 1.13.11.26 peptide-tryptophan 2,3-dioxygenase 542 1.11.1.7 peroxidase 211 1.12.1.1 peroxidase (transferred to EC 1.18.99.1) 315 1.13.12.9 phenylalanine 2-monooxygenase 724 1.11.1.12 phospholipid-hydroperoxide glutathione peroxidase 274 1.13.12.7 Photinus-luciferin 4-monooxygenase (ATP-hydrolysing) 711 XVI Index of Recommended Enzyme Names 1.10.99.1 plastoquinol-plastocyanin reductase 163 1.13.11.3 protocatechuate 3,4-dioxygenase 408 1.13.11.8 protocatechuate 4,5-dioxygenase 447 1.9.3.2 Pseudomonas cytochrome oxidase 35 1.13.11.35 pyrogallol 1,2-oxygenase 605 1.13.11.24 quercetin 2,3-dioxygenase 535 1.11.1.4 recommended name never specified (transferred to EC 1.13.11.11) . 185 1.13.12.5 Renilla-luciferin 2-monooxygenase 704 1.10.3.6 rifamycin-B oxidase 157 1.13.11.29 stizolobate synthase 562 1.13.11.30 stizolobinate synthase 565 1.13.11.18 sulfur dioxygenase 513 1.10.3.8 sulochrin oxidase [(-)-bisdechlorogeodin-forming] 162 (transferred to EC 1.21.3.8) 1.10.3.7 sulochrin oxidase [(+)-bisdechlorogeodin-forming] 161 (transferred to EC 1.21.3.4) 1.10.1.1 trans-acenaphthene-l,2-diol dehydrogenase 76 1.13.11.11 tryptophan 2,3-dioxygenase 457 1.13.99.3 tryptophan 2'-dioxygenase 741 1.13.12.3 tryptophan 2-monooxygenase 687 1.10.2.2 ubiquinol-cytochrome-c reductase 83 1.13.12.8 Watasenia-luciferin 2-monooxygenase 722.
Recommended publications
  • Increased Hydrogen Peroxide Concentration in the Exhaled Breath Condensate of Stable COPD Patients After Nebulized -Acetylcysteine Jacek Rysz, Robert A
    Increased hydrogen peroxide concentration in the exhaled breath condensate of stable COPD patients after nebulized -acetylcysteine Jacek Rysz, Robert A. Stolarek, Rafal Luczynski, Agata Sarniak, Anna Wlodarczyk, Marek Kasielski, Dariusz Nowak To cite this version: Jacek Rysz, Robert A. Stolarek, Rafal Luczynski, Agata Sarniak, Anna Wlodarczyk, et al.. In- creased hydrogen peroxide concentration in the exhaled breath condensate of stable COPD patients after nebulized -acetylcysteine. Pulmonary Pharmacology & Therapeutics, 2007, 20 (3), pp.281. 10.1016/j.pupt.2006.03.011. hal-00499131 HAL Id: hal-00499131 https://hal.archives-ouvertes.fr/hal-00499131 Submitted on 9 Jul 2010 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Author’s Accepted Manuscript Increased hydrogen peroxide concentration in the exhaled breath condensate of stable COPD patients after nebulized N-acetylcysteine Jacek Rysz, Robert A. Stolarek, Rafal Luczynski, Agata Sarniak,Anna Wlodarczyk, Marek Kasielski, Dariusz Nowak PII: S1094-5539(06)00045-9 DOI: doi:10.1016/j.pupt.2006.03.011 www.elsevier.com/locate/ypupt Reference: YPUPT 677 To appear in: Pulmonary Pharmacology & Therapeutics Received date: 2 January 2006 Revised date: 13 March 2006 Accepted date: 15 March 2006 Cite this article as: Jacek Rysz, Robert A.
    [Show full text]
  • Non-Homologous Isofunctional Enzymes: a Systematic Analysis Of
    Omelchenko et al. Biology Direct 2010, 5:31 http://www.biology-direct.com/content/5/1/31 RESEARCH Open Access Non-homologousResearch isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution Marina V Omelchenko, Michael Y Galperin*, Yuri I Wolf and Eugene V Koonin Abstract Background: Evolutionarily unrelated proteins that catalyze the same biochemical reactions are often referred to as analogous - as opposed to homologous - enzymes. The existence of numerous alternative, non-homologous enzyme isoforms presents an interesting evolutionary problem; it also complicates genome-based reconstruction of the metabolic pathways in a variety of organisms. In 1998, a systematic search for analogous enzymes resulted in the identification of 105 Enzyme Commission (EC) numbers that included two or more proteins without detectable sequence similarity to each other, including 34 EC nodes where proteins were known (or predicted) to have distinct structural folds, indicating independent evolutionary origins. In the past 12 years, many putative non-homologous isofunctional enzymes were identified in newly sequenced genomes. In addition, efforts in structural genomics resulted in a vastly improved structural coverage of proteomes, providing for definitive assessment of (non)homologous relationships between proteins. Results: We report the results of a comprehensive search for non-homologous isofunctional enzymes (NISE) that yielded 185 EC nodes with two or more experimentally characterized - or predicted - structurally unrelated proteins. Of these NISE sets, only 74 were from the original 1998 list. Structural assignments of the NISE show over-representation of proteins with the TIM barrel fold and the nucleotide-binding Rossmann fold. From the functional perspective, the set of NISE is enriched in hydrolases, particularly carbohydrate hydrolases, and in enzymes involved in defense against oxidative stress.
    [Show full text]
  • Henrique Pinho Oliveira
    0 UNIVERSIDADE FEDERAL DO CEARÁ CENTRO DE CIÊNCIAS DEPARTAMENTO DE BIOQUÍMICA E BIOLOGIA MOLECULAR PROGRAMA DE PÓS-GRADUAÇÃO EM BIOQUÍMICA HENRIQUE PINHO OLIVEIRA PURIFICAÇÃO, CARACTERIZAÇÃO E ATIVIDADE ANTIFÚNGICA DA Mm -POX, UMA PEROXIDASE DO LÁTEX DE Marsdenia megalantha (GOYDER; MORILLO, 1994). FORTALEZA 2013 1 HENRIQUE PINHO OLVEIRA PURIFICAÇÃO, CARACTERIZAÇÃO E ATIVIDADE ANTIFÚNGICA DA Mm -POX, UMA PEROXIDASE DO LÁTEX DE Marsdenia megalantha (GOYDER; MORILLO, 1994) Tese apresentada ao Curso de Doutorado em Bioquímica do Departamento de Bioquímica e Biologia Molecular da Universidade Federal do Ceará, como parte dos requisitos para obtenção do título de Doutor em Bioquímica. Orientadora: Profa. Dra. Ilka Maria Vasconcelos FORTALEZA 2013 2 3 HENRIQUE PINHO OLIVEIRA PURIFICAÇÃO, CARACTERIZAÇÃO E ATIVIDADE ANTIFÚNGICA DA Mm -POX, UMA PEROXIDASE DO LÁTEX DE Marsdenia megalantha (GOYDER; MORILLO, 1994) Tese apresentada ao Curso de Doutorado em Bioquímica do Departamento de Bioquímica e Biologia Molecular da Universidade Federal do Ceará, como parte dos requisitos para obtenção do título de Doutor em Bioquímica. Aprovada em: ____/____/___ BANCA EXAMINADORA ________________________________________ Profa. Dra. Ilka Maria Vasconcelos Universidade Federal do Ceará (UFC) ________________________________________ Profa. Dra. Daniele de Oliveira Bezerra de Sousa Universidade Federal do Ceará (UFC) ________________________________________ Prof. Dr. Cleverson Diniz Teixeira de Freitas Universidade Federal do Ceará (UFC) ________________________________________ Prof. Dr. Renato de Azevedo Moreira Universidade de Fortaleza (UNIFOR) ________________________________________ Dr. Cleberson de Freitas Fernandes Empresa Brasileira de Pesquisa Agropecuária - Rondônia 4 À minha Mãe Selene, Ao meu Pai Régis, À minha Irmã Cristiane, Às minhas Avós Celina e Laura ( in memorian ), À minha Sherecuda Linda À todos os familiares, Dedico 5 O Mundo está mudado.
    [Show full text]
  • Increased Whitening Efficacy and Reduced Cytotoxicity Are Achieved by the Chemical Activation of a Highly Concentrated Hydrogen Peroxide Bleaching Gel
    Original Article http://dx.doi.org/10.1590/1678-7757-2018-0453 Increased whitening efficacy and reduced cytotoxicity are achieved by the chemical activation of a highly concentrated hydrogen peroxide bleaching gel Abstract Diana Gabriela SOARES1 Objective: This study was designed for the chemical activation of a 35% hydrogen peroxide (H O ) bleaching gel to increase its whitening effectiveness Natália MARCOMINI² 2 2 and reduce its toxicity. Methodology: First, the bleaching gel - associated or Carla Caroline de Oliveira DUQUE³ not with ferrous sulfate (FS), manganese chloride (MC), peroxidase (PR), Ester Alves Ferreira BORDINI³ or catalase (CT) - was applied (3x 15 min) to enamel/dentin discs adapted Uxua Ortecho ZUTA³ to artificial pulp chambers. Then, odontoblast-like MDPC-23 cells were Fernanda Gonçalves BASSO⁴ exposed for 1 h to the extracts (culture medium + components released Josimeri HEBLING⁵ from the product), for the assessment of viability (MTT assay) and oxidative D Carlos Alberto de Souza COSTA⁴ stress (H2DCFDA). Residual H2O2 and bleaching effectiveness ( E) were also evaluated. Data were analyzed with one-way ANOVA complemented with Tukey’s test (n=8. p<0.05). Results: All chemically activated groups minimized MDPC-23 oxidative stress generation; however, significantly higher cell viability was detected for MC, PR, and CT than for plain 35% H2O2 gel. Nevertheless, FS, MC, PR, and CT reduced the amount of residual H2O2 and increased bleaching effectiveness. Conclusion: Chemical activation of 35% H2O2 gel with MC, PR, and CT minimized residual H2O2 and pulp cell toxicity; but PR duplicated the whitening potential of the bleaching gel after a single 45-minute session.
    [Show full text]
  • Korrdel1lic Avhandl Ahmad Zayny
    Faculty of Pharmacy, Uppsala University LICENTIATE THESES 50 Vitamin D metabolism in osteoblast-like cells: effects of drugs on inactivation by CYP24A1 by Ahmad Zayny 2018 Faculty of Pharmacy, Uppsala University LICENTIATE THESES 50 Summary Vitamin D metabolism in osteoblast-like cells: effects of drugs on inactivation by CYP24A1 by Ahmad Zayny 2018 2 This licentiate thesis will be defended on Wednesday, May 30, 2018 at 13:15 in C4:305, BMC, Husargatan 3, Uppsala. The presentation and discussion will be conducted in Swedish. Abstract Zayny, A. 2018 Vitamin D metabolism in osteoblast-like cells: effects of drugs on inactivation by CYP24A1 Vitamin D is essential for bone function, and deficiency in active vitamin D hormone can lead to bone disorders. Long-term treatment with glucocorticoids and antiretroviral drugs used to treat HIV infection, results in osteoporosis and increased risk of fractures. Much remains unclear regarding the effects of these compounds in bone cells. In the current study, human osteosarcoma Saos-2 cells and primary human osteoblasts were found to express mRNA for the vitamin D receptor as well as activating and deactivating enzymes in vitamin D3 metabolism. These bone cells exhibited CYP24A1-mediated 24-hydroxylation, involved in deactivation of the active vitamin form. However, bioactivating vitamin D3 hydroxylase activities were not detected in either of these cells, indicating that local vitamin D bioactivation is not significant in osteoblasts. Several glucocorticoids and antiretroviral drugs, including prednisolone, efavirenz and ritonavir, down regulated CYP24A1 mRNA expression. Prednisolone and ritonavir also down regulated CYP24A1-mediated 24-hydroxylase activity in both Saos-2 and primary human osteoblasts.
    [Show full text]
  • Chloride Peroxidase Cat
    chloride peroxidase Cat. No. EXWM-0491 Lot. No. (See product label) Introduction Description Brings about the chlorination of a range of organic molecules, forming stable C-Cl bonds. Also oxidizes bromide and iodide. Enzymes of this type are either heme-thiolate proteins, or contain vanadate. A secreted enzyme produced by the ascomycetous fungus Caldariomyces fumago (Leptoxyphium fumago) is an example of the heme-thiolate type. It catalyses the production of hypochlorous acid by transferring one oxygen atom from H2O2 to chloride. At a separate site it catalyses the chlorination of activated aliphatic and aromatic substrates, via HClO and derived chlorine species. In the absence of halides, it shows peroxidase (e.g. phenol oxidation) and peroxygenase activities. The latter inserts oxygen from H2O2 into, for example, styrene (side chain epoxidation) and toluene (benzylic hydroxylation), however, these activities are less pronounced than its activity with halides. Has little activity with non-activated substrates such as aromatic rings, ethers or saturated alkanes. The chlorinating peroxidase produced by ascomycetous fungi (e.g. Curvularia inaequalis) is an example of a vanadium chloroperoxidase, and is related to bromide peroxidase (EC 1.11.1.18). It contains vanadate and oxidizes chloride, bromide and iodide into hypohalous acids. In the absence of halides, it peroxygenates organic sulfides and oxidizes ABTS [2,2'-azinobis(3-ethylbenzthiazoline-6-sulfonic acid)] but no phenols. Synonyms chloroperoxidase; CPO; vanadium haloperoxidase Product Information Form Liquid or lyophilized powder EC Number EC 1.11.1.10 CAS No. 9055-20-3 Reaction RH + chloride + H2O2 = RCl + 2 H2O Notes This item requires custom production and lead time is between 5-9 weeks.
    [Show full text]
  • And Dioxygenase Chemistries in a Single Active Site Promotes Heme Degradation
    Unique coupling of mono- and dioxygenase chemistries in a single active site promotes heme degradation Toshitaka Matsuia,1, Shusuke Nambua, Celia W. Gouldingb,c, Satoshi Takahashia, Hiroshi Fujiid, and Masao Ikeda-Saitoa,1 aInstitute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba, Sendai 980-8577, Japan; bDepartment of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697; cDepartment of Pharmaceutical Sciences, University of California, Irvine, CA 92697; and dDepartment of Chemistry, Graduate School of Humanities and Sciences, Nara Women’s University, Kitauoyanishi, Nara 630-8506, Japan Edited by Harry B. Gray, California Institute of Technology, Pasadena, CA, and approved February 26, 2016 (received for review November 26, 2015) − + Bacterial pathogens must acquire host iron for survival and colo- RH + O2 + 2e + 2H → ROH + H2O, [1] nization. Because free iron is restricted in the host, numerous pathogens have evolved to overcome this limitation by using a R + O → RðOÞ . [2] family of monooxygenases that mediate the oxidative cleavage of 2 2 heme into biliverdin, carbon monoxide, and iron. However, the Biological heme degradation proceeds through a unique self- etiological agent of tuberculosis, Mycobacterium tuberculosis, ac- oxidation mechanism where the substrate heme activates O complishes this task without generating carbon monoxide, which 2 potentially induces its latent state. Here we show that this unusual molecules. The canonical enzyme, heme oxygenase (HO), de- heme degradation reaction proceeds through sequential mono- grades heme into ferrous iron, carbon monoxide (CO), and bil- and dioxygenation events within the single active center of MhuD, iverdin by three successive monooxygenation reactions (Fig. 1A) a mechanism unparalleled in enzyme catalysis.
    [Show full text]
  • Supplementary Materials
    Supplementary Materials COMPARATIVE ANALYSIS OF THE TRANSCRIPTOME, PROTEOME AND miRNA PROFILE OF KUPFFER CELLS AND MONOCYTES Andrey Elchaninov1,3*, Anastasiya Lokhonina1,3, Maria Nikitina2, Polina Vishnyakova1,3, Andrey Makarov1, Irina Arutyunyan1, Anastasiya Poltavets1, Evgeniya Kananykhina2, Sergey Kovalchuk4, Evgeny Karpulevich5,6, Galina Bolshakova2, Gennady Sukhikh1, Timur Fatkhudinov2,3 1 Laboratory of Regenerative Medicine, National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, Moscow, Russia 2 Laboratory of Growth and Development, Scientific Research Institute of Human Morphology, Moscow, Russia 3 Histology Department, Medical Institute, Peoples' Friendship University of Russia, Moscow, Russia 4 Laboratory of Bioinformatic methods for Combinatorial Chemistry and Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia 5 Information Systems Department, Ivannikov Institute for System Programming of the Russian Academy of Sciences, Moscow, Russia 6 Genome Engineering Laboratory, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia Figure S1. Flow cytometry analysis of unsorted blood sample. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S2. Flow cytometry analysis of unsorted liver stromal cells. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S3. MiRNAs expression analysis in monocytes and Kupffer cells. Full-length of heatmaps are presented.
    [Show full text]
  • The Role of Regulated Necrosis in Endocrine Diseases
    PERSPECTIVES system results in the typical morphological features such as rapid shrinking of the cell, The role of regulated necrosis nuclear condensation, DNA fragmentation, exposure of phosphatidylserine and a in endocrine diseases process known as membrane blebbing11,12. Phosphatidylserine exposure functions Wulf Tonnus , Alexia Belavgeni , Felix Beuschlein , Graeme Eisenhofer, as an ‘eat me’ signal to macrophages13–15. Martin Fassnacht , Matthias Kroiss , Nils P. Krone, Martin Reincke , Importantly, the plasma membrane remains intact in apoptotically dying cells, Stefan R. Bornstein and Andreas Linkermann a mechanism that prevents the release of Abstract | The death of endocrine cells is involved in type 1 diabetes mellitus, intracellular content to the interstitial and/or autoimmunity, adrenopause and hypogonadotropism. Insights from research on extracellular space. Therefore, apoptosis is immunologically silent. The detection basic cell death have revealed that most pathophysiologically important cell death of apoptosis has been misinterpreted for is necrotic in nature, whereas regular metabolism is maintained by apoptosis decades by the TdT-mediated dUTP-biotin programmes. Necrosis is defined as cell death by plasma membrane rupture, which nick end- labelling (TUNEL) method (BOx 1). allows the release of damage- associated molecular patterns that trigger an Mechanistically, extrinsic apoptosis immune response referred to as necroinflammation. Regulated necrosis comes in is mediated by death receptors such as different forms, such as necroptosis, pyroptosis and ferroptosis. In this Perspective, tumour necrosis factor receptor 1 (TNFR1) or the FAS receptor (also known as with a focus on the endocrine environment, we introduce these cell death CD95)16. To kill a cell through a TNFR1 pathways and discuss the specific consequences of regulated necrosis.
    [Show full text]
  • 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
    [Show full text]
  • Relating Metatranscriptomic Profiles to the Micropollutant
    1 Relating Metatranscriptomic Profiles to the 2 Micropollutant Biotransformation Potential of 3 Complex Microbial Communities 4 5 Supporting Information 6 7 Stefan Achermann,1,2 Cresten B. Mansfeldt,1 Marcel Müller,1,3 David R. Johnson,1 Kathrin 8 Fenner*,1,2,4 9 1Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, 10 Switzerland. 2Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 11 Zürich, Switzerland. 3Institute of Atmospheric and Climate Science, ETH Zürich, 8092 12 Zürich, Switzerland. 4Department of Chemistry, University of Zürich, 8057 Zürich, 13 Switzerland. 14 *Corresponding author (email: [email protected] ) 15 S.A and C.B.M contributed equally to this work. 16 17 18 19 20 21 This supporting information (SI) is organized in 4 sections (S1-S4) with a total of 10 pages and 22 comprises 7 figures (Figure S1-S7) and 4 tables (Table S1-S4). 23 24 25 S1 26 S1 Data normalization 27 28 29 30 Figure S1. Relative fractions of gene transcripts originating from eukaryotes and bacteria. 31 32 33 Table S1. Relative standard deviation (RSD) for commonly used reference genes across all 34 samples (n=12). EC number mean fraction bacteria (%) RSD (%) RSD bacteria (%) RSD eukaryotes (%) 2.7.7.6 (RNAP) 80 16 6 nda 5.99.1.2 (DNA topoisomerase) 90 11 9 nda 5.99.1.3 (DNA gyrase) 92 16 10 nda 1.2.1.12 (GAPDH) 37 39 6 32 35 and indicates not determined. 36 37 38 39 S2 40 S2 Nitrile hydration 41 42 43 44 Figure S2: Pearson correlation coefficients r for rate constants of bromoxynil and acetamiprid with 45 gene transcripts of ECs describing nucleophilic reactions of water with nitriles.
    [Show full text]
  • Substrate-Mediated Reduction of the Diiron Center for 5-Demethoxyubiquinone Hydroxylation
    Aging-Associated Enzyme Human Clock-1: Substrate-Mediated Reduction of the Diiron Center for 5-Demethoxyubiquinone Hydroxylation The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Lu, Tsai-Te, Seung Jae Lee, Ulf-Peter Apfel, and Stephen J. Lippard. “Aging-Associated Enzyme Human Clock-1: Substrate-Mediated Reduction of the Diiron Center for 5-Demethoxyubiquinone Hydroxylation.” Biochemistry 52, no. 13 (April 2, 2013): 2236–2244. As Published http://dx.doi.org/10.1021/bi301674p Publisher American Chemical Society (ACS) Version Author's final manuscript Citable link http://hdl.handle.net/1721.1/95488 Terms of Use Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. NIH Public Access Author Manuscript Biochemistry. Author manuscript; available in PMC 2014 April 02. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Biochemistry. 2013 April 2; 52(13): 2236–2244. doi:10.1021/bi301674p. Aging-Associated Enzyme Human Clock-1: Substrate-Mediated Reduction of the Diiron Center for 5-Demethoxyubiquinone Hydroxylation† Tsai-Te Lu, Seung Jae Lee, Ulf-Peter Apfel, and Stephen J. Lippard* Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States Abstract The mitochondrial membrane-bound enzyme Clock-1 (CLK-1) extends the average longevity of mice and C. elegans, as demonstrated for Δclk-1 constructs for both organisms. Such an apparent impact on aging and the presence of a carboxylate-bridged diiron center in the enzyme inspired the present work.
    [Show full text]