DOCSLIB.ORG

Detection of Bacterial Sulfatase Activity Through Liquid- and Solid-Phase Colony-Based Assays

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Detection of Bacterial Sulfatase Activity Through Liquid- and Solid-Phase Colony-Based Assays Yoon et al. AMB Expr (2017) 7:150 DOI 10.1186/s13568-017-0449-3 ORIGINAL ARTICLE Open Access Detection of bacterial sulfatase activity through liquid‑ and solid‑phase colony‑based assays Hey Young Yoon1†, Hyung Jun Kim2†, Soojin Jang2 and Jong‑In Hong1* Abstract Bacterial arylsulfatases are crucial to biosynthesis in many microorganisms, as bacteria often utilize aryl sulfates as a source of sulfur. The bacterial sulfatases are associated with pathogenesis and are applied in many areas such as industry and agriculture. We developed an activity-based probe 1 for detection of bacterial sulfatase activity through liquid- and solid-phase colony-based assays. Probe 1 is hydrolyzed by sulfatase to generate fuorescent N-methyl isoindole, which is polymerized to form colored precipitates. These fuorescent and colorimetric properties of probe 1 induced upon treatment of sulfatases were successfully utilized for liquid-phase sulfatase activity assays for colonies and lysates of Klebsiella aerogenes, Mycobacterium avium and Mycobacterium smegmatis. In addition, probe 1 allowed solid-phase colony-based assays of K. aerogenes through the formation of insoluble colored precipitates, thus ena‑ bling accurate staining of target colonies under heterogeneous conditions. Keywords: Bacterial sulfatase, Activity-based probe, N-methyl isoindole, Colony-based assay, Liquid-phase assay, Solid-phase assay Introduction 2015). Teir activities are strongly infuenced by bacterial Sulfur is a chemical element essential to all organisms, as growth environmental conditions and thus their meas- it is required for the biosynthesis of cysteine and methio- urements can be used for soil quality assessment (Garcia- nine; it is also involved in many redox reactions that take Sanchez et al. 2016; Klose et al. 1999). In addition, it was place in biological systems (Kertesz 2000). Microorgan- suggested that sulfatase activity is related with the deg- isms are capable of acquiring sulfur for biosynthesis by radation of endosulfan, an extensively used insecticide assimilating inorganic sulfates or organosulfur com- (Kalyani et al. 2009; Narkhede et al. 2015). Recently, it pounds, such as sulfonates and sulfate esters (Kertesz was reported that sulfatases are potentially implicated in 2000; Stipanuk 1986). Bacterial arylsulfatases catalyze bacterial pathogenesis (Hickey et al. 2015). Furthermore, the hydrolysis of aromatic sulfate esters and participate bacterial sulfatases might be involved in decomposition in the metabolic pathways through which sulfur is pro- of sulfated mucins (Murty et al. 1992) and reconstruction cured by organosulfur compounds. Considering the of extracellular structures by desulfation of glycosami- ability to hydrolyze organosulfur compounds, bacterial noglycans (Mougous et al. 2002) for bacterial infection. arylsulfatases would be useful for many areas such as However, despite of the various usages and the impor- industry and agriculture (Stressler et al. 2016). In prac- tance of sulfatase activity, only a few bacterial sulfatases tice, bacterial arylsulfatases are applied in the desulfa- were characterized. tion of agar (Kim et al. 2004; Lim et al. 2004; Wang et al. Sulfatases contain the conserved Cys/Ser-X-Pro-X- Arg motif in their active sites. Te frst residue of the *Correspondence: [email protected] motif, which can be either cysteine or serine, is post- †Hey Young Yoon and Hyung Jun Kim contributed equally to this work translationally modifed to form C­α-formylglycine 1 Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea (FGly), a unique amino acid that is the key catalytic Full list of author information is available at the end of the article residue for sulfate ester cleavage (Hanson et al. 2004; © The Author(s) 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Yoon et al. AMB Expr (2017) 7:150 Page 2 of 8 Knaust et al. 1998). In eukaryotes, the frst residue of Activity-based probes, based on detecting specifc the motif is cysteine; inability to post-translationally enzymatic activity in a cellular context, are powerful modify this residue to form FGly in humans results in tools for enzyme activity assays (Heal et al. 2011). Previ- a rare lysosomal storage disease called multiple sul- ously reported activity-based probes for sulfatase activity fatase defciency (MSD) (Dierks et al. 2003; Diez-Roux assays contained luminophores and sulfate esters, with and Ballabio 2005; Hanson et al. 2004). In prokaryotes, sulfatase activity inducing an optical response (Beatty the frst residue of the active site motif, i.e., the FGly et al. 2013; Park et al. 2012; Rush et al. 2010; Smith progenitor, can be either cysteine or serine (Dierks et al. 2014). Although those probes were characterized et al. 1998; Marquordt et al. 2003; Miech et al. 1998). by fast response times and low detection limits, they Sulfatases are believed to have either diferent FGly for- were deployed in purifed enzyme solutions or bacterial mation pathways or a common pathway with diferent lysates. modulating cofactors causing diferent localizations We previously reported an activity-based probe 1 (Kertesz 2000). Tese reports indicate that post-trans- (Scheme 1), which enables detection of sulfatase activ- lational modifcations of sulfatases can regulate their ity in purifed enzyme solutions through fuorescence activity, localization and/or stability, and all expressed enhancement (Yoon and Hong 2017). Probe 1 consists sulfatases may not be capable of hydrolyzing sulfate of sulfate ester as a substrate and benzaldehyde as a esters (Hanson et al. 2004; Souf et al. 2015). Tus, it is responsive unit, which are linked with a self-immolative necessary to develop diverse assay methods for detect- moiety. Te cleavage of the sulfate ester in probe 1 by ing sulfatase activity. sulfatase is followed by intramolecular cyclization, result- Determination of microorganisms expressing arylsul- ing in the formation of N-methyl isoindole which emits fatase requires a simple and easy assay method. Many fuorescence at 415 nm. However, N-methyl isoindole is methods for detection of arylsulfatase activity used bac- unstable and easily undergoes autooxidation and polym- teria cell lysates which were prepared through time–con- erization (Bonnett et al. 1973; Kochi and Singleton 1968; suming and complicated processes. Colony-based assays Rettig and Wirz 1976). Te polymerization of N-methyl are simple and thus can reduce sample preparation time. isoindole would trigger the formation of colored precipi- In addition, they also allow functional information to be tates when a higher concentration of probe 1 was incu- acquired in an organism’s physiological environment (An bated with sulfatase for a longer period of time. Tese and Tolliday 2010). Solid-phase assays are proper ways properties of probe 1 enabled us to detect sulfatase activ- to screen and isolate the potential bacterial strains that ity through liquid- and solid-phase colony-based assays express arylsulfatases. Solid-phase assays that exhibit (Scheme 1). sharp and clear image changes according to sulfatase activity are particularly useful in directly detecting indi- Materials and methods vidual colonies of interest (Baud et al. 2015; Green et al. Cultures and growth conditions 2014; Weiss et al. 2014) and they could ofer easy meth- Klebsiella aerogenes was obtained from Hideko Urushi- ods for industrial applications (Bric et al. 1991; Kasana hara at University of Tsukuba. Mycobacterium avium et al. 2008). Terefore, a colony-based solid-phase assay 104, and Mycobacterium smegmatis mc2-155 (ATCC method would be most appropriate one to study bacterial 700084™) were obtained from Yonsei University. Staph- arylsulfatases. ylococcus aureus (ATCC 700698™) was purchased from colored precipitation Scheme 1 Strategy of probe 1 for sulfatase activity detection Yoon et al. AMB Expr (2017) 7:150 Page 3 of 8 American Type Culture Collection (ATCC). For the papers (Whatman) were soaked in a solution of probe growth of K. aerogenes and S. aureus, Nutrient broth 1 (5 mM) in 50 mM Tris bufer. Te membranes were (NB) (BD Difco) was prepared according to the manufac- placed on top of the flter paper soaked in probe 1 solu- turer’s instruction, and the media was supplemented with tion, and incubated 24 h at 37 °C. 1.5% (w/v) agar to make growth plates. For the growth of M. avium and M. smegmatis, 7H9 (BD Difco) media was Results prepared according to the manufacturer’s instruction and Sulfatase activity tests supplemented with 0.5% (w/v) BSA, 0.08% (w/v) NaCl, To evaluate the ability of probe 1 to detect sulfatase activ- 0.2% (w/v) dextrose, 0.1% (v/v) tween 80, and 2% (v/v) ity, we compared the fuorescence intensities and color glycerol to make the complete media. Also, 7H11 (BD changes of probe 1 in the presence or absence of com- Difco) growth plate was prepared according to the manu- mercially available arylsulfatases from Helix pomatia facturer’s instruction, and supplemented with 0.5% (v/v) and A. aerogenes. We used 1 mM probe 1 and 0.1 mg/ glycerol, 0.05% (v/v) tween 80, 10% (v/v) OADC solution. ml of sulfatase from H. pomatia, dissolved in 50 mM Tris Te bacteria were grown at 37 °C, and the growth was bufer at pH 7.4. For about one hour after the initiation monitored by the optical density at 600 nm. of the reaction with the sulfatase, the fuorescence inten- Ф sity increased in a time-dependent manner ( F = 0.146; Enzymatic assays of purifed sulfatase with probe 1 the quantum yield was determined using tryptophan Ф Probe 1 was synthesized according to modifed literature ( F = 0.12 in water) as a standard) (Brouwer 2011). Ten, procedures (Yoon and Hong 2017).
Load more

Recommended publications
  • Identification and Characterisation of Mucin Abnormalities in the Ganglionic Bowel in Hirschsprung’S Disease
    IDENTIFICATION AND CHARACTERISATION OF MUCIN ABNORMALITIES IN THE GANGLIONIC BOWEL IN HIRSCHSPRUNG’S DISEASE By Ruth Marian Speare Submitted for MD (Res) 1 Abstract Hirschsprung’s disease (HD) is a congenital abnormality of unknown origin, characterised by a lack of ganglion cells in the distal colon which results in functional colonic obstruction. The major cause of morbidity and mortality in these children results from an inflammatory condition called enterocolitis. Mucins are large glycoproteins produced by intestinal cells which are a vital part of the colonic defensive barrier to infection. Previous work has found that this barrier is deficient in children with HD in the aganglionic colon and in the immediately adjacent ganglionic colon and that this is related to the risk of developing enterocolitis. This study aimed to further investigate the mucin defensive barrier in a greater region of the ganglionic colon in HD, to establish the extent of any mucin deficiencies and whether these were confined to a limited region close to the aganglionic colon. Mucosal biopsies were collected at intervals along the colon at the time of corrective surgery or colostomy closure in the controls. Organ culture with radioactive mucin precursors was performed and the mucin produced was purified and analysed, results quantified by DNA content in the sample. Lectin binding studies were also carried out. Patients were found to produce lower levels of new mucins most distally, but much higher levels five centimetres proximal when compared to controls. The rest of the colon studied also showed changes in mucin production, with a lack of production of gel-forming mucins and sulphated secreted mucins in Hirschsprung’s disease higher up the colon.
    [Show full text]
  • Mucin Glycoproteins Are Ubiquitous in Mucous Secretions on Cell Surfaces and in Body fluids
    Chapter 9 – O-GalNAc Glycans - Essentials of Glycobiology 2nd edition Intestinal mucosal barrier function in health and disease. Turner, JR Nature Rev. Immunology 9: 799 (2009) From Mucins to Mucus Thornton DJ and Sheehan JK, Proc Am Thorac Soc., 1:54 (2004) Mucin structure, aggregation, physiological functions and biomedical applications Bansil R. and Turner BS Curr Opin in Colloid & Interface Sci, 11:164 (2006) Mucins in the mucosal barrier to infection Linden et al, Nature Immunology 1: 183 (2008) The cancer glycocalyx mechanically primes integrin-mediated growth and survival. Paszek et al, Nature 511: 319 (2014) Chapter 9 – O-GalNAc Glycans Essentials of Glycobiology 2nd edition 4/14/2016 O-GalNAc Glycans - Essentials of Glycobiology - NCBI Bookshelf NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health. Varki A, Cummings RD, Esko JD, et al., editors. Essentials of Glycobiology. 2nd edition. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 2009. Chapter 9O-GalNAc Glycans Inka Brockhausen, Harry Schachter, and Pamela Stanley. Correction O-glycosylation is a common covalent modification of serine and threonine residues of mammalian glycoproteins. This chapter describes the structures, biosynthesis, and functions of glycoproteins that are often termed mucins. In mucins, O-glycans are covalently α-linked via an N-acetylgalactosamine (GalNAc) moiety to the -OH of serine or threonine by an O-glycosidic bond, and the structures are named mucin O-glycans or O-GalNAc glycans. The focus of this chapter is on mucins and mucin-like glycoproteins that are heavily O-glycosylated, although glycoproteins that carry only one or a few O- GalNAc glycans are also briefly discussed.
    [Show full text]
  • Two Glycosulfatases from the Liver of a Marine Gastropod , Charonia Lampas
    J. Biochem., 79, 27-34 (1976) Two Glycosulfatases from the Liver of a Marine Gastropod , Charonia lampas Partial Purification and Properties1 Hiroshi HATANAKA, Yoko OGAWA , and Fujio EGAMI Mitsubishi-Kasei Institute of Life Sciences , Minamiooya, Machida-shi, Tokyo 194 Received for publication , July 9, 1975 Two glycosulfatases [EC 3.1 .6.3], I and ‡U, were purified 31 .3- and 33.9-fold respectively, from a crude extract of the liver of Charonia lampas . The purification was carried out by the following chromatographic procedures ; phosphocellulose , S ephadex G-150, Concanavalin A-Sepharose and isoelectric focussing . The enzyme preparations obtained were practically free from arylsulfatase [EC 3.1.6.1] contami nation. Both glycosulfatases are probably glycoproteins differing in their carbohydrate moieties. The molecular weights of glycosulfatase I and H were estimated to be about 112,000 and 79 ,000, respectively. They had the same optimum pH of 5.5, and the same Km value of 25.0mM for glucose 6-sulfate . As a result of recent investigations on sul yet been fully investigated. Glycosulfatase was fatase reactions, the physiological significance found first in molluscs by Soda and co-workers of arylsulfatase [EC 3. 1. 6. 1] is gradually being (10) and later in microorganisms, but its oc- elucidated. The hydrolysis of naturally oc currence in higher animals is doubtful (11). curring sugar-sulfate derivatives by arylsul In the present investigation, we studied fatase has been reported in the cases of sulfo the partial purification and some properties of galactolipids (1-5), UDP - N- acetylgalacto two glycosulfatases from the liver of a marine samine 4-sulfate (6, 7), and ascorbate 2-sulfate gastropod, Charonia lampas.
    [Show full text]
  • Molecular and Biochemical Characterisation of Siap As a Sialic Acid Binding Protein Component of a TRAP Transporter for Sialic Acid
    Molecular and biochemical characterisation of SiaP as a sialic acid binding protein component of a TRAP transporter for sialic acid Adam Paul Hopkins A thesis submitted for the degree of Doctor of Philosophy University of York Department of Biology July 2010 Abstract Sialic acid utilisation plays an important role in the growth and persistence of the obligate human mucosal pathogen Haemophilus influenzae, which causes respiratory tract infections, septicaemia and meningitis. Like many other bacteria, H. influenzae can use host-derived sialic acids as carbon, nitrogen and energy sources, but also as a terminal modification on the LPS to better evade the human immune system. H. influenzae takes up exogenous sialic acid via a tripartite ATP-independent periplasmic (TRAP) transporter, SiaPQM. This possesses an extracytoplasmic substrate binding protein (SBP), SiaP, which binds the substrate in the periplasm and delivers it to the specific membrane permease, SiaQM. SiaP contains two globular domains, which close around the substrate upon binding. Here, the mechanism of sialic acid binding by SiaP is investigated using site-directed mutagenesis of residues in the ligand binding site and analogues of sialic acid. These, and several mutations on the surface of SiaP, were investigated for their effect on transport by SiaPQM in vitro, using SiaQM reconstituted into proteoliposomes, and in vivo, using expression of siaPQM in an E. coli strain lacking its native sialic acid transporter, NanT. It is demonstrated that stabilisation of the carboxylate group of sialic acid by the totally conserved Arginine-147 is important for high-affinity ligand binding, but is not essential for transport. Mutation of Aparagine-150 to Aspartate abolishes the function of the transporter without affecting ligand binding, suggesting the existence of a critical interaction between the components of the transporter.
    [Show full text]
  • A Single Bacterial Sulfatase Is Required for Metabolism of Colonic Mucin O-Glycans and Intestinal Colonization by a Symbiotic Hu
    bioRxiv preprint doi: https://doi.org/10.1101/2020.11.20.392076; this version posted November 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 2 A single bacterial sulfatase is required for metabolism of colonic mucin O-glycans 3 and intestinal colonization by a symbiotic human gut bacterium 4 5 *1,2Ana S. Luis, 2Chunsheng Jin, 1Gabriel Vasconcelos Pereira, 1Robert W. P. Glowacki, 6 1Sadie Gugel, 1Shaleni Singh, 3Dominic P. Byrne, 1Nicholas Pudlo, 3James A London, 7 4Arnaud Baslé, 5Mark Reihill, 5Stefan Oscarson, 3Patrick A. Eyers, 6Mirjam, Czjzek, 8 6Gurvan Michel, 6Tristan Barbeyron, 3Edwin A Yates, 2Gunnar C. Hansson, 2Niclas G. 9 Karlsson, *,3Alan Cartmell, *1Eric C. Martens 10 11 12 13 1Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 14 48109, USA 15 2Department of Medical Biochemistry, Institute for Biomedicine, Sahlgrenska Academy, 16 University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden 17 3Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and 18 Integrative Biology, University of Liverpool, Liverpool L69 3BX, United Kingdom 19 4Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon 20 Tyne, United Kingdom 21 5Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 22 4, Ireland. 23 6Sorbonne Université, Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine 24 Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France.
    [Show full text]
  • 12) United States Patent (10
    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.
    [Show full text]
  • Biomarker Identification in Human Lung Adenocarcinoma
    Research Collection Doctoral Thesis Activity-based proteomics biomarker identification in human lung adenocarcinoma Author(s): Wiedl, Thomas Publication Date: 2011 Permanent Link: https://doi.org/10.3929/ethz-a-006698733 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library Diss. ETH Nr. 19704 Activity-based proteomics: biomarker identification in human lung adenocarcinoma A dissertation submitted to the ETH Zurich for the degree of Doctor of Sciences (Dr. sc. ETH Zurich) presented by Thomas Wiedl Dipl. Ing., Vienna University of Technology, Austria Born March 30, 1981 Citizen of Austria accepted on the recommendation of Prof. Dr. Rudolf Aebersold (examiner) Prof. Dr. Walter Weder (co-examiner) Prof. Dr. Holger Moch (co-examiner) Prof. Dr. Stephan Sieber (co-examiner) 2011 Table of contents SUMMARY 6 ZUSAMMENFASSUNG 8 ACKNOWLEDGEMENTS 10 ABBREVIATIONS 12 1. INTRODUCTION 14 1.1 LUNG CANCER : CLASSIFICATION , EPIDEMIOLOGY AND PROGNOSIS 14 1.2 MOLECULAR EVOLUTION OF LUNG CANCER 16 1.3 LUNG CANCER AND THE BIOMARKER CONCEPT : STATUS QUO 18 1.4 MASS SPECTROMETRY (MS) BASED PROTEOMICS 20 1.5 ACTIVITY -BASED PROTEOMICS : A NOVEL STRATEGY FOR BIOMARKER DISCOVERY 23 1.6 THE SERINE HYDROLASE SUPERFAMILY 26 1.7 LUNG CANCER IN THE FUTURE 29 2. MATERIAL AND METHODS 30 2.1 SAMPLE COLLECTION 30 2.2 CELL CULTURE AND LYSIS 31 2.3 WESTERN BLOT 31 2.4 ACTIVITY -BASED PROBE 32 2.5 PROTEOME PREPARATION FOR LC-MS/MS ANALYSIS 33 2.6 LC-MS/MS ANALYSIS 35 2.7 DATABASE SEARCH AND LABEL -FREE QUANTIFICATION 36 2.8 STATISTICAL ANALYSIS 37 3.
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2012/0266329 A1 Mathur Et Al
    US 2012026.6329A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0266329 A1 Mathur et al. (43) Pub. Date: Oct. 18, 2012 (54) NUCLEICACIDS AND PROTEINS AND CI2N 9/10 (2006.01) METHODS FOR MAKING AND USING THEMI CI2N 9/24 (2006.01) CI2N 9/02 (2006.01) (75) Inventors: Eric J. Mathur, Carlsbad, CA CI2N 9/06 (2006.01) (US); Cathy Chang, San Marcos, CI2P 2L/02 (2006.01) CA (US) CI2O I/04 (2006.01) CI2N 9/96 (2006.01) (73) Assignee: BP Corporation North America CI2N 5/82 (2006.01) Inc., Houston, TX (US) CI2N 15/53 (2006.01) CI2N IS/54 (2006.01) CI2N 15/57 2006.O1 (22) Filed: Feb. 20, 2012 CI2N IS/60 308: Related U.S. Application Data EN f :08: (62) Division of application No. 1 1/817,403, filed on May AOIH 5/00 (2006.01) 7, 2008, now Pat. No. 8,119,385, filed as application AOIH 5/10 (2006.01) No. PCT/US2006/007642 on Mar. 3, 2006. C07K I4/00 (2006.01) CI2N IS/II (2006.01) (60) Provisional application No. 60/658,984, filed on Mar. AOIH I/06 (2006.01) 4, 2005. CI2N 15/63 (2006.01) Publication Classification (52) U.S. Cl. ................... 800/293; 435/320.1; 435/252.3: 435/325; 435/254.11: 435/254.2:435/348; (51) Int. Cl. 435/419; 435/195; 435/196; 435/198: 435/233; CI2N 15/52 (2006.01) 435/201:435/232; 435/208; 435/227; 435/193; CI2N 15/85 (2006.01) 435/200; 435/189: 435/191: 435/69.1; 435/34; CI2N 5/86 (2006.01) 435/188:536/23.2; 435/468; 800/298; 800/320; CI2N 15/867 (2006.01) 800/317.2: 800/317.4: 800/320.3: 800/306; CI2N 5/864 (2006.01) 800/312 800/320.2: 800/317.3; 800/322; CI2N 5/8 (2006.01) 800/320.1; 530/350, 536/23.1: 800/278; 800/294 CI2N I/2 (2006.01) CI2N 5/10 (2006.01) (57) ABSTRACT CI2N L/15 (2006.01) CI2N I/19 (2006.01) The invention provides polypeptides, including enzymes, CI2N 9/14 (2006.01) structural proteins and binding proteins, polynucleotides CI2N 9/16 (2006.01) encoding these polypeptides, and methods of making and CI2N 9/20 (2006.01) using these polynucleotides and polypeptides.
    [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]
  • Bacterial Glycosulphatases and Sulphomucin Degradation
    PEDIATRIC GASTROENTEROLOGY Bacterial glycosulphatases and sulphomucin degradation Anthony M Roberton BSc(Hons) DPhil, Damian P Wright MSc AM Roberton, DP Wright. Bacterial glycosulphatases and sul- Glycosulfatases bactériennes et dégradation de phomucin degradation. Can J Gastroenterol 1997;11(4):361- 366. The presence of a high bacterial population in a region of the la sulfomucine gastrointestinal tract is usually associated with the secretion of sul- RÉSUMÉ : La présence d’une forte population bactérienne dans une ré- phomucins into the mucus gel covering that region. The term ‘su- gion du tractus digestif est habituellement associée à la sécrétion de sul- lphomucin’ is a histochemical description of the staining fomucines dans le gel muqueux qui tapisse cette région. Le terme properties of mucin. At present this term can only be qualitatively sulfomucine est une description histochimique des propriétés colorantes de related to the percentage of sulphate in the mucin molecule, la mucine. À l’heure actuelle, ce terme ne peut être que qualitativement as- which makes the term difficult to use in a biochemical and func- socié au pourcentage de sulfate présent dans la molécule de mucine, ce qui tional sense. Sulphomucins are thought to carry out the normal rend son emploi difficile dans un sens biochimique et fonctionnel. Les sul- functions attributed to mucins; in addition, heavy sulphation fomucines accompliraient des fonctions normalement attribuées aux mu- rate-limits the degradation of mucins by bacterial mucin- cines; de plus, de forts taux de sulfatation limitent la dégradation des degrading glycosidases. A number of mucin-specific glycosul- mucines par les glycosidases responsables de la dégradation de la mucine phatases have been reported in bacteria, although only two such bactérienne.
    [Show full text]
  • Universal Protein Families and the Functional Content of the Last Universal Common Ancestor
    J Mol Evol (1999) 49:413–423 © Springer-Verlag New York Inc. 1999 Universal Protein Families and the Functional Content of the Last Universal Common Ancestor Nikos Kyrpides,1,2 Ross Overbeek,2 Christos Ouzounis3 1 Department of Microbiology, University of Illinois at Urbana–Champaign, 407 South Goodwin Avenue, Urbana IL 61801, USA 2 Mathematics and Computer Science Division, Argonne National Laboratory, 9700 South Case Avenue, Argonne IL 60439, USA 3 Computational Genomics Group, Research Programme, The European Bioinformatics Institute, EMBL Cambridge Outstation, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK Abstract. The phylogenetic distribution of Metha- ties of a complete set of archaeal proteins with the other nococcus jannaschii proteins can provide, for the first two domains, Bacteria and Eukarya. This universal set of time, an estimate of the genome content of the last com- protein families present in all domains can then be used mon ancestor of the three domains of life. Relying on as an estimate for the genome content of the Last Uni- annotation and comparison with reference to the species versal Common Ancestor (Woese 1982; Woese and Fox distribution of sequence similarities results in 324 pro- 1977). Evidently, factors such as gene loss, horizontal teins forming the universal family set. This set is very transfer across domains and species peculiarities make well characterized and relatively small and nonredun- this task difficult, especially when only interspecies com- dant, containing 301 biochemical functions, of which parisons are used (Becerra et al. 1997). Previous such 246 are unique. This universal function set contains approaches have ignored the above problems (Mush- mostly genes coding for energy metabolism or informa- egian and Koonin 1996), resulting in descriptions that tion processing.
    [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]