Halfway to Hypusine—Structural Basis for Substrate Recognition by Human
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Yeast Genome Gazetteer P35-65
gazetteer Metabolism 35 tRNA modification mitochondrial transport amino-acid metabolism other tRNA-transcription activities vesicular transport (Golgi network, etc.) nitrogen and sulphur metabolism mRNA synthesis peroxisomal transport nucleotide metabolism mRNA processing (splicing) vacuolar transport phosphate metabolism mRNA processing (5’-end, 3’-end processing extracellular transport carbohydrate metabolism and mRNA degradation) cellular import lipid, fatty-acid and sterol metabolism other mRNA-transcription activities other intracellular-transport activities biosynthesis of vitamins, cofactors and RNA transport prosthetic groups other transcription activities Cellular organization and biogenesis 54 ionic homeostasis organization and biogenesis of cell wall and Protein synthesis 48 plasma membrane Energy 40 ribosomal proteins organization and biogenesis of glycolysis translation (initiation,elongation and cytoskeleton gluconeogenesis termination) organization and biogenesis of endoplasmic pentose-phosphate pathway translational control reticulum and Golgi tricarboxylic-acid pathway tRNA synthetases organization and biogenesis of chromosome respiration other protein-synthesis activities structure fermentation mitochondrial organization and biogenesis metabolism of energy reserves (glycogen Protein destination 49 peroxisomal organization and biogenesis and trehalose) protein folding and stabilization endosomal organization and biogenesis other energy-generation activities protein targeting, sorting and translocation vacuolar and lysosomal -
Anti-Inflammatory Role of Curcumin in LPS Treated A549 Cells at Global Proteome Level and on Mycobacterial Infection
Anti-inflammatory Role of Curcumin in LPS Treated A549 cells at Global Proteome level and on Mycobacterial infection. Suchita Singh1,+, Rakesh Arya2,3,+, Rhishikesh R Bargaje1, Mrinal Kumar Das2,4, Subia Akram2, Hossain Md. Faruquee2,5, Rajendra Kumar Behera3, Ranjan Kumar Nanda2,*, Anurag Agrawal1 1Center of Excellence for Translational Research in Asthma and Lung Disease, CSIR- Institute of Genomics and Integrative Biology, New Delhi, 110025, India. 2Translational Health Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India. 3School of Life Sciences, Sambalpur University, Jyoti Vihar, Sambalpur, Orissa, 768019, India. 4Department of Respiratory Sciences, #211, Maurice Shock Building, University of Leicester, LE1 9HN 5Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia- 7003, Bangladesh. +Contributed equally for this work. S-1 70 G1 S 60 G2/M 50 40 30 % of cells 20 10 0 CURI LPSI LPSCUR Figure S1: Effect of curcumin and/or LPS treatment on A549 cell viability A549 cells were treated with curcumin (10 µM) and/or LPS or 1 µg/ml for the indicated times and after fixation were stained with propidium iodide and Annexin V-FITC. The DNA contents were determined by flow cytometry to calculate percentage of cells present in each phase of the cell cycle (G1, S and G2/M) using Flowing analysis software. S-2 Figure S2: Total proteins identified in all the three experiments and their distribution betwee curcumin and/or LPS treated conditions. The proteins showing differential expressions (log2 fold change≥2) in these experiments were presented in the venn diagram and certain number of proteins are common in all three experiments. -
Generate Metabolic Map Poster
Authors: Pallavi Subhraveti Anamika Kothari Quang Ong Ron Caspi An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Ingrid Keseler Peter D Karp Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Csac1394711Cyc: Candidatus Saccharibacteria bacterium RAAC3_TM7_1 Cellular Overview Connections between pathways are omitted for legibility. Tim Holland TM7C00001G0420 TM7C00001G0109 TM7C00001G0953 TM7C00001G0666 TM7C00001G0203 TM7C00001G0886 TM7C00001G0113 TM7C00001G0247 TM7C00001G0735 TM7C00001G0001 TM7C00001G0509 TM7C00001G0264 TM7C00001G0176 TM7C00001G0342 TM7C00001G0055 TM7C00001G0120 TM7C00001G0642 TM7C00001G0837 TM7C00001G0101 TM7C00001G0559 TM7C00001G0810 TM7C00001G0656 TM7C00001G0180 TM7C00001G0742 TM7C00001G0128 TM7C00001G0831 TM7C00001G0517 TM7C00001G0238 TM7C00001G0079 TM7C00001G0111 TM7C00001G0961 TM7C00001G0743 TM7C00001G0893 TM7C00001G0630 TM7C00001G0360 TM7C00001G0616 TM7C00001G0162 TM7C00001G0006 TM7C00001G0365 TM7C00001G0596 TM7C00001G0141 TM7C00001G0689 TM7C00001G0273 TM7C00001G0126 TM7C00001G0717 TM7C00001G0110 TM7C00001G0278 TM7C00001G0734 TM7C00001G0444 TM7C00001G0019 TM7C00001G0381 TM7C00001G0874 TM7C00001G0318 TM7C00001G0451 TM7C00001G0306 TM7C00001G0928 TM7C00001G0622 TM7C00001G0150 TM7C00001G0439 TM7C00001G0233 TM7C00001G0462 TM7C00001G0421 TM7C00001G0220 TM7C00001G0276 TM7C00001G0054 TM7C00001G0419 TM7C00001G0252 TM7C00001G0592 TM7C00001G0628 TM7C00001G0200 TM7C00001G0709 TM7C00001G0025 TM7C00001G0846 TM7C00001G0163 TM7C00001G0142 TM7C00001G0895 TM7C00001G0930 Detoxification Carbohydrate Biosynthesis DNA combined with a 2'- di-trans,octa-cis a 2'- Amino Acid Degradation an L-methionyl- TM7C00001G0190 superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. -
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 -
Stem Cells® Original Article
® Stem Cells Original Article Properties of Pluripotent Human Embryonic Stem Cells BG01 and BG02 XIANMIN ZENG,a TAKUMI MIURA,b YONGQUAN LUO,b BHASKAR BHATTACHARYA,c BRIAN CONDIE,d JIA CHEN,a IRENE GINIS,b IAN LYONS,d JOSEF MEJIDO,c RAJ K. PURI,c MAHENDRA S. RAO,b WILLIAM J. FREEDa aCellular Neurobiology Research Branch, National Institute on Drug Abuse, Department of Health and Human Services (DHHS), Baltimore, Maryland, USA; bLaboratory of Neuroscience, National Institute of Aging, DHHS, Baltimore, Maryland, USA; cLaboratory of Molecular Tumor Biology, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA; dBresaGen Inc., Athens, Georgia, USA Key Words. Embryonic stem cells · Differentiation · Microarray ABSTRACT Human ES (hES) cell lines have only recently been compared with pooled human RNA. Ninety-two of these generated, and differences between human and mouse genes were also highly expressed in four other hES lines ES cells have been identified. In this manuscript we (TE05, GE01, GE09, and pooled samples derived from describe the properties of two human ES cell lines, GE01, GE09, and GE07). Included in the list are genes BG01 and BG02. By immunocytochemistry and reverse involved in cell signaling and development, metabolism, transcription polymerase chain reaction, undifferenti- transcription regulation, and many hypothetical pro- ated cells expressed markers that are characteristic of teins. Two focused arrays designed to examine tran- ES cells, including SSEA-3, SSEA-4, TRA-1-60, TRA-1- scripts associated with stem cells and with the 81, and OCT-3/4. Both cell lines were readily main- transforming growth factor-β superfamily were tained in an undifferentiated state and could employed to examine differentially expressed genes. -
A Novel Mouse Model for Inhibition of DOHH-Mediated Hypusine Modification Reveals a Crucial Function in Embryonic Development, P
© 2014. Published by The Company of Biologists Ltd | Disease Models & Mechanisms (2014) 7, 963-976 doi:10.1242/dmm.014449 RESEARCH ARTICLE A novel mouse model for inhibition of DOHH-mediated hypusine modification reveals a crucial function in embryonic development, proliferation and oncogenic transformation Henning Sievert1, Nora Pällmann1,2,*, Katharine K. Miller3,*, Irm Hermans-Borgmeyer3, Simone Venz4, Ataman Sendoel5,6, Michael Preukschas1, Michaela Schweizer3, Steffen Boettcher6, P. Christoph Janiesch3, Thomas Streichert7, Reinhard Walther4, Michael O. Hengartner5, Markus G. Manz6, Tim H. Brümmendorf8, Carsten Bokemeyer1, Melanie Braig1, Joachim Hauber2, Kent E. Duncan3 and Stefan Balabanov1,6,‡ ABSTRACT factor 5A (eIF5A), represents an essential mechanism in the control The central importance of translational control by post-translational of proliferation of eukaryotic cells (Cooper et al., 1982). This modification has spurred major interest in regulatory pathways that modification leads to the activation of eIF5A and is mediated by control translation. One such pathway uniquely adds hypusine to deoxyhypusine synthase (DHS), which catalyses the transfer of a 4- eukaryotic initiation factor 5A (eIF5A), and thereby affects protein aminobutyl moiety of spermidine to the ε-amino group of Lys50 to synthesis and, subsequently, cellular proliferation through an form an intermediate residue, deoxyhypusine (Dhp50) (Park et al., unknown mechanism. Using a novel conditional knockout mouse 1981). Subsequently, deoxyhypusine hydroxylase (DOHH) -
Interactions of Natural Polyamines with Mammalian Proteins
Article in press - uncorrected proof BioMol Concepts, Vol. 2 (2011), pp. 79–94 • Copyright ᮊ by Walter de Gruyter • Berlin • New York. DOI 10.1515/BMC.2011.007 Review Interactions of natural polyamines with mammalian proteins Inge Schuster1 and Rita Bernhardt2,* ecules, such as phospholipids or nucleotides, thereby mas- 1 Institute for Theoretical Chemistry, University Vienna, sively affecting their structures and functions (9, 10). A-1090 Vienna, Austria Accordingly, polyamines were found to modulate numerous 2 Institute of Biochemistry, Saarland University, Campus regulatory processes in model systems that range from cel- B2.2, D-66123 Saarbru¨cken, Germany lular signaling to the control of gene expression and trans- lation and offer explanations for the obvious involvement of * Corresponding author polyamines in the regulation of cell growth, differentiation, e-mail: [email protected] and death wreviewed in (1, 11–14)x. The broad actions of polyamines on essential life functions are reflected by their effects on global gene expression. A recent study in a yeast Abstract mutant, an eukaryotic system comprising a three times small- er genome than mammalians, showed a significant regulation The ubiquitously expressed natural polyamines putrescine, of some 10% of the genome in (direct or indirect) response spermidine, and spermine are small, flexible cationic com- to spermidine or spermine (15). The essential requirement pounds that exert pleiotropic actions on various regulatory for polyamines and balanced levels of polyamines is under- systems and, accordingly, are essentially involved in diverse lined from studying knockouts that lack distinct genes life functions. These roles of polyamines result from their involved in polyamine synthesis and are not viable (10). -
Norspermine Substitutes for Thermospermine in the Control of Stem Elongation in Arabidopsis Thaliana
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS Letters 584 (2010) 3042–3046 journal homepage: www.FEBSLetters.org Norspermine substitutes for thermospermine in the control of stem elongation in Arabidopsis thaliana Jun-Ichi Kakehi a, Yoshitaka Kuwashiro a, Hiroyasu Motose a, Kazuei Igarashi b, Taku Takahashi a,* a Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan b Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan article info abstract Article history: Thermospermine is a structural isomer of spermine and is required for stem elongation in Arabid- Received 26 March 2010 opsis thaliana. We noted the C3C3 arrangement of carbon chains in thermospermine (C3C3C4), Revised 16 May 2010 which is not present in spermine (C3C4C3), and examined if it is functionally replaced with norsper- Accepted 17 May 2010 mine (C3C3C3) or not. Exogenous application of norspermine to acl5, a mutant defective in the syn- Available online 24 May 2010 thesis of thermospermine, partially suppressed its dwarf phenotype, and down-regulated the level Edited by Ulf-Ingo Flügge of the acl5 transcript which is much higher than that of the ACL5 transcript in the wild type. Further- more, in the Zinnia culture, differentiation of mesophyll cells into tracheary elements was blocked by thermospermine and norspermine but not by spermine. Our results indicate that norspermine Keywords: Arabidopsis can functionally substitute for thermospermine. Thermospermine Ó 2010 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. Norspermine Polyamine Stem elongation Xylem 1. -
O O2 Enzymes Available from Sigma Enzymes Available from Sigma
COO 2.7.1.15 Ribokinase OXIDOREDUCTASES CONH2 COO 2.7.1.16 Ribulokinase 1.1.1.1 Alcohol dehydrogenase BLOOD GROUP + O O + O O 1.1.1.3 Homoserine dehydrogenase HYALURONIC ACID DERMATAN ALGINATES O-ANTIGENS STARCH GLYCOGEN CH COO N COO 2.7.1.17 Xylulokinase P GLYCOPROTEINS SUBSTANCES 2 OH N + COO 1.1.1.8 Glycerol-3-phosphate dehydrogenase Ribose -O - P - O - P - O- Adenosine(P) Ribose - O - P - O - P - O -Adenosine NICOTINATE 2.7.1.19 Phosphoribulokinase GANGLIOSIDES PEPTIDO- CH OH CH OH N 1 + COO 1.1.1.9 D-Xylulose reductase 2 2 NH .2.1 2.7.1.24 Dephospho-CoA kinase O CHITIN CHONDROITIN PECTIN INULIN CELLULOSE O O NH O O O O Ribose- P 2.4 N N RP 1.1.1.10 l-Xylulose reductase MUCINS GLYCAN 6.3.5.1 2.7.7.18 2.7.1.25 Adenylylsulfate kinase CH2OH HO Indoleacetate Indoxyl + 1.1.1.14 l-Iditol dehydrogenase L O O O Desamino-NAD Nicotinate- Quinolinate- A 2.7.1.28 Triokinase O O 1.1.1.132 HO (Auxin) NAD(P) 6.3.1.5 2.4.2.19 1.1.1.19 Glucuronate reductase CHOH - 2.4.1.68 CH3 OH OH OH nucleotide 2.7.1.30 Glycerol kinase Y - COO nucleotide 2.7.1.31 Glycerate kinase 1.1.1.21 Aldehyde reductase AcNH CHOH COO 6.3.2.7-10 2.4.1.69 O 1.2.3.7 2.4.2.19 R OPPT OH OH + 1.1.1.22 UDPglucose dehydrogenase 2.4.99.7 HO O OPPU HO 2.7.1.32 Choline kinase S CH2OH 6.3.2.13 OH OPPU CH HO CH2CH(NH3)COO HO CH CH NH HO CH2CH2NHCOCH3 CH O CH CH NHCOCH COO 1.1.1.23 Histidinol dehydrogenase OPC 2.4.1.17 3 2.4.1.29 CH CHO 2 2 2 3 2 2 3 O 2.7.1.33 Pantothenate kinase CH3CH NHAC OH OH OH LACTOSE 2 COO 1.1.1.25 Shikimate dehydrogenase A HO HO OPPG CH OH 2.7.1.34 Pantetheine kinase UDP- TDP-Rhamnose 2 NH NH NH NH N M 2.7.1.36 Mevalonate kinase 1.1.1.27 Lactate dehydrogenase HO COO- GDP- 2.4.1.21 O NH NH 4.1.1.28 2.3.1.5 2.1.1.4 1.1.1.29 Glycerate dehydrogenase C UDP-N-Ac-Muramate Iduronate OH 2.4.1.1 2.4.1.11 HO 5-Hydroxy- 5-Hydroxytryptamine N-Acetyl-serotonin N-Acetyl-5-O-methyl-serotonin Quinolinate 2.7.1.39 Homoserine kinase Mannuronate CH3 etc. -
Isolation and Characterization of S-Adenosylmethionine Synthase Gene from Cucumber and Responsive to Abiotic Stress T
Plant Physiology and Biochemistry 141 (2019) 431–445 Contents lists available at ScienceDirect Plant Physiology and Biochemistry journal homepage: www.elsevier.com/locate/plaphy Research article Isolation and characterization of S-Adenosylmethionine synthase gene from cucumber and responsive to abiotic stress T ∗ Mei-Wen Hea, Yu Wanga, Jian-Qiang Wua, Sheng Shua,b, Jin Suna,b, Shi-Rong Guoa,b, a Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China b Suqian Academy of Protected Horticulture, Nanjing Agricultural University, Suqian, 223800, China ARTICLE INFO ABSTRACT Keywords: S-adenosylmethionine synthetase (SAMS) catalyzes methionine and ATP to generate S-adenosyl-L-methionine Cucumis sativus (SAM). In plants, accumulating SAMS genes have been characterized and the majority of them are reported to S-adenosylmethionine synthetase participate in development and stress response. In this study, two putative SAMS genes (CsSAMS1 and CsSAMS2) Gene expression were identified in cucumber (Cucumis Sativus L.). They displayed 95% similarity and had a high identity with Function their homologous of Arabidopsis thaliana and Nicotiana tabacum. The qRT-PCR test showed that CsSAMS1 was Salt stress predominantly expressed in stem, male flower, and young fruit, whereas CsSAMS2 was preferentially accumu- lated in stem and female flower. And they displayed differential expression profiles under stimuli, including NaCl, ABA, SA, MeJA, drought and low temperature. To elucidate the function of cucumber SAMS, the full- length CDS of CsSAMS1 was cloned, and prokaryotic expression system and transgenic materials were con- structed. Expressing CsSAMS1 in Escherichia coli BL21 (DE3) improved the growth of the engineered strain under salt stress. -
Deoxyhypusine Synthase As an Antimalarial Target
Validation of Plasmodium falciparum deoxyhypusine synthase as an antimalarial target Aiyada Aroonsri1, Navaporn Posayapisit1, Jindaporn Kongsee2, Onsiri Siripan1,3, Danoo Vitsupakorn1, Sugunya Utaida2, Chairat Uthaipibull1, Sumalee Kamchonwongpaisan1 and Philip J. Shaw1 1 Protein-Ligand Engineering and Molecular Biology Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand 2 Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Pathum Thani, Thailand 3 Present address: Fisheries Industrial Technology Research and Development Division, Department of Fisheries, Bangkok, Thailand ABSTRACT Background: Hypusination is an essential post-translational modification in eukaryotes. The two enzymes required for this modification, namely deoxyhypusine synthase (DHS) and deoxyhypusine hydrolase are also conserved. Plasmodium falciparum human malaria parasites possess genes for both hypusination enzymes, which are hypothesized to be targets of antimalarial drugs. Methods: Transgenic P. falciparum parasites with modification of the PF3D7_1412600 gene encoding Pf DHS enzyme were created by insertion of the glmS riboswitch or the M9 inactive variant. The Pf DHS protein was studied in transgenic parasites by confocal microscopy and Western immunoblotting. The biochemical function of Pf DHS enzyme in parasites was assessed by hypusination and nascent protein synthesis assays. Gene essentiality was assessed by competitive growth assays and chemogenomic profiling. Results: Clonal transgenic parasites with integration of glmS riboswitch downstream Submitted 9 August 2018 of the Pf DHS gene were established. Pf DHS protein was present in the cytoplasm of Accepted 5 March 2019 Published 17 April 2019 transgenic parasites in asexual stages. The Pf DHS protein could be attenuated fi Corresponding author vefold in transgenic parasites with an active riboswitch, whereas Pf DHS protein Philip J. -
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US007635572B2 (12) UnitedO States Patent (10) Patent No.: US 7,635,572 B2 Zhou et al. (45) Date of Patent: Dec. 22, 2009 (54) METHODS FOR CONDUCTING ASSAYS FOR 5,506,121 A 4/1996 Skerra et al. ENZYME ACTIVITY ON PROTEIN 5,510,270 A 4/1996 Fodor et al. MICROARRAYS 5,512,492 A 4/1996 Herron et al. 5,516,635 A 5/1996 Ekins et al. (75) Inventors: Fang X. Zhou, New Haven, CT (US); 5,532,128 A 7/1996 Eggers Barry Schweitzer, Cheshire, CT (US) 5,538,897 A 7/1996 Yates, III et al. s s 5,541,070 A 7/1996 Kauvar (73) Assignee: Life Technologies Corporation, .. S.E. al Carlsbad, CA (US) 5,585,069 A 12/1996 Zanzucchi et al. 5,585,639 A 12/1996 Dorsel et al. (*) Notice: Subject to any disclaimer, the term of this 5,593,838 A 1/1997 Zanzucchi et al. patent is extended or adjusted under 35 5,605,662 A 2f1997 Heller et al. U.S.C. 154(b) by 0 days. 5,620,850 A 4/1997 Bamdad et al. 5,624,711 A 4/1997 Sundberg et al. (21) Appl. No.: 10/865,431 5,627,369 A 5/1997 Vestal et al. 5,629,213 A 5/1997 Kornguth et al. (22) Filed: Jun. 9, 2004 (Continued) (65) Prior Publication Data FOREIGN PATENT DOCUMENTS US 2005/O118665 A1 Jun. 2, 2005 EP 596421 10, 1993 EP 0619321 12/1994 (51) Int. Cl. EP O664452 7, 1995 CI2O 1/50 (2006.01) EP O818467 1, 1998 (52) U.S.