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Lahham M, Jha S, Goj D, Macheroux P, Wallner S. The family of sarcosine oxidases: Same reaction, different products. Arch Biochem Biophys 2021; 704:108868. [PMID: 33812916 DOI: 10.1016/j.abb.2021.108868] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 12/11/2022]
Abstract
The subfamily of sarcosine oxidase is a set of enzymes within the larger family of amine oxidases. It is ubiquitously distributed among different kingdoms of life. The member enzymes catalyze the oxidization of an N-methyl amine bond of amino acids to yield unstable imine species that undergo subsequent spontaneous non-enzymatic reactions, forming an array of different products. These products range from demethylated simple species to complex alkaloids. The enzymes belonging to the sarcosine oxidase family, namely, monomeric and heterotetrameric sarcosine oxidase, l-pipecolate oxidase, N-methyltryptophan oxidase, NikD, l-proline dehydrogenase, FsqB, fructosamine oxidase and saccharopine oxidase have unique features differentiating them from other amine oxidases. This review highlights the key attributes of the sarcosine oxidase family enzymes, in terms of their substrate binding motif, type of oxidation reaction mediated and FAD regeneration, to define the boundaries of this group and demarcate these enzymes from other amine oxidase families.
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Affiliation(s)
- Majd Lahham
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria; Department of Biochemistry and Microbiology, Aljazeera Private University, Ghabagheb, Syria
| | - Shalinee Jha
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Dominic Goj
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Silvia Wallner
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria.
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Noell SE, Giovannoni SJ. SAR11 bacteria have a high affinity and multifunctional glycine betaine transporter. Environ Microbiol 2019; 21:2559-2575. [PMID: 31090982 DOI: 10.1111/1462-2920.14649] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/06/2019] [Indexed: 11/29/2022]
Abstract
Marine bacterioplankton face stiff competition for limited nutrient resources. SAR11, a ubiquitous clade of very small and highly abundant Alphaproteobacteria, are known to devote much of their energy to synthesizing ATP-binding cassette periplasmic proteins that bind substrates. We hypothesized that their small size and relatively large periplasmic space might enable them to outcompete other bacterioplankton for nutrients. Using uptake experiments with 14 C-glycine betaine, we discovered that two strains of SAR11, Candidatus Pelagibacter sp. HTCC7211 and Cand. P. ubique HTCC1062, have extraordinarily high affinity for glycine betaine (GBT), with half-saturation (K s ) values around 1 nM and specific affinity values between 8 and 14 L mg cell-1 h-1 . Competitive inhibition studies indicated that the GBT transporters in these strains are multifunctional, transporting multiple substrates in addition to GBT. Both strains could use most of the transported compounds for metabolism and ATP production. Our findings indicate that Pelagibacter cells are primarily responsible for the high affinity and multifunctional GBT uptake systems observed in seawater. Maximization of whole-cell affinities may enable these organisms to compete effectively for nutrients during periods when the gross transport capacity of the heterotrophic plankton community exceeds the supply, depressing ambient concentrations.
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Affiliation(s)
- Stephen E Noell
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
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Mihalik SJ, McGuinness M, Watkins PA. Purification and characterization of peroxisomal L-pipecolic acid oxidase from monkey liver. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(19)67723-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Der Garabedian PA, Vermeersch JJ. Lysine degradation in Candida. Characterization and probable role of L-norleucine-leucine, 4-aminobutyrate and delta-aminovalerate:2-oxoglutarate aminotransferases. Biochimie 1989; 71:497-503. [PMID: 2503054 DOI: 10.1016/0300-9084(89)90180-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Three enzymes partially purified that catalyze respectively the transamination of L-norleucine, 4-aminobutyrate and delta-aminovalerate with alpha-ketoglutarate as aminoacceptor were characterized and isolated from L-lysine adapted cell of Candida guilliermondii var. membranaefaciens. The transaminases have a maximum activity in the pH range of 7.8-8.5 and at 55 degrees C, 45 degrees C and 40 degrees C respectively. alpha-Ketoglutarate and to a lesser extent pyridoxal-5'-phosphate were effective protecting agents against rise in temperature. The enzymes exhibit absorption maximum at 280 nm, 330 nm and 410 nm. The fact that L-norleucine-leucine aminotransferase, 4-aminobutyrate aminotransferase and delta-aminovalerate aminotransferase are strongly induced by growing the yeast Candida on L-lysine suggests new hypothetic pathways for the catabolism of L-lysine where the main substrate of each aminotransferase could be an intermediary metabolite.
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Affiliation(s)
- P A Der Garabedian
- Laboratoire d'Enzymologie, Université Pierre et Marie Curie, UER 58, Paris, France
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Der Garabedian PA, Lotti AM, Vermeersch JJ. 4-Aminobutyrate:2-oxoglutarate aminotransferase from Candida. Purification and properties. EUROPEAN JOURNAL OF BIOCHEMISTRY 1986; 156:589-96. [PMID: 3699025 DOI: 10.1111/j.1432-1033.1986.tb09618.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
An enzyme which catalyzes the transamination of 4-aminobutyrate with 2-oxoglutarate was purified 588-fold to homogeneity from Candida guilliermondii var. membranaefaciens, grown with 4-aminobutyrate as sole source of nitrogen. An apparent relative molecular mass of 107,000 was estimated by gel filtration. The enzyme was found to be a dimer made up of two subunits identical in molecular mass (Mr 55,000). The enzyme has a maximum activity in the pH range 7.8-8.0 and a temperature optimum of 45 degrees C. 2-Oxoglutarate protects the enzyme from heat inactivation better than pyridoxal 5'-phosphate. The absorption spectrum of the enzyme exhibits two maxima at 412 nm and 330 nm. The purified enzyme catalyzes the transamination of omega-amino acids; 4-aminobutyrate is the best amino donor and low activity is observed with beta-alanine. The Michaelis constants are 1.5 mM for 2-oxoglutarate and 2.3 mM for 4-aminobutyrate. Several amino acids, such as alpha,beta-alanine and 2-aminobutyrate, are inhibitors (Ki = 38.7 mM, Ki = 35.5 mM and Ki = 33.2 mM respectively). Propionic and butyric acids are also inhibitors (Ki = 3 mM and Ki = 2 mM).
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Chang YF, Charles AK, Tilkin RB. Assay of delta 1-piperideine-2-carboxylate and synthesis of L-[14C]pipecolate from DL-[14C]pipecolate. Anal Biochem 1982; 125:376-85. [PMID: 7181096 DOI: 10.1016/0003-2697(82)90019-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Abstract
Pseudomonas putida metabolizes D-lysine to delta 1-piperideine-2-carboxylate and L-pipecolate. The second step of this catabolic pathway is catalyzed by delta 1-piperideine-2-carboxylate reductase. This enzyme was isolated and purified from cells grown on DL-lysine as substrate. The enzyme was very unstable, resulting in low recovery of activity and low purity after a six-step purification procedure. The enzyme had a pH optimum of 8.0 to 8.3. The Km values for delta 1-piperideine-2-carboxylate and NADPH were 0.23 and 0.13 mM, respectively. NADPH at concentrations above 0.15 mM was inhibitory to the enzyme. Delta 1-pyrroline-5-carboxylate, pyroglutamate, and NADH were poor substrates or coenzyme for delta 1-piperideine-2-carboxylate reductase. The enzyme reaction from delta 1-piperideine-2-carboxylate to L-pipecolate was irreversible. EDTA, sodium pyrophosphate, and dithiothreitol at concentrations of 1 mM protected the enzyme during storage. The enzyme was inhibited almost totally by Zn2+, Mn2+, Hg2+ Co2+, and p-chloromercuribenzoate at concentrations of 0.1 mM. The enzyme had a molecular weight of about 200,000. Both D-lysine and L-lysine were good inducers for the enzyme. Neither delta1-piperideine-2-carboxylate nor L-pipecolate was an effective inducer for the enzyme. P. putida cells grew on D-lysine only after a 5- to 8-h lag, which could be abolished by adding a supplement of 0.01% alpha-ketoglutarate or other readily metabolizable compounds. Such a supplement also converted the noncoordinate induction of this enzyme and pipecolate oxidase, both of the D-lysine pathway, to coordinacy. However, this effect was not observed if the enzyme pair was from different pathways of lysine metabolism in this organism (i.e., the D- and L-lysine pathways).
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Dancis J, Hutzler J. Comparative rates of metabolism of pipecolic acid in several animal species. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. B, COMPARATIVE BIOCHEMISTRY 1982; 73:1011-2. [PMID: 6817963 DOI: 10.1016/0305-0491(82)90351-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
1. The rate of metabolism of pipecolic acid, measured in liver and kidney, varied 1000 fold among 10 animal species. Degradation of L-pipecolic acid by kidney in rat and mouse was 0.11 and 0.31 pmoles/min/mg protein, respectively; in monkey and human. 3.0 and 6.5; in guinea-pig and rabbit 101 and 106. 2. Activity with D-pipecolic acid was consistently 50-60% higher than the L-isomer except in the rabbit. 3. Degradation of L-lysine presumably through the saccharopine-alpha-aminoadipic acid pathway, was effective in all species, contrasting with the variable performance in the pipecolic acid-alpha-aminoadipic acid pathway.
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Dancis J, Hutzler J. The metabolism of D- and L-pipecolic acid in the rabbit and rat. BIOCHIMICA ET BIOPHYSICA ACTA 1981; 675:411-5. [PMID: 6791703 DOI: 10.1016/0304-4165(81)90034-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The metabolism of D- and L-pipecolic acid has been investigated in rabbits and rats. A rapid evolution of 14CO2 followed the injection of either D- or L-pipe[6-14C]colic acid into rabbits. Rabbit kidney slices degraded to CO2 both isomers of lysine and of pipecolic acid. Rabbit liver was effective with only the L-isomers. In the rat, very little of injected L-pipecolic acid was catabolized to CO2, and large amounts were excreted unchanged into the urine, L-Lysine was efficiently metabolized to CO2 by rat liver and kidney slices but not D-lysine or either isomer of pipecolic acid. Rat kidney converted D-lysine to L-pipecolic acid. The L-isomer was identified by co-precipitation of the radioactive product with authentic compounds.
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Jensen RA, Calhoun DH. Intracellular roles of microbial aminotransferases: overlap enzymes across different biochemical pathways. Crit Rev Microbiol 1981; 8:229-66. [PMID: 7009061 DOI: 10.3109/10408418109085080] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Kopchick JJ, Hartline RA. alpha-Hydroxyglutarate as an intermediate in the catabolism of alpha-aminoadipate by Pseudomonas putida. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(18)50753-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Vanderbilt AS, Gaby NS, Rodwell VW. Intermediates and enzymes between alpha-ketoarginine and gamma-guanidinobutyrate in the L-arginine catabolic pathway of Pseudomonas putida. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41184-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Pekala PH, Perfetti T, Hartline RA. Physiological basis for preferential uptake of D-alpha-aminoadipate over the L-isomer by Alcaligenes denitrificans. BIOCHIMICA ET BIOPHYSICA ACTA 1975; 394:65-75. [PMID: 1138928 DOI: 10.1016/0005-2736(75)90205-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Alcaligenes denitrificans, pre-incubated with D-alpha-aminoadipate and assayed for L-isomer uptake without removal of extracellular D-isomer, exhibits a reduced rate of uptake and a reduced level at which steady state is achieved. During D- or L-isomer uptake, intracellular alpha-aminoadipate is exclusively the L-configuration. These data are consistent with an intracellular, mediated reduction in L-isomer uptake as the physiological basis for preferential D-alpha-aminoadipate uptake by A. denitrificans growing on racemic alpha-aminoadipate. Translocated D-alpha-aminoadipate is rapidly metabolized to form an L-isomer pool which subsequently reduces the rate of L-isomer uptake and the level at which steady state occurs resulting in a preferred D-isomer uptake. Competitive inhibition of L-alpha-aminoadipate uptake by the D-isomer or a difference in the maximum rates of uptate uptake is an inducible process expressed only in the presence of that compound and while uptake of L-alpha-animoadipate is also inducible there is a low rate of constitutive uptake. While L-alpha-aminoadipate uptake occurs against a concentration gradient, uptake of the D-isomer is not against a gradient. D- and L-isomer uptake are active processes since both are inhibited by azide, cyanide and 2,4-dinitrophenol.
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Chang YF, Adams E. D-lysine catabolic pathway in Pseudomonas putida: interrelations with L-lysine catabolism. J Bacteriol 1974; 117:753-64. [PMID: 4359655 PMCID: PMC285570 DOI: 10.1128/jb.117.2.753-764.1974] [Citation(s) in RCA: 44] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The isolation of several mutant strains blocked in l-lysine degradation has permitted an assessment of the physiological significance of enzymatic reactions related to lysine metabolism in Pseudomonas putida. Additional studies with intact cells involved labeling of metabolic intermediates from radioactive l- or d-lysine, and patterns of enzyme induction in both wild-type and mutant strains. These studies lead to the conclusions that from l-lysine, the obligatory pathway is via delta-aminovaleramide, delta-aminovalerate, glutaric semialdehyde, and glutarate, and that no alternative pathways from l-lysine exist in our strain. A distinct pathway from d-lysine proceeds via Delta(1)-piperideine-2-carboxylate, l-pipecolate, and Delta(1)-piperideine-6-carboxylate (alpha-aminoadipic semialdehyde). The two pathways are independent in the sense that certain mutants, unable to grow on l-lysine, grow at wild-type rates of d-lysine, utilizing the same intermediates as the wild type, as inferred from labeling studies. This finding implies that lysine racemase in our strain, while detectable in cell extracts, is not physiologically functional in intact cells at a rate that would permit growth of mutants blocked in the l-lysine pathway. Pipecolate oxidase, a d-lysine-related enzyme, is induced by d-lysine and less efficiently by l-lysine. Aminooxyacetate virtually abolishes the inducing activity of l-lysine for this enzyme, suggesting that lysine racemase, although functionally inactive for growth purposes, may still have regulatory significance in permitting cross-induction of d-lysine-related enzymes by l-lysine, and vice versa. This finding suggests a mechanism in bacteria for maintaining regulatory patterns in pathways that may have lost their capacity to support growth. In addition, enzymatic studies are reported which implicate Delta(1)-piperideine-2-carboxylate reductase as an early step in the d-lysine pathway.
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Pekala P, Hartline RA. Isolation of radioactive D- and L-alpha-aminoadipate of high specific activity by selective bacterial metabolism. Anal Biochem 1973; 55:411-9. [PMID: 4750683 DOI: 10.1016/0003-2697(73)90131-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Jacobsen GB, Rodwell VW. A Bacillus Ribonucleic Acid Phosphodiesterase with Associated 5′-Nucleotidase Activity. J Biol Chem 1972. [DOI: 10.1016/s0021-9258(19)44830-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Perfetti R, Campbell RJ, Titus J, Hartline RA. Catabolism of Pipecolate to Glutamate in Pseudomonas putida. J Biol Chem 1972. [DOI: 10.1016/s0021-9258(19)45142-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Hartline RA, Rodwell VW. Metabolism of pipecolic acid in a Pseudomonas species. VI. Precursors of glutamate. Arch Biochem Biophys 1971; 142:32-9. [PMID: 5545486 DOI: 10.1016/0003-9861(71)90256-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Guirguis MA, Vancura V. The oxidation of pipecolic acid in preincubated soils. Folia Microbiol (Praha) 1970; 15:459-67. [PMID: 5515455 DOI: 10.1007/bf02880190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Bensch WR, Rodwell VW. Purification and Properties of 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase from Pseudomonas. J Biol Chem 1970. [DOI: 10.1016/s0021-9258(18)62916-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Abstract
Oxidation of d-alpha-hydroxyglutarate to alpha-ketoglutarate is catalyzed by d-alpha-hydroxyglutarate oxidoreductase, an inducible membrane-bound enzyme of the electron transport particle [ETP; a comminuted cytoplasmic membrane preparation with enzymic properties and chemical composition resembling beef heart mitochondrial ETP (1)] of Pseudomonas putida P2 (P2-ETP). Treatment of P2-ETP with a nonionic detergent yields a preparation with the sedimentation characteristics of a soluble enzyme, but which retains an intact electron transport chain. Oxygen acts solely as a terminal electron acceptor and may be replaced by ferricyanide, 2,6-dichlorophenol indophenol, or mammalian cytochrome c. The oxidoreductase is specific for the d-isomer (K(m) = 4.0 x 10(-4)m for dl-alpha-hydroxyglutarate) and is distinct both from l- and d-malate dehydrogenases. Spectral studies suggest that the carrier sequence is substrate --> flavine or nonheme iron --> cyt b --> [cyt c] --> oxygen.
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Lindstedt S, Lindstedt G, Mitoma C. Studies on the metabolism of lysine and 5-hydroxylysine. Arch Biochem Biophys 1967; 119:336-46. [PMID: 6052426 DOI: 10.1016/0003-9861(67)90462-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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