Skip to main content
NCBI home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1994 Mar 15;91(6):2120–2124. doi: 10.1073/pnas.91.6.2120

RNA polymerase binding using a strongly acidic hydrophobic-repeat region of sigma 54.

Y Tintut 1, C Wong 1, Y Jiang 1, M Hsieh 1, J D Gralla 1
PMCID: PMC43321  PMID: 8134358

Abstract

sigma 54 is a rare bacterial protein that substitutes for sigma 70 in the case of Escherichia coli genes transcribed by certain activators with enhancer protein-like properties. It contains a strongly acidic region of previously unknown function. Gel mobility-shift assays using sigma 54 deletion mutants show that this region is essential for sigma 54 to bind the core RNA polymerase and recruit it to the promoter. Multiple-point mutational analysis shows that the acidic amino acids and overlapping periodic hydrophobic amino acids are necessary for this binding. Related sequences are not found within the core binding determinant of sigma 70, which binds the same core RNA polymerase. This comparison suggests that the core RNA polymerase interacts differently with the two sigma factors, likely contributing to the critical differences in transcription mechanism in the two cases.

Full text

PDF
2120

Images in this article

2121Image
on p.2121
2121Image
on p.2121
2122Image
on p.2122
2122Image
on p.2122

Selected References

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

  1. Brendel V., Karlin S. Association of charge clusters with functional domains of cellular transcription factors. Proc Natl Acad Sci U S A. 1989 Aug;86(15):5698–5702. doi: 10.1073/pnas.86.15.5698. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Buck M., Cannon W. Specific binding of the transcription factor sigma-54 to promoter DNA. Nature. 1992 Jul 30;358(6385):422–424. doi: 10.1038/358422a0. [DOI] [PubMed] [Google Scholar]
  3. Buratowski S., Hahn S., Guarente L., Sharp P. A. Five intermediate complexes in transcription initiation by RNA polymerase II. Cell. 1989 Feb 24;56(4):549–561. doi: 10.1016/0092-8674(89)90578-3. [DOI] [PubMed] [Google Scholar]
  4. Cannon W., Claverie-Martin F., Austin S., Buck M. Core RNA polymerase assists binding of the transcription factor sigma 54 to promoter DNA. Mol Microbiol. 1993 Apr;8(2):287–298. doi: 10.1111/j.1365-2958.1993.tb01573.x. [DOI] [PubMed] [Google Scholar]
  5. Collado-Vides J., Magasanik B., Gralla J. D. Control site location and transcriptional regulation in Escherichia coli. Microbiol Rev. 1991 Sep;55(3):371–394. doi: 10.1128/mr.55.3.371-394.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Dombroski A. J., Walter W. A., Record M. T., Jr, Siegele D. A., Gross C. A. Polypeptides containing highly conserved regions of transcription initiation factor sigma 70 exhibit specificity of binding to promoter DNA. Cell. 1992 Aug 7;70(3):501–512. doi: 10.1016/0092-8674(92)90174-b. [DOI] [PubMed] [Google Scholar]
  7. Giniger E., Ptashne M. Transcription in yeast activated by a putative amphipathic alpha helix linked to a DNA binding unit. Nature. 1987 Dec 17;330(6149):670–672. doi: 10.1038/330670a0. [DOI] [PubMed] [Google Scholar]
  8. Gralla J. D. Transcriptional control--lessons from an E. coli promoter data base. Cell. 1991 Aug 9;66(3):415–418. doi: 10.1016/0092-8674(81)90001-5. [DOI] [PubMed] [Google Scholar]
  9. Hope I. A., Mahadevan S., Struhl K. Structural and functional characterization of the short acidic transcriptional activation region of yeast GCN4 protein. Nature. 1988 Jun 16;333(6174):635–640. doi: 10.1038/333635a0. [DOI] [PubMed] [Google Scholar]
  10. Hsieh M., Tintut Y., Gralla J. D. Functional roles for the glutamines within the glutamine-rich region of the transcription factor sigma 54. J Biol Chem. 1994 Jan 7;269(1):373–378. [PubMed] [Google Scholar]
  11. Hunt T. P., Magasanik B. Transcription of glnA by purified Escherichia coli components: core RNA polymerase and the products of glnF, glnG, and glnL. Proc Natl Acad Sci U S A. 1985 Dec;82(24):8453–8457. doi: 10.1073/pnas.82.24.8453. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Ingles C. J., Shales M., Cress W. D., Triezenberg S. J., Greenblatt J. Reduced binding of TFIID to transcriptionally compromised mutants of VP16. Nature. 1991 Jun 13;351(6327):588–590. doi: 10.1038/351588a0. [DOI] [PubMed] [Google Scholar]
  13. Kustu S., Santero E., Keener J., Popham D., Weiss D. Expression of sigma 54 (ntrA)-dependent genes is probably united by a common mechanism. Microbiol Rev. 1989 Sep;53(3):367–376. doi: 10.1128/mr.53.3.367-376.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Lesley S. A., Brow M. A., Burgess R. R. Use of in vitro protein synthesis from polymerase chain reaction-generated templates to study interaction of Escherichia coli transcription factors with core RNA polymerase and for epitope mapping of monoclonal antibodies. J Biol Chem. 1991 Feb 5;266(4):2632–2638. [PubMed] [Google Scholar]
  15. Lesley S. A., Burgess R. R. Characterization of the Escherichia coli transcription factor sigma 70: localization of a region involved in the interaction with core RNA polymerase. Biochemistry. 1989 Sep 19;28(19):7728–7734. doi: 10.1021/bi00445a031. [DOI] [PubMed] [Google Scholar]
  16. Lin Y. S., Green M. R. Mechanism of action of an acidic transcriptional activator in vitro. Cell. 1991 Mar 8;64(5):971–981. doi: 10.1016/0092-8674(91)90321-o. [DOI] [PubMed] [Google Scholar]
  17. Lin Y. S., Ha I., Maldonado E., Reinberg D., Green M. R. Binding of general transcription factor TFIIB to an acidic activating region. Nature. 1991 Oct 10;353(6344):569–571. doi: 10.1038/353569a0. [DOI] [PubMed] [Google Scholar]
  18. Lonetto M., Gribskov M., Gross C. A. The sigma 70 family: sequence conservation and evolutionary relationships. J Bacteriol. 1992 Jun;174(12):3843–3849. doi: 10.1128/jb.174.12.3843-3849.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Merrick M., Gibbins J., Toukdarian A. The nucleotide sequence of the sigma factor gene ntrA (rpoN) of Azotobacter vinelandii: analysis of conserved sequences in NtrA proteins. Mol Gen Genet. 1987 Dec;210(2):323–330. doi: 10.1007/BF00325701. [DOI] [PubMed] [Google Scholar]
  20. Mitchell P. J., Tjian R. Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. Science. 1989 Jul 28;245(4916):371–378. doi: 10.1126/science.2667136. [DOI] [PubMed] [Google Scholar]
  21. Ninfa A. J., Reitzer L. J., Magasanik B. Initiation of transcription at the bacterial glnAp2 promoter by purified E. coli components is facilitated by enhancers. Cell. 1987 Sep 25;50(7):1039–1046. doi: 10.1016/0092-8674(87)90170-x. [DOI] [PubMed] [Google Scholar]
  22. Popham D. L., Szeto D., Keener J., Kustu S. Function of a bacterial activator protein that binds to transcriptional enhancers. Science. 1989 Feb 3;243(4891):629–635. doi: 10.1126/science.2563595. [DOI] [PubMed] [Google Scholar]
  23. Popham D., Keener J., Kustu S. Purification of the alternative sigma factor, sigma 54, from Salmonella typhimurium and characterization of sigma 54-holoenzyme. J Biol Chem. 1991 Oct 15;266(29):19510–19518. [PubMed] [Google Scholar]
  24. Reitzer L. J., Bueno R., Cheng W. D., Abrams S. A., Rothstein D. M., Hunt T. P., Tyler B., Magasanik B. Mutations that create new promoters suppress the sigma 54 dependence of glnA transcription in Escherichia coli. J Bacteriol. 1987 Sep;169(9):4279–4284. doi: 10.1128/jb.169.9.4279-4284.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Reitzer L. J., Magasanik B. Transcription of glnA in E. coli is stimulated by activator bound to sites far from the promoter. Cell. 1986 Jun 20;45(6):785–792. doi: 10.1016/0092-8674(86)90553-2. [DOI] [PubMed] [Google Scholar]
  26. Reitzer L. J., Movsas B., Magasanik B. Activation of glnA transcription by nitrogen regulator I (NRI)-phosphate in Escherichia coli: evidence for a long-range physical interaction between NRI-phosphate and RNA polymerase. J Bacteriol. 1989 Oct;171(10):5512–5522. doi: 10.1128/jb.171.10.5512-5522.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Roberts S. G., Ha I., Maldonado E., Reinberg D., Green M. R. Interaction between an acidic activator and transcription factor TFIIB is required for transcriptional activation. Nature. 1993 Jun 24;363(6431):741–744. doi: 10.1038/363741a0. [DOI] [PubMed] [Google Scholar]
  28. Sasse-Dwight S., Gralla J. D. Probing the Escherichia coli glnALG upstream activation mechanism in vivo. Proc Natl Acad Sci U S A. 1988 Dec;85(23):8934–8938. doi: 10.1073/pnas.85.23.8934. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Sasse-Dwight S., Gralla J. D. Role of eukaryotic-type functional domains found in the prokaryotic enhancer receptor factor sigma 54. Cell. 1990 Sep 7;62(5):945–954. doi: 10.1016/0092-8674(90)90269-k. [DOI] [PubMed] [Google Scholar]
  30. Su W., Porter S., Kustu S., Echols H. DNA-looping and enhancer activity: association between DNA-bound NtrC activator and RNA polymerase at the bacterial glnA promoter. Proc Natl Acad Sci U S A. 1990 Jul;87(14):5504–5508. doi: 10.1073/pnas.87.14.5504. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Sundaresan V., Jones J. D., Ow D. W., Ausubel F. M. Klebsiella pneumoniae nifA product activates the Rhizobium meliloti nitrogenase promoter. Nature. 1983 Feb 24;301(5902):728–732. doi: 10.1038/301728a0. [DOI] [PubMed] [Google Scholar]
  32. Wang W., Carey M., Gralla J. D. Polymerase II promoter activation: closed complex formation and ATP-driven start site opening. Science. 1992 Jan 24;255(5043):450–453. doi: 10.1126/science.1310361. [DOI] [PubMed] [Google Scholar]
  33. Wong C., Gralla J. D. A role for the acidic trimer repeat region of transcription factor sigma 54 in setting the rate and temperature dependence of promoter melting in vivo. J Biol Chem. 1992 Dec 5;267(34):24762–24768. [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES