The transcription regulator AllR senses both allantoin and glyoxylate and controls a set of genes for degradation and reutilization of purines

References

1. Bouvier J., Patte J. C., Stragier P. 1984; Multiple regulatory signals in the control region of the Escherichia coli carAB operon. Proc Natl Acad Sci U S A 81:4139–4143
   [Google Scholar]
2. Chang Y. Y., Wang A. Y., Cronan J. E. Jr 1993; Molecular cloning, DNA sequencing, and biochemical analysis of Escherichia coli glyoxylate carboligase. J Biol Chem 268:3911–3919
   [Google Scholar]
3. Cusa E., Obradors N., Baldoma L., Badia J., Aguilar J. 1999; Genetic analysis of a chromosomal region containing genes required for assimilation of allantoin nitrogen and linked glyoxylate metabolism in Escherichia coli . J Bacteriol 181:7479–7484
   [Google Scholar]
4. Donald L. J., Hosfield D. J., Cuvelier S. L., Ens W., Standing K. G., Duckworth H. W. 2001; Mass spectrometric study of the Escherichia coli repressor proteins, IclR and GclR, and their complexes with DNA. Protein Sci 10:1370–1380
   [Google Scholar]
5. Dubey A. K., Baker C. S., Suzuki K., Jones A. D., Pnadit P., Romeo T., Babitzke P. 2003; CsrA regulates translation of the Escherichia coli carbon starvation gene, cstA, by blocking ribosome access to the cstA transcript. J Bacteriol 185:4450–4460
   [Google Scholar]
6. Ellington A. D., Szostak J. W. 1990; In vitro selection of DNA molecules that bind specific ligands. Nature 346:818–822
   [Google Scholar]
7. Liu M. Y., Yang H., Romeo T. 1995; The product of the pleiotropic Escherichia coli gene csrA modulates glycogen biosynthesis via effects on mRNA stability. J Bacteriol 177:2663–2672
   [Google Scholar]
8. Lorca G. L., Ezersky A., Lunin V. V., Walker J. R., Altamentova S., Evdokimova E., Vedadi M., Bochkarev A., Savchenko A. 2007; Glyoxylate and pyruvate are antagonistic effectors of the Escherichia coli IclR transcriptional regulator. J Biol Chem 282:16476–16491
   [Google Scholar]
9. Makinoshima H., Nishimura A., Ishihama A. 2002; Fractionation of Escherichia coli cell populations at different stages during growth transition to stationary phase. Mol Microbiol 43:269–279
   [Google Scholar]
10. Muse W. B., Rosario C. J., Bender R. A. 2003; Nitrogen regulation of the codBA (cytosine deaminase) operon from Escherichia coli by the nitrogen assimilation control protein, NAC. J Bacteriol 185:2920–2926
    [Google Scholar]
11. Ogasawara H., Hasegawa A., Kanda E., Miki T., Yamamoto K., Ishihama A. 2007a; Genomic SELEX search for target promoters under the control of the PhoQP–RstBA signal cascade. J Bacteriol 187:4791–4799
    [Google Scholar]
12. Ogasawara H., Ishida Y., Yamada K., Yamamoto K., Ishihama A. 2007b; PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli . J Bacteriol 189:5534–5541
    [Google Scholar]
13. Rintoul M. R., Cusa E., Baldoma L., Badia J., Reitzer L., Aguilar J. 2002; Regulation of the Escherichia coli allantoin regulon: coordinated function of the repressor AllR and the activator AllS. J Mol Biol 324:599–610
    [Google Scholar]
14. Shimada T., Makinoshima H., Ogawa Y., Miki T., Maeda M., Ishihama A. 2004; Classification and strength measurement of stationary-phase promoters by use of a newly developed promoter cloning vector. J Bacteriol 186:7112–7122
    [Google Scholar]
15. Shimada T., Fujita N., Maeda M., Ishihama A. 2005; Systematic search for the Cra-binding promoters using genomic SELEX system. Genes Cells 10:907–918
    [Google Scholar]
16. Shimada T., Hirao K., Kori A., Yamamoto K., Ishihama A. 2007; RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines. Mol Microbiol 66:744–779
    [Google Scholar]
17. Singer B. S., Shtatland T., Brown D., Gold L. 1997; Libraries for genomic SELEX. Nucleic Acids Res 25:781–786
    [Google Scholar]
18. Tuerk C., Gold L. 1990; Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505–510
    [Google Scholar]
19. Vogels G. D., van der Drift C. 1976; Degradation of purines and pyrimidines by microorganisms. Bacteriol Rev 40:403–468
    [Google Scholar]
20. Walker J. R., Altamentova S., Ezersky A., Lorca G., Skarina T., Kudritska M., Ball L. J., Bochkarev A., Savchenkom A. 2006; Structural and biochemical study of effector molecule recognition by the E. coli glyoxylate and allantoin utilization regulatory protein AllR. J Mol Biol 358:810–828
    [Google Scholar]
21. Yamada M., Izu H., Nitta T., Kurihara K., Sakurai T. 1998; High temperature, nonradioactive primer extension assay for determination of a transcription initiation site. Biotechniques 25:72–75
    [Google Scholar]
22. Yamamoto K., Ishihama A. 2003; Two different modes of transcription repression of the Escherichia coli acetate operon by IclR. Mol Microbiol 47:183–194
    [Google Scholar]
23. Yamamoto K., Ogasawara H., Fujita N., Ustumi R., Ishihama A. 2002; Novel mode of transcription regulation of divergently overlapping promoters by PhoP, the regulator of two-component system sensing external magnesium availability. Mol Microbiol 45:423–438
    [Google Scholar]
24. Zimmer D. P., Soupene E., Lee H. L., Wendisch V. F., Khodursky A. B., Peter B. J., Bender R. A., Kustu S. 2000; Nitrogen regulatory protein C-controlled genes of Escherichia coli; scavenging as a defense against nitrogen limitation. Proc Natl Acad Sci U S A 97:14674–14679
    [Google Scholar]