Skip to main content
PMC home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1996 Nov;178(21):6238–6249. doi: 10.1128/jb.178.21.6238-6249.1996

Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promoters.

A S Lynch 1, E C Lin 1
PMCID: PMC178496  PMID: 8892825

Abstract

ArcA protein bearing an amino-terminal, oligohistidine extension has been purified, and its DNA binding activity has been characterized with or without prior incubation with carbamoyl phosphate. Electrophoretic mobility shift assays and DNase I protection assays indicate that where the phosphorylated form of the ArcA protein (ArcA-P) is expected to act as a transcriptional repressor (e.g., of lctPRD and gltA-sdhCDAB), the effect is likely to be mediated by sequestration of cis-controlling transcriptional regulatory elements. In contrast, in the case of cydAB, for which ArcA-P is expected to function as a transcriptional activator, two discrete binding sites have been identified upstream of a known promoter, and activation from these sites is likely to be mediated by a mechanism typical of the type I class of prokaryotic transcriptional activators. An additional ArcA-P binding site has also been located downstream of the known promoter, and a distinct role for this site in the regulation of the cydAB operon during anoxic growth transitions is suggested. These results are discussed within the framework of an overall model of signaling by the Arc two-component signal transduction system in response to changes in aerobiosis.

Full Text

The Full Text of this article is available as a PDF (1.7 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Beck C. F., Warren R. A. Divergent promoters, a common form of gene organization. Microbiol Rev. 1988 Sep;52(3):318–326. doi: 10.1128/mr.52.3.318-326.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Boucher P. E., Menozzi F. D., Locht C. The modular architecture of bacterial response regulators. Insights into the activation mechanism of the BvgA transactivator of Bordetella pertussis. J Mol Biol. 1994 Aug 19;241(3):363–377. doi: 10.1006/jmbi.1994.1513. [DOI] [PubMed] [Google Scholar]
  3. Compan I., Touati D. Anaerobic activation of arcA transcription in Escherichia coli: roles of Fnr and ArcA. Mol Microbiol. 1994 Mar;11(5):955–964. doi: 10.1111/j.1365-2958.1994.tb00374.x. [DOI] [PubMed] [Google Scholar]
  4. Compan I., Touati D. Interaction of six global transcription regulators in expression of manganese superoxide dismutase in Escherichia coli K-12. J Bacteriol. 1993 Mar;175(6):1687–1696. doi: 10.1128/jb.175.6.1687-1696.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cotter P. A., Chepuri V., Gennis R. B., Gunsalus R. P. Cytochrome o (cyoABCDE) and d (cydAB) oxidase gene expression in Escherichia coli is regulated by oxygen, pH, and the fnr gene product. J Bacteriol. 1990 Nov;172(11):6333–6338. doi: 10.1128/jb.172.11.6333-6338.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cotter P. A., Gunsalus R. P. Contribution of the fnr and arcA gene products in coordinate regulation of cytochrome o and d oxidase (cyoABCDE and cydAB) genes in Escherichia coli. FEMS Microbiol Lett. 1992 Feb 1;70(1):31–36. doi: 10.1016/0378-1097(92)90558-6. [DOI] [PubMed] [Google Scholar]
  7. Darlison M. G., Guest J. R. Nucleotide sequence encoding the iron-sulphur protein subunit of the succinate dehydrogenase of Escherichia coli. Biochem J. 1984 Oct 15;223(2):507–517. doi: 10.1042/bj2230507. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Deretic V., Leveau J. H., Mohr C. D., Hibler N. S. In vitro phosphorylation of AlgR, a regulator of mucoidy in Pseudomonas aeruginosa, by a histidine protein kinase and effects of small phospho-donor molecules. Mol Microbiol. 1992 Oct;6(19):2761–2767. doi: 10.1111/j.1365-2958.1992.tb01455.x. [DOI] [PubMed] [Google Scholar]
  9. Dong J. M., Taylor J. S., Latour D. J., Iuchi S., Lin E. C. Three overlapping lct genes involved in L-lactate utilization by Escherichia coli. J Bacteriol. 1993 Oct;175(20):6671–6678. doi: 10.1128/jb.175.20.6671-6678.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Drapal N., Sawers G. Purification of ArcA and analysis of its specific interaction with the pfl promoter-regulatory region. Mol Microbiol. 1995 May;16(3):597–607. doi: 10.1111/j.1365-2958.1995.tb02422.x. [DOI] [PubMed] [Google Scholar]
  11. Fang H., Gennis R. B. Identification of the transcriptional start site of the cyd operon from Escherichia coli. FEMS Microbiol Lett. 1993 Apr 1;108(2):237–242. doi: 10.1111/j.1574-6968.1993.tb06105.x. [DOI] [PubMed] [Google Scholar]
  12. Feng J., Atkinson M. R., McCleary W., Stock J. B., Wanner B. L., Ninfa A. J. Role of phosphorylated metabolic intermediates in the regulation of glutamine synthetase synthesis in Escherichia coli. J Bacteriol. 1992 Oct;174(19):6061–6070. doi: 10.1128/jb.174.19.6061-6070.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Fiedler U., Weiss V. A common switch in activation of the response regulators NtrC and PhoB: phosphorylation induces dimerization of the receiver modules. EMBO J. 1995 Aug 1;14(15):3696–3705. doi: 10.1002/j.1460-2075.1995.tb00039.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Fu H. A., Iuchi S., Lin E. C. The requirement of ArcA and Fnr for peak expression of the cyd operon in Escherichia coli under microaerobic conditions. Mol Gen Genet. 1991 Apr;226(1-2):209–213. doi: 10.1007/BF00273605. [DOI] [PubMed] [Google Scholar]
  15. Guest J. R., Russell G. C. Complexes and complexities of the citric acid cycle in Escherichia coli. Curr Top Cell Regul. 1992;33:231–247. doi: 10.1016/b978-0-12-152833-1.50018-6. [DOI] [PubMed] [Google Scholar]
  16. Holman T. R., Wu Z., Wanner B. L., Walsh C. T. Identification of the DNA-binding site for the phosphorylated VanR protein required for vancomycin resistance in Enterococcus faecium. Biochemistry. 1994 Apr 19;33(15):4625–4631. doi: 10.1021/bi00181a024. [DOI] [PubMed] [Google Scholar]
  17. Iuchi S., Aristarkhov A., Dong J. M., Taylor J. S., Lin E. C. Effects of nitrate respiration on expression of the Arc-controlled operons encoding succinate dehydrogenase and flavin-linked L-lactate dehydrogenase. J Bacteriol. 1994 Mar;176(6):1695–1701. doi: 10.1128/jb.176.6.1695-1701.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Iuchi S., Cameron D. C., Lin E. C. A second global regulator gene (arcB) mediating repression of enzymes in aerobic pathways of Escherichia coli. J Bacteriol. 1989 Feb;171(2):868–873. doi: 10.1128/jb.171.2.868-873.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Iuchi S., Chepuri V., Fu H. A., Gennis R. B., Lin E. C. Requirement for terminal cytochromes in generation of the aerobic signal for the arc regulatory system in Escherichia coli: study utilizing deletions and lac fusions of cyo and cyd. J Bacteriol. 1990 Oct;172(10):6020–6025. doi: 10.1128/jb.172.10.6020-6025.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Iuchi S., Lin E. C. Adaptation of Escherichia coli to redox environments by gene expression. Mol Microbiol. 1993 Jul;9(1):9–15. doi: 10.1111/j.1365-2958.1993.tb01664.x. [DOI] [PubMed] [Google Scholar]
  21. Iuchi S., Lin E. C. Adaptation of Escherichia coli to respiratory conditions: regulation of gene expression. Cell. 1991 Jul 12;66(1):5–7. doi: 10.1016/0092-8674(91)90130-q. [DOI] [PubMed] [Google Scholar]
  22. Iuchi S., Lin E. C. arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways. Proc Natl Acad Sci U S A. 1988 Mar;85(6):1888–1892. doi: 10.1073/pnas.85.6.1888. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Iuchi S., Matsuda Z., Fujiwara T., Lin E. C. The arcB gene of Escherichia coli encodes a sensor-regulator protein for anaerobic repression of the arc modulon. Mol Microbiol. 1990 May;4(5):715–727. doi: 10.1111/j.1365-2958.1990.tb00642.x. [DOI] [PubMed] [Google Scholar]
  24. Iuchi S. Phosphorylation/dephosphorylation of the receiver module at the conserved aspartate residue controls transphosphorylation activity of histidine kinase in sensor protein ArcB of Escherichia coli. J Biol Chem. 1993 Nov 15;268(32):23972–23980. [PubMed] [Google Scholar]
  25. Kenney L. J., Bauer M. D., Silhavy T. J. Phosphorylation-dependent conformational changes in OmpR, an osmoregulatory DNA-binding protein of Escherichia coli. Proc Natl Acad Sci U S A. 1995 Sep 12;92(19):8866–8870. doi: 10.1073/pnas.92.19.8866. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Li J., Kustu S., Stewart V. In vitro interaction of nitrate-responsive regulatory protein NarL with DNA target sequences in the fdnG, narG, narK and frdA operon control regions of Escherichia coli K-12. J Mol Biol. 1994 Aug 12;241(2):150–165. doi: 10.1006/jmbi.1994.1485. [DOI] [PubMed] [Google Scholar]
  27. Lukat G. S., McCleary W. R., Stock A. M., Stock J. B. Phosphorylation of bacterial response regulator proteins by low molecular weight phospho-donors. Proc Natl Acad Sci U S A. 1992 Jan 15;89(2):718–722. doi: 10.1073/pnas.89.2.718. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. McCleary W. R., Stock J. B., Ninfa A. J. Is acetyl phosphate a global signal in Escherichia coli? J Bacteriol. 1993 May;175(10):2793–2798. doi: 10.1128/jb.175.10.2793-2798.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Minagawa J., Nakamura H., Yamato I., Mogi T., Anraku Y. Transcriptional regulation of the cytochrome b562-o complex in Escherichia coli. Gene expression and molecular characterization of the promoter. J Biol Chem. 1990 Jul 5;265(19):11198–11203. [PubMed] [Google Scholar]
  30. Park S. J., McCabe J., Turna J., Gunsalus R. P. Regulation of the citrate synthase (gltA) gene of Escherichia coli in response to anaerobiosis and carbon supply: role of the arcA gene product. J Bacteriol. 1994 Aug;176(16):5086–5092. doi: 10.1128/jb.176.16.5086-5092.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Park S. J., Tseng C. P., Gunsalus R. P. Regulation of succinate dehydrogenase (sdhCDAB) operon expression in Escherichia coli in response to carbon supply and anaerobiosis: role of ArcA and Fnr. Mol Microbiol. 1995 Feb;15(3):473–482. doi: 10.1111/j.1365-2958.1995.tb02261.x. [DOI] [PubMed] [Google Scholar]
  32. Quail M. A., Guest J. R. Purification, characterization and mode of action of PdhR, the transcriptional repressor of the pdhR-aceEF-lpd operon of Escherichia coli. Mol Microbiol. 1995 Feb;15(3):519–529. doi: 10.1111/j.1365-2958.1995.tb02265.x. [DOI] [PubMed] [Google Scholar]
  33. Rice C. W., Hempfling W. P. Oxygen-limited continuous culture and respiratory energy conservation in Escherichia coli. J Bacteriol. 1978 Apr;134(1):115–124. doi: 10.1128/jb.134.1.115-124.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Schröder I., Wolin C. D., Cavicchioli R., Gunsalus R. P. Phosphorylation and dephosphorylation of the NarQ, NarX, and NarL proteins of the nitrate-dependent two-component regulatory system of Escherichia coli. J Bacteriol. 1994 Aug;176(16):4985–4992. doi: 10.1128/jb.176.16.4985-4992.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Tardat B., Touati D. Iron and oxygen regulation of Escherichia coli MnSOD expression: competition between the global regulators Fur and ArcA for binding to DNA. Mol Microbiol. 1993 Jul;9(1):53–63. doi: 10.1111/j.1365-2958.1993.tb01668.x. [DOI] [PubMed] [Google Scholar]
  36. Tseng C. P., Albrecht J., Gunsalus R. P. Effect of microaerophilic cell growth conditions on expression of the aerobic (cyoABCDE and cydAB) and anaerobic (narGHJI, frdABCD, and dmsABC) respiratory pathway genes in Escherichia coli. J Bacteriol. 1996 Feb;178(4):1094–1098. doi: 10.1128/jb.178.4.1094-1098.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Unden G., Becker S., Bongaerts J., Holighaus G., Schirawski J., Six S. O2-sensing and O2-dependent gene regulation in facultatively anaerobic bacteria. Arch Microbiol. 1995 Aug;164(2):81–90. [PubMed] [Google Scholar]
  38. Unden G., Trageser M., Duchêne A. Effect of positive redox potentials (greater than +400 mV) on the expression of anaerobic respiratory enzymes in Escherichia coli. Mol Microbiol. 1990 Feb;4(2):315–319. doi: 10.1111/j.1365-2958.1990.tb00598.x. [DOI] [PubMed] [Google Scholar]
  39. Wall D., Delaney J. M., Fayet O., Lipinska B., Yamamoto T., Georgopoulos C. arc-dependent thermal regulation and extragenic suppression of the Escherichia coli cytochrome d operon. J Bacteriol. 1992 Oct;174(20):6554–6562. doi: 10.1128/jb.174.20.6554-6562.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Wilde R. J., Guest J. R. Transcript analysis of the citrate synthase and succinate dehydrogenase genes of Escherichia coli K12. J Gen Microbiol. 1986 Dec;132(12):3239–3251. doi: 10.1099/00221287-132-12-3239. [DOI] [PubMed] [Google Scholar]
  41. Wood D., Darlison M. G., Wilde R. J., Guest J. R. Nucleotide sequence encoding the flavoprotein and hydrophobic subunits of the succinate dehydrogenase of Escherichia coli. Biochem J. 1984 Sep 1;222(2):519–534. doi: 10.1042/bj2220519. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES