GRAS Notice 807, Streptococcus Salivarius

Total Page:16

File Type:pdf, Size:1020Kb

GRAS Notice 807, Streptococcus Salivarius GRAS Notice (GRN) No. 807 https://www.fda.gov/food/generally-recognized-safe-gras/gras-notice-inventory • • :.•• BLIS Technologies July 26, 2018 Dr. Paulette Gaynor Office of Food Additive Safety (HFS-200) Center for Food Safety and Applied Nutrition Food and Drug Administration 5001 Campus Drive College Park, MD 20740-3835 Dear Dr. Gaynor: Re GRAS Exemption Claim for Streptococcus salivarius M18 In accordance with 21 CFR §170 Subpart E consisting of §§170.203 through 170.285, BLIS Technologies Ltd. hereby informs the U.S. Food and Drug Administration (FDA) of the conclusion that Streptococcus salivarius M18, is Generally Recognized as Safe (GRAS) for its intended conditions of use in food as described in the enclosed notice, and therefore is not subject to the premarket approval requirements of the Federal Food, Drug, and Cosmetic Act. I verify that the enclosed electronic files were scanned for viruses prior to submission and are thus certified as being virus-free using Symantec Endpoint Protection Virus and Spyware Protection. Should you have any questions or concerns regarding this GRAS Notice, please do not hesitate to contact me at any point during the review process so that we may provide a response in a timely manner. Sincerely, Brian Watson CEO BUS Technologies Ltd. 81 Glasgow Street South Dunedin, Dunedin 9012 New Zealand [email protected] AUG 9 201 OFFICE OF FOOD AODmVE SAFETI Bir Techtrologres lrmited: 81 Gia go11 1 Strf!l!t, South Oumulin 91111. PO Ro:,; .:!:10, . Owredm 9r,4 4. New Zrml,11111 T: 6./ 3 -17./ 098 E.- mli, u bli .:o 111 W: www.hlis.co.11:. GRAS Notice for Streptococcus Salivarius M18 Part 1. §170.225 Signed Statements and Certification In accordance with 21 CFR §170 Subpart E consisting of §§170.203 through 170.285, BUS Technologies Ltd. (BUS) hereby informs the U.S. Food and Drug Administration (FDA) that Streptococcus salivarius M18 (5. salivarius M18), as manufactured by BUS, is not subject to the premarket approval requirements of the Federal Food, Drug, and Cosmetic Act based on BUS's view that the notified substance is Generally Recognized as Safe (GRAS) under the conditions of its intended use described in Section 1.3 below. In addition, as a responsible official of BLIS, Brian Watson hereby certifies that all data and information presented in this notice represents a complete, representative, and balanced submission, and which considered all unfavorable as well as favorable information known to BUS and pertinent to the evaluation of the safety and GRAS status of 5. sa/ivarius M18 as an ingredient for addition to food. Signed, Brian Watson Date CEO [email protected] 1.1 Name and Address of Notifier BLIS Technologies Ltd. 81 Glasgow Street South Dunedin 1 Dunedin 9012 New Zealand 1.2 Common Name of Notified Substance Streptococcus salivarius M18 1.3 Conditions of Use BUS Technologies Ltd. (BUS) intends to market a freeze-dried powder of 5. salivarius M18 as a food ingredient in the United States (U.S.) for use in a variety of conventional food and beverage products [i.e., baby, infant, and toddler foods (excluding infant formula); baked goods and baking mixes; beverage and beverage bases; breakfast cereals; cheeses; chewing gum; dairy product analogs; frozen dairy desserts and mixes; gelatins, puddings, and fillings; grain products and pastas; hard candy; milk, whole and skim; milk products; nuts and nut products; processed fruits and fruit juices; soft candy; sweet sauces, toppings, and syrups] at a level of 20 mg per seNing (providing a minimum of 1xl09 colony-forming units [CFU]/serving). The individual proposed food-uses and use-levels for 5. salivarius M18 employed in the current intake analysis are summarized in Table 1.3-1. Food codes representative of each proposed food-use were chosen BUS Technologies Ltd. 4 July 26 1h , 2018 GRAS NOTICE FOR STREPTOCOCCUS SALIVARIUS M18 PREPARED FOR: Office of Food Additive Safety (HFS-200) Center for Food Safety and Applied Nutrition Food and Drug Administration 5001 Campus Drive College Park, MD 20740 USA SUBMITTED BY: BLIS Technologies Ltd. 81 Glasgow Street South Dunedin Dunedin 9012 New Zealand DATE: 26 July 2018 GRAS Notice for Streptococcus Salivarius M18 TABLE OF CONTENTS Part 1. §170.225 Signed Statements and Certification ..................................................................................... 4 1.1 Name and Address of Notifier .................................................................................................. 4 1.2 Common Name of Notified Substance ..................................................................................... 4 1.3 Conditions of Use ...................................................................................................................... 4 1.4 Basis for GRAS ........................................................................................................................... 6 1.5 Availability of Information ........................................................................................................ 6 1.6 Freedom of Information Act, 5 U.S.C. 552 ................................................................................ 7 Part 2. §170.230 Identity, Method of Manufacture, Specifications, and Physical or Technical Effect ............. 7 2.1 Identity ...................................................................................................................................... 7 2.1.1 Trade Name ................................................................................................................. 7 2.1.2 Taxonomic Lineage ...................................................................................................... 7 2.1.3 History .......................................................................................................................... 8 2.1.4 Phenotypic Identity ...................................................................................................... 8 2.1.5 Genotypic Characterization ....................................................................................... 11 2.2 Manufacturing ........................................................................................................................ 16 2.3 Product Specifications and Batch Analyses ............................................................................ 17 2.3.1 Proposed Product Specifications ............................................................................... 17 2.3.2 Batch Analyses ........................................................................................................... 17 2.4 Stability ................................................................................................................................... 18 2.4.1 Storage Stability ......................................................................................................... 18 Part 3. §170.235 Dietary Exposure .................................................................................................................. 19 3.1 History of Use in Food ............................................................................................................. 19 3.2 Estimated Consumption of S. salivarius M18 from All Intended Conditions of Use in Food ........................................................................................................................................ 20 Part 4. §170.240 Self-Limiting Levels of Use ................................................................................................... 20 Part 5. §170.245 Experience Based on Common Use in Food Before 1958 ................................................... 21 Part 6. §170.250 Narrative and Safety Information ........................................................................................ 21 6.1 Introduction ............................................................................................................................ 21 6.2 Colonization and Metabolic Fate ............................................................................................ 22 6.2.1 Effects on Oral Microbiota ......................................................................................... 23 6.2.2 Effects on Gastrointestinal Microbiota ...................................................................... 24 6.3 Toxicology Studies .................................................................................................................. 24 6.3.1 Toxicity Studies on S. salivarius K12 .......................................................................... 25 6.3.2 Other Animal Studies ................................................................................................. 26 6.3.3 Genotoxicity Studies .................................................................................................. 29 6.4 Human Studies ........................................................................................................................ 29 6.4.1 Studies with S. salivarius M18 ................................................................................... 29 6.4.2 Studies with S. salivarius K12 ..................................................................................... 30 BLIS Technologies Ltd. 1 July 26th, 2018 6.5 Safety of Organism/Pathogenicity .......................................................................................... 34 6.5.1 Case Reports of Human Infection Related to Streptococcus salivarius ..................... 34 6.5.2 Bioinformatic Analyses for Virulence
Recommended publications
  • The Influence of Probiotics on the Firmicutes/Bacteroidetes Ratio In
    microorganisms Review The Influence of Probiotics on the Firmicutes/Bacteroidetes Ratio in the Treatment of Obesity and Inflammatory Bowel disease Spase Stojanov 1,2, Aleš Berlec 1,2 and Borut Štrukelj 1,2,* 1 Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia; [email protected] (S.S.); [email protected] (A.B.) 2 Department of Biotechnology, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia * Correspondence: borut.strukelj@ffa.uni-lj.si Received: 16 September 2020; Accepted: 31 October 2020; Published: 1 November 2020 Abstract: The two most important bacterial phyla in the gastrointestinal tract, Firmicutes and Bacteroidetes, have gained much attention in recent years. The Firmicutes/Bacteroidetes (F/B) ratio is widely accepted to have an important influence in maintaining normal intestinal homeostasis. Increased or decreased F/B ratio is regarded as dysbiosis, whereby the former is usually observed with obesity, and the latter with inflammatory bowel disease (IBD). Probiotics as live microorganisms can confer health benefits to the host when administered in adequate amounts. There is considerable evidence of their nutritional and immunosuppressive properties including reports that elucidate the association of probiotics with the F/B ratio, obesity, and IBD. Orally administered probiotics can contribute to the restoration of dysbiotic microbiota and to the prevention of obesity or IBD. However, as the effects of different probiotics on the F/B ratio differ, selecting the appropriate species or mixture is crucial. The most commonly tested probiotics for modifying the F/B ratio and treating obesity and IBD are from the genus Lactobacillus. In this paper, we review the effects of probiotics on the F/B ratio that lead to weight loss or immunosuppression.
    [Show full text]
  • The Efficacy and Tolerability of Streptococcus Salivarius 24SMB
    European Review for Medical and Pharmacological Sciences 2019; 23(1 Suppl.): 67-72 The efficacy and tolerability of Streptococcus salivarius 24SMB and Streptococcus oralis 89a administered as nasal spray in the treatment of recurrent upper respiratory tract infections in children D. PASSALI1, G.C. PASSALI2, E. VESPERINI3, S. COCCA3, I.C. VISCONTI4, M. RALLI4, L.M. BELLUSSI1 1Department of Medicine, Surgery and Neuroscience, ENT Clinic, University of Siena, Siena, Italy 2ENT Clinic, Catholic University of Sacred Heart, Rome, Italy 3Department of Ear, Nose and Throat, San Giovanni Hospital, Rome, Italy 4Department of Sense Organs, Sapienza University of Rome, Rome, Italy Abstract. – OBJECTIVE: Nasal administration Key Words of Streptococcus salivarius 24SMB and Strepto- Streptococcus salivarius 24SMB, Streptococcus ora- coccus oralis 89a has been proposed to reduce lis 89 a, Pharyngitis, Adenotonsillitis, Acute otitis media. the risk of new episodes of adenoiditis, tonsillitis and acute rhinosinusitis in children. PATIENTS AND METHODS: We enrolled 202 List of Abbreviations children with a recent diagnosis of recurrent upper URT: upper respiratory tract; TLR: Toll-like Receptors; respiratory tract infection. All the patients were COPD: Chronic Obstructive Pulmonary Disease; LPS: treated twice daily for 7 days each month for 3 lipopolysaccharide; AOM: acute otitis media. consecutive months with a nasal spray whose active agents were two specific bacterial strains: Streptococcus salivarius 24SMB and Streptococ- cus oralis 89a. Evaluation was performed at the end of treatment and at follow-up at 3, 6, and 12 months. Introduction RESULTS: Patients who completed the entire 90-day course of bacteriotherapy and the follow-up period showed a 64.3% reduction in their episodes The capability of microbes to adapt to their of upper respiratory tract infections compared to environment is evident in the human body as in the number of episodes recorded in the previous other living organisms.
    [Show full text]
  • Streptococcus Salivarius Meningitis in Immunocompetent
    ISSN: 2643-4008 Elsawy et al. Int Arch Med Microbiol 2018, 1:004 Volume 1 | Issue 1 Open Access International Archives of Medical Microbiology CASE REPORT Streptococcus salivarius Meningitis in Immunocompetent: A Case Report Abdelrahman M Elsawy1*, Hani S Faidah2 and Elrashdy M Redwan3 1Department of Microbiology, Al-Azhar Faculty of Medicine, Egypt Check for 2Department of Microbiology, Umm Al-Qura University, Saudi Arabia updates 3Biological Science Department, King Abdulaziz University, Saudi Arabia *Corresponding author: Elsawy AM, Department of Microbiology, Al-Azhar Faculty of Medicine, Egypt; P.O. Box 13765, Makkah 21599, Saudi Arabia, Tel: 00966555-38337, E-mail: [email protected] is a Joint commission international (JCI) accredited, Abstract with a history of high grade of fever 2 days ago, inter- Streptococcus salivarius (S. salivarius) is a rare cause of pu- rulent meningitis. We report a case of meningitis due to S. mittent, relieved by paracetamol, severe headache and salivarius in 15-years-old Sudanese boy. Diagnosis was es- generalized fatigability. On day of admission, he devel- tablished based on Cerebrospinal fluid (CSF) findings. The oped one episode of tonic clonic convulsion at home patient responded well to systemic antibiotics and recovered and three times in emergency room. He was intubated completely without any neurological complications after proper and admitted in ICU. supportive measures. In this patient the meningitis caused by S. salivarius was thought to be spontaneous. The importance Assessment of vital signs on presentation revealed of bacteriological diagnosis and proper antibiotic treatment for a temperature of 39.2 °C, pulse of 112 beats per min- S. salivarius meningitis is discussed.
    [Show full text]
  • The Enzymatic Conversion of Phosphonates to Phosphate by Bacteria
    Available online at www.sciencedirect.com The enzymatic conversion of phosphonates to phosphate by bacteria 1 Siddhesh S Kamat and Frank M Raushel Phosphonates are ubiquitous organophosphorus compounds annually into the environment in the form of herbicides that contain a characteristic C–P bond which is chemically inert and detergent wastes. With such large quantities of and hydrolytically stable. Bacteria have evolved pathways to phosphonates being released into the environment, there metabolize these phosphonate compounds and utilize the is a significant interest in understanding the mechanisms products of these pathways as nutrient sources. This review by which phosphonates are degraded or metabolized by aims to present all of the known bacterial enzymes capable of bacterial species [1]. The abundance and universal preva- transforming phosphonates to phosphates. There are three lence of phosphonates in the environment has led to the major classes of enzymes known to date performing such evolution of several bacterial species that are able to transformations: phosphonatases, the C-P lyase complex and metabolize and utilize phosphonates as carbon and phos- an oxidative pathway for C–P bond cleavage. A brief phorus sources [2–4]. There are three known classes of description of each class is presented. enzymes or enzymatic systems that have been mechan- istically characterized which are capable of breaking the Addresses C–P bonds of phosphonate compounds. These include Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, TX 77843, United States phosphonate hydrolases, the C-P lyase complex, and an oxidative pathway. Corresponding author: Raushel, Frank M ([email protected]) 1 Present address: The Skaggs Institute for Chemical Biology and Phosphonate hydrolases Department of Chemical Physiology, The Scripps Research Institute, La Phosphonate hydrolases have been generically referred to Jolla, CA 92037, United States.
    [Show full text]
  • Multi-Enzymatic Cascades in the Synthesis of Modified Nucleosides
    biomolecules Article Multi-Enzymatic Cascades in the Synthesis of Modified Nucleosides: Comparison of the Thermophilic and Mesophilic Pathways Ilja V. Fateev , Maria A. Kostromina, Yuliya A. Abramchik, Barbara Z. Eletskaya , Olga O. Mikheeva, Dmitry D. Lukoshin, Evgeniy A. Zayats , Maria Ya. Berzina, Elena V. Dorofeeva, Alexander S. Paramonov , Alexey L. Kayushin, Irina D. Konstantinova * and Roman S. Esipov Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 GSP, B-437 Moscow, Russia; [email protected] (I.V.F.); [email protected] (M.A.K.); [email protected] (Y.A.A.); [email protected] (B.Z.E.); [email protected] (O.O.M.); [email protected] (D.D.L.); [email protected] (E.A.Z.); [email protected] (M.Y.B.); [email protected] (E.V.D.); [email protected] (A.S.P.); [email protected] (A.L.K.); [email protected] (R.S.E.) * Correspondence: [email protected]; Tel.: +7-905-791-1719 ! Abstract: A comparative study of the possibilities of using ribokinase phosphopentomutase ! nucleoside phosphorylase cascades in the synthesis of modified nucleosides was carried out. Citation: Fateev, I.V.; Kostromina, Recombinant phosphopentomutase from Thermus thermophilus HB27 was obtained for the first time: M.A.; Abramchik, Y.A.; Eletskaya, a strain producing a soluble form of the enzyme was created, and a method for its isolation and B.Z.; Mikheeva, O.O.; Lukoshin, D.D.; chromatographic purification was developed. It was shown that cascade syntheses of modified nu- Zayats, E.A.; Berzina, M.Y..; cleosides can be carried out both by the mesophilic and thermophilic routes from D-pentoses: ribose, Dorofeeva, E.V.; Paramonov, A.S.; 2-deoxyribose, arabinose, xylose, and 2-deoxy-2-fluoroarabinose.
    [Show full text]
  • The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
    Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota.
    [Show full text]
  • Streptococci
    STREPTOCOCCI Streptococci are Gram-positive, nonmotile, nonsporeforming, catalase-negative cocci that occur in pairs or chains. Older cultures may lose their Gram-positive character. Most streptococci are facultative anaerobes, and some are obligate (strict) anaerobes. Most require enriched media (blood agar). Streptococci are subdivided into groups by antibodies that recognize surface antigens (Fig. 11). These groups may include one or more species. Serologic grouping is based on antigenic differences in cell wall carbohydrates (groups A to V), in cell wall pili-associated protein, and in the polysaccharide capsule in group B streptococci. Rebecca Lancefield developed the serologic classification scheme in 1933. β-hemolytic strains possess group-specific cell wall antigens, most of which are carbohydrates. These antigens can be detected by immunologic assays and have been useful for the rapid identification of some important streptococcal pathogens. The most important groupable streptococci are A, B and D. Among the groupable streptococci, infectious disease (particularly pharyngitis) is caused by group A. Group A streptococci have a hyaluronic acid capsule. Streptococcus pneumoniae (a major cause of human pneumonia) and Streptococcus mutans and other so-called viridans streptococci (among the causes of dental caries) do not possess group antigen. Streptococcus pneumoniae has a polysaccharide capsule that acts as a virulence factor for the organism; more than 90 different serotypes are known, and these types differ in virulence. Fig. 1 Streptococci - clasiffication. Group A streptococci causes: Strep throat - a sore, red throat, sometimes with white spots on the tonsils Scarlet fever - an illness that follows strep throat. It causes a red rash on the body.
    [Show full text]
  • Antimicrobial and Antibiofilm Activity of the Probiotic Strain Streptococcus
    antibiotics Article Antimicrobial and Antibiofilm Activity of the Probiotic Strain Streptococcus salivarius K12 against Oral Potential Pathogens Andrea Stašková 1, Miriam Sondorová 2,*, Radomíra Nemcová 2, Jana Kaˇcírová 2 and Marián Mad’ar 2 1 Clinic of Stomatology and Maxillofacial Surgery, Faculty of Medicine, University of Pavol Jozef Šafárik in Košice, 040 01 Košice, Slovakia; [email protected] 2 Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Košice, 041 81 Košice, Slovakia; [email protected] (R.N.); [email protected] (J.K.); [email protected] (M.M.) * Correspondence: [email protected] Abstract: Oral probiotics are increasingly used in the harmonization of the oral microbiota in the prevention or therapy of various oral diseases. Investigation of the antimicrobial activity of the bacteriocinogenic strain Streptococcus salivarius K12 against oral pathogens shows promising results, not only in suppressing growth, but also in eliminating biofilm formation. Based on these findings, we decided to investigate the antimicrobial and antibiofilm activity of the neutralized cell-free supernatant (nCFS) of S. salivarius K12 at various concentrations against selected potential oral pathogens under in vitro conditions on polystyrene microtiter plates. The nCFS of S. salivarius K12 significantly reduced growth (p < 0.01) in Streptococcus mutans Clarke with increasing concentration from 15 to 60 mg/mL and also in Staphylococcus hominis 41/6 at a concentration of 60 mg/mL (p < 0.001). Biofilm formation significantly decreased (p < 0.001) in Schaalia odontolytica P10 at nCFS Citation: Stašková, A.; Sondorová, M.; Nemcová, R.; Kaˇcírová, J.; Mad’ar, concentrations of 60 and 30 mg/mL.
    [Show full text]
  • Identification of Clinically Relevant Streptococcus and Enterococcus
    pathogens Article Identification of Clinically Relevant Streptococcus and Enterococcus Species Based on Biochemical Methods and 16S rRNA, sodA, tuf, rpoB, and recA Gene Sequencing Maja Kosecka-Strojek 1,* , Mariola Wolska 1, Dorota Zabicka˙ 2 , Ewa Sadowy 3 and Jacek Mi˛edzobrodzki 1 1 Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland; [email protected] (M.W.); [email protected] (J.M.) 2 Department of Molecular Microbiology, National Medicines Institute, 00-725 Warsaw, Poland; [email protected] 3 Department of Epidemiology and Clinical Microbiology, National Medicines Institute, 00-725 Warsaw, Poland; [email protected] * Correspondence: [email protected]; Tel.: +48-12-664-6365 Received: 13 October 2020; Accepted: 9 November 2020; Published: 11 November 2020 Abstract: Streptococci and enterococci are significant opportunistic pathogens in epidemiology and infectious medicine. High genetic and taxonomic similarities and several reclassifications within genera are the most challenging in species identification. The aim of this study was to identify Streptococcus and Enterococcus species using genetic and phenotypic methods and to determine the most discriminatory identification method. Thirty strains recovered from clinical samples representing 15 streptococcal species, five enterococcal species, and four nonstreptococcal species were subjected to bacterial identification by the Vitek® 2 system and Sanger-based sequencing methods targeting the 16S rRNA, sodA, tuf, rpoB, and recA genes. Phenotypic methods allowed the identification of 10 streptococcal strains, five enterococcal strains, and four nonstreptococcal strains (Leuconostoc, Granulicatella, and Globicatella genera). The combination of sequencing methods allowed the identification of 21 streptococcal strains, five enterococcal strains, and four nonstreptococcal strains.
    [Show full text]
  • Analogous Enzymes: Independent Inventions in Enzyme Evolution Michael Y
    Downloaded from genome.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press RESEARCH Analogous Enzymes: Independent Inventions in Enzyme Evolution Michael Y. Galperin,1 D. Roland Walker,1,2 and Eugene V. Koonin1,3 1National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894 USA; 2Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218 USA It is known that the same reaction may be catalyzed by structurally unrelated enzymes. We performed a systematic search for such analogous (as opposed to homologous) enzymes by evaluating sequence conservation among enzymes with the same enzyme classification (EC) number using sensitive, iterative sequence database search methods. Enzymes without detectable sequence similarity to each other were found for 105 EC numbers (a total of 243 distinct proteins). In 34 cases, independent evolutionary origin of the suspected analogous enzymes was corroborated by showing that they possess different structural folds. Analogous enzymes were found in each class of enzymes, but their overall distribution on the map of biochemical pathways is patchy, suggesting multiple events of gene transfer and selective loss in evolution, rather than acquisition of entire pathways catalyzed by a set of unrelated enzymes. Recruitment of enzymes that catalyze a similar but distinct reaction seems to be a major scenario for the evolution of analogous enzymes, which should be taken into account for functional annotation of genomes. For many analogous enzymes, the bacterial form of the enzyme is different from the eukaryotic one; such enzymes may be promising targets for the development of new antibacterial drugs.
    [Show full text]
  • Modeling and Computational Prediction of Metabolic Channelling
    MODELING AND COMPUTATIONAL PREDICTION OF METABOLIC CHANNELLING by Christopher Morran Sanford A thesis submitted in conformity with the requirements for the degree of Master of Science Graduate Department of Molecular Genetics University of Toronto © Copyright by Christopher Morran Sanford 2009 Abstract MODELING AND COMPUTATIONAL PREDICTION OF METABOLIC CHANNELLING Master of Science 2009 Christopher Morran Sanford Graduate Department of Molecular Genetics University of Toronto Metabolic channelling occurs when two enzymes that act on a common substrate pass that intermediate directly from one active site to the next without allowing it to diffuse into the surrounding aqueous medium. In this study, properties of channelling are investigated through the use of computational models and cell simulation tools. The effects of enzyme kinetics and thermodynamics on channelling are explored with the emphasis on validating the hypothesized roles of metabolic channelling in living cells. These simulations identify situations in which channelling can induce acceleration of reaction velocities and reduction in the free concentration of intermediate metabolites. Databases of biological information, including metabolic, thermodynamic, toxicity, inhibitory, gene fusion and physical protein interaction data are used to predict examples of potentially channelled enzyme pairs. The predictions are used both to support the hypothesized evolutionary motivations for channelling, and to propose potential enzyme interactions that may be worthy of future investigation. ii Acknowledgements I wish to thank my supervisor Dr. John Parkinson for the guidance he has provided during my time spent in his lab, as well as for his extensive help in the writing of this thesis. I am grateful for the advice of my committee members, Prof.
    [Show full text]
  • One-Pot Enzymatic Transformation of D-Pentoses Into Nucleosides
    98 The Open Conference Proceedings Journal, 2010, 1, 98-102 Open Access A New Strategy for the Synthesis of Nucleosides: One-Pot Enzymatic Transformation of D-Pentoses into Nucleosides Anatoly I. Miroshnikov1, Roman S. Esipov1, at’yana I. Muravyova1, Irina D. Konstantinova1, Ilja V. Fateev1 and Igor A. Mikhailopulo*,2 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow B-437, Russian Federation, 2Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Acad. Kuprevicha 5/2, Republic of Belarus Abstract: A possibility of the one-pot synthesis of purine and pyrimidine nucleosides employing pure recombinant ribokinase, phosphopentomutase and nucleoside phosphorylases in a caskade transformation of D-pentoses into nucleosides is demonstrated. Preliminary results of this study point to reliability to develop practical methods for the preparation of a number of biologically important nucleosides. Keywords: Nucleosides, one-pot transformation of pentoses into nucleosides. INTRODUCTION ribokinase (RK) [D-pentose pentose-5-phosphates (D-PF- 5P)], PPM [D-PF-5P -D-pentofuranose 1-phosphates During recent years, a chemo-enzymatic approach to the (-D-PF-1P)], and nucleoside phosphorylases (NP’s) (-D- synthesis of nucleosides attracts continuously growing PF-1P + heterobase -D-nucleosides) coupled with the interest (for recent reviews, see [1]). There are three lines of appropriate pyrimidine or purine heterobases (Scheme 1). investigation in this field of research, viz., (i) The preparation of pure recombinant RK as well as uridine transglycosylation reaction consisting of the transfer of a (UP), thymidine (TP) and purine nucleoside (PNP) pentofuranosyl moiety of commercially available phosphorylases was described by us earlier [5, 6].
    [Show full text]