Skip to main content
NCBI home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1996 Nov;178(21):6319–6326. doi: 10.1128/jb.178.21.6319-6326.1996

Structure and function of the Pseudomonas putida integration host factor.

R Calb 1, A Davidovitch 1, S Koby 1, H Giladi 1, D Goldenberg 1, H Margalit 1, A Holtel 1, K Timmis 1, J M Sanchez-Romero 1, V de Lorenzo 1, A B Oppenheim 1
PMCID: PMC178507  PMID: 8892836

Abstract

Integration host factor (IHF) is a DNA-binding and -bending protein that has been found in a number of gram-negative bacteria. Here we describe the cloning, sequencing, and functional analysis of the genes coding for the two subunits of IHF from Pseudomonas putida. Both the ihfA and ihfB genes of P. putida code for 100-amino-acid-residue polypeptides that are 1 and 6 residues longer than the Escherichia coli IHF subunits, respectively. The P. putida ihfA and ihfB genes can effectively complement E. coli ihf mutants, suggesting that the P. putida IHF subunits can form functional heterodimers with the IHF subunits of E. coli. Analysis of the amino acid differences between the E. coli and P. putida protein sequences suggests that in the evolution of IHF, amino acid changes were mainly restricted to the N-terminal domains and to the extreme C termini. These changes do not interfere with dimer formation or with DNA recognition. We constructed a P. putida mutant strain carrying an ihfA gene knockout and demonstrated that IHF is essential for the expression of the P(U) promoter of the xyl operon of the upper pathway of toluene degradation. It was further shown that the ihfA P. putida mutant strain carrying the TOL plasmid was defective in the degradation of the aromatic model compound benzyl alcohol, proving the unique role of IHF in xyl operon promoter regulation.

Full Text

The Full Text of this article is available as a PDF (518.5 KB).

Selected References

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

  1. Abril M. A., Ramos J. L. Physical organization of the upper pathway operon promoter of the Pseudomonas TOL plasmid. Sequence and positional requirements for XylR-dependent activation of transcription. Mol Gen Genet. 1993 May;239(1-2):281–288. doi: 10.1007/BF00281629. [DOI] [PubMed] [Google Scholar]
  2. Drlica K., Rouviere-Yaniv J. Histonelike proteins of bacteria. Microbiol Rev. 1987 Sep;51(3):301–319. doi: 10.1128/mr.51.3.301-319.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Fernández S., Shingler V., De Lorenzo V. Cross-regulation by XylR and DmpR activators of Pseudomonas putida suggests that transcriptional control of biodegradative operons evolves independently of catabolic genes. J Bacteriol. 1994 Aug;176(16):5052–5058. doi: 10.1128/jb.176.16.5052-5058.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Flamm E. L., Weisberg R. A. Primary structure of the hip gene of Escherichia coli and of its product, the beta subunit of integration host factor. J Mol Biol. 1985 May 25;183(2):117–128. doi: 10.1016/0022-2836(85)90206-2. [DOI] [PubMed] [Google Scholar]
  5. Freundlich M., Ramani N., Mathew E., Sirko A., Tsui P. The role of integration host factor in gene expression in Escherichia coli. Mol Microbiol. 1992 Sep;6(18):2557–2563. doi: 10.1111/j.1365-2958.1992.tb01432.x. [DOI] [PubMed] [Google Scholar]
  6. Friedman D. I. Integration host factor: a protein for all reasons. Cell. 1988 Nov 18;55(4):545–554. doi: 10.1016/0092-8674(88)90213-9. [DOI] [PubMed] [Google Scholar]
  7. Gamas P., Burger A. C., Churchward G., Caro L., Galas D., Chandler M. Replication of pSC101: effects of mutations in the E. coli DNA binding protein IHF. Mol Gen Genet. 1986 Jul;204(1):85–89. doi: 10.1007/BF00330192. [DOI] [PubMed] [Google Scholar]
  8. Giladi H., Goldenberg D., Koby S., Oppenheim A. B. Enhanced activity of the bacteriophage lambda PL promoter at low temperature. Proc Natl Acad Sci U S A. 1995 Mar 14;92(6):2184–2188. doi: 10.1073/pnas.92.6.2184. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Giladi H., Koby S., Gottesman M. E., Oppenheim A. B. Supercoiling, integration host factor, and a dual promoter system, participate in the control of the bacteriophage lambda pL promoter. J Mol Biol. 1992 Apr 20;224(4):937–948. doi: 10.1016/0022-2836(92)90461-r. [DOI] [PubMed] [Google Scholar]
  10. Gober J. W., Shapiro L. Integration host factor is required for the activation of developmentally regulated genes in Caulobacter. Genes Dev. 1990 Sep;4(9):1494–1504. doi: 10.1101/gad.4.9.1494. [DOI] [PubMed] [Google Scholar]
  11. Granston A. E., Nash H. A. Characterization of a set of integration host factor mutants deficient for DNA binding. J Mol Biol. 1993 Nov 5;234(1):45–59. doi: 10.1006/jmbi.1993.1562. [DOI] [PubMed] [Google Scholar]
  12. Haluzi H., Goitein D., Koby S., Mendelson I., Teff D., Mengeritsky G., Giladi H., Oppenheim A. B. Genes coding for integration host factor are conserved in gram-negative bacteria. J Bacteriol. 1991 Oct;173(19):6297–6299. doi: 10.1128/jb.173.19.6297-6299.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Hoover T. R., Santero E., Porter S., Kustu S. The integration host factor stimulates interaction of RNA polymerase with NIFA, the transcriptional activator for nitrogen fixation operons. Cell. 1990 Oct 5;63(1):11–22. doi: 10.1016/0092-8674(90)90284-l. [DOI] [PubMed] [Google Scholar]
  14. Lee B., Richards F. M. The interpretation of protein structures: estimation of static accessibility. J Mol Biol. 1971 Feb 14;55(3):379–400. doi: 10.1016/0022-2836(71)90324-x. [DOI] [PubMed] [Google Scholar]
  15. Lee E. C., Hales L. M., Gumport R. I., Gardner J. F. The isolation and characterization of mutants of the integration host factor (IHF) of Escherichia coli with altered, expanded DNA-binding specificities. EMBO J. 1992 Jan;11(1):305–313. doi: 10.1002/j.1460-2075.1992.tb05053.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lerner C. G., Inouye M. Low copy number plasmids for regulated low-level expression of cloned genes in Escherichia coli with blue/white insert screening capability. Nucleic Acids Res. 1990 Aug 11;18(15):4631–4631. doi: 10.1093/nar/18.15.4631. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Marqués S., Ramos J. L. Transcriptional control of the Pseudomonas putida TOL plasmid catabolic pathways. Mol Microbiol. 1993 Sep;9(5):923–929. doi: 10.1111/j.1365-2958.1993.tb01222.x. [DOI] [PubMed] [Google Scholar]
  18. Mengeritsky G., Goldenberg D., Mendelson I., Giladi H., Oppenheim A. B. Genetic and biochemical analysis of the integration host factor of Escherichia coli. J Mol Biol. 1993 Jun 5;231(3):646–657. doi: 10.1006/jmbi.1993.1316. [DOI] [PubMed] [Google Scholar]
  19. Oberto J., Drlica K., Rouvière-Yaniv J. Histones, HMG, HU, IHF: Même combat. Biochimie. 1994;76(10-11):901–908. doi: 10.1016/0300-9084(94)90014-0. [DOI] [PubMed] [Google Scholar]
  20. Pérez-Martín J., de Lorenzo V. In vitro activities of an N-terminal truncated form of XylR, a sigma 54-dependent transcriptional activator of Pseudomonas putida. J Mol Biol. 1996 May 17;258(4):575–587. doi: 10.1006/jmbi.1996.0270. [DOI] [PubMed] [Google Scholar]
  21. Short J. M., Fernandez J. M., Sorge J. A., Huse W. D. Lambda ZAP: a bacteriophage lambda expression vector with in vivo excision properties. Nucleic Acids Res. 1988 Aug 11;16(15):7583–7600. doi: 10.1093/nar/16.15.7583. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Stenzel T. T., Patel P., Bastia D. The integration host factor of Escherichia coli binds to bent DNA at the origin of replication of the plasmid pSC101. Cell. 1987 Jun 5;49(5):709–717. doi: 10.1016/0092-8674(87)90547-2. [DOI] [PubMed] [Google Scholar]
  23. Tanaka I., Appelt K., Dijk J., White S. W., Wilson K. S. 3-A resolution structure of a protein with histone-like properties in prokaryotes. Nature. 1984 Aug 2;310(5976):376–381. doi: 10.1038/310376a0. [DOI] [PubMed] [Google Scholar]
  24. Thompson J. F., Waechter-Brulla D., Gumport R. I., Gardner J. F., Moitoso de Vargas L., Landy A. Mutations in an integration host factor-binding site: effect on lambda site-specific recombination and regulatory implications. J Bacteriol. 1986 Dec;168(3):1343–1351. doi: 10.1128/jb.168.3.1343-1351.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Toussaint B., David L., de Sury d'Aspremont R., Vignais P. M. The IHF proteins of Rhodobacter capsulatus and Pseudomonas aeruginosa. Biochimie. 1994;76(10-11):951–957. doi: 10.1016/0300-9084(94)90020-5. [DOI] [PubMed] [Google Scholar]
  26. Toussaint B., Delic-Attree I., Vignais P. M. Pseudomonas aeruginosa contains an IHF-like protein that binds to the algD promoter. Biochem Biophys Res Commun. 1993 Oct 15;196(1):416–421. doi: 10.1006/bbrc.1993.2265. [DOI] [PubMed] [Google Scholar]
  27. Vis H., Mariani M., Vorgias C. E., Wilson K. S., Kaptein R., Boelens R. Solution structure of the HU protein from Bacillus stearothermophilus. J Mol Biol. 1995 Dec 8;254(4):692–703. doi: 10.1006/jmbi.1995.0648. [DOI] [PubMed] [Google Scholar]
  28. Weisberg R. A., Freundlich M., Friedman D., Gardner J., Goosen N., Nash H., Oppenheim A., Rouvière-Yaniv J. Nomenclature of the genes encoding IHF. Mol Microbiol. 1996 Feb;19(3):642–642. doi: 10.1046/j.1365-2958.1996.t01-2-442924.x. [DOI] [PubMed] [Google Scholar]
  29. Werner M. H., Clore G. M., Gronenborn A. M., Nash H. A. Symmetry and asymmetry in the function of Escherichia coli integration host factor: implications for target identification by DNA-binding proteins. Curr Biol. 1994 Jun 1;4(6):477–487. doi: 10.1016/s0960-9822(00)00108-1. [DOI] [PubMed] [Google Scholar]
  30. White M. F., Kahn C. R. The insulin signaling system. J Biol Chem. 1994 Jan 7;269(1):1–4. [PubMed] [Google Scholar]
  31. White S. W., Appelt K., Wilson K. S., Tanaka I. A protein structural motif that bends DNA. Proteins. 1989;5(4):281–288. doi: 10.1002/prot.340050405. [DOI] [PubMed] [Google Scholar]
  32. Wozniak D. J., Ohman D. E. Involvement of the alginate algT gene and integration host factor in the regulation of the Pseudomonas aeruginosa algB gene. J Bacteriol. 1993 Jul;175(13):4145–4153. doi: 10.1128/jb.175.13.4145-4153.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Yang C. C., Nash H. A. The interaction of E. coli IHF protein with its specific binding sites. Cell. 1989 Jun 2;57(5):869–880. doi: 10.1016/0092-8674(89)90801-5. [DOI] [PubMed] [Google Scholar]
  34. Zulianello L., de la Gorgue de Rosny E., van Ulsen P., van de Putte P., Goosen N. The HimA and HimD subunits of integration host factor can specifically bind to DNA as homodimers. EMBO J. 1994 Apr 1;13(7):1534–1540. doi: 10.1002/j.1460-2075.1994.tb06415.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. de Lorenzo V., Herrero M., Metzke M., Timmis K. N. An upstream XylR- and IHF-induced nucleoprotein complex regulates the sigma 54-dependent Pu promoter of TOL plasmid. EMBO J. 1991 May;10(5):1159–1167. doi: 10.1002/j.1460-2075.1991.tb08056.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES