Novel Amidohydrolytic Reactions in Oxidative Pyrimidine Metabolism: Analysis of the Barbiturase Reaction and Discovery of a Novel Enzyme, Ureidomalonase

Soong, Chee-Leong; Ogawa, Jun; Shimizu, Sakayu

doi:10.1006/bbrc.2001.5356

Cited by 27 publications

(26 citation statements)

References 9 publications

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“…Second, urease activity was detected when cells were grown on cyanuric acid (1,5,10). Third, metabolism of compounds structurally analogous to cyanuric acid, such as barbituric acid, proceeds via urea (37). Fourth, mutants blocked in complete cyanuric acid metabolism accumulated an organic product that, after workup and chromatography, was identified as urea (10).…”

Section: Discussionmentioning

confidence: 99%

Allophanate Hydrolase, Not Urease, Functions in Bacterial Cyanuric Acid Metabolism

Cheng

Shapir

Sadowsky

et al. 2005

Appl Environ Microbiol

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Growth substrates containing an s-triazine ring are typically metabolized by bacteria to liberate 3 mol of ammonia via the intermediate cyanuric acid. Over a 25-year period, a number of original research papers and reviews have stated that cyanuric acid is metabolized in two steps to the 2-nitrogen intermediate urea. In the present study, allophanate, not urea, was shown to be the 2-nitrogen intermediate in cyanuric acid metabolism in all the bacteria examined. Six different experimental results supported this conclusion: (i) synthetic allophanate was shown to readily decarboxylate to form urea under acidic extraction and chromatography conditions used in previous studies; (ii) alkaline extraction methods were used to stabilize and detect allophanate in bacteria actively metabolizing cyanuric acid; (iii) the kinetic course of allophanate formation and disappearance was consistent with its being an intermediate in cyanuric acid metabolism, and no urea was observed in those experiments; (iv) protein extracts from cells grown on cyanuric acid contained allophanate hydrolase activity; (v) genes encoding the enzymes AtzE and AtzF, which produce and hydrolyze allophanate, respectively, were found in several cyanuric acidmetabolizing bacteria; and (vi) TrzF, an AtzF homolog found in Enterobacter cloacae strain 99, was cloned, expressed in Escherichia coli, and shown to have allophanate hydrolase activity. In addition, we have observed that there are a large number of genes homologous to atzF and trzF distributed in phylogenetically distinct bacteria. In total, the data indicate that s-triazine metabolism in a broad class of bacteria proceeds through allophanate via allophanate hydrolase, rather than through urea using urease.

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Section: Discussionmentioning

confidence: 99%

Allophanate Hydrolase, Not Urease, Functions in Bacterial Cyanuric Acid Metabolism

Cheng

Shapir

Sadowsky

et al. 2005

Appl Environ Microbiol

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“…AtzD and TrzD were identified as being homologous, but they were not connected to any other proteins or protein families in those studies (12,20,26). Barbiturase was first purified to homogeneity from Rhodococcus erythropolis JCM3132 and shown to catalyze the hydrolytic opening of barbituric acid, an intermediate in the oxidative pyrimidine catabolic pathway (34,35). Those studies reported that barbiturase was homologous to AtzD and TrzD (34,35).…”

mentioning

confidence: 99%

“…Barbiturase was first purified to homogeneity from Rhodococcus erythropolis JCM3132 and shown to catalyze the hydrolytic opening of barbituric acid, an intermediate in the oxidative pyrimidine catabolic pathway (34,35). Those studies reported that barbiturase was homologous to AtzD and TrzD (34,35). One of the reports found zinc to be present in the enzyme preparations and thus proposed that barbiturase was homologous to members of the amidohydrolase superfamily (35).…”

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confidence: 99%

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Defining Sequence Space and Reaction Products within the Cyanuric Acid Hydrolase (AtzD)/Barbiturase Protein Family

Seffernick

Erickson

Cameron

et al. 2012

Journal of Bacteriology

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“…The URC pathway is found in several fungi and bacteria, while the oxidative and Rut pathways have been found in only a few bacteria (6)(7)(8)(9). The reductive pathway starts with the reduction of uracil to dihydrouracil by a dihydropyrimidine dehydrogenase (EC 1.3.1.2), an enzyme which has not been found in any fungi.…”

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confidence: 99%

Global Expression Analysis of the Yeast Lachancea (Saccharomyces) kluyveri Reveals New URC Genes Involved in Pyrimidine Catabolism

et al. 2014

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bPyrimidines are important nucleic acid precursors which are constantly synthesized, degraded, and rebuilt in the cell. Four degradation pathways, two of which are found in eukaryotes, have been described. One of them, the URC pathway, has been initially discovered in our laboratory in the yeast Lachancea kluyveri. Here, we present the global changes in gene expression in L. kluyveri in response to different nitrogen sources, including uracil, uridine, dihydrouracil, and ammonia. The expression pattern of the known URC genes, URC1-6, helped to identify nine putative novel URC genes with a similar expression pattern. The microarray analysis provided evidence that both the URC and PYD genes are under nitrogen catabolite repression in L. kluyveri and are induced by uracil or dihydrouracil, respectively. We determined the function of URC8, which was found to catalyze the reduction of malonate semialdehyde to 3-hydroxypropionate, the final degradation product of the pathway. The other eight genes studied were all putative permeases. Our analysis of double deletion strains showed that the L. kluyveri Fui1p protein transported uridine, just like its homolog in Saccharomyces cerevisiae, but we demonstrated that is was not the only uridine transporter in L. kluyveri. We also showed that the L. kluyveri homologs of DUR3 and FUR4 do not have the same function that they have in S. cerevisiae, where they transport urea and uracil, respectively. In L. kluyveri, both of these deletion strains grew normally on uracil and urea.

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Novel Amidohydrolytic Reactions in Oxidative Pyrimidine Metabolism: Analysis of the Barbiturase Reaction and Discovery of a Novel Enzyme, Ureidomalonase

Cited by 27 publications

References 9 publications

Allophanate Hydrolase, Not Urease, Functions in Bacterial Cyanuric Acid Metabolism

Allophanate Hydrolase, Not Urease, Functions in Bacterial Cyanuric Acid Metabolism

Defining Sequence Space and Reaction Products within the Cyanuric Acid Hydrolase (AtzD)/Barbiturase Protein Family

Global Expression Analysis of the Yeast Lachancea (Saccharomyces) kluyveri Reveals New URC Genes Involved in Pyrimidine Catabolism

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