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Schirmer M, Stražar M, Avila-Pacheco J, Rojas-Tapias DF, Brown EM, Temple E, Deik A, Bullock K, Jeanfavre S, Pierce K, Jin S, Invernizzi R, Pust MM, Costliow Z, Mack DR, Griffiths AM, Walters T, Boyle BM, Kugathasan S, Vlamakis H, Hyams J, Denson L, Clish CB, Xavier RJ. Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course. Cell Host Microbe 2024; 32:209-226.e7. [PMID: 38215740 PMCID: PMC10923022 DOI: 10.1016/j.chom.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 11/08/2023] [Accepted: 12/15/2023] [Indexed: 01/14/2024]
Abstract
Understanding the role of the microbiome in inflammatory diseases requires the identification of microbial effector molecules. We established an approach to link disease-associated microbes to microbial metabolites by integrating paired metagenomics, stool and plasma metabolomics, and culturomics. We identified host-microbial interactions correlated with disease activity, inflammation, and the clinical course of ulcerative colitis (UC) in the Predicting Response to Standardized Colitis Therapy (PROTECT) pediatric inception cohort. In severe disease, metabolite changes included increased dipeptides and tauro-conjugated bile acids (BAs) and decreased amino-acid-conjugated BAs in stool, whereas in plasma polyamines (N-acetylputrescine and N1-acetylspermidine) increased. Using patient samples and Veillonella parvula as a model, we uncovered nitrate- and lactate-dependent metabolic pathways, experimentally linking V. parvula expansion to immunomodulatory tryptophan metabolite production. Additionally, V. parvula metabolizes immunosuppressive thiopurine drugs through xdhA xanthine dehydrogenase, potentially impairing the therapeutic response. Our findings demonstrate that the microbiome contributes to disease-associated metabolite changes, underscoring the importance of these interactions in disease pathology and treatment.
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Affiliation(s)
- Melanie Schirmer
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Translational Microbiome Data Integration, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
| | - Martin Stražar
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Eric M Brown
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Emily Temple
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amy Deik
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin Bullock
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah Jeanfavre
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kerry Pierce
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shen Jin
- Translational Microbiome Data Integration, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | | | - Marie-Madlen Pust
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Zach Costliow
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David R Mack
- Division of Gastroenterology, Hepatology & Nutrition, Children's Hospital of Eastern Ontario and University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Anne M Griffiths
- Division of Gastroenterology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Thomas Walters
- Division of Gastroenterology, Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Brendan M Boyle
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Subra Kugathasan
- Department of Pediatrics, Emory University, Atlanta, GA 30322, USA
| | - Hera Vlamakis
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jeffrey Hyams
- Connecticut Children's Medical Center, Division of Digestive Diseases, Hartford, CT 06106, USA
| | - Lee Denson
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Clary B Clish
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Hobson PN, Bousfield S, Summers R, Kirsch EJ. Anaerobic digestion of organic matter. ACTA ACUST UNITED AC 2009. [DOI: 10.1080/10643387409381614] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Whiteley HR. The Mechanism of Propionic Acid Formation by Succinate Decarboxylation: I. The Activation of Succinate. Proc Natl Acad Sci U S A 2006; 39:772-9. [PMID: 16589332 PMCID: PMC1063856 DOI: 10.1073/pnas.39.8.772] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- H R Whiteley
- Hopkins Marine Station, Pacific Grove, California
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McCormick NG, Ordal EJ, Whiteley HR. DEGRADATION OF PYRUVATE BY MICROCOCCUS LACTILYTICUS I. : General Properties of the Formate-Exchange Reaction. J Bacteriol 2006; 83:887-98. [PMID: 16561936 PMCID: PMC279371 DOI: 10.1128/jb.83.4.887-898.1962] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
McCormick, N. G. (University of Washington, Seattle), E. J. Ordal, and H. R. Whiteley. Degradation of pyruvate by Micrococcus lactilyticus. I. General properties of the formate-exchange reaction (J. Bacteriol. 83:887-898. 1962.-At an alkaline pH, extracts of Micrococcus lactilyticus(2) catalyze the phosphoroclastic degradation of pyruvate to formate and acetyl phosphate and the rapid exchange of formate into the carboxyl group of pyruvate. At an acid pH, hydrogen, carbon dioxide, and acetyl phosphate are produced, and carbon dioxide is exchanged into the carboxyl group of pyruvate. A concentration of approximately 1 m phosphate is required for the phosphoroclastic reaction and formate exchange; the production of carbon dioxide and hydrogen is greatly inhibited by high concentrations of phosphate. Formate exchange requires a divalent metal ion and is stimulated by reducing agents and an atmosphere of hydrogen. Inhibition by p-chloromercuribenzoate, Zn(++), Cd(++), and arsenite indicates that sulfhydryl groups on the enzyme are involved in the reaction; the inhibition by arsenite and Cd(++) may be relieved by 2,3-dimercaptopropanol, suggesting that vicinal dithiols may be required. Inhibition by hypophosphite may reflect a competition with formate for a site on the enzyme. At an alkaline pH, alpha-ketobutyrate is degraded to propionate and formate, whereas alpha-ketoglutarate is fermented to succinate, propionate, carbon dioxide, hydrogen, and formate. Formate is exchanged into the carboxyl groups of alpha-ketobutyrate and alpha-ketoglutarate under these conditions. Only traces of alpha-ketovalerate and alpha-ketoisovalerate are fermented at an alkaline pH and the exchange of formate into these compounds is very low.The addition of viologen dyes under the conditions used for formate exchange causes a reduction of pyruvate, alpha-ketobutyrate, alpha-ketovalerate, and alpha-ketoisovalerate to the corresponding alpha-hydroxy acids.
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Affiliation(s)
- N G McCormick
- Department of Microbiology, University of Washington, Seattle, Washington
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WOOLFOLK CA, WHITELEY HR. Reduction of inorganic compounds with molecular hydrogen by Micrococcus lactilyticus. I. Stoichiometry with compounds of arsenic, selenium, tellurium, transition and other elements. J Bacteriol 1998; 84:647-58. [PMID: 14001842 PMCID: PMC277940 DOI: 10.1128/jb.84.4.647-658.1962] [Citation(s) in RCA: 136] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Woolfolk, C. A. (University of Washington, Seattle) and H. R. Whiteley. Reduction of inorganic compounds with molecular hydrogen by Micrococcus lactilyticus. I. Stoichiometry with compounds of arsenic, selenium, tellurium, transition and other elements. J. Bacteriol. 84:647-658. 1962.-Extracts of Micrococcus lactilyticus (Veillonella alcalescens) oxidize molecular hydrogen at the expense of certain compounds of arsenic, bismuth, selenium, tellurium, lead, thallium, vanadium, manganese, iron, copper, molybdenum, tungsten, osmium, ruthenium, gold, silver, and uranium, as well as molecular oxygen. Chemical and manometric data indicate that the following reductions are essentially quantitative: arsenate to arsenite, pentavalent and trivalent bismuth to the free element, selenite via elemental selenium to selenide, tellurate and tellurite to tellurium, lead dioxide and manganese dioxide to the divalent state, ferric to ferrous iron, osmium tetroxide to osmate ion, osmium dioxide and trivalent osmium to the metal, uranyl uranium to the tetravalent state, vanadate to the level of vanadyl, and polymolybdate ions to molybdenum blues with an average valence for molybdenum of +5. The results of a study of certain other hydrogenase-containing bacteria with respect to their ability to carry out some of the same reactions are also presented.
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WOOLFOLK CA. Reduction of inorganic compounds with molecular hydrogen by Micrococcus lactilyticus. II. Stoichiometry with inorganic sulfur compounds. J Bacteriol 1998; 84:659-68. [PMID: 14001843 PMCID: PMC277941 DOI: 10.1128/jb.84.4.659-668.1962] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Woolfolk, C. A. (University of Washington, Seattle). Reduction of inorganic compounds with molecular hydrogen by Micrococcus lactilyticus. II. Stoichiometry with inorganic sulfur compounds. J. Bacteriol. 84:659-668. 1962.-Extracts of Micrococcus lactilyticus (Veillonella alcalescens) are capable of utilizing molecular hydrogen for the reduction of metabisulfite (pyrosulfite) to thiosulfate via dithionite as an intermediate. The first step of metabisulfite reduction (i.e., to dithionite) is reversible, and, when dithionite is added as a substrate, there is an evolution of molecular hydrogen accompanied by the formation of equilibrium concentrations of metabisulfite. Kinetic studies indicate that dithionite may be directly reduced to thiosulfate without the formation of sulfoxylate as an intermediate. Although tetrathionate is reduced to thiosulfate with an uptake of hydrogen, polythionates probably are not formed as intermediates in the reduction of metabisulfite to thiosulfate.
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VALENTINE RC, JACKSON RL, WOLFE RS. Role of ferredoxin in hydrogen metabolism of Micrococcus lactilyticus. Biochem Biophys Res Commun 1998; 7:453-6. [PMID: 13924344 DOI: 10.1016/0006-291x(62)90334-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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OSTER MO, WOOD NP. FORMATE--PYRUVATE EXCHANGE REACTION IN STREPTOCOCCUS FAECALIS. II. REACTION CONDITIONS FOR CELL EXTRACTS. J Bacteriol 1996; 87:104-13. [PMID: 14102842 PMCID: PMC276968 DOI: 10.1128/jb.87.1.104-113.1964] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oster, M. O. (A. & M. College of Texas, College Station), and N. P. Wood. Formate-pyruvate exchange reaction in Streptococcus faecalis. II. Reaction conditions for cell extracts. J. Bacteriol. 87:104-113. 1964.-In contrast to intact cells of Streptococcus faecalis, no stimulation of the formate-pyruvate exchange reaction was observed in cell extracts when yeast extract was added to the reaction mixture. A heated extract of Micrococcus lactilyticus, vitamin K(5), ferrous sulfate, and ferrous ammonium sulfate stimulated an active exchange by protecting the system from oxygen. Tetrahydrofolate, 2,3-dimercaptopropanol, and sodium sulfide provided partial protection, whereas ascorbate, glutathione, sodium hydrosulfite, ammonium sulfide, and sodium bisulfite gave insufficient protection or were inhibitory. Oxidation-reduction (O-R) indicators were not inhibitory and were used to estimate the O-R potentials of reaction mixtures. A potential at least as negative as -125 mv was estimated to be necessary to preserve or initiate formate-pyruvate exchange activity. The reaction operated over a narrow pH range when strict anaerobic conditions were not maintained but, when the system was suitably poised, the pH range was broader. The influence of high phosphate concentrations was less under strictly anaerobic conditions, and orthophosphate could be replaced by small amounts of pyrophosphate. Effect of temperature, time, and amount of extract is presented. Addition of reduced benzyl viologen and hydrogen-saturated palladium in the buffer during 8 hr of dialysis prevented inactivation of extracts. Recovery of activity could be obtained after ammonium sulfate treatment when a combination of palladium chloride, neutral red, and hydrogen bubbling were used.
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Abstract
Rogosa, M. (National Institute of Dental Research, U.S. Public Health Service, Bethesda, Md.), and Ferial S. Bishop. The genus Veillonella. II. Nutritional studies. J. Bacteriol. 87:574-580. 1964.-A medium is described for the study of the vitamin, hypoxanthine, putrescine, or cadaverine requirements of 86 Veillonella isolates from man, rabbit, rat, and hamster. No organism required riboflavine or folic acid for growth. Niacin and calcium pantothenate were often stimulatory, but in nearly all cases were dispensable. Biotin and p-aminobenzoic acid were frequently stimulatory and sometimes indispensable for continued growth. V. parvula (antigenic group VI) required pyridoxal and thiamine and did not require putrescine or cadaverine. V. alcalescens (antigenic group IV) required pyridoxal, generally required thiamine, and also required putrescine or cadaverine. Of the isolates, 25 from the rat and 3 from the hamster (antigenic group II) generally behaved like V. parvula, except that a putrescine or cadaverine requirement was often observed. Spermine, spermidine, and agmatine could not replace putrescine or cadaverine. Although succinate is metabolized by resting cells, the organisms could not grow with succinate as an energy source.
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Abstract
Valentine, R. C. (University of Illinois, Urbana) and R. S. Wolfe. Role of ferredoxin in the metabolism of molecular hydrogen. J. Bacteriol. 85:1114-1120. 1963.-The metabolism of molecular hydrogen by Clostridium pasteurianum, Micrococcus lactilyticus (Veillonella alcalescens), and several other anaerobic bacteria was studied. Oxidation of hydrogen, using several electron-accepting substrates including triphosphopyridine nucleotide, uric acid, xanthine, nitrite, and hydroxylamine, required ferredoxin in conjunction with hydrogenase. Evolution of hydrogen from pyruvate, alpha-ketoglutarate, hypoxanthine, and dithionite was mediated by ferredoxin. On the basis of these findings, a unitary hypothesis for biological hydrogen evolution is proposed in which ferredoxin plays a key role.
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Abstract
From a general standpoint, the formation of molecular hydrogen can be considered a device for disposal of electrons released in metabolic oxidations. We presume that this means of performing anaerobic oxidations is of ancient origin and that the hydrogen-evolving system of strict anaerobes represents a primitive form of cytochrome oxidase, which in aerobes effects the terminal step of respiration, namely the disposal of electrons by combination with molecular oxygen. We further assume that the original pattern of reactions leading to H(2) production has become modified in various ways (with respect to both mechanisms and functions) during the course of biochemical evolution, and we believe that this point of view suggests profitable approaches for clarifying a number of problems in the intermediary metabolism of microorganisms which produce or utilize H(2). Of special general importance in this connection is the basic problem of defining more precisely the fundamental elements in the regulatory control of anaerobic energy metabolism. Among the more specific aspects awaiting further elucidation are: the relations between formation of H(2) and use of H(2) as a primary reductant for biosynthetic purposes; the various forms of direct and indirect interactions between hydrogenase and N(2) reduction systems; and the transitional stages between anaerobic and aerobic energy-metabolism patterns of facultative organisms.
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Bollag J, Kaiser J. The transformation of heterocyclic aromatic compounds and their derivatives under anaerobic conditions. ACTA ACUST UNITED AC 1991. [DOI: 10.1080/10643389109388419] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Abstract
Based on the finding that Methanococcus vannielii can employ any of several purines as the sole nitrogen source, an investigation was undertaken to elucidate the pathways of purine metabolism in this organism. Cell-free extracts of M. vannielii converted guanine, uric acid, and hypoxanthine to xanthine and also formed guanine from guanine nucleotides or guanosine. The conversions of guanine and uric acid to xanthine appear to occur by pathways similar to those described in clostridia. The conversion of hypoxanthine to xanthine, however, is different than that described for Clostridium cylindrosporum and C. acidiurici, but is similar to that of C. purinolyticum, and apparently involves the direct oxidation of hypoxanthine to xanthine.
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DeMoll E, Tsai L. Utilization of purines or pyrimidines as the sole nitrogen source by Methanococcus vannielii. J Bacteriol 1986; 167:681-4. [PMID: 3090020 PMCID: PMC212943 DOI: 10.1128/jb.167.2.681-684.1986] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Studies of biosynthetic pathways with purines as substrates showed that Methanococcus vannielii was capable of degrading xanthine to an extent that several of the carbon atoms were converted to CO2. Experiments to determine whether this catabolic activity could satisfy the entire nitrogen requirement for growth of M. vannielii showed that urate, guanine, xanthine, or hypoxanthine, but not adenine, could serve as the sole nitrogen source. The pyrimidines uracil and thymine, but not cytosine, were also degraded to serve as a source of nitrogen. Although urate was extensively degraded, it did not replace formate as the sole carbon source for growth of M. vannielii under the conditions imposed.
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Eubacterium angustum sp. nov., a Gram-positive anaerobic, non-sporeforming, obligate purine fermenting organism. Arch Microbiol 1984. [DOI: 10.1007/bf00409763] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Dürre P, Andreesen JR. Anaerobic degradation of uric acid via pyrimidine derivatives by selenium-starved cells of Clostridium purinolyticum. Arch Microbiol 1982; 131:255-60. [PMID: 6808963 DOI: 10.1007/bf00405889] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Clostridium purinolyticum decomposed uric acid via pyrimidine derivatives under selenium starvation conditions. Products were acetate, formate, glycine, ammonia, and CO2. 4,5-Diaminouracil could be identified as an intermediate after converting the labile substance into 6,7-dimethyllumazine. The breakdown of uric acid was inhibited by EDTA. High-pressure liquid chromatography methods have been developed for the simultaneous determination of uric acid, 4,5-diaminouracil, and 6,7-dimethyllumazine. The significance of the new pathway is discussed.
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Potrikus CJ, Breznak JA. Anaerobic Degradation of Uric Acid by Gut Bacteria of Termites. Appl Environ Microbiol 1980; 40:125-32. [PMID: 16345588 PMCID: PMC291535 DOI: 10.1128/aem.40.1.125-132.1980] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A study was done of anaerobic degradation of uric acid (UA) by representative strains of uricolytic bacteria isolated from guts of
Reticulitermes flavipes
termites.
Streptococcus
strain UAD-1 degraded UA incompletely, secreting a fluorescent compound into the medium, unless formate (or a formicogenic compound) was present as a cosubstrate. Formate functioned as a reductant, and its oxidation to CO
2
by formate dehydrogenase provided 2H
+
+ 2e
−
needed to drive uricolysis to completion. Uricolysis by
Streptococcus
UAD-1 thus corresponded to the following equation: 1UA + 1formate → 4CO
2
+ 1acetate + 4NH
3
. Urea did not appear to be an intermediate in CO
2
and NH
3
formation during uricolysis by strain UAD-1. Formate dehydrogenase and uricolytic activities of strain UAD-1 were inducible by growth of cells on UA.
Bacteroides termitidis
strain UAD-50 degraded UA as follows: 1UA → 3.5 CO
2
+ 0.75acetate + 4NH
3
. Exogenous formate was neither required for nor stimulatory to uricolysis by strain UAD-50. Studies of UA catabolism by
Citrobacter
strains were limited, because only small amounts of UA were metabolized by cells in liquid medium. Uricolytic activity of such bacteria in situ could be important to the carbon, nitrogen, and energy economy of
R. flavipes
.
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Affiliation(s)
- C J Potrikus
- Department of Microbiology and Public Health, Michigan State University, East Lansing, Michigan 48824
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Wagner R, Andreesen JR. Selenium requirement for active xanthine dehydrogenase from Clostridium acidiurici and Clostridium cylindrosporum. Arch Microbiol 1979; 121:255-60. [PMID: 518233 DOI: 10.1007/bf00425064] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The xanthine dehydrogenase of Clostridium acidiurici and C. cylindrosporum was assayed with methyl viologen as acceptor. In C. acidiurici the basal activity level was about 0.3 mumol/min x mg of protein. Cells grown on uric acid in the presence of 10(-7) M selenite showed a 14-fold increase in xanthine dehydrogenase activity, which decreased with higher selenite concentrations (10(-5) M). The supplementation with 10(-7) M molybdate or tungstate was without effect. High concentrations of tungstate decreased the xanthine dehydrogenase if selenite was also present. In comparison, high concentrations of molybdate affected only a small decrease in activity level at the optimal concentration for selenite and relieved to some degree the inhibitory effect of 10(-5) M selenite. With hypoxanthine and xanthine as substrates for growth again only the addition of selenite was necessary to show a similar increase in xanthine dehydrogenase activity. C. acidiurici could be grown in a mineral medium. Both xanthine dehydrogenase and formate dehydrogenase exhibited the highest level of activity if selenite and tungstate were present in that medium. In C. cyclindrosporum the basal activity level of xanthine dehydrogenase was about 0.95 mumol/min x mg of protein. The addition of 10(-7) M selenite to the growth medium increased the activity level about 3-fold, but the highest level (3.7 U/mg) was reached if 10(-7) M molybdate was also added. The presence of tungstate resulted in a decreased enzyme activity.
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Marr JJ, Berens RL, Nelson DJ. Purine metabolism in Leishmania donovani and Leishmania braziliensis. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 544:360-71. [PMID: 719006 DOI: 10.1016/0304-4165(78)90104-6] [Citation(s) in RCA: 173] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We have studied purine metabolism in the culture forms of Leishmania donovani and Leishmania braziliensis. These organisms are incapable of synthesizing purines de novo from glycine, serine, or formate and require an exogenous purine for growth. This requirement is better satisfied by adenosine or hypoxanthine than by guanosine. Both adenine and inosine are converted to a common intermediate, hypoxanthine, before transformation to nucleotides. This is due to the activity of an adenine aminohydrolase ((EC 3.5.4.2), a rather unusual finding in a eukaryotic cell. There is a preferential synthesis of adenine nucleotides, even when guanine or xanthine are used as precursors. The pathways of purine nucleotide interconversions in these Leishmania resemble those found in mammalian cells except for the absence of de novo purine biosynthesis and the presence of an adenine-deaminating activiting.
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Kidder GW, Dewey VC, Nolan LL. Adenine deaminase of a eukaryotic animal cell, Crithidia fasciculata. Arch Biochem Biophys 1977; 183:7-12. [PMID: 20850 DOI: 10.1016/0003-9861(77)90412-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Woolfolk CA, Downard JS. Distribution of xanthine oxidase and xanthine dehydrogenase specificity types among bacteria. J Bacteriol 1977; 130:1175-91. [PMID: 863854 PMCID: PMC235341 DOI: 10.1128/jb.130.3.1175-1191.1977] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A diverse collection of xanthine-metabolizing bacteria was examined for xanthine-, 1-methylxanthine-, and 3-methylxanthine-oxidizing activity. Both particulate and soluble fractions of extracts from aerobically grown gram-negative bacteria exhibited oxidation of all three substrates; however, when facultative gram-negative bacteria were grown anaerobically, low particulate and 3-methylxanthine activities were detected. Gram-positive and obligately anaerobic bacteria showed no particulate activity or 3-methylxanthine oxidation. Substrate specificity studies indicate two types of enzyme distributed among the bacteria along taxonomic lines, although other features indicate diversity of the enzyme within these two major groups. The soluble and particulate enzymes from Pseudomonas putida and the enzyme from Arthrobacter S-2 were examined as type examples with a series of purine and analogues differing in the number and position of oxygen groups. Each preparation was active with a variety of compounds, but the compounds and position attacked by each enzyme was different, both from the other enzymes examined and from previously investigated enzymes. The soluble enzyme from Pseudomonas was inhibited in a competitive manner by uric acid, whereas the Arthrobacter enzyme was not. This was correlated with the ability of Pseudomonas, but not Arthrobacter, to incorporate radioactivity from [2-14C]uric acid into cellular material.
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Vogels GD, Van der Drift C. Degradation of purines and pyrimidines by microorganisms. BACTERIOLOGICAL REVIEWS 1976; 40:403-68. [PMID: 786256 PMCID: PMC413962 DOI: 10.1128/br.40.2.403-468.1976] [Citation(s) in RCA: 253] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Abstract
Seven Bacillus strains including one of the original Bacillus fastidiosus strains of Den Dooren de Jong could grow on urate, allantoin, and, except one, on allantoate. No growth could be detected on adenine, guanine, hypoxanthine, xanthine, and on degradation products of allantoate. Some strains grew very slowly in complex media. The metabolic pathway from urate to glyoxylate involved uricase, S(+)-allantoinase, allantoate amidohydrolase, S(-)-ureidoglycolase, and, in some strains, urease.
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Bentley CM, Dawes EA. The energy-yielding reactions of Peptococcus prévotii, their behaviour on starvation and the role and regulation of threonine dehydratase. Arch Microbiol 1974; 100:363-87. [PMID: 4155937 DOI: 10.1007/bf00446329] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Dalton H, Zubieta J. Ferredoxin from Veillonella alcalescens. BIOCHIMICA ET BIOPHYSICA ACTA 1973; 322:133-40. [PMID: 4355309 DOI: 10.1016/0005-2795(73)90183-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Abstract
Three strains of Veillonella, representing two species, were unable to utilize carbohydrates as energy sources for growth. Ribose, however, was utilized biosynthetically by all three strains. Exponentially growing cultures removed (14)C-ribose from the growth medium and retained radioactivity throughout the growth cycle. The kinetics of removal of ribose from the growth medium was found to depend on the initial ribose concentration. Uptake by resting cells was found to require active metabolism, was greatly stimulated by the presence of an energy source, and was insensitive to the presence of other pentoses. Fractionation of cells showed that the ribose was used for synthesis of acid-precipitable material, with as much as 92% of the radioactivity being found in the nucleic acid fraction. The intracellular distribution of ribose radioactivity did not change during growth after uptake was completed.
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Smith ST, Rajagopalan K, Handler P. Purification and Properties of Xanthine Dehydrogenase from Micrococcus lactilyticus. J Biol Chem 1967. [DOI: 10.1016/s0021-9258(18)95785-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Abstract
Ackrell, B. A. C. (University of Hawaii, Honolulu), R. N. Asato, and H. F. Mower. Multiple forms of bacterial hydrogenases. J. Bacteriol. 92:828-838. 1966.-Extracts of certain bacterial species have been shown by disc electrophoresis on polyacrylamide gel to contain multiple hydrogenase systems. The hydrogenase enzymes comprising these systems have different electrophoretic mobilities and produce a band pattern that is unique for each bacterial species. Of 20 bacterial species known to possess hydrogenase activity and which were examined by this technique, only the activities of Clostridium tetanomorphum and C. thermosaccharolyticum could be attributed, at pH 8.3, to a single hydrogenase enzyme. This multiplicity of hydrogenase forms was found both in bacteria which contain mostly soluble hydrogenases and in those where the hydrogenase is predominantly associated with particulate material. When solubilization of this particulate material could be effected, at least two solubilized hydrogenases were released, and, of these, one would have the same electrophoretic properties (i.e., R(F)) as one of the soluble hydrogenases already present in small amounts within the cell. Different growth conditions for various types of bacteria, such as the nitrogen source, the degree of aeration, and photosynthetic versus aerobic growth in the dark, as well as the conditions under which the cells were stored, markedly affected the hydrogenase activity of the cells, but not their hydrogenase band pattern. The disc electrophoresis technique proved to be 10 times more sensitive than the manometric technique in detecting hydrogenase activity.
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Whiteley H, Osborn M, Huennekens F. Purification and Properties of the Formate-activating Enzyme from Micrococcus aerogenes. J Biol Chem 1959. [DOI: 10.1016/s0021-9258(18)70046-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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VAN NIEL CB. Introductory remarks on the comparative biochemistry of micro-organisms. JOURNAL OF CELLULAR PHYSIOLOGY. SUPPLEMENT 1953; 41:11-38. [PMID: 13052628 DOI: 10.1002/jcp.1030410404] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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LYONS DC. The present concept of cellular and environmental influences on mouth-inhabiting acidogenic bacteria; a review. ORAL SURGERY, ORAL MEDICINE, AND ORAL PATHOLOGY 1952; 5:1104-18. [PMID: 13003146 DOI: 10.1016/0030-4220(52)90214-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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HARE R, WILDY P, BILLETT FS, TWORT DN. The anaerobic cocci: gas formation, fermentation reactions, sensitivity to antibiotics and sulphonamides; classification. J Hyg (Lond) 1952; 50:295-319. [PMID: 12990792 PMCID: PMC2235172 DOI: 10.1017/s0022172400019628] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
1. A total of ninety-nine strains of anaerobic cocci from human beings have been studied and six groups demarcated on the basis of gas formation and fermentation reactions.2.Gas formation by strains of group I is due to fermentation of glucose, laevu-lose or maltose, with a sulphur compound as an activator and with the production of gas rich in CO2.3.Gas formation by strains of groups II, III and V is due to fermentation of different organic acids, sulphur not being required, and accompanied by the production of gases containing a high proportion of H2.4.Two groups, IV and VI, do not from gas, but the latter has marked fermentation abilities.There is correlation between microscopic apperances, probable pathogenicity, sensitivity to antibiotics and sulphonamides and the groups demarcated.Ninety-two out of ninety-nine strains isolated from human beings could be placed in one or other group.We are greatly indebted to Dr H. J. Parish of the Wellcome Research Laboratories for a sample of Polymyxin E, to Prof. L. Young for much assistance and advice and to those colleagues, particularly Dr R. M. Caiman of Queen Charlotte's Hospital, who sent us strains.
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