Advertisement

Role of HU in Regulation of gal Promoters

  • Dale E. A. Lewis
  • Sang Jun Lee
  • Sankar Adhya

Abstract

HU is one of the histone-like DNA binding proteins, which are involved in maintaining the nucleoid structure in bacteria. HU has also been shown to ­participate in transcriptional regulation of specific promoters. In this chapter, we provide an overview of the mechanism of HU action in the transcriptional ­regulation of the two promoters of the gal operon in E. coli by providing results of genetic, biophysical and biochemical experiments both in vivo and in vitro.

Keywords

Anti-parallel DNA Looping Atomic Force Microscopy gal Operon GalR HU 

Notes

Acknowledgements

Much of the work described in this chapter is from the authors’ laboratory. We gratefully acknowledge the contributions of many of our past and present colleagues and collaborators too numerous to list. We are supported by the Intramural Research Program of the National Institutes of Health, the National Cancer Institute, the Center for Cancer Research. We thank Dr. Dhruba Chattoraj for suggestions and critical reading of the manuscript.

References

  1. Adhya S, Echols H (1966) Glucose effect and the galactose enzymes of Escherichia coli: correlation between glucose inhibition of induction and inducer transport. J Bacteriol 92:601-608PubMedGoogle Scholar
  2. Adhya S, Miller W (1979) Modulation of the two promoters of the galactose operon of Escherichia coli. Nature 279:492-494CrossRefPubMedGoogle Scholar
  3. Adhya S, Geanacopoulos M, Lewis DE, Roy S, Aki T (1998) Transcription regulation by repressosome and by RNA polymerase contact. Cold Spring Harb Symp Quant Biol 63:1-9CrossRefPubMedGoogle Scholar
  4. Aki T, Adhya S (1997) Repressor induced site-specific binding of HU for transcriptional regulation. EMBO J 16:3666-3674CrossRefPubMedGoogle Scholar
  5. Aki T, Choy HE, Adhya S (1996) Histone-like protein HU as a specific transcriptional regulator: co-factor role in repression of gal transcription by GAL repressor. Genes Cells 1:179-188CrossRefPubMedGoogle Scholar
  6. Alberti S, Oehler S, von Wilcken-Bergmann B, Kramer H, Muller-Hill B (1991) Dimer-to-tetramer assembly of Lac repressor involves a leucine heptad repeat. New Biol 3:57-62PubMedGoogle Scholar
  7. Alberti S, Oehler S, von Wilcken-Bergmann B, Muller-Hill B (1993) Genetic analysis of the leucine heptad repeats of Lac repressor: evidence for a 4-helical bundle. EMBO J 12:3227-3236PubMedGoogle Scholar
  8. Bonnefoy E, Rouvière-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 10:687-696PubMedGoogle Scholar
  9. Bonnefoy E, Takahashi M, Yaniv JR (1994) DNA-binding parameters of the HU protein of Escherichia coli to cruciform DNA. J Mol Biol 242:116-129CrossRefPubMedGoogle Scholar
  10. Borowiec JA, Zhang L, Sasse-Dwight S, Gralla JD (1987) DNA supercoiling promotes formation of a bent repression loop in lac DNA. J Mol Biol 196:101-111CrossRefPubMedGoogle Scholar
  11. Bouffard GG, Rudd KE, Adhya SL (1994) Dependence of lactose metabolism upon mutarotase encoded in the gal operon in Escherichia coli. J Mol Biol 244:269-278CrossRefPubMedGoogle Scholar
  12. Brenowitz M, Jamison E, Majumdar A, Adhya S (1990) Interaction of the Escherichia coli Gal repressor protein with its DNA operators in vitro. Biochemistry 29:3374-3383CrossRefPubMedGoogle Scholar
  13. Brenowitz M, Mandal N, Pickar A, Jamison E, Adhya S (1991) DNA-binding properties of a lac repressor mutant incapable of forming tetramers. J Biol Chem 266:1281-1288PubMedGoogle Scholar
  14. Buttin G (1963) Regulatory mechanisms in the biosynthesis of the enzymes of galactose metabolism in Escherichia coli K 12. Ii. the genetic determinism of the regulation. J Mol Biol 7:183-205CrossRefPubMedGoogle Scholar
  15. Castaing 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 270:10291-10296CrossRefPubMedGoogle Scholar
  16. Charlier M, Maurizot JC, Zaccai G (1980) Neutron scattering studies of lac repressor. Nature 286:423-425CrossRefPubMedGoogle Scholar
  17. Charvin G, Allemand JF, Strick TR, Bensimon D, Croquette V (2004) Twisting DNA: single molecule studies. Contemp Phys 45:383-403CrossRefGoogle Scholar
  18. Choy HE, Adhya S (1992) Control of gal transcription through DNA looping: inhibition of the initial transcribing complex. Proc Natl Acad Sci USA 89:11264-11268CrossRefPubMedGoogle Scholar
  19. Choy HE, Park SW, Aki T, Parrack P, Fujita N, Ishihama A, Adhya S (1995a) Repression and activation of transcription by Gal and Lac repressors: involvement of alpha subunit of RNA polymerase. EMBO J 14:4523-4529PubMedGoogle Scholar
  20. Choy HE, Park SW, Parrack P, Adhya S (1995b) Transcription regulation by inflexibility of promoter DNA in a looped complex. Proc Natl Acad Sci USA 92:7327-7331CrossRefPubMedGoogle Scholar
  21. Choy HE, Hanger RR, Aki T, Mahoney M, Murakami K, Ishihama A, Adhya S (1997) Repression and activation of promoter-bound RNA polymerase activity by Gal repressor. J Mol Biol 272:293-300CrossRefPubMedGoogle Scholar
  22. Craigie R, Mizuuchi K (1985) Mechanism of transposition of bacteriophage Mu: structure of a transposition intermediate. Cell 41:867-876CrossRefPubMedGoogle Scholar
  23. Dandanell G, Hammer K (1985) Two operator sites separated by 599 base pairs are required for deoR repression of the deo operon of Escherichia coli. EMBO J 4:3333-3338PubMedGoogle Scholar
  24. Dickerson RE (1998) DNA bending: the prevalence of kinkiness and the virtues of normality. Nucleic Acids Res 26:1906-1926CrossRefPubMedGoogle Scholar
  25. Drlica K (1987) The nucleoid. In: Neidhardt FC, Ingraham JL, Low KB, Magasanik B, Schaechter M, Umbarger HE (eds) Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. American Society for Microbiology, Washington, DC, pp 91-103Google Scholar
  26. Drlica K, Rouvière-Yaniv J (1987) Histonelike proteins of bacteria. Microbiol Rev 51:301-319PubMedGoogle Scholar
  27. Dunn TM, Schleif R (1984) Deletion analysis of the Escherichia coli ara PC and PBAD promoters. J Mol Biol 180:201-204CrossRefPubMedGoogle Scholar
  28. Echols H, Reznichek J, Adhya S (1963) Complementation, recombination, and suppression in galactose negative mutants of E. coli. Proc Natl Acad Sci USA 50:286-293CrossRefPubMedGoogle Scholar
  29. Friedman AM, Fischmann TO, Steitz TA (1995) Crystal structure of lac repressor core tetramer and its implications for DNA looping. Science 268:1721-1727CrossRefPubMedGoogle Scholar
  30. Geanacopoulos M, Vasmatzis G, Lewis DE, Roy S, Lee B, Adhya S (1999) GalR mutants defective in repressosome formation. Genes Dev 13:1251-1262CrossRefPubMedGoogle Scholar
  31. Geanacopoulos M, Vasmatzis G, Zhurkin VB, Adhya S (2001) Gal repressosome contains an antiparallel DNA loop. Nat Struct Biol 8:432-436CrossRefPubMedGoogle Scholar
  32. Griffith J, Hochschild A, Ptashne M (1986) DNA loops induced by cooperative binding of lambda repressor. Nature 322:750-752CrossRefPubMedGoogle Scholar
  33. Grove A, Galeone A, Mayol L, Geiduschek EP (1996) Localized DNA flexibility contributes to target site selection by DNA-bending proteins. J Mol Biol 260:120-125CrossRefPubMedGoogle Scholar
  34. Haber R, Adhya S (1988) Interaction of spatially separated protein-DNA complexes for control of gene expression: operator conversions. Proc Natl Acad Sci USA 85:9683-9687CrossRefPubMedGoogle Scholar
  35. Hahn S, Hendrickson W, Schleif R (1986) Transcription of Escherichia coli ara in vitro. The cyclic AMP receptor protein requirement for PBAD induction that depends on the presence and orientation of the araO2 site. J Mol Biol 188:355-367CrossRefPubMedGoogle Scholar
  36. Hochschild A, Ptashne M (1986) Homologous interactions of lambda repressor and lambda Cro with the lambda operator. Cell 44:925-933CrossRefPubMedGoogle Scholar
  37. Irani MH, Orosz L, Adhya S (1983) A control element within a structural gene: the gal operon of Escherichia coli. Cell 32:783-788CrossRefPubMedGoogle Scholar
  38. Kabsch W, Sander C, Trifonov EN (1982) The ten helical twist angles of B-DNA. Nucleic Acids Res 10:1097-1104CrossRefPubMedGoogle Scholar
  39. Kano Y, Wada M, Nagase T, Imamoto F (1986) Genetic characterization of the gene hupB encoding the HU-1 protein of Escherichia coli. Gene 45:37-44CrossRefPubMedGoogle Scholar
  40. Kano Y, Osato K, Wada M, Imamoto F (1987) Cloning and sequencing of the HU-2 gene of Escherichia coli. Mol Gen Genet 209:408-410CrossRefPubMedGoogle Scholar
  41. Kar S, Adhya S (2001) Recruitment of HU by piggyback: a special role of GalR in repressosome assembly. Genes Dev 15:2273-2281CrossRefPubMedGoogle Scholar
  42. Kobryn K, Lavoie BD, Chaconas G (1999) Supercoiling-dependent site-specific binding of HU to naked Mu DNA. J Mol Biol 289:777-784CrossRefPubMedGoogle Scholar
  43. Kramer H, Niemoller M, Amouyal M, Revet B, von Wilcken-Bergmann B, Muller-Hill B (1987) lac repressor forms loops with linear DNA carrying two suitably spaced lac operators. EMBO J 6:1481-1491PubMedGoogle Scholar
  44. Kramer H, Amouyal M, Nordheim A, Muller-Hill B (1988) DNA supercoiling changes the spacing requirement of two lac operators for DNA loop formation with lac repressor. EMBO J 7:547-556PubMedGoogle Scholar
  45. Kuhnke G, Krause A, Heibach C, Gieske U, Fritz HJ, Ehring R (1986) The upstream operator of the Escherichia coli galactose operon is sufficient for repression of transcription initiated at the cyclic AMP-stimulated promoter. EMBO J 5:167-173PubMedGoogle Scholar
  46. Lavoie BD, Chaconas G (1993) Site-specific HU binding in the Mu transpososome: conversion of a sequence-independent DNA-binding protein into a chemical nuclease. Genes Dev 7:2510-2519CrossRefPubMedGoogle Scholar
  47. Lavoie BD, Shaw GS, Millner A, Chaconas G (1996) Anatomy of a flexer-DNA complex inside a higher-order transposition intermediate. Cell 85:761-771CrossRefPubMedGoogle Scholar
  48. Law SM, Bellomy GR, Schlax PJ, Record MT Jr (1993) In vivo thermodynamic analysis of repression with and without looping in lac constructs. Estimates of free and local lac repressor concentrations and of physical properties of a region of supercoiled plasmid DNA in vivo. J Mol Biol 230:161-173CrossRefPubMedGoogle Scholar
  49. Lee DH, Schleif RF (1989) In vivo DNA loops in araCBAD: size limits and helical repeat. Proc Natl Acad Sci USA 86:476-480CrossRefPubMedGoogle Scholar
  50. Lewis DE (2003) Identification of promoters of Escherichia coli and phage in transcription section plasmid pSA850. Methods Enzymol 370:618-645CrossRefPubMedGoogle Scholar
  51. Lewis DE, Adhya S (2002) In vitro repression of the gal promoters by GalR and HU depends on the proper helical phasing of the two operators. J Biol Chem 277:2498-2504CrossRefPubMedGoogle Scholar
  52. Lewis M, Chang G, Horton NC, Kercher MA, Pace HC, Schumacher MA, Brennan RG, Lu P (1996) Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science 271:1247-1254CrossRefPubMedGoogle Scholar
  53. Lewis DE, 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 Microbiol 31:451-461CrossRefPubMedGoogle Scholar
  54. Lia G, Bensimon D, Croquette V, Allemand JF, Dunlap D, Lewis DE, Adhya S, Finzi L (2003) Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping. Proc Natl Acad Sci USA 100:11373-11377CrossRefPubMedGoogle Scholar
  55. Lia G, Semsey S, Lewis DE, Adhya S, Bensimon D, Dunlap D, Finzi L (2008) The antiparallel loops in gal DNA. Nucleic Acids Res 36:4204-4210CrossRefPubMedGoogle Scholar
  56. Lobell RB, Schleif RF (1990) DNA looping and unlooping by AraC protein. Science 250:528-532CrossRefPubMedGoogle Scholar
  57. Majumdar A, Adhya S (1984) Demonstration of two operator elements in gal: in vitro repressor binding studies. Proc Natl Acad Sci USA 81:6100-6104CrossRefPubMedGoogle Scholar
  58. Majumdar A, Adhya S (1987) Probing the structure of gal operator-repressor complexes. Conformation change in DNA. J Biol Chem 262:13258-13262PubMedGoogle Scholar
  59. Majumdar A, Rudikoff S, Adhya S (1987) Purification and properties of Gal repressor:pL-galR fusion in pKC31 plasmid vector. J Biol Chem 262:2326-2331PubMedGoogle Scholar
  60. Mandal N, Su W, Haber R, Adhya S, Echols H (1990) DNA looping in cellular repression of transcription of the galactose operon. Genes Dev 4:410-418CrossRefPubMedGoogle Scholar
  61. Mossing MC, Record MT Jr (1986) Upstream operators enhance repression of the lac promoter. Science 233:889-892CrossRefPubMedGoogle Scholar
  62. Muller J, Oehler S, Muller-Hill B (1996) Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator. J Mol Biol 257:21-29CrossRefPubMedGoogle Scholar
  63. Muller J, Barker A, Oehler S, Muller-Hill B (1998) Dimeric lac repressors exhibit phase-dependent co-operativity. J Mol Biol 284:851-857CrossRefPubMedGoogle Scholar
  64. Murphy LD, Zimmerman SB (2000) Multiple restraints to the unfolding of spermidine nucleoids from Escherichia coli. J Struct Biol 132:46-62CrossRefPubMedGoogle Scholar
  65. Musso RE, Di Lauro R, Adhya S, de Crombrugghe B (1977) Dual control for transcription of the galactose operon by cyclic AMP and its receptor protein at two interspersed promoters. Cell 12:847-854CrossRefPubMedGoogle Scholar
  66. Oberto J, Drlica K, Rouvière-Yaniv J (1994) Histones, HMG, HU, IHF: meme combat. Biochimie 76:901-908CrossRefPubMedGoogle Scholar
  67. Oehler S, Eismann ER, Kramer H, Muller-Hill B (1990) The three operators of the lac operon cooperate in repression. EMBO J 9:973-979PubMedGoogle Scholar
  68. Pennington MR (2006) Sigma coupling to photons: hidden scalar in gammagamma -> pi0pi0. Phys Rev Lett 97:011601CrossRefPubMedGoogle Scholar
  69. Perez N, Rehault M, Amouyal M (2000) A functional assay in Escherichia coli to detect non-assisted interaction between galactose repressor dimers. Nucleic Acids Res 28:3600-3604CrossRefPubMedGoogle Scholar
  70. Pettijohn DE (1988) Histone-like proteins and bacterial chromosome structure. J Biol Chem 263:12793-12796PubMedGoogle Scholar
  71. Pettijohn DE (1996) The nucleoid. In: Curtis R, Ingraham JL, Lin ECC, Low KB, Magasanik B, and Reznikoff WS et al. (eds) Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd edn. American Society for Microbiology, Washington, DC, pp 158-166Google Scholar
  72. Pontiggia A, Negri A, Beltrame M, Bianchi ME (1993) Protein HU binds specifically to kinked DNA. Mol Microbiol 7:343-350CrossRefPubMedGoogle Scholar
  73. Ptashne M (1986) Gene regulation by proteins acting nearby and at a distance. Nature 322:697-701CrossRefPubMedGoogle Scholar
  74. Reitzer LJ, Magasanik B (1986) Transcription of glnA in E. coli is stimulated by activator bound to sites far from the promoter. Cell 45:785-792CrossRefPubMedGoogle Scholar
  75. Rhodes D, Klug A (1980) Helical periodicity of DNA determined by enzyme digestion. Nature 286:573-578CrossRefPubMedGoogle Scholar
  76. Rice PA, Yang S, Mizuuchi K, Nash HA (1996) Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell 87:1295-1306CrossRefPubMedGoogle Scholar
  77. Rouvière-Yaniv J (1978) Localization of the HU protein on the Escherichia coli nucleoid. Cold Spring Harb Symp Quant Biol 42(Pt 1):439-447PubMedGoogle Scholar
  78. Rouvière-Yaniv J, Gros F (1975) Characterization of a novel, low-molecular-weight DNA-binding protein from Escherichia coli. Proc Natl Acad Sci USA 72:3428-3432CrossRefPubMedGoogle Scholar
  79. Roy S, Semsey S, Liu M, Gussin GN, Adhya S (2004) GalR represses galP1 by inhibiting the rate-determining open complex formation through RNA polymerase contact: a GalR negative control mutant. J Mol Biol 344:609-618CrossRefPubMedGoogle Scholar
  80. Roy S, Dimitriadis EK, Kar S, Geanacopoulos M, Lewis MS, Adhya S (2005) Gal repressor-operator-HU ternary complex: pathway of repressosome formation. Biochemistry 44:5373-5380CrossRefPubMedGoogle Scholar
  81. Schleif R (1987) Gene regulation: why should DNA loop? Nature 327:369-370CrossRefPubMedGoogle Scholar
  82. Schumacher MA, Choi KY, Zalkin H, Brennan RG (1994) Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices. Science 266:763-770CrossRefPubMedGoogle Scholar
  83. Semsey S, Geanacopoulos M, Lewis DE, Adhya S (2002) Operator-bound GalR dimers close DNA loops by direct interaction: tetramerization and inducer binding. EMBO J 21:4349-4356CrossRefPubMedGoogle Scholar
  84. Semsey S, Tolstorukov MY, Virnik K, Zhurkin VB, Adhya S (2004) DNA trajectory in the Gal repressosome. Genes Dev 18:1898-1907CrossRefPubMedGoogle Scholar
  85. Shapiro JA, Adhya SL (1969) The galactose operon of E. coli K-12. II. A deletion analysis of operon structure and polarity. Genetics 62:249-264PubMedGoogle Scholar
  86. Shore D, Baldwin RL (1983) Energetics of DNA twisting I. Relation between twist and cyclization probability. J Mol Biol 170:957-981CrossRefPubMedGoogle Scholar
  87. Surette MG, Buch SJ, Chaconas G (1987) Transpososomes: stable protein-DNA complexes involved in the in vitro transposition of bacteriophage Mu DNA. Cell 49:253-262CrossRefPubMedGoogle Scholar
  88. Tanaka H, Goshima N, Kohno K, Kano Y, Imamoto F (1993) Properties of DNA-binding of HU heterotypic and homotypic dimers from Escherichia coli. J Biochem 113:568-572PubMedGoogle Scholar
  89. Tullius TD, Dombroski BA (1985) Iron(II) EDTA used to measure the helical twist along any DNA molecule. Science 230:679-681CrossRefPubMedGoogle Scholar
  90. Virnik K, Lyubchenko YL, Karymov MA, Dahlgren P, Tolstorukov MY, Semsey S, Zhurkin VB, Adhya S (2003) “Antiparallel” DNA loop in gal repressosome visualized by atomic force microscopy. J Mol Biol 334:53-63CrossRefPubMedGoogle Scholar
  91. von Wilcken-Bergmann B, Muller-Hill B (1982) Sequence of galR gene indicates a common evolutionary origin of lac and gal repressor in Escherichia coli. Proc Natl Acad Sci USA 79:2427-2431CrossRefGoogle Scholar
  92. Wang JC (1979) Helical repeat of DNA in solution. Proc Natl Acad Sci USA 76:200-203CrossRefPubMedGoogle Scholar
  93. Wang JC, Giaever GN (1988) Action at a distance along a DNA. Science 240:300-304CrossRefPubMedGoogle Scholar
  94. Wang MD, Schnitzer MJ, Yin H, Landick R, Gelles J, Block SM (1998) Force and velocity measured for single molecules of RNA polymerase. Science 282:902-907CrossRefPubMedGoogle Scholar
  95. Weickert MJ, Adhya S (1992) A family of bacterial regulators homologous to Gal and Lac repressors. J Biol Chem 267:15869-15874PubMedGoogle Scholar
  96. Yang B, Larson TJ (1996) Action at a distance for negative control of transcription of the glpD gene encoding sn-glycerol 3-phosphate dehydrogenase of Escherichia coli K-12. J Bacteriol 178:7090-7098PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Dale E. A. Lewis
    • 1
  • Sang Jun Lee
    • 1
  • Sankar Adhya
    • 1
  1. 1.Laboratory of Molecular BiologyNational Cancer InstituteBethesdaUSA

Personalised recommendations