Skip to main content
SpringerLink
Log in

Comparison of the Local Concentration of the HU Protein for Particular Regions of Genomic DNA in Escherichia coli Cells in Vivo

  • Review and Experimantal Articles
  • Published:
Molecular Biology Aims and scope Submit manuscript

Abstract

HU, a nonspecific histone-like DNA-binding protein, is a major component of the bacterial nucleoid. HU is referred to as an accessory factor in forming and maintaining specific DNA conformations in complex DNA-protein assemblies and as a protein involved in DNA compaction. The HU distribution along the bacterial chromosome in vivo was studied by comparing the local concentration of HU for individual DNA sequences. The method included covalent fixation of DNA-protein contacts with formaldehyde and immuno-precipitation of covalent DNA-protein complexes with anti-HU antibodies. The HU local concentration was assayed in Escherichia coli cells during exponential or stationary growth and was compared for the origin of replication oriC; the promoter and structural regions of hupA and hupB, which code for HU subunits; and the structural regions of dps and glgS, which are activated at the stationary growth phase. During exponential growth, the local concentration of HU was much the same on all DNA sequences examined and did not depend on the transcriptional activity of the genes. During the stationary phase, the HU local concentration was similarly equal on all sequences but was two times higher than at the exponential phase.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

REFERENCES

  1. Sinden R., Pettijohn D. 1981. Chromosomes in living Escherichia coli cells are segregated into domain of supercoiling. Proc. Natl. Acad. Sci. USA. 78, 224–228.

    PubMed  Google Scholar 

  2. Higgins N.P., Yang X., Fu Q., Roth J.R. 1996. Surveying a supercoil domain by using the gamma delta resolution system in Salmonella typhimurium. J. Bacteriol. 178, 2825–2835.

    PubMed  Google Scholar 

  3. Pettijohn D.E. 1996. In: Escherichia coli and Salmonella typhimurium: Cellular and Molecular biology. Eds. Curtis R., Ingraham J.L., Lin E.C.C., Low K.B., Magasanik B., Reznikoff W.S., Rieley M., Schaechter M., Umbarger H.E. Washington, DC: Am. Soc. Microbiol. 158–166.

    Google Scholar 

  4. Rouviere-Yaniv J., Gros F. 1975. Characterization of novel, low-molecular-weight DNA-binding protein from Escherichia coli. Proc. Natl. Acad. Sci. USA. 72, 3428–3432.

    PubMed  Google Scholar 

  5. Rouviere-Yaniv J. 1978. Localization of HU protein in the E. coli nucleoid. Cold Spring Harbor Symp. Quant. Biol. 42, 439–447.

    PubMed  Google Scholar 

  6. Rouviere-Yaniv J., Kjeldgaard N.O. 1979. Native Escherihia coli HU protein is a heterotypic dimer. FEBS Lett. 106, 297–300.

    PubMed  Google Scholar 

  7. Bonnefoy E., Rouviere-Yaniv J. 1991. HU and IHF, two homologous histone-like proteins of Escherichia coli, form different protein-DNA complexes with short DNA fragments. EMBO J. 10, 687–696.

    PubMed  Google Scholar 

  8. Krylov A., Zasedateleva O.A., Prokopenko D.V., Rouviere-Yaniv J., Mirzabekov A.D. 2001. Massive parallel analysis of the binding specificity of histone-like protein HU to single-and double-stranded DNA with generic oligodeoxyribonucleotide microchips. Nucleic Acids Res. 29, 2654–2660.

    Article  PubMed  Google Scholar 

  9. Pontiggia A., Negri A., Beltrame M., Bianchi M.E. 1993. Protein HU binds specifically to kinked DNA. Mol. Microbiol. 7, 343–350.

    PubMed  Google Scholar 

  10. Bonnefoy E., Takahashi M., Rouviere-Yaniv J. 1994. DNA-binding parameters of the HU protein of Escherichia coli to cruciform DNA. J. Mol. Biol. 242, 116–129.

    Article  PubMed  Google Scholar 

  11. Castang B., Zelwer C., Laval J., Boiteux S. 1995. HU protein of Escherichia coli binds specifically to DNA that contains single-strand breaks or gaps. J. Biol. Chem. 270, 10291–10295.

    Article  PubMed  Google Scholar 

  12. Hodges-Garcia Y., Hegerman P.J., Pettijohn D.E. 1989. DNA ring closure mediated by protein HU. J. Biol. Chem. 264, 14621–14623.

    PubMed  Google Scholar 

  13. Kamashev D., Balandina A., Rouviere-Yaniv J. 1999. The binding motif recognized by HU on both nicked and cruciform DNA. EMBO J. 18, 101–111.

    Article  Google Scholar 

  14. Flashner Y., Gralla J.D. 1988. DNA dynamic flexibility and protein recognition: Differential stimulation by bacterial histone-like protein HU. Cell. 54, 713–721.

    Article  PubMed  Google Scholar 

  15. Preobrajenskaya O., Boullard A., Boubrik F., Schnarr M., Rouviere-Yaniv J. 1994. The protein HU can displace the lexA repressor from its DNA-binding sites. Mol. Microbiol. 13, 459–467.

    PubMed  Google Scholar 

  16. Bonnefoy E., Rouviere-Yaniv J. 1992. HU, the major histone-like protein of E. coli, modulates the binding of IHF to oriC. EMBO J. 11, 4489–4496.

    PubMed  Google Scholar 

  17. White S.W., Wilson K.S., Appelt K., Tanaka I. 1999. The high resolution structure of the DNA-binding protein HU from B. stearothermophilus. Acta Crystallogr. D. 55, 801–809.

    Article  PubMed  Google Scholar 

  18. Kamashev D., Rouviere-Yaniv J. 2000. The histone-like protein HU binds specifically to DNA recombination and repair intermediates. EMBO J. 19, 6527–6535.

    Article  PubMed  Google Scholar 

  19. Wery M., Woldringh C.L., Rouviere-Yaniv J. 2001. HUGFP and DAPI co-localize on the Escherichia coli nucleoid. Biochimie. 83, 193–200.

    Article  PubMed  Google Scholar 

  20. Wada M., Kano Y., Ogawa T., Okasaki T., Imamoto F. 1988. Construction and characterization of the deletion mutant of hupA and hupB genes in Escherichia coli. J. Mol. Biol. 204, 581–591.

    Article  PubMed  Google Scholar 

  21. Huisman O., Faelen M., Girard D., Jaffe A., Toussaint A., Rouviere-Yaniv J. 1989. Multiple defects in Escherichia coli mutants lacking HU protein. J. Bacteriol. 171, 3704–3712.

    PubMed  Google Scholar 

  22. Boubrik F., Rouviere-Yaniv J. 1995. Increased sensitivity to γ-irradiation in bacteria lacking protein HU. Proc. Natl. Acad. Sci. USA. 92, 3958–3962.

    PubMed  Google Scholar 

  23. Painbeni E., Caroff M., Rouviere-Yaniv J. 1997. Alterations of the outer membrane composition in Escherichia coli lacking the histone-like protein HU. Proc. Natl. Acad. Sci. USA. 94, 6712–6717.

    Article  PubMed  Google Scholar 

  24. Li S., Waters R. 1998. Escherichia coli lacking protein HU are UV sensitive due to a role for HU in homologous recombination. J. Bacteriol. 180, 3750–3756.

    PubMed  Google Scholar 

  25. Bahloul A., Boubrik F., Rouviere-Yaniv J. 2001. Roles of Escherichia coli histone-like protein HU in DNA replication: HU-beta suppresses the thermosensitivity of dnaA46ts. Biochimie. 83, 219–229.

    Article  PubMed  Google Scholar 

  26. Haykinson M.J., Johnson R.C. 1993. DNA looping and the helical repeat in vitro and in vivo: Effect of HU protein and enhancer location on Hin invertasome assembly. EMBO J. 12, 2503–2512.

    PubMed  Google Scholar 

  27. Malik M., Bensaid A., Rouviere-Yaniv J., Drlica K. 1996. Histone-like protein HU and bacterial DNA topology: Suppression of an HU deficiency by gyrase mutations. J. Mol. Biol. 256, 66–76.

    Article  PubMed  Google Scholar 

  28. Bensaid A., Almeida A., Drilca K., Rouviere-Yaniv J. 1996. Cross-talk between topoisomerase I and HU in Escherichia coli. J. Mol. Biol. 265, 292–300.

    Article  Google Scholar 

  29. Hecht A., Grunstein. 1999. Mapping DNA interaction sites of chromosomal proteins using immunoprecipita-tion and polymerase chain reaction. Methods Enzymol. 304, 399–414.

    PubMed  Google Scholar 

  30. Orlando V. 2000. Mapping chromosomal proteins in vivo by formaldehyde-crosslinked chromatin immunoprecipitation. Trends Biochem. Sci. 25, 99–104.

    Article  PubMed  Google Scholar 

  31. Pellegrini O., Oberto J., Pinson V., Wery M., Rouviere-Yaniv J. 2000. Overproduction and improved strategies to purify the three native forms of nuclease free HU protein. Biochimie. 82, 1–13.

    Article  PubMed  Google Scholar 

  32. Briat J.-F., Letoffe S., Marche R., Rouviere-Yaniv J. 1984. Similarity between the bacterial histone-like protein HU and a protein from spinach chloroplasts. FEBS Lett. 172, 75–79.

    Article  Google Scholar 

  33. Ausubel F.M., Brent R., Kingston R., Moore D.D., Seidman J.G., Smith J.A., Struhl K. 1999. Short Protocols in Molecular Biology. N.Y.: Wiley.

    Google Scholar 

  34. Krolenko E.V., Kamashev D.V., Balandina A.V., Karpov V.L., Rouviere-Yaniv J., Preobrajenskaya O.V. 1999. Immunochemical detection of histone-like bacterial protein HU in covalently linked DNA-protein complexes obtained in vitro and in vivo. Mol. Biol. 33, 44–446.

    Google Scholar 

  35. Claret L., Rouviere-Yaniv J. 1997. Variation in HU composition during growth of Escherichia coli: The heterodimer is required for long-term survival. J. Mol. Biol. 273, 93–104.

    Article  PubMed  Google Scholar 

  36. Almiron M., Link A., Furlong D., Kolter R. 1992. A novel DNA binding protein with regulatory and protective roles in starved Escherichia coli. Genes Dev. 6, 2646–2654.

    PubMed  Google Scholar 

  37. Hengge-Aronis R., Fisher D. 1992. Identification and molecular analysis of glgS, a novel growth phase-regulated and rpoS-dependent gene involved in glycogen synthesis in Escherichia coli. Mol. Microbiol. 6, 187–1886.

    Google Scholar 

  38. Aki T., Adhya S. 1997. Repressor induced site-specific binding of HU for transcriptional regulation. EMBO J. 16, 3666–3674.

    Article  PubMed  Google Scholar 

  39. Lewis D.E., Geanacopoulos M., Adhya S. 1999. Role of HU and DNA supercoiling in transcription repression: Specialized nucleoprotein repression complex at gal promoters in Escherichia coli. Mol. Micobiol. 31, 451–461.

    Article  Google Scholar 

  40. Kar S., Adhya S. 2001. Recruitment of HU by piggy-back: A special role of GalR in repressosome assembly. Genes Dev. 15, 2273–2281.

    Article  PubMed  Google Scholar 

  41. Nash H.A. 1996. The HU and IHF proteins: Accessory factors for complex protein-DNA assemblies. In: Regulation of gene expression in Escherichia coli. Eds. Lin E. C.C., Lynch A.S., R.G. Landes Comp. 149–179.

  42. Dame R.T., Goosen N. 2002. HU: promoting or counteracting DNA compaction? FEBS Lett. 529, 151–156.

    Article  PubMed  Google Scholar 

  43. Manna D., Gowrishankar J. 1994. Evidence for involvement of proteins HU and RpoS in transcription of the osmoresponsive proU operon in Escherichia coli. J. Bacteriol. 176, 5378–5384.

    PubMed  Google Scholar 

  44. Morales P., Rouviere-Yaniv J., Dreyfus M. 2002. The histone-like protein HU does not obstruct movement of T7 RNA polymerase in Escherichia coli cells but stimulates its activity. J. Bacteriol. 184, 1565–1570.

    Article  PubMed  Google Scholar 

  45. Rouviere-Yaniv J., Yaniv M., Germond J.E. 1979. E. coli DNA binding protein HU forms nucleosome-like structure with circular double-stranded DNA. Cell. 17, 265–274.

    Article  PubMed  Google Scholar 

  46. Tanaka H., Yasuzawa K., Kohno K., Goshima N., Kano Y., Saiki T., Imamoto F. 1995. Role of HU proteins in forming and constraining supercoils of chromosomal DNA in Escherichia coli. Mol. Gen. Genet. 248, 518–526.

    PubMed  Google Scholar 

  47. Dorman C.J. 2002. DNA topology and regulation of bacterial gene expression. In: Signals, Switches, Regulons and Cascades: Control of Bacterial Gene Expression. Eds. Hodgson D.A., Thomas C.M. Cambridge: Cambridge Univ. Press. 41–56.

    Google Scholar 

  48. Balke V.L., Gralla J.D. 1987. Changes in linking number of supercoiled DNA accompany growth transitions in Escherichia coli. J. Bacteriol. 169, 4499–4506.

    PubMed  Google Scholar 

  49. Huisman G.W., Siegle D.A., Zambrano M.M., Kolter R. 1996. Morphological and physiological changes during stationary phase. In: Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. Eds. Curtis R., Ingraham J.L., Lin E.C.C., Low K.B., Magasanik B., Reznikoff W.S., Rieley M., Schaechter M., Umbarger H.E. Washington, DC.: Am. Soc. Microbiol. 1672–1682.

    Google Scholar 

  50. Hengge-Aronis R. 1996. Regulation of gene expression during entry into stationary phase. In: Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. Eds. Curtis R., Ingraham J.L., Lin E.C.C., Low K.B., Magasanik B., Reznikoff W.S., Rieley M., Schaechter M., Umbarger H.E. Washington, DC: Am. Soc. Microbiol. 1497–1512.

    Google Scholar 

  51. Hengge-Aronis R. 1993. Survival of hunger and stress: The role of rpoS in early stationary phase regulation in E. coli. Cell. 72, 165–168.

    Article  PubMed  Google Scholar 

  52. Azam T.A., Iwata A., Nishimura A., Ueda S., Ishihama A. 1999. Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J. Bacteriol. 181, 6361–6370.

    PubMed  Google Scholar 

  53. Balandina A., Claret L., Hengge-Aronis R., Rouvier-Yaniv J. 2001. The Escherichia coli histone-like protein HU regulates rpoS translation. Mol. Microbiol. 39, 1069–1079.

    Article  PubMed  Google Scholar 

  54. Pinson V., Takahashi M., Rouvier-Yaniv J. 1999. Differential binding of Escherichia coli HU, homodimeric forms and heterodimeric form to linear, gapped and cruciform DNA. J. Mol. Biol. 287, 485–497.

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia

    O. V. Preobrajenskaya, E. S. Starodubova & V. L. Karpov

  2. Institute de Biologie Physico-Chimique, Paris, 75005, France

    J. Rouviere-Yaniv

Authors
  1. O. V. Preobrajenskaya
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. E. S. Starodubova
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. V. L. Karpov
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. J. Rouviere-Yaniv
    View author publications

    You can also search for this author in PubMed Google Scholar

Additional information

__________

Translated from Molekulyarnaya Biologiya, Vol. 39, No. 4, 2005, pp. 678–686.

Original Russian Text Copyright © 2005 by Preobrajenskaya, Starodubova, Karpov, Rouviere-Yaniv.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Preobrajenskaya, O.V., Starodubova, E.S., Karpov, V.L. et al. Comparison of the Local Concentration of the HU Protein for Particular Regions of Genomic DNA in Escherichia coli Cells in Vivo . Mol Biol 39, 585–592 (2005). https://doi.org/10.1007/s11008-005-0074-0

Download citation

  • Received:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11008-005-0074-0

Key words

Search

Navigation