Bacterial Glycosulphatases and Sulphomucin Degradation

Total Page:16

File Type:pdf, Size:1020Kb

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. Un nombre de glycosulfatases spécifiques aux mucines ont été enzymes have been purified. These enzymes remove part of the signalés dans les bactéries, bien que peu seulement des ces enzymes aient sulphate content from sulphomucins and make them more suscep- été purifiées. Ces enzymes éliminent une partie de la teneur en sulfates des tible to further enzymic degradation. The variety of chain loca- sulfomucines et les rendent plus sujettes à la dégradation enzymatique. La tions and sugar attachment sites of sulphate esters on the mucin variété des localisations des chaînes et des types de fixation aux atomes de oligosaccharides, taken together with the data on the enzymes, sucre des esters de sulfate sur les oligosaccharides de mucine étudiés dans le suggest there will be a spectrum of bacterial glycosulphatases, with contexte des données recueillies sur les enzymes donnent à penser qu’il ex- different properties, cellular locations and substrate specificities. iste un large spectre de glycosulfatases bactériennes dotées de propriétés de Bacterial glycosulphatases have the potential to modify sulphated localisation cellulaire et de spécificité des substrats différentes. Elles peu- glycoconjugates at mucosal surfaces and should prove useful as vent modifier les glycoconjugués sulfatés sur les surfaces muqueuses et biochemical tools for the study of sulphated glycoconjugates. devraient se révéler utiles à titre d’outils biochimiques pour l’étude des gly- Key Words: Glycosulphatase, Mucin, Sulphomucin coconjugués sulfatés. he digestive tract is covered by a viscoelastic mucus gel, simplification of the complexity of the molecule. It is more Tin which the main structural molecules are the mucins. accurate to picture the mucin oligosaccharide chains as con- These have been categorized historically as neutral mucins, taining a mixture of sialic acid and sulphate groups in various sialomucins or sulphomucins on the basis of the density and ratios (Figure 1d). The terms ‘sialomucin’, ‘sulphomucin’ or types of acidic groups present in their oligosaccharide side ‘neutral mucin’ then more correctly describe the predomi- chains. However, this categorization, depicted schemati- nance of sialic acid or sulphate acidic groups or their scarcity cally in Figures 1a to 1c, implies a structure that is an over- in the mucin molecule. Recent analyses of oligosaccharide This paper was part of a symposium entitled “Selected topics in pediatric gastroenterology and nutrition” held in October 1995 to honour the academic career of Dr Gordon G Forstner School of Biological Sciences, University of Auckland, Auckland, New Zealand Correspondence: Dr AM Roberton, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand. Telephone 64-9-373-7599 ext 8233, fax 64-9-373-7414 Can J Gastroenterol Vol 11 No 4 May/June 1997 361 Roberton and Wright lium. Sulphomucins can be visualized in mucin-secreting cells and the overlying mucus layer by staining with high iron diamine (HID) at pH 1.5, Alcian blue at pH 1.0, or HID and Alcian blue at pH 2.5 (3). When colon tissue is treated with the last of these techniques, the sulphomucins in the crypt goblet cells stain dark brown with HID, while the sia- lomucins, containing mucin with less sulphate and larger amounts of sialic acid, stain blue with Alcian blue. There is some difficulty in using the term sulphomucin in a biochemical context. The term was coined by histochem- ists to describe mucins that stain with HID or Alcian blue at pH 1. However, while this characterization broadly relates to the name, the percentage of sulphate in mucin (ie, grams of sulphate/100 g mucin) needed to give a positive stain is un- known (4). Table 1 (5-10) shows the sulphate content of a selection of isolated human mucins from saliva and intes- tines. The small intestinal mucins would presumably be clas- sified histochemically as sialomucins rather than sulpho- mucins, and the unfractionated colonic mucin (9) would be a mixture of sialomucins and sulphomucins. It is clear that small intestinal mucins (sialomucins) contain sulphate, al- though in lesser amounts than colonic mucin. The quantity of sulphate needed to qualify a mucin for categorization as a Figure 1) Classes of mucins. Stylized diagrams of (a) neutral mucin sulphomucin is unclear. Perhaps the borderline should not chain, (b) sialomucin chain and (c) sulphomucin chain. These concepts be defined until the properties that sulphate imparts to a mu- are oversimplified because they show only one type of acidic group within cin are better understood, and until it is known whether all the mucin. A more realistic concept of an acidic mucin chain containing sulphate groups should be considered equivalent despite dif- both sulphate and sialic acid groups within the molecule is shown in (d) ferent chain locations and sugar attachment sites. So there is a problem in defining boundaries within which to define the TABLE 1 term sulphomucin. Sulphate contents of human salivary and intestinal mucins ROLES OF SULPHOMUCINS Sulphate What are the sulphomucins doing in the digestive tract? Pre- Mucin content* Reference sumably they possess many of the functions of all mucins, in- Saliva (submandibular-sublingual, high 7.0 5 cluding participating in the barrier role and protecting the molecular weight mucin, MG1) underlying surface from the aggressive and damaging luminal Small intestine 0.45 6 1.6 7 factors in the particular region. They also lubricate the mu- Ileum (ileal conduit) 1.2 8 cosal surface, preventing abrasion by food or fecal particles Colon (cystic fibrosis patient) 2.0 9 during passage through the tract. They are part of the un- Colon (isolated sulphomucin fraction) 6.5 10 stirred water layer through which all substances must diffuse *Grams sulphate/100 g mucin to enter or leave the epithelial cell surface during absorption and secretion. Mucins are the main structural molecules of the visco-elastic mucus gel, and their reduced viscosity and chain structures have shown that both sulphate and sialic calcium binding activity both increase with sulphate con- acid groups can be present within a single oligosaccharide tent, although the values are also affected by forming com- chain (1,2). plexes with other components of the mucin layer (11). Sulphomucins may be a target for certain bacterial receptors. SULPHOMUCINS In addition, there is accumulating evidence that sulpho- In humans the mouth and the colon are the two main re- mucins rate-limit mucin degradation by mucin-degrading gions of the digestive tract containing sulphomucins. As a bacterial enzymes. The evidence for the last of these roles is general rule, the areas of digestive tract that are the habitat summarized below. of large numbers of microorganisms are also rich in secreted sulphomucins, suggesting that these two phenomena have EVIDENCE THAT SULPHOMUCINS RATE-LIMIT become linked during evolution. The converse is not true MUCIN DEGRADATION BY BACTERIAL ENZYMES because there are other areas that secrete sulphomucins but The first line of evidence comes from the general rule that, do not have a large bacterial population, such as the submu- under normal conditions, the presence of a large bacterial cosal esophageal glands and the pancreaticobiliary epithe- population in a region of an animal digestive tract coincides 362 Can J Gastroenterol Vol 11 No 4 May/June 1997 Sulphomucins and glycosulphatases with the presence of sulphomucins. This is teleological evi- TABLE 2 dence that the two have evolved together, and the latter Sulphated sugars in mucins may be necessary to control the former. Sulphated sugar Origin Reference Second, evidence that sulphated glycopeptides inhibit N-acetylglucosamine-
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]
  • 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.
    [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]
  • 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]