DOCSLIB.ORG

UNIVERSITY of CALIFORNIA RIVERSIDE Engineering Human

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
UNIVERSITY of CALIFORNIA RIVERSIDE Engineering Human UNIVERSITY OF CALIFORNIA RIVERSIDE Engineering Human Paraoxonase 2 for Quorum Quenching A Dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Biochemistry and Molecular Biology by Xin Li September 2017 Dissertation Committee: Dr. Xin Ge, Chairperson Dr. Ashok Mulchandani Dr. Manuela Martins-Green Copyright by Xin Li 2017 The Dissertation of Xin Li is approved: Committee Chairperson University of California, Riverside Acknowledgement After an intensive period, today is the day: writing this note of thanks is the finishing touch on my dissertation. It has been five years of intense learning for me, not only in the scientific arena, but also on a personal level. Writing this dissertation has had a big impact on me. I would like to reflect on the people who have supported and helped me so much throughout this time. I would express my deepest gratitude to my parents for their continuous love and non-stop support. They are my dearest friends, great listeners, talented cook, and strong allies. At the most depressed time, with their endless love and giving, I did not give up myself. They always wish their baby girl happy, respect her decisions even though sometimes they are ridiculous, and most importantly, they have faith in her. I cannot thank you enough. My sincere thanks to my advisor Dr. Xin Ge. Thank you for giving me the opportunity to be one of your graduate students. During the past four years working with you, I have learnt quite a few from you, such as scientific thinking, efficient planning, abilities to solve research problems. I would like to thank you for your patience. This training makes me become stronger, smarter, and wiser (at least in my opinion, haha!). I also want to give my sincere thanks to Dr. Ashok Mulchandani and Dr. Manuela Martins-Green. You gave me enlightening suggestions for my projects when I had difficulty solving the puzzles. Also, your support and understanding iv game me a lot of strength when I had concerns about my abilities. I am very grateful for your unselfish assistance. I would like to thank Dr. Richard Debus, Dr. Dr. Meng Chen, lab safety manager Joshua Halford, TA coworkers Kyu Lee, Carlos Rodriguez, Matthew Young. During many of these busy quarters, you all like great friends to me. Your wisdom, your stories and your experience were warm, funny, and impressive. You were all brightened and smoothed my days. I would like to thank my lab members, Long Chen, Tyler Lopez, Dr. Chuan Chen, Kibaek Lee, Matthew Chow, Evan Kruchowy; and my undergraduates, Christopher Wang, Guan-Ju Lai, Ran Ye, Jaspreet Wadhwa, Anson Tsang. Thank you all for your daily support, suggestions and discussions, all the scientific sparkling during this time. I am lucky to have you all as my colleagues and closest friends. I want to take this opportunity to thank my friends, Fei Bu, Yang Yu, Xuye Lang, Chuanxiao Chen, Chen Geng, Qi Ai, Chunyu Chen, and my roommates Jie Shi, Chenwei Tian, Honghong Wu who have helped me and had great life experience with me. Last but not the least, I would like to express my heart-felt gratitude to Jan Schlemmer. Your love and support, your humor and kindness, made my life colorful. I cannot walk this far without you. v ABSTRACT OF THE DISSERTATION Engineering Human Paraoxonase 2 for Quorum Quenching by Xin Li Doctor of Philosophy, Graduate Program in Biochemistry and Molecular Biology University of California, Riverside, September 2017 Dr. Xin Ge, Chairperson The rapid emergence of antibiotic-resistant bacteria results in a global health crisis. Among approaches to fighting against antibiotic resistance, this study focuses on quorum sensing (QS) quenching. The QS system regulates the expression of non-essential functions – virulence factors – by sensing their own population density. QS inhibitors interfere with QS communication, thus disrupting biofilm formation and inhibiting the expression of virulence factors. Different from antibiotics, manipulating QS system may halt the development of resistance. Another approach to disrupting QS is the use of quorum quenching (QQ) enzymes to abolish the biological activity of autoinducers (AIs). The first report of degradation AIs was lactonase aiiA isolated from Bacillus sp. 240B. We used aiiA for our studies as a positive QQ enzyme control because of its broad-spectrum vi AHL-degrading ability. For therapeutic purposes, prokaryotic enzymes are very likely to generate adverse immune responses. Subsequently, it would be desirable to have a therapeutic quality enzyme that is as close as possible to the native human protein. Currently, no such enzyme meets all these requirements. Human paraoxonases (huPONs) have been discovered to have AHL- lactonase-like activity, hydrolyzing lactones of various modifications, and carbon chain lengths. HuPONs in particular modulates the stress response of endothelial cells to oxidized phospholipids as well as a bacterial quorum-sensing molecule. However, huPONs are difficult to express in soluble forms, and when heterogeneously expressed, the yield is considerably low. Thus, we intend to enhance the performance of huPON2 by improving its solubility, yield, and activity. By replacing the hydrophobic helices of huPON2 with degenerate short peptide linkers, we isolated human PON2 variants exhibiting high levels of soluble expression. Engineered huPON2s are biologically functional in P. aeruginosa swimming, swarming motility and biofilm formation tests and have lactone hydrolysis activities toward a spectrum of QS molecules. Finally, I introduced random mutations to the soluble expressed huPON2s to improve its catalytic activity. This engineered huPON2 as a quorum quenching enzyme shed light on a novel selection pressure-free selection approach to fight against pathogenic infections. vii Table of Contents 1 Chapter 1 Introduction ....................................................................................... 1 1.1 THREAT OF ANTIBIOTIC RESISTANCE ........................................................................... 1 1.2 MOLECULAR MECHANISMS OF ANTIBIOTICS RESISTANCE ............................................ 3 1.2.1 PREVENTION OF ACCESS TO TARGET ....................................................................... 4 1.2.2 TARGETS PROTECTION ............................................................................................. 7 1.2.3 DIRECT MODIFICATION OF ANTIBIOTIC MOLECULE..................................................... 8 1.3 DEVELOPMENT OF NOVEL ANTIBIOTICS ..................................................................... 10 1.3.1 PEPTIDOMIMETIC ANTIMICROBIALS .......................................................................... 11 1.3.2 AMINOGLYCOSIDES AND DERIVATIVES .................................................................... 13 1.3.3 NANOPARTICLES..................................................................................................... 14 1.3.4 PROBIOTICS APPROACHES ...................................................................................... 15 1.4 QUORUM SENSING QUENCHING ................................................................................. 17 1.4.1 QUORUM SENSING SYSTEM .................................................................................... 17 1.4.2 QUORUM QUENCHING............................................................................................. 25 1.4.3 HUMAN PARAOXONASES ......................................................................................... 30 1.5 OUTLINES 32 1.6 REFERENCES 34 2 Chapter 2 Engineering Soluble Human Paraoxonase 2 for Quorum Quenching 49 2.1 ABSTRACT 49 2.2 INTRODUCTION 50 2.3 METHODS 54 viii 2.3.1 DESIGN AND CONSTRUCTION OF THE HUPON2 LIBRARY. ........................................ 54 2.3.2 SELECTION OF SOLUBLE EXPRESSED HUPON2 VARIANTS....................................... 56 2.3.3 CLONING, EXPRESSION, AND PURIFICATION OF MBP FUSED HUPON2 VARIANTS. ... 56 2.3.4 LACTONASE ACTIVITY ASSAYS................................................................................. 57 2.3.5 BIOLUMINESCENCE QUORUM SENSING BIOASSAY. .................................................. 59 2.3.6 P. AERUGINOSA PAO1 SWARMING AND SWIMMING MOTILITY TESTS........................ 60 2.4 RESULTS AND DISCUSSION ........................................................................................ 60 2.4.1 GENERATION OF SOLUBLE EXPRESSED HUPON2 VARIANTS. ................................... 60 2.4.2 QUORUM QUENCHING ACTIVITY OF HELIX-FREE SOLUBLE HUPON 2S. .................... 72 2.4.3 INHIBITION OF P. AERUGINOSA SWIMMING AND SWARMING MOTILITIES. ................... 75 2.4.4 PROMISCUOUS HYDROLYSIS ACTIVITIES OF SOLUBLE HUPON2. ............................. 81 2.5 CONCLUSION 86 2.6 REFERENCE 88 3 Chapter 3 Engineering Human Paraoxonase 2 for Enhanced Quorum- Quenching Activity 95 3.1 ABSTRACT 95 3.2 INTRODUCTION 96 3.3 MATERIALS AND METHODS ........................................................................................ 97 3.3.1 GENERATION OF HUPON2 RANDOM MUTAGENESIS LIBRARY .................................. 97 3.3.2 BIOLUMINESCENCE QUORUM QUENCHING SCREENING ASSAY ................................. 98 3.3.3 EXPRESSION AND PURIFICATION OF HUPON2 VARIANTS ......................................... 98 3.3.4 SDS-PAGE AND WESTERN BLOTTING .................................................................... 99 3.3.5 LACTONASE ACTIVITY ASSAYS............................................................................... 100 ix 3.3.6
Load more

Recommended publications
  • Identification of a Second Type of AHL- Lactonase from Rhodococcus Sp
    J. Microbiol. Biotechnol. 2020. 30(6): 937–945 https://doi.org/10.4014/jmb.2001.01006 Identification of a Second Type of AHL- Lactonase from Rhodococcus sp. BH4, belonging to the α/β Hydrolase Superfamily Du-Hwan Ryu1†, Sang-Won Lee1†, Viktorija Mikolaityte1, Yea-Won Kim1, Haeyoung Jeong2, Sang Jun Lee3, Chung-Hak Lee4, and Jung-Kee Lee1* 1Department of Biomedicinal Science and Biotechnology, Paichai University, Daejeon 35345, Republic of Korea 2Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea 3Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea 4School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea N-acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) plays a major role in development of biofilms, which contribute to rise in infections and biofouling in water-related industries. Interference in QS, called quorum quenching (QQ), has recieved a lot of attention in recent years. Rhodococcus spp. are known to have prominent quorum quenching activity and in previous reports it was suggested that this genus possesses multiple QQ enzymes, but only one gene, qsdA, which encodes an AHL-lactonase belonging to phosphotriesterase family, has been identified. Therefore, we conducted a whole genome sequencing and analysis of Rhodococcus sp. BH4 isolated from a wastewater treatment plant. The sequencing revealed another gene encoding a QQ enzyme (named jydB) that exhibited a high AHL degrading activity. This QQ enzyme had a 46% amino acid sequence similarity with the AHL-lactonase (AidH) of Ochrobactrum sp. T63. HPLC analysis and AHL restoration experiments by acidification revealed that the jydB gene encodes an AHL-lactonase which shares the known characteristics of the α/β hydrolase family.
    [Show full text]
  • United States Patent (19) 11 Patent Number: 6,146,860 Asakura Et Al
    USOO6146860A United States Patent (19) 11 Patent Number: 6,146,860 Asakura et al. (45) Date of Patent: Nov. 14, 2000 54) MANUFACTURE OF L-ASCORBIC ACID Bublitz, et al., “The role of aldonolactonase in the conver AND D-ERYTHORBIC ACID sion of L-gulonate to L-ascorbate,” Biochimica et Bio physica, vol. 47, pp. 288-297 (1961). 75 Inventors: Akira Asakura, Fujisawa; Tatsuo Derwent English language abstract of De 196 04 798 A1 Hoshino, Kamakura; Tatsuya Kiyasu, (document B2). Fujisawa; Masako Shinjoh, Kamakura, Zachariou, et al., “Glucose-Fructose Oxidoreductase, a New all of Japan Enzyme Isolated from Zymomonas mobilis That is Respon sible for Sorbitol Production,” Journal of Bacteriology, 73 Assignee: Roche Vitamins Inc., Parsippany, N.J. 167(3): 863–869 (1986). Hucho, et al., “Glucono-6-Lactonase From Escherichia 21 Appl. No.: 09/484,966 Coli,” Biochimica et Biophysica Acta, 276:176-179 (1982). Shimizu, et al., “Purification and Characterization of a 22 Filed: Jan. 18, 2000 Novel Lactonohydrolase, Catalyzing the Hydrolysis of 30 Foreign Application Priority Data Aldonate Lactones and Aromatic Lactones, from Fusarium oxysporum,” Eur, J. Biochem., 209:383-390 (1992). Jan. 18, 1999 EP European Pat. Off. .............. 991OO785 Kanagasundaram, et al., “Isolation and Characterization of the gene encoding gluconolactonase from Zymomonas 51) Int. Cl." ............................... C12P 17/04; C12N 9/18 52 U.S. C. ... 435/126; 435/137; 435/195; mobilis,” Biochimica et Biophysica Acta, 1171: (1992). 435/196; 435/197 Primary Examiner Herbert J. Lilling 58 Field of Search ..................................... 435/126, 137, Attorney, Agent, or Firm Mark E. Waddell; Stephen M. 435/195, 196, 197 Haracz; Bryan Cave LLP 56) References Cited 57 ABSTRACT U.S.
    [Show full text]
  • Thermostable Enzymes Important for Industrial Biotechnology
    Thermostable Enzymes Important For Industrial Biotechnology Submitted by Aaron Charles Westlake to the University of Exeter as a thesis for the degree of Doctor of Philosophy in Biological Science in September 2018 This thesis is available for Library use on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. I certify that all material in this thesis which is not my own work has been identified and that no material has previously been submitted and approved for the award of a degree by this or any other University. Aaron Charles Westlake [1] Abstract The use of enzymes in technology is of increasing commercial interest due to their high catalytic efficiency and specificity and the lowering of manufacturing costs. Enzymes are also becoming more widely utilised because they are more environmentally friendly compared to chemical methods. Firstly, they carry out their reactions at ambient temperatures requiring less energy to achieve the high temperatures and pressures that many chemical methods require. Secondly, they can substitute for toxic chemical catalysts which need careful disposal. In this project two classes of enzymes of industrial interest from thermophiles were investigated, lactonase enzymes and 1-deoxy-D-xylulose 5-phosphate (DXP) synthases. A quorum sensing lactonase from Vulcanisaeta moutnovskia, a thermoacidophilic anaerobic crenarchaeon, was expressed in high levels in an Escherichia coli host, then purified and characterised with a range of industrially relevant substrates. These enzymes are of industrial interest for water treatment and bioreactors for their ability to prevent biofilm formation in bacteria. This enzyme showed different specificity to another well characterised quorum sensing lactonase from a thermophilic crenarchaeon, Sulfolobus solfataricus.
    [Show full text]
  • Fermentation Processes for the Production of Ethanol Fermentationsverfahren Zur Herstellung Von Ethanol Processus De Fermentation Pour La Production De L’Éthanol
    (19) TZZ_¥_T (11) EP 1 654 374 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12P 1/00 (2006.01) 24.05.2017 Bulletin 2017/21 (86) International application number: (21) Application number: 04776399.0 PCT/US2004/018342 (22) Date of filing: 09.06.2004 (87) International publication number: WO 2005/005646 (20.01.2005 Gazette 2005/03) (54) FERMENTATION PROCESSES FOR THE PRODUCTION OF ETHANOL FERMENTATIONSVERFAHREN ZUR HERSTELLUNG VON ETHANOL PROCESSUS DE FERMENTATION POUR LA PRODUCTION DE L’ÉTHANOL (84) Designated Contracting States: (56) References cited: AT BE BG CH CY CZ DE DK EE ES FI FR GB GR WO-A1-96/13580 WO-A1-2004/029193 HU IE IT LI LU MC NL PL PT RO SE SI SK TR US-A- 4 288 550 US-A- 4 316 956 US-A- 4 642 236 US-A- 5 464 761 (30) Priority: 10.06.2003 US 459315 • SHIIBA ET AL.: ’Chemical Changes During (43) Date of publication of application: Sponge-Dough Fermentation’ CEREAL 10.05.2006 Bulletin 2006/19 CHEMISTRY vol. 67, no. 4, 1990, pages 350 - 355, XP008091326 (73) Proprietor: Novozymes North America, Inc. • VANDAMME ET AL.: ’Bioflavours and fragrances Franklinton, NC 27525 (US) via fermentation and biocatalysis’ J. CHEM. TECHNOL. BIOTECHNOL. vol. 77, no. 12, 2002, (72) Inventor: GRICHKO, Varvara pages 1323 - 1332, XP008093071 Raleigh, NC 27614 (US) (74) Representative: Kofoed, Gertrud Sonne et al Novozymes A/S Patents Krogshoejvej 36 2880 Bagsvaerd (DK) Note: Within nine months of the publication of the mention of the grant of the European patent in the European Patent Bulletin, any person may give notice to the European Patent Office of opposition to that patent, in accordance with the Implementing Regulations.
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 8,561,811 B2 Bluchel Et Al
    USOO8561811 B2 (12) United States Patent (10) Patent No.: US 8,561,811 B2 Bluchel et al. (45) Date of Patent: Oct. 22, 2013 (54) SUBSTRATE FOR IMMOBILIZING (56) References Cited FUNCTIONAL SUBSTANCES AND METHOD FOR PREPARING THE SAME U.S. PATENT DOCUMENTS 3,952,053 A 4, 1976 Brown, Jr. et al. (71) Applicants: Christian Gert Bluchel, Singapore 4.415,663 A 1 1/1983 Symon et al. (SG); Yanmei Wang, Singapore (SG) 4,576,928 A 3, 1986 Tani et al. 4.915,839 A 4, 1990 Marinaccio et al. (72) Inventors: Christian Gert Bluchel, Singapore 6,946,527 B2 9, 2005 Lemke et al. (SG); Yanmei Wang, Singapore (SG) FOREIGN PATENT DOCUMENTS (73) Assignee: Temasek Polytechnic, Singapore (SG) CN 101596422 A 12/2009 JP 2253813 A 10, 1990 (*) Notice: Subject to any disclaimer, the term of this JP 2258006 A 10, 1990 patent is extended or adjusted under 35 WO O2O2585 A2 1, 2002 U.S.C. 154(b) by 0 days. OTHER PUBLICATIONS (21) Appl. No.: 13/837,254 Inaternational Search Report for PCT/SG2011/000069 mailing date (22) Filed: Mar 15, 2013 of Apr. 12, 2011. Suen, Shing-Yi, et al. “Comparison of Ligand Density and Protein (65) Prior Publication Data Adsorption on Dye Affinity Membranes Using Difference Spacer Arms'. Separation Science and Technology, 35:1 (2000), pp. 69-87. US 2013/0210111A1 Aug. 15, 2013 Related U.S. Application Data Primary Examiner — Chester Barry (62) Division of application No. 13/580,055, filed as (74) Attorney, Agent, or Firm — Cantor Colburn LLP application No.
    [Show full text]
  • Acyl Homoserine Lactonase (Aiia) from Bacillus Thuringiensis 147-115-16 Strain Revista Colombiana De Biotecnología, Vol
    Revista Colombiana de Biotecnología ISSN: 0123-3475 [email protected] Universidad Nacional de Colombia Colombia Florez, Álvaro M.; González, Adriana; Pedroza, Carmen J.; Correa, Elizabeth; Rueda, Nohora J.; Orduz, Sergio Identification, cloning and lactonase activity of recombinant protein of N -acyl homoserine lactonase (AiiA) from Bacillus thuringiensis 147-115-16 strain Revista Colombiana de Biotecnología, vol. XVI, núm. 1, julio, 2014, pp. 153-162 Universidad Nacional de Colombia Bogotá, Colombia Disponible en: http://www.redalyc.org/articulo.oa?id=77631180018 Cómo citar el artículo Número completo Sistema de Información Científica Más información del artículo Red de Revistas Científicas de América Latina, el Caribe, España y Portugal Página de la revista en redalyc.org Proyecto académico sin fines de lucro, desarrollado bajo la iniciativa de acceso abierto ARTÍCULO DE INVESTIGACIÓN Identification, cloning and lactonase activity of recombinant protein of N-acyl homoserine lactonase (AiiA) from Bacillus thuringiensis 147-115-16 strain Identificación, clonación y actividad lactonasa de la proteína recombinante de N-ácil homoserina lactonasa (AiiA) de Bacillus thuringiensis cepa 147-115-16 Álvaro M. Florez*|, Adriana González*, Carmen J. Pedroza**, Elizabeth Correa**, Nohora J. Rueda*, Sergio Orduz** Abstract The quorum-quenching N-acyl homoserine lactonases are a family of bacterial metalloenzymes that participate in degra- dation of N-acyl homoserine lactones (AHLs), disrupting the quorum sensing system of gram negative bacterial species. From a collection of Bacillus thuringiensis strains isolated in Colombia from plants and exhibiting toxic activity against lepi- dopteran insects, 310 bacterial isolates were tested to determine lactonase activity by using biosensor systems in presence of synthetic N-hexanoyl-L-homoserine lactone (C6-HSL) and N-octanoyl-L-homoserine lactone (C8-HSL).
    [Show full text]
  • Carboxylic Ester Hydrolases in Bacteria: Active Site, Structure, Function and Application
    crystals Review Carboxylic Ester Hydrolases in Bacteria: Active Site, Structure, Function and Application Changsuk Oh 1 , T. Doohun Kim 2,* and Kyeong Kyu Kim 1,* 1 Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea; [email protected] 2 Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul 04310, Korea * Correspondence: [email protected] (T.D.K.); [email protected] (K.K.K.) Received: 4 October 2019; Accepted: 7 November 2019; Published: 14 November 2019 Abstract: Carboxylic ester hydrolases (CEHs), which catalyze the hydrolysis of carboxylic esters to produce alcohol and acid, are identified in three domains of life. In the Protein Data Bank (PDB), 136 crystal structures of bacterial CEHs (424 PDB codes) from 52 genera and metagenome have been reported. In this review, we categorize these structures based on catalytic machinery, structure and substrate specificity to provide a comprehensive understanding of the bacterial CEHs. CEHs use Ser, Asp or water as a nucleophile to drive diverse catalytic machinery. The α/β/α sandwich architecture is most frequently found in CEHs, but 3-solenoid, β-barrel, up-down bundle, α/β/β/α 4-layer sandwich, 6 or 7 propeller and α/β barrel architectures are also found in these CEHs. Most are substrate-specific to various esters with types of head group and lengths of the acyl chain, but some CEHs exhibit peptidase or lactamase activities. CEHs are widely used in industrial applications, and are the objects of research in structure- or mutation-based protein engineering. Structural studies of CEHs are still necessary for understanding their biological roles, identifying their structure-based functions and structure-based engineering and their potential industrial applications.
    [Show full text]
  • All Enzymes in BRENDA™ the Comprehensive Enzyme Information System
    All enzymes in BRENDA™ The Comprehensive Enzyme Information System http://www.brenda-enzymes.org/index.php4?page=information/all_enzymes.php4 1.1.1.1 alcohol dehydrogenase 1.1.1.B1 D-arabitol-phosphate dehydrogenase 1.1.1.2 alcohol dehydrogenase (NADP+) 1.1.1.B3 (S)-specific secondary alcohol dehydrogenase 1.1.1.3 homoserine dehydrogenase 1.1.1.B4 (R)-specific secondary alcohol dehydrogenase 1.1.1.4 (R,R)-butanediol dehydrogenase 1.1.1.5 acetoin dehydrogenase 1.1.1.B5 NADP-retinol dehydrogenase 1.1.1.6 glycerol dehydrogenase 1.1.1.7 propanediol-phosphate dehydrogenase 1.1.1.8 glycerol-3-phosphate dehydrogenase (NAD+) 1.1.1.9 D-xylulose reductase 1.1.1.10 L-xylulose reductase 1.1.1.11 D-arabinitol 4-dehydrogenase 1.1.1.12 L-arabinitol 4-dehydrogenase 1.1.1.13 L-arabinitol 2-dehydrogenase 1.1.1.14 L-iditol 2-dehydrogenase 1.1.1.15 D-iditol 2-dehydrogenase 1.1.1.16 galactitol 2-dehydrogenase 1.1.1.17 mannitol-1-phosphate 5-dehydrogenase 1.1.1.18 inositol 2-dehydrogenase 1.1.1.19 glucuronate reductase 1.1.1.20 glucuronolactone reductase 1.1.1.21 aldehyde reductase 1.1.1.22 UDP-glucose 6-dehydrogenase 1.1.1.23 histidinol dehydrogenase 1.1.1.24 quinate dehydrogenase 1.1.1.25 shikimate dehydrogenase 1.1.1.26 glyoxylate reductase 1.1.1.27 L-lactate dehydrogenase 1.1.1.28 D-lactate dehydrogenase 1.1.1.29 glycerate dehydrogenase 1.1.1.30 3-hydroxybutyrate dehydrogenase 1.1.1.31 3-hydroxyisobutyrate dehydrogenase 1.1.1.32 mevaldate reductase 1.1.1.33 mevaldate reductase (NADPH) 1.1.1.34 hydroxymethylglutaryl-CoA reductase (NADPH) 1.1.1.35 3-hydroxyacyl-CoA
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2015/0240226A1 Mathur Et Al
    US 20150240226A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0240226A1 Mathur et al. (43) Pub. Date: Aug. 27, 2015 (54) NUCLEICACIDS AND PROTEINS AND CI2N 9/16 (2006.01) METHODS FOR MAKING AND USING THEMI CI2N 9/02 (2006.01) CI2N 9/78 (2006.01) (71) Applicant: BP Corporation North America Inc., CI2N 9/12 (2006.01) Naperville, IL (US) CI2N 9/24 (2006.01) CI2O 1/02 (2006.01) (72) Inventors: Eric J. Mathur, San Diego, CA (US); CI2N 9/42 (2006.01) Cathy Chang, San Marcos, CA (US) (52) U.S. Cl. CPC. CI2N 9/88 (2013.01); C12O 1/02 (2013.01); (21) Appl. No.: 14/630,006 CI2O I/04 (2013.01): CI2N 9/80 (2013.01); CI2N 9/241.1 (2013.01); C12N 9/0065 (22) Filed: Feb. 24, 2015 (2013.01); C12N 9/2437 (2013.01); C12N 9/14 Related U.S. Application Data (2013.01); C12N 9/16 (2013.01); C12N 9/0061 (2013.01); C12N 9/78 (2013.01); C12N 9/0071 (62) Division of application No. 13/400,365, filed on Feb. (2013.01); C12N 9/1241 (2013.01): CI2N 20, 2012, now Pat. No. 8,962,800, which is a division 9/2482 (2013.01); C07K 2/00 (2013.01); C12Y of application No. 1 1/817,403, filed on May 7, 2008, 305/01004 (2013.01); C12Y 1 1 1/01016 now Pat. No. 8,119,385, filed as application No. PCT/ (2013.01); C12Y302/01004 (2013.01); C12Y US2006/007642 on Mar. 3, 2006.
    [Show full text]
  • Characterization of Aiik, an AHL Lactonase, from Kurthia Huakui
    www.nature.com/scientificreports OPEN Characterization of AiiK, an AHL lactonase, from Kurthia huakui LAM0618T and its application Received: 15 May 2017 Accepted: 5 April 2018 in quorum quenching on Published: xx xx xxxx Pseudomonas aeruginosa PAO1 Weiwei Dong1,2, Jie Zhu3, Xiang Guo2, Delong Kong2, Qi Zhang3, Yiqing Zhou2, Xiaoyang Liu2, Shumiao Zhao1 & Zhiyong Ruan2 N-Acyl homoserine lactones (AHLs) act as the key quorum sensing (QS) signal molecules in gram- negative bacteria, which coordinates gene expression and then activates various processes, including bioflm formation and production of virulence factors in some pathogens. Quorum quenching (QQ), which is the inactivation of the signal molecules by means of enzymatic degradation or modifcation, inhibits the processes of QS rather than killing the pathogens and is a promising antipathogenic strategy to control the bacterial pathogens. In this study, an AHL lactonase gene (named aiiK) was cloned from Kurthia huakuii LAM0618T and the AHL lactonase AiiK was expressed by Escherichia coli. AiiK exhibits a variable substrate spectrum and efcient degradation of the AHL compounds. The enzyme assays demonstrated that AiiK behaves as an AHL lactonase that can hydrolyze the −1 −1 lactone bond of the AHLs. The total hydrolytic efciency of AiiK for C10-HSL is 3.9 s ·mM . AiiK can also maintain 20% activity after 12 h incubation at 37 °C and demonstrate great resistance to α-chymotrypsin, trypsin, and protease K. Furthermore, AiiK signifcantly inhibits the bioflm formation and attenuates extracellular proteolytic activity and pyocyanin production of Pseudomonas aeruginosa PAO1, which indicates the potential application of AiiK as a biocontrol agent or an anti-pathogenic drug.
    [Show full text]
  • Springer Handbook of Enzymes
    Dietmar Schomburg Ida Schomburg (Eds.) Springer Handbook of Enzymes Alphabetical Name Index 1 23 © Springer-Verlag Berlin Heidelberg New York 2010 This work is subject to copyright. All rights reserved, whether in whole or part of the material con- cerned, specifically the right of translation, printing and reprinting, reproduction and storage in data- bases. The publisher cannot assume any legal responsibility for given data. Commercial distribution is only permitted with the publishers written consent. Springer Handbook of Enzymes, Vols. 1–39 + Supplements 1–7, Name Index 2.4.1.60 abequosyltransferase, Vol. 31, p. 468 2.7.1.157 N-acetylgalactosamine kinase, Vol. S2, p. 268 4.2.3.18 abietadiene synthase, Vol. S7,p.276 3.1.6.12 N-acetylgalactosamine-4-sulfatase, Vol. 11, p. 300 1.14.13.93 (+)-abscisic acid 8’-hydroxylase, Vol. S1, p. 602 3.1.6.4 N-acetylgalactosamine-6-sulfatase, Vol. 11, p. 267 1.2.3.14 abscisic-aldehyde oxidase, Vol. S1, p. 176 3.2.1.49 a-N-acetylgalactosaminidase, Vol. 13,p.10 1.2.1.10 acetaldehyde dehydrogenase (acetylating), Vol. 20, 3.2.1.53 b-N-acetylgalactosaminidase, Vol. 13,p.91 p. 115 2.4.99.3 a-N-acetylgalactosaminide a-2,6-sialyltransferase, 3.5.1.63 4-acetamidobutyrate deacetylase, Vol. 14,p.528 Vol. 33,p.335 3.5.1.51 4-acetamidobutyryl-CoA deacetylase, Vol. 14, 2.4.1.147 acetylgalactosaminyl-O-glycosyl-glycoprotein b- p. 482 1,3-N-acetylglucosaminyltransferase, Vol. 32, 3.5.1.29 2-(acetamidomethylene)succinate hydrolase, p. 287 Vol.
    [Show full text]
  • Discovery of an L‑Fucono-1,5-Lactonase from Cog3618 of the Amidohydrolase Superfamily † § ‡ ‡ Merlin Eric Hobbs, Matthew Vetting, Howard J
    Article pubs.acs.org/biochemistry Discovery of an L‑Fucono-1,5-lactonase from cog3618 of the Amidohydrolase Superfamily † § ‡ ‡ Merlin Eric Hobbs, Matthew Vetting, Howard J. Williams, Tamari Narindoshvili, ‡ § § § Devon M. Kebodeaux, Brandan Hillerich, Ronald D. Seidel, Steven C. Almo,*, † ‡ and Frank M. Raushel*, , † Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States ‡ Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States § Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States *S Supporting Information ABSTRACT: A member of the amidohydrolase superfamily, BmulJ_04915 from Burkholderia multivorans, of unknown function was determined to hydrolyze a series of sugar lactones: L-fucono-1,4-lactone, D-arabino-1,4-lactone, L-xylono- 1,4-lactone, D-lyxono-1,4-lactone, and L-galactono-1,4-lactone. The highest activity was shown for L-fucono-1,4-lactone with a −1 × 5 −1 −1 kcat value of 140 s and a kcat/Km value of 1.0 10 M s at pH 8.3. The enzymatic product of an adjacent L-fucose dehydrogenase, BmulJ_04919, was shown to be L-fucono-1,5- lactone via nuclear magnetic resonance spectroscopy. L- Fucono-1,5-lactone is unstable and rapidly converts non- enzymatically to L-fucono-1,4-lactone. Because of the chemical instability of L-fucono-1,5-lactone, 4-deoxy-L-fucono-1,5-lac- tone was enzymatically synthesized from 4-deoxy-L-fucose using L-fucose dehydrogenase. BmulJ_04915 hydrolyzed 4-deoxy-L- −1 × 6 −1 −1 fucono-1,5-lactone with a kcat value of 990 s and a kcat/Km value of 8.0 10 M s at pH 7.1.
    [Show full text]