Skip to main content
SpringerLink
Log in

The HU and IHF Proteins: Accessory Factors for Complex Protein-DNA Assemblies

  • Chapter
Regulation of Gene Expression in Escherichia coli

Abstract

The apparatus required for the regulation of gene expression varies widely in complexity. At one extreme, regulation can be achieved by one or two proteins acting at a DNA locus that encompasses 30–50 bp. However, such a simple picture is not usually (if ever) the whole story. Much more common are complex systems that typically involve several proteins acting over much larger segments of DNA. At these extended loci, one finds that function depends not only on a principal actor and a regulator (e.g., RNA polymerase and a transcriptional activator) but also on additional components. This chapter focuses on two of the best studied of such accessory factors: HU and IHF. We review the structure of these proteins, their influence on DNA conformation and topology, the regulation of their expression, their function in several well-studied systems, and their roles in homeostasis of E. coli. In order to focus on these questions, the present work has not presented all that is known about these proteins. More information can be found in several other surveys.1–6 For reviews of other accessory factors of E. coli—e.g., Fis, H-NS, Crp and Lrp—the reader is directed to chapters 12 and 20 of this volume and to other sources.7–11

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Drlica K, Rouviére-Yaniv J. Histonelike proteins of bacteria. Microbiol Rev 1987; 51:301–319.

    Google Scholar 

  2. Friedman DI. Integration host factor: A protein for all reasons. Cell 1988; 55:545–554.

    Google Scholar 

  3. Pettijohn DE. Histone-like proteins and bacterial chromosome structure. J Biol Chem 1988; 263:12793–12796.

    Google Scholar 

  4. Schmid MB, Johnson RC. Southern revival—news of bacterial chromatin. The New Biologist 1991; 3:945–950.

    Google Scholar 

  5. Freundlich M, Ramani N, Mathew E et al. The role of integration host factor in gene expression in Escherichia coli. Mol Microbiol 1992; 6:2557–2563.

    Google Scholar 

  6. Oberto J, Drlica K, Rouviére-Yaniv J. Histones, HMG, HU, IHF: Même combat. Biochimie 1994; 76:901–908.

    Google Scholar 

  7. Finkel SE, Johnson RC. Mol Microbiol 1992; 6:3257–3265.

    Google Scholar 

  8. Crothers DM, Steitz TA. Transcriptional activation by Escherichia coli CAP protein. In: McKinght SL, Yamamoto KR, eds. Transcriptional Regulation. Cold Spring Harbor: Cold Spring Harbor Press, 1992:501–534.

    Google Scholar 

  9. Ussery DW, Hinton JCD, Jordi BJAM et al. The chromatin-associated protein H-NS. Biochimie 1994; 76:968–980.

    Google Scholar 

  10. Calvo JM, Matthews RG. The leucine-responsive regulatory protein, a global regulator of metabolism in Escherichia coli.. Microbiol Rev 1994; 58:466–490.

    Google Scholar 

  11. Kolb A, Busby S, Buc H et al. Transcriptional regulation by cAMP and its receptor protein. Annu Rev Biochem 1993; 62:749–795.

    Google Scholar 

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

    Google Scholar 

  13. Nash HA, Mizuuchi K, Weisberg RA et al. Integrative recombination of bacteriophage lambda-the biochemical approach to DNA insertion. In: Bukhari AI, Shapiro JA, Adhya SL, eds. DNA insertion elements, plas-mids, and episomes. Cold Spring Harbor: Cold Spring Harbor Press, 1977:363–373.

    Google Scholar 

  14. Miller HI, Kikuchi A, Nash HA et al. Site-specific recombination of bacteriophage λ: the role of host gene products. Cold Spring Harb Symp Quant Biol 1979; 43:1121–1126.

    Google Scholar 

  15. Craigie R, Arndt-Jovin DJ, Mizuuchi K. A defined system for the DNA strand-transfer reaction at the initiation of bacteriophage Mu transposition: protein and DNA substrate requirements. Proc Natl Acad Sci USA 1985; 82:7570–7574.

    Google Scholar 

  16. Geiduschek EP, Schneider GJ, Sayre MH. TF1, a bacteriophage-specific DNA-binding and DNA bending protein. J Struc Biol 1990; 104:84–90.

    Google Scholar 

  17. Neilan JG, Lu Z, Kutish GF et al. An African swine fever virus gene with similarity to bacterial DNA binding proteins, bacterial integration host factors, and the Bacillus phage SPO1 transcription factor, TF1. Nucleic Acids Res 1993; 21:1496.

    Google Scholar 

  18. Rouviére-Yaniv J, Kjeldgaard NO. Native Escherichia coli HU protein is a heterotypic dimer. FEBS Letters 1979; 106:297–300.

    Google Scholar 

  19. Wada M, Kano Y, Ogawa T et al. Construction and characterization of the deletion mutant of hupA and hupB genes in Escherichia coli. J Mol Biol 1988; 204:581–591.

    Google Scholar 

  20. Huisman O, Faelen M, Girard D et al. Multiple defects in Escherichia coli mutants lacking HU protein. J Bacteriol 1989; 171:3704–3712.

    Google Scholar 

  21. Werner MH, Clore GM, Gronenborn AM et al. Symmetry and asymmetry in the function of Escherichia coli integration host factor: Implications for target identification by DNA-binding proteins. Curr Biol 1994; 4: 477–487.

    Google Scholar 

  22. Zulianello L, de la Gorgue de Rosny E, van Ulsen P et al. The HimA and HimD subunits of integration host factor can specifically bind to DNA as homodimers. EMBO J 1994; 13:1534–1540.

    Google Scholar 

  23. Tanaka I, Appelt K, Dijk J et al. 3-xÅ resolution structure of a protein with histone-like properties in prokaryotes. Nature 1984; 310:376–381.

    Google Scholar 

  24. White SW, Appelt K, Wilson KS et al. A protein structural motif that bends DNA. Proteins: Struct, Funct, and Genet 1989; 5:281–288.

    Google Scholar 

  25. Yang CC, Nash HA. The interaction of E. coli IHF protein with its specific binding sites. Cell 1989; 57:869–880.

    Google Scholar 

  26. Lee EC, Hales LM, Gumport RI et al. The isolation and characterization of mutants of the integration host factor (IHF) of Escherichia coli with altered, expanded DNA-binding specificities. EMBO J 1992; 11:305–313.

    Google Scholar 

  27. Granston AE, Nash HA Characterization of a set of integration host factor mutants deficient for DNA binding. J Mol Biol 1993; 234 45–59.

    Google Scholar 

  28. Yang S, Nash H. Specific photocrosslinking of DNA-protein complexes: identification of contacts between integration host factor and its target DNA. Proc Natl Acad Sci USA 1994; 91; 12183–12187.

    Google Scholar 

  29. Vis H, Boelens R, Mariani M et al. 1H, 13C, and 15N resonance assignments and secondary structure analysis of the HU protein from Bacillus stearothermophilus using two- and three- dimensional double- and triple-resonance heteronuclear magnetic resonance spectroscopy. Biochem 1994; 33:14858–14870.

    Google Scholar 

  30. Gualerzi CO, Losso MA, Lammi M et al. Proteins from the prokaryotic nucleoid. Structural and functional characterization of the Escherichia coli DNA-binding proteins NS (HU) and H-NS. In: Gualerzi CO, Pon CL, eds. Bacterial Chromatin. Heidelberg: Springer-Verlag, 1986:101–134.

    Google Scholar 

  31. Mendelson I, Gottesman M, Oppenheim AB. HU and integration host factor function as auxiliary proteins in cleavage of phage lambda cohesive ends by terminase. J Bacteriol 1991; 173:1670–1676.

    Google Scholar 

  32. Skorupski K, Sauer B, Sternberg N. Faithful cleavage of the P1 packaging site (pac) requires two phage proteins, PacA and PacB, and two Escherichi coli proteins, IHF and HU. J Mol Biol 1994; 243:268–282.

    Google Scholar 

  33. Broyles SS, Pettijohn DE. Interaction of the Escherichia coli HU protein with DNA. Evidence for formation of nucleosome-like structures with altered DNA helical pitch. J Mol Biol 1986; 187:47–60.

    Google Scholar 

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

    Google Scholar 

  35. Bonnefoy E, Almeida A, Rouviere-Yaniv J. Lon-dependent regulation of the DNA binding protein HU in Escherichia coli. Proc Natl Acad Sci USA 1989; 86:7691–7695.

    Google Scholar 

  36. Shindo H, Furubayashi A, Shimizu M et al. Preferential binding of E. coli histone-like protein HUα to negatively supercoiled DNA. Nucleic Acids Res 1992; 20:1553–1558.

    Google Scholar 

  37. Tanaka H, Goshima N, Kohno K et al. Properties of DNA-binding of HU heterotypic and homotypic dimers from Escherichia coli. J Biochem 1993; 113:568–572.

    Google Scholar 

  38. Winkelman JW, Hatfield GWJ. Characterization of the integration host factor binding site in the ilvPG1 promoter region of the ilvGMEDA Operon of Escherichia coli. J Biol Chem 1990; 265:10055–10060.

    Google Scholar 

  39. Kur J, Hasan N, Szybalski W. Physical and biological consequences of interactions between integration host factor (IHF) and coliphage lambda late p’ R promoter and its mutants. Gene 1989; 81:1–15.

    Google Scholar 

  40. Gardner JF, Nash HA. Role of Escherichia coli IHF protein in lambda site-specific recombination. A mutational analysis of binding sites. J Mol Biol 1986; 191:181–189.

    Google Scholar 

  41. Prentki P, Chandler M, Galas DJ. Escherichia coli integration host factor bends the DNA at the ends of IS 1 and in an insertion hotspot with multiple IHF binding sites. EMBO J 1987; 6:2479–2487.

    Google Scholar 

  42. Mengeritsky G, Goldenberg D, Mendelson I et al. Genetic and biochemical analysis of the integration host factor of Escherichia coli. J Mol Biol 1993; 231:646–657.

    Google Scholar 

  43. Yang S-W, Nash HA. Comparison of protein binding to DNA in vivo and in vitro: defining an effective intracellular target. EMBO J 1995; (in press)..

    Google Scholar 

  44. . Wang S, Cosstick R, Gardner JF et al. The specific binding of integration host factor involves both major and minor grooves of DNA. Biochemistry 1995; 34:13082–13090.

    Google Scholar 

  45. Morse BK, Michalczyk R, Kosturko LD. Multiple molecules of integration host factor (IHF) at a single DNA binding site, the bacteriophage X cos II site. Biochimie 1994; 76:1005–1018.

    Google Scholar 

  46. . Goodrich JA, Schwartz ML, McClure WR. Searching for and predicting the activity of sites for DNA binding proteins: compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF). Nucleic Acids Res 1990; 18: 4993–5000.

    Google Scholar 

  47. . Boccard F, Prentki P. Specific interaction of IHF with RIBs, a class of bacterial repetitive DNA elements located at the 3′ end of transcription units. EMBO 1993; 12:5019–5027.

    Google Scholar 

  48. Oppenheim AB, Rudd KE, Mendelson I et al. Integration host factor binds to a unique class of complex repetitive extragenic DNA sequences in Escherichia coli. Mol Microbiol 1993; 10:113–122.

    Google Scholar 

  49. Bachellier S, Perrin D, Hofnung M et al. Bacterial interspersed mosaic elements (BIMEs) are present in the genome of Klebsiella. Mol Microbiol 1993; 7:537–544.

    Google Scholar 

  50. Boffini A, Prentki P. Identification of protein binding sites in genomic DNA by two-dimensional gel electrophoresis. Nucleic Acids Res 1991; 19:1369–1374.

    Google Scholar 

  51. Rouviére-Yaniv J, Yaniv M. E. coli DNA binding protein HU forms nu-cleosome-like structure with circular double-stranded DNA. Cell 1979; 17:265–274.

    Google Scholar 

  52. Wang JC, Giaever GN. Action at a distance along a DNA. Science 1988; 240:300–304.

    Google Scholar 

  53. Hodges-Garcia Y, Hagerman PJ, Pettijohn DE. DNA ring closure mediated by protein HU. J Biol Chem 1989; 264:14621–14623.

    Google Scholar 

  54. Pauli TT, Haykinson MJ, Johnson RC. The nonspecific DNA-binding and -bending proteins HMG1 and HMG2 promote the assembly of complex nucleoprotein structures. Genes Dev 1993; 7:1521–1534.

    Google Scholar 

  55. Wu HM, Crothers DM. The locus of sequence-directed and protein-induced DNA bending. Nature 1984; 308:509–513.

    Google Scholar 

  56. Zinkel SS, Crothers DM. Comparative gel electrophoresis measurement of the DNA bend angle induced by the catabolite activator protein. Biopolymers 1990; 29:29–38.

    Google Scholar 

  57. Thompson JF, Landy A. Empirical estimation of protein-induced DNA bending angles: applications to lambda site-specific recombination complexes. Nucleic Acids Res 1988; 16:9687–9705.

    Google Scholar 

  58. Kosturko LD, Daub E, Murialdo H. The interaction of E. coli integration host factor and lambda cos DNA: multiple complex formation and protein-induced bending. Nucleic Acids Res 1989; 17:317–334.

    Google Scholar 

  59. Yang S-M, Kahn JD, Crothers DM. 1995; (in preparation).

    Google Scholar 

  60. Schneider GJ, Sayre MH, Geiduschek EP. DNA-bending properties of TF1. J Mol Biol 1991; 221:777–794.

    Google Scholar 

  61. Kim JL, Nikolov DB, Burley SK. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 1993; 365:520–527.

    Google Scholar 

  62. Kim Y, Geiger JH, Hahn S et al. Crystal structure of a yeast TBP/TATA-box complex. Nature 1993; 365:512–520.

    Google Scholar 

  63. Kahn JD, Crothers DM. Protein-induced bending and DNA cyclization. Proc Natl Acad Sci USA 1992: 89:6343–6347.

    Google Scholar 

  64. Teter B, PhD Thesis (University of S. California, 1991).

    Google Scholar 

  65. Sun D, Harshey RM, Hurley LH. IHF-induced DNA bending studied by DNA cyclization. 1995; (in preparation).

    Google Scholar 

  66. Pontiggia A, Negri A, Beltrame M et al. Protein HU binds specifically to kinked DNA. Mol Microbiol 1993; 7:343–350.

    Google Scholar 

  67. Castaing B, Zelwer C, Laval J et al. HU protein of Escherichia coli binds specifically to DNA that contains single-strand breaks or gaps. J Biol Chem 1995; 270:10291–10296.

    Google Scholar 

  68. Craig NL, Nash HA. E. coli integration host factor binds to specific sites in DNA. Cell 1984; 39:707–716.

    Google Scholar 

  69. Zulianello L, van Ulsen P, van de Putte P et al. Participation of the flank regions of the IHF protein in the specificity and stability of DNA-bind-ing. J Biol Chem 1995; 270:17902–17907.

    Google Scholar 

  70. Lavoie BD, Chaconas G. Site-specific HU binding in the Mu transposo-some: conversion of a sequence-independent DNA-binding protein into a chemical nuclease. Genes Dev 1993; 7:2510–2519.

    Google Scholar 

  71. Neidhardt FC. Multigene Systems and Regulons. In: Neidhardt FC ed. Escherichia coli and Salmonella typhimurium. Washington, DC: American Society for Microbiology, 1987:1313–1317.

    Google Scholar 

  72. Magasanik B, Neidhardt FC. Regulation of carbon and nitrogen utilization. In: Neidhardt FC, ed. Escherichia coli and Salmonella typhimurium. Washington DC: American Society for Microbiology, 1987:1318–1325.

    Google Scholar 

  73. Ball CA, Osuna R, Ferguson KC et al. Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli. J Bacteriol 1992; 174:8043–8056.

    Google Scholar 

  74. Ninnemann O, Koch C, Kahmann R. The E. coli fis promoter is subject to stringent control and autoregulation. EMBO 1992; 11:1075–1083.

    Google Scholar 

  75. Ditto MD, Roberts D, Weisberg RA. Growth phase variation of integration host factor level in Escherichia coli. J Bacteriol 1994; 176:3738–3748.

    Google Scholar 

  76. Kohno K, Wada M, Kano Y et al. Promoters and autogenous control of the Escherichia coli hupA and hupB genes. J Mol Biol 1990; 213:27–36.

    Google Scholar 

  77. . Bushman W, Thompson JF, Vargas L et al. Control of directionality in lambda site specific recombination. Science 1985; 230, 906–911.

    Google Scholar 

  78. Nash HA, Robertson CA, Flamm E et al. Overproduction of Escherichia coli integration host factor, a protein with nonidentical subunits. J Bacteriol 1987; 169:4124–4127.

    Google Scholar 

  79. Aviv M, Giladi H, Schreiber G et al. Expression of the genes coding for the Escherichia coli integration host factor are controlled by growth phase, rpoS, ppGpp and by autoregulation. Mol Microbiol 1994; 14:1021–1031.

    Google Scholar 

  80. Mechulam Y, Blanquet S, Fayat GJ. Dual level control of the Escherichia coli pheST-himA operon expression tRNAPhe -dependent attenuation and transcriptional operator-repressor control by himA and the SOS network. J Mol Biol 1987; 197:453–470.

    Google Scholar 

  81. Flamm EL, Weisberg RA. Primary structure of the hip gene of Escherichia coli and of its product, the β subunit of integration host factor. J Mol Biol 1985; 183:117–128.

    Google Scholar 

  82. Miller HI, Kirk M, Echols H. SOS induction and autoregulation of the himA gene for site-specific recombination in Escherichia coli. Proc Natl Acad Sci USA 1981; 78:6754–6758.

    Google Scholar 

  83. Peterson KR, Mount DW. Differential repression of SOS genes by unstable LexA4l (Tsl-1) protein causes a “split-phenotype” in Escherichia coli K-12. J Mol Biol 1987; 193:27–40.

    Google Scholar 

  84. Mahan MJ, Slauch JM, Mekalanos JJ. Selection of bacterial virulence genes that are specifically induced in host tissues. Science 1993; 259:686–688.

    Google Scholar 

  85. Neidhardt FC. Chemical composition of Escherichia coli. In: Neidhardt FC ed. Escherichia coli and Salmonella typhimurium. Washington DC: American Society for Microbiology, 1987:3–6.

    Google Scholar 

  86. von Hippel PH, Revzin A, Gross CA et al. Non-specific DNA binding of genome regulating proteins as a biological control mechanism: 1. The lac operon: equilibrium aspects. Proc Nat Acad Sci USA 1974; 71:4808–4812.

    Google Scholar 

  87. Lin S-Y, Riggs AD. The general affinity of lac repressor for E. coli DNA: implications for gene regulation in procaryotes and eucaryotes. Cell 1975; 4:107–111.

    Google Scholar 

  88. Stickle DF, Vossen KM, Riley DA et al. Free DNA concentration in E. coli estimated by an analysis of competition for DNA binding proteins. J Theor Biol 1994; 168:1–12.

    Google Scholar 

  89. Grosschedl R, Giese K, Pagel J. HMG domain proteins: Architectural elements in the assembly of nucleoprotein structures. Trends Genet 1994; 10:94–100.

    Google Scholar 

  90. Richet E, Abcarian P, Nash HA. The interaction of recombination proteins with supercoiled DNA: defining the role of supercoiling in lambda integrative recombination. Cell 1986; 46:1011–1021.

    Google Scholar 

  91. Robertson CA., Nash HA. Bending of the bacteriophage λ attachment site by Escherichia coli integration host factor. J Biol Chem 1988; 263:3554–3557.

    Google Scholar 

  92. Goodman SD, Nash HA. Functional replacement of a protein-induced bend in a DNA recombination site. Nature 1989; 341:251–244.

    Google Scholar 

  93. Goodman SD, Nicholson SC, Nash HA. Deformation of DNA during site-specific recombination of bacteriophage λ replacement of IHF protein by HU protein or sequence-directed bends. Proc Natl Acad Sci USA 1992; 89:11910–11914.

    Google Scholar 

  94. Moitoso de Vargas L, Kim S, Landy A. DNA looping generated by DNA bending protein IHF and the two domains of lambda integrase. Science 1989; 244:1457–1461.

    Google Scholar 

  95. Kim S, de Vargas LM, Nunes-Düby SE et al. Mapping of a higher order protein-DNA complex: two kinds of long-range interactions in λ attL. Cell 1990; 63:773–781.

    Google Scholar 

  96. Nash HA. Bending and supercoiling of DNA at the attachment site of bacteriophage λ Trends Biochem Sci 1990; 15:222–227.

    Google Scholar 

  97. Landy A. Mechanistic and structural complexity in the site-specific recombination pathways of Int and FLP. Curr Opin Genet Devel 1993; 3:699–707.

    Google Scholar 

  98. Tang RS, Draper DE. Bulge loops used to measure the helical twist of RNA in solution. Biochemistry 1990; 29:5232–5237.

    Google Scholar 

  99. Kustu S, Santero E, Keener J et al. Expression of a54 (ntrA)-dependent genes is probably united by a common mechanism. Microbiol Rev 1989; 53:367–376.

    Google Scholar 

  100. Hoover TR, Santero E, Porter S et al. The integration host factor stimulates interaction of RNA polymerase with NIFA, the transcriptional activator for nitrogen fixation operons. Cell 1990; 63:11–22.

    Google Scholar 

  101. Claverie-Martin F, Magasanik BJ. Positive and negative effects of DNA bending on activation of transcription from a distant site. J Mol Biol 1992; 227:996–1008.

    Google Scholar 

  102. Perez-Martin J, Timmis KN, de Lorenzo VJ. Co-regulation by bent DNA. J Biol Chem 1994; 269:22657–22662.

    Google Scholar 

  103. Molina-López J, Govantes F, Santero EJ. Geometry of the process of transcription activation at the σ54-dependent nifH promoter of Klebsiella pneumoniae. J Biol Chem 1994; 269:25419–25425.

    Google Scholar 

  104. Krause HM, Higgins NP. Positive and negative regulation of the Mu operator by Mu repressor and Escherichia coli integration host factor. J Biol Chem 1986; 261:3744–3752.

    Google Scholar 

  105. van Rijn PA, van de Putte P, Goosen, N. Analysis of the IHF binding site in the regulatory region of bacteriophage Mu. Nucleic Acids Res 1991; 19:2825–2834.

    Google Scholar 

  106. Alazard R, Bétermier M, Chandler M. Escherichia coli integration host factor stabilizes bacteriophage Mu repressor interactions with operator DNA in vitro. Mol Microbiol 1992; 6:1707–1714.

    Google Scholar 

  107. Betermier M, Rousseau P, Alazard R et al. Mutual stabilisation of bacteriophage Mu repressor and histone like proteins in a nucleoprotein structure. J Mol Biol 1995; 249:332–341.

    Google Scholar 

  108. Mizuuchi M, Mizuuchi K. Efficient Mu transposition requires interaction of transposase with a DNA sequence at the Mu operator: implications for regulation. Cell 1989; 58:399–408.

    Google Scholar 

  109. Lleung PC, Teplow DB, Harshey. Interaction of distinct domains in Mu transposase with Mu DNA ends and an internal transpositional enhancer. Nature 1989; 338:656–658.

    Google Scholar 

  110. Surette MG, Chaconas G. The Mu transpositional enhancer can function in trans: requirement of the enhancer for synapsis but not strand cleavage. Cell 1992; 68:1101–1108.

    Google Scholar 

  111. Surette MG, Lavoie BD, Chaconas G. Action at a distance in Mu DNA transposition: an enhancer-like element is the site of action of supercoil-ing relief activity by integration host factor (IHF). EMBO J 1989; 8:3483–3489.

    Google Scholar 

  112. Vologodskii AV, Cozzarelli NR. Conformational and thermodynamic properties of supercoiled DNA. Ann Rev Biophys Biomol Struct 1994; 23:609–643.

    Google Scholar 

  113. Kornberg A, Baker TA. DNA replication. Second Edition. New York: WH Freeman & Co, 1992.

    Google Scholar 

  114. Polaczek P. Bending of the origin of replication of E. coli by binding of IHF at a specific site. The New Biologist 1990; 2:265–271.

    Google Scholar 

  115. Filutowicz M, Roll J. The requirement of IHF protein for extrachromosomal replication of the Escherichia coli oriC in a mutant deficient in DNA polymerase I activity. The New Biologist 1990; 2:818–827.

    Google Scholar 

  116. Roth A, Urmoneit B, Messer W. Functions of histone-like proteins in the initiation of DNA replication at oriC of Escherichia coli. Biochimie 1994; 6:917–923.

    Google Scholar 

  117. Kano Y, Ogawa T, Ogura T et al. Participation of the histone-like protein HU and of IHF in minichromosomal maintenance in Escherichia coli. Gene 1991; 103:25–30.

    Google Scholar 

  118. Hwang DS, Kornberg AJ. Opening of the replication origin of Escherichia coli by DnaA protein with protein HU or IHF. J Biol Chem 1992; 267:23083–23086.

    Google Scholar 

  119. Cassler MR, Grimwade JE, Leonard AC. Cell cycle-specific changes in nucleoprotein complexes at a chromosomal replication origin. EMBO J 1995; (in press).

    Google Scholar 

  120. Lu M, Campbell JL, Boye E et al. SeqA: a negative modulator of replication initiation in E. coli. Cell 1994; 77:413–426.

    Google Scholar 

  121. Boye E, Lyngstadaas A, Løbner-Olesen A et al. Regulation of DNA replication in Escherichia coli. In: Fanning E, Knippers R, Winnacher E-L, eds. DNA Replication and the Cell Cycle. Heidelberg: Springer-Verlag, 1992; 15–26.

    Google Scholar 

  122. Kleckner N, Chalmers R, Kwon D et al. Tn10 and IS10 transposition and chromosome rearrangements: mechanism and regulation in vivo and in vitro. In: Saedler H, Gierl A, eds. Transposable Elements. Current Topics in Microbiology and Immunology. New York: Springer-Verlag, 1995; (in press).

    Google Scholar 

  123. Morisato D, Kleckner N. TnlO transposition and circle formation in vitro. Cell 1987; 51:101–111.

    Google Scholar 

  124. Chalmers RM, Kleckner NJ. Tn10/IS10 Transposase purification, activation, and in vitro reaction. J Biol Chem 1994; 269:8029–8035.

    Google Scholar 

  125. Signon L, Kleckner N. Negative and positive regulation of Tn10/IS10-promoted recombination by IHF: two distinguishable processes inhibit transposition off of multicopy plasmid replicons and activate chromosomal events that favor evolution of new transposons. Genes Dev 1995; 9:1123–1136.

    Google Scholar 

  126. Goosen N, van de Putte P. The regulation of transcription initiation by integration host factor. Mol Microbiol 1995; 16:1–7.

    Google Scholar 

  127. Pereira RF, Ortuno MJ, Lawther RP. Binding of integration host factor (IHF) to the ilvGp1 promoter of the ilvGMEDA Operon of Escherichia coli K12. Nucleic Acids Res 1988; 16:5973–5989.

    Google Scholar 

  128. Pagel JM, Winkelman JW, Adams CW et al. DNA topology-mediated regulation of transcription initiation from the tandem promoters of the ilvGMEDA operon of Escherichia coli. J Mol Biol 1992; 224:919–935.

    Google Scholar 

  129. Huisman O, Errada PR, Signon L et al. Mutational analysis of IS10’s outside end. EMBO J 1989; 8:2101–2109.

    Google Scholar 

  130. Giladi H, Igarashi K, Ishihama A et al. Stimulation of the phage λ pL promoter by integration host factor requires the carboxy terminus of the α-subunit of RNA polymerase. J Mol Biol 1992; 227:985–990.

    Google Scholar 

  131. Giladi H, Gottesman M, Oppenheim AB. Integration host factor stimulates the phage lambda pL promoter. J Mol Biol 1990; 213:109–121.

    Google Scholar 

  132. Giladi H, Koby S, Gottesman ME et al. Supercoiling, integration host factor, and a dual promoter system, participate in the control of the bacteriophage λ pL promoter. J Mol Biol 1992; 224:937–948.

    Google Scholar 

  133. Higgins NP, Collier DA, Kilpatrick MW et al. Supercoiling and integration host factor change the DNA conformation and alter the flow of convergent transcription in phage mu. J Biol Chem 1989; 264:3035–3042.

    Google Scholar 

  134. van Rijn PA, Goosen N, van de Putte P. Integration host factor of Escherichia coli regulates early and repressor transcription of bacteriophage Mu by two different mechanisms. Nucleic Acid Res 1988; 16:4595–4605.

    Google Scholar 

  135. Mizuuchi K. Transpositional recombination: mechanistic insights from studies of Mu and other elements. Annu Rev Biochem 1992; 61: 1011–1051.

    Google Scholar 

  136. Mizuuchi M, Baker T, Mizuuchi K. Assembly of the active form of the transposase-Mu DNA complex: a critical control point in Mu transposition. Cell 1992; 70:303–311.

    Google Scholar 

  137. Surette MG, Chaconas GJ. A protein factor which reduces the negative supercoiling requirment in the Mu DNA strand transfer reaction is Escherichia coli integration host factor. J Biol Chem 1989; 264:3028–3034.

    Google Scholar 

  138. Lavoie BD, Chaconas GJ. Immunoelectron microscopic analysis of the A, B, and HU protein content of bacteriophage Mu transpososomes. J Biol Chem 1990; 265:1623–1627.

    Google Scholar 

  139. Lavoie BD, Chaconas GJ. A second high affinity HU binding site in the phage Mu transpososome. J Biol Chem 1994; 269:15571–15576.

    Google Scholar 

  140. Johnson R. Mechanism of site-specific DNA inversion in bacteria. Curr Opin Genet Devel 1991; 1:412–416.

    Google Scholar 

  141. Johnson RC, Bruist MF, Simon MI. Host protein requirements for in vitro site-specific DNA inversion. Cell 1986; 46:531–539.

    Google Scholar 

  142. Pauli TT, Haykinson MJ, Johnson RC. HU and functional analogs in eukaryotes promote Hin invertasome assembly. Biochimie 1994; 76:992–1004.

    Google Scholar 

  143. Haykinson MJ, Johnson RC. DNA looping and the helical repeat in vitro and in vivo: effect of Hu protein and enhancer location on Hin invertasome assembly. EMBO J 1993; 12:2503–2512.

    Google Scholar 

  144. Hillyard DR, Edlund M, Hughes KT et al. Subunit-specific phenotypes of Salmonella typhimurium HU mutants. J Bacteriol 1990; 172:5402–5407.

    Google Scholar 

  145. Wada M, Kutsukake K, Komano T et al. Participation of the hup gene product in site-specific DNA inversion in Escherichia coli. Gene 1989; 76:345–352.

    Google Scholar 

  146. Koch C, Kahmann RJ. Purification and properties of the Escherichia coli host factor required for inversion of the G segment in bacteriophage Mu. J Biol Chem 1986; 261:15673–15678.

    Google Scholar 

  147. Pauli TT, Johnson RC. DNA looping by Saccharomyces cerevisiae high mobility group proteins NHP6A/B. J Biol Chem 1995; 270:8744–8754.

    Google Scholar 

  148. Bianchi ME. Prokaryotic HU and eukaryotic HMG1: a kinked relationship. Mol Microbiol 1994; 4:1–5.

    Google Scholar 

  149. Segall AM, Goodman SD, Nash HA. Architectural elements in nucle-oprotein complexes. EMBO J 1994; 13:4536–4548.

    Google Scholar 

  150. Nash HA, Robertson CA. Purification and properties of the Escherichia coli protein factor required for λ integrative recombination. J Biol Chem 1981; 256:9246–9253.

    Google Scholar 

  151. Gamas P, Burger AC, Churchward G et al. Replication of pSC101: effects of mutations in the E. coli DNA binding protein IHF. Mol Gen Genet 1986; 204:85–89.

    Google Scholar 

  152. Stenzel TT, 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; 49:709–717.

    Google Scholar 

  153. Hoyt MA, Knight DM, Das A et al. Control of phage λ development by stability and synthesis of cII protein: role of the viral cIII and host hflA, himA and himD genes. Cell 1982; 31:565–573.

    Google Scholar 

  154. Mahajna J, Oppenheim AB, Rattray A et al. Translation initiation of bacteriophage lambda gene cII requires integration host factor. J Bacteriol 1986; 165:167–174.

    Google Scholar 

  155. Rabin RS, Collins LA, Stewart V. In vivo requirement of integration host factor for nar (nitrate reductase) Operon expression in Escherichia coli K-12. Proc Natl Acad Sci USA 1992; 89:8701–8705.

    Google Scholar 

  156. Schröder I, Darie S, Gunsalus RP. Activation of the Escherichia coli nitrate reductase (narGHJT) Operon by NarL and Fnr requires integration host factor. J Biol Chem 1993; 268:771–774.

    Google Scholar 

  157. Wu Y, Datta PJ. Integration host factor is required for positive regulation of the tdc operon of Escherichia coli. J Bacteriol 1992; 174:233–240.

    Google Scholar 

  158. Weiss DS, Klose KE, Hoover TR et al. Prokaryotic transcriptional enhancers. In: McKinght SL, Yamamoto KR eds. Transcriptional Regulation. Cold Spring Harbor: Cold Spring Harbor Press, 1992:667–694.

    Google Scholar 

  159. Pérez-Martín J, de Lorenzo V. Integration host factor (IHF) suppresses promiscuous activation of the σ54-dependent promoter Pu of Pseudomaonas putita. Proc Natl Acad Sci USA 1995; 92:7277–7281.

    Google Scholar 

  160. Ogawa T, Wada M, Kano Y et al. DNA replication in Escherichia coli mutants that lack protein HU. J Bacteriol 1989; 171:5672–5679.

    Google Scholar 

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

    Google Scholar 

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

    Google Scholar 

  163. Travers AA, Ner SS, Churchill, MEA. DNA chaperones: a solution to a persistence problem. Cell 1994; 77:167–169.

    Google Scholar 

  164. Schneider GJ, Geiduschek EP. Stoichiometry of DNA binding by the bacteriophage SPO1-encoded type II DNA-binding protein TF1. J Biol Chem 1990; 265:10198–10200.

    Google Scholar 

  165. Kano Y, Imamoto F. Requirement of integration host factor (IHF) for growth of Escherichia coli deficient in HU protein. Gene 1990; 89:133–137.

    Google Scholar 

  166. Friedman DI, Olson EJ, Carver D et al. Synergistic effect of himA and gyrB mutations: evidence that Him functions control expression of ilv and xyl genes. J Bacteriol 1984; 157:484–489.

    Google Scholar 

  167. Roberts DE. Genetic analysis of mutants of E. coli affected for Tn10 transposition. (Harvard University, 1986).

    Google Scholar 

  168. Yasuzawa K, Hayashi N, Goshima N et al. Histone-like proteins are required for cell growth and constraint of supercoils in DNA. Gene 1992; 122:9–15.

    Google Scholar 

  169. Goshima N, Kano Y, Tanaka H et al. IHF supresses the inhibitory effect of H-NS on HU function in the hin inversion system. Gene 1994; 141:17–23.

    Google Scholar 

  170. Kano Y, Yasuzawa K, Tanaka H et al. Propagation of phage Mu in IHF-deficient Escherichia coli in the absence of the H-NS histone-like protein. Gene 1993; 126:93–97.

    Google Scholar 

  171. Sayre MH, Geiduschek EP. Construction and properties of a temperature-sensitive mutation in the gene for the bacteriophage SPO1 DNA-binding protein TF1. J Bacteriol 1990; 172:4672–4681.

    Google Scholar 

  172. Hayes JJ, Wolffe AP. The interaction of transcription factors with nu-cleosomal DNA. BioEssays 1992; 14:597–603.

    Google Scholar 

  173. Ramakrishnan V. Histone structure. Curr Opin Struct Biol 1994; 4:44–50.

    Google Scholar 

  174. Wallrath LL, Lu Q, Granok H et al. Architectural variations of inducible eukaryotic promoters: preset and remodeling chromatin structures. Bioessays 1994; 16:165–170.

    Google Scholar 

  175. Sandman K, Perler FB, Reeve JN. Histone-encoding genes from Pyrococcus: evidence for members of the HMF family of archaeal histories in a non-methanogenic Archaeon. Gene 1994; 150:207–208.

    Google Scholar 

  176. Dürrenberger M, Bjornsti MA, Uetz T et al. J Bacteriol 1988; 170:4757–4768.

    Google Scholar 

  177. Shellman VL, Pettijohn DE. Introduction of proteins into living bacterial cells: distribution of labeled HU protein in Escherichia coli. J Bacteriol 1991; 173:3047–3059.

    Google Scholar 

  178. Revzin A. Techniques for characterizing nonspecific DNA-protein interactions. In: Reuzin A, ed. The Biology of Nonspecific DNA-Protein Interactions. Ann Arbor: CRC Press, 1990:6–31.

    Google Scholar 

  179. Toussaint B, Delic-Attree I, De Sury d’Aspremont R et al. Purification of the integration host factor homolog of Rhodobacter capsulatus: cloning and sequencing of the hip gene, which encodes the ß subunit. J Bacteriol 1993; 175:6499–6504.

    Google Scholar 

  180. Kim S, Landy A. Lambda Int protein bridges between higher order complexes at two distant chromosomal loci attL and attR. Science 1992; 256:198–203.

    Google Scholar 

  181. Richet E, Abcarian P, Nash HA. Synapsis of attachment sites during lambda integrative recombination involves capture of a naked DNA by a protein-DNA complex. Cell 1988; 52:9–17.

    Google Scholar 

  182. Pérez-Martín J, Rojo F, de Lorezo V. Promoters responsive to DNA bending: A common theme in prokaryotic gene expressionn. Microbiol Rev 1994; 58:268–290

    Google Scholar 

Download references

Authors
  1. Howard A. Nash
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

Copyright information

© 1996 R.G. Landes Company

About this chapter

Cite this chapter

Nash, H.A. (1996). The HU and IHF Proteins: Accessory Factors for Complex Protein-DNA Assemblies. In: Regulation of Gene Expression in Escherichia coli . Springer, Boston, MA. https://doi.org/10.1007/978-1-4684-8601-8_8

Download citation

  • DOI: https://doi.org/10.1007/978-1-4684-8601-8_8

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4684-8603-2

  • Online ISBN: 978-1-4684-8601-8

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation