1887

Abstract

Purines are degraded via uric acid to yield allantoin. Under anaerobic conditions, allantoin is further degraded via carbamoylphosphate to &SetFont Typeface="11"; to provide a nitrogen source and, under aerobic conditions, to 3-phosphoglycerate via glyoxylate for energy production. In this study, we found that a DNA-binding transcription factor AllR, together with AllS, plays a key role in switching control of two pathways, nitrogen assimilation and energy production. The repressor function of AllR is activated in the presence of allantoin, the common substrate for both pathways, leading to repression of the genes for energy production. On the other hand, when glyoxylate is accumulated, AllR is inactivated for derepression of the pathway for energy production. RutR, the master regulator for pyrimidines and arginine, is also involved in this pathway-switching control.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.2008/020016-0
2008-11-01
2024-12-14
Loading full text...

Full text loading...

/deliver/fulltext/micro/154/11/3366.html?itemId=/content/journal/micro/10.1099/mic.0.2008/020016-0&mimeType=html&fmt=ahah

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]
/content/journal/micro/10.1099/mic.0.2008/020016-0
Loading
/content/journal/micro/10.1099/mic.0.2008/020016-0
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error