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  • The Pennsylvania State University the Graduate School Department
    The Pennsylvania State University The Graduate School Department of Chemistry SUBSTRATE POSITIONING AND CHANNELING OF ESCHERICHIA COLI QUINOLINATE SYNTHASE A Thesis in Chemistry by Lauren A. Sites 2012 Lauren A. Sites Submitted in Partial Fulfillment of the Requirements for the Degree of Master of Science December 2012 ii The thesis of Lauren A. Sites was reviewed and approved* by the following: Squire J. Booker Associate Professor of Chemistry Thesis Advisor Carsten Krebs Professor of Chemistry Scott A. Showalter Assistant Professor of Chemistry Kenneth S. Feldman Professor of Chemistry Head of Department *Signatures are on file in the Graduate School iii ABSTRACT The essential cofactor nicotinamide adenine dinucleotide (NAD) is consumed in many metabolic reactions in the cell, necessitating the need to synthesize NAD. In most bacteria, the de novo pathway to form NAD begins with two unique enzymes that have been extensively studied herein. The first enzyme in the pathway, L-aspartate oxidase, performs a two-electron oxidation of L-aspartate to form iminoaspartate. This flavin containing enzyme can undergo multiple catalytic turnovers given the oxidants, fumarate or molecular oxygen, to afford the oxidized form of the enzyme. The second enzyme in the pathway, quinolinate synthase or NadA, condenses iminoaspartate and dihydroxyacetone phosphate to form quinolinic acid, the backbone of the pyridine ring of NAD. Many have postulated that these two enzymes can operate as an enzyme complex, yet no substantial evidence of this complex has been demonstrated. Investigations to examine the possible protein-protein interactions of the two enzymes were carried out, yet no obvious interaction was seen by the techniques employed.
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  • Propranolol-Mediated Attenuation of MMP-9 Excretion in Infants with Hemangiomas
    Supplementary Online Content Thaivalappil S, Bauman N, Saieg A, Movius E, Brown KJ, Preciado D. Propranolol-mediated attenuation of MMP-9 excretion in infants with hemangiomas. JAMA Otolaryngol Head Neck Surg. doi:10.1001/jamaoto.2013.4773 eTable. List of All of the Proteins Identified by Proteomics This supplementary material has been provided by the authors to give readers additional information about their work. © 2013 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 10/01/2021 eTable. List of All of the Proteins Identified by Proteomics Protein Name Prop 12 mo/4 Pred 12 mo/4 Δ Prop to Pred mo mo Myeloperoxidase OS=Homo sapiens GN=MPO 26.00 143.00 ‐117.00 Lactotransferrin OS=Homo sapiens GN=LTF 114.00 205.50 ‐91.50 Matrix metalloproteinase‐9 OS=Homo sapiens GN=MMP9 5.00 36.00 ‐31.00 Neutrophil elastase OS=Homo sapiens GN=ELANE 24.00 48.00 ‐24.00 Bleomycin hydrolase OS=Homo sapiens GN=BLMH 3.00 25.00 ‐22.00 CAP7_HUMAN Azurocidin OS=Homo sapiens GN=AZU1 PE=1 SV=3 4.00 26.00 ‐22.00 S10A8_HUMAN Protein S100‐A8 OS=Homo sapiens GN=S100A8 PE=1 14.67 30.50 ‐15.83 SV=1 IL1F9_HUMAN Interleukin‐1 family member 9 OS=Homo sapiens 1.00 15.00 ‐14.00 GN=IL1F9 PE=1 SV=1 MUC5B_HUMAN Mucin‐5B OS=Homo sapiens GN=MUC5B PE=1 SV=3 2.00 14.00 ‐12.00 MUC4_HUMAN Mucin‐4 OS=Homo sapiens GN=MUC4 PE=1 SV=3 1.00 12.00 ‐11.00 HRG_HUMAN Histidine‐rich glycoprotein OS=Homo sapiens GN=HRG 1.00 12.00 ‐11.00 PE=1 SV=1 TKT_HUMAN Transketolase OS=Homo sapiens GN=TKT PE=1 SV=3 17.00 28.00 ‐11.00 CATG_HUMAN Cathepsin G OS=Homo
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  • Pseudouridine Synthase 1: a Site-Specific Synthase Without Strict Sequence Recognition Requirements Bryan S
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Published online 18 November 2011 Nucleic Acids Research, 2012, Vol. 40, No. 5 2107–2118 doi:10.1093/nar/gkr1017 Pseudouridine synthase 1: a site-specific synthase without strict sequence recognition requirements Bryan S. Sibert and Jeffrey R. Patton* Department of Pathology, Microbiology and Immunology, University of South Carolina, School of Medicine, Columbia, SC 29208 USA Received May 20, 2011; Revised October 19, 2011; Accepted October 22, 2011 ABSTRACT rRNA and snRNA and requires Dyskerin or its homologs Pseudouridine synthase 1 (Pus1p) is an unusual (Cbf5p in yeast for example) and RNP cofactors [most site-specific modification enzyme in that it can often H/ACA small nucleolar ribonucleoprotein particles modify a number of positions in tRNAs and can rec- (snoRNPs)] that enable one enzyme to recognize many ognize several other types of RNA. No consensus different sites for modification on different substrates recognition sequence or structure has been identi- (17–25). The other pathway for É formation employs fied for Pus1p. Human Pus1p was used to determine site-specific É synthases that require no cofactors to rec- which structural or sequence elements of human ognize and modify the RNA substrate. A number of en- tRNASer are necessary for pseudouridine ()) forma- zymes have been identified in this pathway and are grouped in six families that all share a common basic tion at position 28 in the anticodon stem-loop (ASL). Ser structure (4). It is safe to say the cofactor ‘guided’ pathway Some point mutations in the ASL stem of tRNA has received a great deal of attention because of its simi- had significant effects on the levels of modification larity to aspects of RNA editing, but the site-specific and compensatory mutation, to reform the base pseudouridine synthases accomplish the same task, on pair, restored a wild-type level of ) formation.
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  • TITLE PAGE Oxidative Stress and Response to Thymidylate Synthase
    Downloaded from molpharm.aspetjournals.org at ASPET Journals on October 2, 2021 -Targeted -Targeted 1 , University of of , University SC K.W.B., South Columbia, (U.O., Carolina, This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted.
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  • 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
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  • Microbial Production of Methyl Anthranilate, a Grape Flavor Compound
    Microbial production of methyl anthranilate, a grape flavor compound Zi Wei Luoa,b,1, Jae Sung Choa,b,1, and Sang Yup Leea,b,c,d,2 aMetabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology, 34141 Daejeon, Republic of Korea; bSystems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Korea Advanced Institute of Science and Technology, 34141 Daejeon, Republic of Korea; cBioProcess Engineering Research Center, Korea Advanced Institute of Science and Technology, 34141 Daejeon, Republic of Korea; and dBioInformatics Research Center, Korea Advanced Institute of Science and Technology, 34141 Daejeon, Republic of Korea Contributed by Sang Yup Lee, April 5, 2019 (sent for review March 6, 2019; reviewed by Jay D. Keasling and Blaine A. Pfeifer) Methyl anthranilate (MANT) is a widely used compound to give While these biotransformation procedures are considered more grape scent and flavor, but is currently produced by petroleum-based natural and ecofriendly compared with chemical synthesis, their processes. Here, we report the direct fermentative production of actual use is limited due to low yields, long reaction times, and MANT from glucose by metabolically engineered Escherichia coli and formation of byproducts (5). In addition, the chemical and bio- Corynebacterium glutamicum strains harboring a synthetic plant- transformation processes mentioned
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  • Davidge JBC Supplementary.Pdf
    promoting access to White Rose research papers Universities of Leeds, Sheffield and York http://eprints.whiterose.ac.uk/ White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/7923/ (includes links to Main Article, Supplementary Material and Figures) Published paper Davidge, K.S., Sanguinetti, G., Yee, C.H., Cox, A.G., McLeod, C.W., Monk, C.E., Mann, B.E., Motterlini, R. and Poole, R.K. (2009) Carbon monoxide-releasing antibacterial molecules target respiration and global transcriptional regulators. Journal of Biological Chemistry, 284 (7). pp. 4516-4524. http://dx.doi.org/10.1074/jbc.M808210200 Supplementary Material White Rose Research Online [email protected] Supplementary Material Carbon monoxide-releasing antibacterial molecules target respiration and global transcriptional regulators Kelly S Davidge, Guido Sanguinetti, Chu Hoi Yee, Alan G Cox, Cameron W McLeod, Claire E Monk, Brian E Mann, Roberto Motterlini and Robert K Poole Contents Page Number Supplementary Figure S1 3 Inhibition by CORM-3 of E. coli cultures grown in defined medium anaerobically and aerobically Supplementary Figure S2 4 Viability assays showing survival of anaerobically and aerobically E. coli in defined growth medium Supplementary Figure S3 5 Reaction of terminal oxidases in vivo on addition of RuCl2(DMSO)4 to intact cells in a dual-wavelength spectrophotometer Supplementary Figure S4 6 CORM-3 generates carbonmonoxycytochrome bd in vivo and depresses synthesis of cytochrome bo' Supplementary Figure S5 7 Expression of spy-lacZ activity
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  • Insensitive 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthaset LISA M
    JOURNAL OF BACTERIOLOGY, Nov. 1990, p. 6581-6584 Vol. 172, No. 11 0021-9193/90/116581-04$02.00/0 Copyright X 1990, American Society for Microbiology Cloning of an aroF Allele Encoding a Tyrosine- Insensitive 3-Deoxy-D-arabino-Heptulosonate 7-Phosphate Synthaset LISA M. WEAVER AND KLAUS M. HERRMANN* Department ofBiochemistry, Purdue University, West Lafayette, Indiana 47907 Received 9 May 1990/Accepted 10 August 1990 In Escherichia coli, genes aroF+, aroG+, and aroH+ encode isoenzymes of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthases that are feedback inhibited by tyrosine, phenylalanine, and tryptophan, respectively. A single base pair change in aroF causes a Pro-148-to-Leu-148 substitution and results in a tyrosine-insensitive enzyme. In bacteria and plants, the aromatic amino acids phenyl- plasmid, designated pLW22, contained an 8-kb insert that alanine, tyrosine, and tryptophan are synthesized via the hybridized to the 714-bp DdeI (Fig. 1) aroF probe (6, 11). shikimate pathway (7, 13). The first enzyme of this pathway Digestion of pLW22 with HindIII-BglII gave a 950-bp frag- is 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) ment that hybridized to the probe. This result was unex- synthase (EC 4.1.2.15). In Escherichia coli, the three un- pected, since the corresponding wild-type fragment is 1.8 kb linked genes aroF+, aroG+, and aroH+ (1) encode three in size. Subsequent detailed restriction analysis and hybrid- isoenzymes of DAHP synthase that are sensitive to tyrosine, ization of pLW22 with the 796-bp DdeI (Fig. 1) aroF probe phenylalanine, and tryptophan, respectively (2).
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  • Letters to Nature
    letters to nature Received 7 July; accepted 21 September 1998. 26. Tronrud, D. E. Conjugate-direction minimization: an improved method for the re®nement of macromolecules. Acta Crystallogr. A 48, 912±916 (1992). 1. Dalbey, R. E., Lively, M. O., Bron, S. & van Dijl, J. M. The chemistry and enzymology of the type 1 27. Wolfe, P. B., Wickner, W. & Goodman, J. M. Sequence of the leader peptidase gene of Escherichia coli signal peptidases. Protein Sci. 6, 1129±1138 (1997). and the orientation of leader peptidase in the bacterial envelope. J. Biol. Chem. 258, 12073±12080 2. Kuo, D. W. et al. Escherichia coli leader peptidase: production of an active form lacking a requirement (1983). for detergent and development of peptide substrates. Arch. Biochem. Biophys. 303, 274±280 (1993). 28. Kraulis, P.G. Molscript: a program to produce both detailed and schematic plots of protein structures. 3. Tschantz, W. R. et al. Characterization of a soluble, catalytically active form of Escherichia coli leader J. Appl. Crystallogr. 24, 946±950 (1991). peptidase: requirement of detergent or phospholipid for optimal activity. Biochemistry 34, 3935±3941 29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and (1995). the thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281±296 (1991). 4. Allsop, A. E. et al.inAnti-Infectives, Recent Advances in Chemistry and Structure-Activity Relationships 30. Meritt, E. A. & Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505± (eds Bently, P. H. & O'Hanlon, P. J.) 61±72 (R. Soc. Chem., Cambridge, 1997).
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  • 1577 MOLECULAR BIOLOGY of PYRIDINE NUCLEOTIDE and NICOTINE BIOSYNTHESIS Akir
    [Frontiers in Bioscience 9, 1577-1586, May 1, 2004] MOLECULAR BIOLOGY OF PYRIDINE NUCLEOTIDE AND NICOTINE BIOSYNTHESIS Akira Katoh and Takashi Hashimoto Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan TABLE OF CONTENTS 1. Abstract 2. Introduction 3. de novo NAD biosynthesis in bacteria: Aspartate pathway 4. de novo NAD biosynthesis in animals: Kynurenine pathway 5. de novo DNA biosynthesis in plants: Precursor feeding studies 6. de novo NAD biosynthesis in plants: Aspartate pathway 7. de novo NAD biosynthesis in plants: Kynurenine pathway 8. NAD salvage pathway in bacteria, yeast and mammals 9. NAD salvage pathway in plants 10. Nicotine biosynthesis in tobacco 11. Pathway regulation 12. Acknowledgment 13. References 1. ABSTRACT Nicotinamide adenine dinucleotide (NAD) is a the pyruvate dehydrogenase complex in the citric acid ubiquitous coenzyme in oxidation-reduction reactions. cycle. Recent animal and fungal studies show that it also plays important roles in transcriptional regulation, NAD also regulates gene expression by longevity, and age-associated diseases. NAD is modulating activities of some animal transcription synthesized de novo from aspartic acid in E. coli or factors (2). NADH enhances the heterodimerization of from tryptophan in animals, by way of quinolinic acid. BMAL1 and BMAL2, the transcription factors involved Although the number of biochemical studies on NAD is in the circadian clock (3), and their DNA binding very limited, a bioinformatic search of genome activity, whereas NAD attenuates these activities. The databases suggests that Arabidopsis (dicots) synthesizes binding of the co-repressor CtBP to transcriptional NAD from aspartic acid whereas rice (monocots) may repressors is reported to be regulated by NAD and utilize both aspartate and tryptophan as starting amino NADH (4).
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  • Advancing a Systems Cell-Free Metabolic Engineering Approach to Natural Product Synthesis and Discovery
    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2020 Advancing a systems cell-free metabolic engineering approach to natural product synthesis and discovery Benjamin Mohr University of Tennessee Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Mohr, Benjamin, "Advancing a systems cell-free metabolic engineering approach to natural product synthesis and discovery. " PhD diss., University of Tennessee, 2020. https://trace.tennessee.edu/utk_graddiss/6837 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Benjamin Mohr entitled "Advancing a systems cell-free metabolic engineering approach to natural product synthesis and discovery." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Energy Science and Engineering. Mitchel Doktycz, Major Professor We have read this dissertation and recommend its acceptance: Jennifer Morrell-Falvey, Dale Pelletier, Michael Simpson, Robert Hettich Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Advancing a systems cell-free metabolic engineering approach to natural product synthesis and discovery A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Benjamin Pintz Mohr December 2019 c by Benjamin Pintz Mohr, 2019 All Rights Reserved.
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  • Medical Bacteriology
    LECTURE NOTES Degree and Diploma Programs For Environmental Health Students Medical Bacteriology Abilo Tadesse, Meseret Alem University of Gondar In collaboration with the Ethiopia Public Health Training Initiative, The Carter Center, the Ethiopia Ministry of Health, and the Ethiopia Ministry of Education September 2006 Funded under USAID Cooperative Agreement No. 663-A-00-00-0358-00. Produced in collaboration with the Ethiopia Public Health Training Initiative, The Carter Center, the Ethiopia Ministry of Health, and the Ethiopia Ministry of Education. Important Guidelines for Printing and Photocopying Limited permission is granted free of charge to print or photocopy all pages of this publication for educational, not-for-profit use by health care workers, students or faculty. All copies must retain all author credits and copyright notices included in the original document. Under no circumstances is it permissible to sell or distribute on a commercial basis, or to claim authorship of, copies of material reproduced from this publication. ©2006 by Abilo Tadesse, Meseret Alem All rights reserved. Except as expressly provided above, no part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or by any information storage and retrieval system, without written permission of the author or authors. This material is intended for educational use only by practicing health care workers or students and faculty in a health care field. PREFACE Text book on Medical Bacteriology for Medical Laboratory Technology students are not available as need, so this lecture note will alleviate the acute shortage of text books and reference materials on medical bacteriology.
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