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A previously undescribed pathway for pyrimidine catabolism
- Kevin D. Loh*,†,
- Prasad Gyaneshwar*,‡,
- Eirene Markenscoff Papadimitriou*,§,
- Rebecca Fong*,
- Kwang-Seo Kim*,
- Rebecca Parales¶,
- Zhongrui Zhou‖,
- William Inwood*, and
- Sydney Kustu*,**
- *Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720-3102;
- ¶Section of Microbiology, 1 Shields Avenue, University of California, Davis, CA 95616; and
- ‖College of Chemistry, 8 Lewis Hall, University of California, Berkeley, CA 94720-1460
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Contributed by Sydney Kustu, January 19, 2006
Abstract
The b1012 operon of Escherichia coli K-12, which is composed of seven unidentified ORFs, is one of the most highly expressed operons under control of nitrogen regulatory protein C. Examination of strains with lesions in this operon on Biolog Phenotype MicroArray (PM3) plates and subsequent growth tests indicated that they failed to use uridine or uracil as the sole nitrogen source and that the parental strain could use them at room temperature but not at 37°C. A strain carrying an ntrB(Con) mutation, which elevates transcription of genes under nitrogen regulatory protein C control, could also grow on thymidine as the sole nitrogen source, whereas strains with lesions in the b1012 operon could not. Growth-yield experiments indicated that both nitrogens of uridine and thymidine were available. Studies with [14C]uridine indicated that a three-carbon waste product from the pyrimidine ring was excreted. After trimethylsilylation and gas chromatography, the waste product was identified by mass spectrometry as 3-hydroxypropionic acid. In agreement with this finding, 2-methyl-3-hydroxypropionic acid was released from thymidine. Both the number of available nitrogens and the waste products distinguished the pathway encoded by the b1012 operon from pyrimidine catabolic pathways described previously. We propose that the genes of this operon be named rutA–G for pyrimidine utilization. The product of the divergently transcribed gene, b1013, is a tetracycline repressor family regulator that controls transcription of the b1012 operon negatively.
Footnotes
- **To whom correspondence should be addressed. E-mail: kustu{at}nature.berkeley.edu
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↵ †Present address: 71-254 CHS, Department of Epidemiology, University of California School of Public Health, Los Angeles, CA 90095-1772.
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↵ ‡Present address: Biotechnology Institute, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN 55108.
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↵ §Present address: Département de Microbiologie et Médecine Moléculaire, Université de Geneva, 1, Rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
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Author contributions: K.D.L., P.G., K.-S.K., W.I., and S.K. designed research; K.D.L., P.G., E.M.P., R.F., K.-S.K., Z.Z., and W.I. performed research; Z.Z. contributed new reagents/analytic tools; P.G., R.P., Z.Z., W.I., and S.K. analyzed data; and S.K. wrote the paper.
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Conflict of interest statement: No conflicts declared.
- Abbreviations:
- NtrC,
- nitrogen regulatory protein C
- © 2006 by The National Academy of Sciences of the USA
