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Indirect Effects of DNA Sequence on Transcriptional Activation by Prokaryotic DNA Binding Proteins

  • Chapter
Book cover Mechanisms of Transcription

Part of the book series: Nucleic Acids and Molecular Biology ((NUCLEIC,volume 11))

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Abstract

Most prokaryotic transcriptional activators are sequence-specific DNA binding proteins which activate transcription at various promoters by increasing the rate of transcription initiation by RNA polymerase. In these organisms, the activator protein binds to a specific DNA sequence at or near the promoter, influencing RNA polymerase by making direct contacts with the promoter-bound polymerase. Several studies have shown that changing the juxtaposition of the activator binding site with respect to the promoter can dramatically influence the effectiveness of the activator protein (Gaston et al. 1990; Lavigne et al. 1992; Joung et al. 1993; Woody et al. 1993). These observations indicate that proper alignment of the activator surface and the RNA polymerase are crucial for functional catalysis of transcription initiation by the activator protein. Hence, alterations in the geometry of the ternary complex formed between the polymerase, the activator protein, and DNA may be expected to influence the efficiency of transcription initiation.

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References

  • Ansari AZ, Chael ML, O’Halloran TV (1992) Allosteric underwinding of DNA is a critical step in positive control of transcription by Hg-MerR. Nature 355:87–89

    Article  PubMed  CAS  Google Scholar 

  • Ansari AZ, Bradner JE, O’Halloran TV (1995) DNA-bend modulation in a repressor-to-activator switching mechanism. Nature 374:371–375

    Article  PubMed  CAS  Google Scholar 

  • Assa-Munt N, Mortishire-Smith RJ, Aurora R, Herr W, Wright PE (1993) The solution structure of the Oct-1 POU-specific domain reveals a striking similarity to the bacteriophage lambda repressor DNA-binding domain. Cell 73:193–205

    Article  PubMed  CAS  Google Scholar 

  • Attey A, Belyaeva T, Savery N, Hoggett J, Fujita N, Ishihama A, Busby S (1994) Interactions between the cyclic AMP receptor protein and the alpha subunit of RNA polymerases at the Escherichia coli galactose operon PI promoter. Nucleic Acids Res 22:4375–4380

    Article  PubMed  CAS  Google Scholar 

  • Bell A, Gaston K, Williams R, Chapman K, Kolb A, Buc H, Minchin S, Williams J, Busby S (1990) Mutations that alter the ability of the Escherichia coli cyclic AMP receptor protein to activate transcription. Nucleic Acids Res 18:7243–7250

    Article  PubMed  CAS  Google Scholar 

  • Bell AC, Koudelka GB (1993) Operator sequence context influences amino acid-base-pair interactions in 434 repressor-operator complexes. J Mol Biol 234:542–553

    Article  PubMed  CAS  Google Scholar 

  • Bell AC, Koudelka GB (1995) How 434 repressor discriminates between OR1 and OR3. The influence of contacted and noncontacted base pairs. J Biol Chem 270:1205–1212

    Article  PubMed  CAS  Google Scholar 

  • Blatter EE, Ross W, Tang H, Gourse RL, Ebright RH (1994) Domain organization of RNA polymerase a subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding. Cell 78:889–896

    Article  PubMed  CAS  Google Scholar 

  • Busby S, Ebright RH (1994) Promoter structure, promoter recognition, and transcription activation in prokaryotes. Cell 79:743–746

    Article  PubMed  CAS  Google Scholar 

  • Bushman FD (1993) The bacteriophage 434 right operator. Roles of Or1, Or2 and Or3. J Mol Biol 230:28–40

    Article  PubMed  CAS  Google Scholar 

  • Bushman FD, Ptashne M (1986) Activation of transcription by the bacteriophage 434 repressor. Proc Natl Acad Sci USA 83:9353–9357

    Article  PubMed  CAS  Google Scholar 

  • Bushman FD, Ptashne M (1988) Turning lambda Cro into a transcriptional activator. Cell 54:191–197

    Article  PubMed  CAS  Google Scholar 

  • Claverie-Martin F, Magasanik B (1991) Role of integration host factor in the regulation of the glnHp2 promoter of Escherichia coli. Proc Natl Acad Sci USA 88:1631–1635

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Dekker N, Cox M, Boelens R, Verrijzer CP, Van der Vliet PC, Kaptein R (1993) Solution structure of the POU-specific DNA-binding domain of Oct-1. Nature 362:852–855

    Article  PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Ebright RH, Cossart P, Gicquel-Sanzey B, Beckwith J (1984) Mutations that alter the DNA sequence specificity of the catabolite gene activator protein of E. coli. Nature 311:232–235

    Article  PubMed  CAS  Google Scholar 

  • Ebright RH, Kolb A, Buc H, Kunkel TA, Krakow JS, Beckwith J (1987) Role of glutamic acid-181 in DNA-sequence recognition by the catabolite gene activator protein (CAP) of Escherichia coli: altered DNA-sequence-recognition properties of [Vall81]CAP and [Leul81]CAP. Proc Natl Acad Sci USA 84:6083–6087

    Article  PubMed  CAS  Google Scholar 

  • Ebright RH, Ebright YW, Gunasekera A (1989) Consensus DNA site for the Escherichia coli catabolite gene activator protein (CAP): CAP exhibits a 450-fold higher affinity for the consensus DNA site than for the E. coli lac DNA site. Nucleic Acids Res 17:10295–10305

    Article  PubMed  CAS  Google Scholar 

  • Flatow U, Rajendrakumar GV, Garges S (1996) Analysis of the spacer DNA between the cyclic AMP receptor protein binding site and the lac promoter. J Bacteriol 178:2436–2439

    PubMed  CAS  Google Scholar 

  • Freundlich M, Ramani N, Mathew E, Sirko A, Tsui P (1992) The role of integration host factor in gene expression in Escherichia coli. Mol Microbiol 6:2557–2563

    Article  PubMed  CAS  Google Scholar 

  • Gartenberg MR, Crothers DM (1986) DNA sequence determinants of CAP-induced bending and protein binding affinity. Nature 333:824–829

    Article  Google Scholar 

  • Gaston K, Bell A, Kolb A, Buc H, Busby S (1990) Stringent spacing requirements for transcription activation by CRP. Cell 62:733–743

    Article  PubMed  CAS  Google Scholar 

  • Gent ME, Gronenborn AM, Davies RW, Clore GM (1987) Probing the sequence-specific interaction of the cyclic AMP receptor protein with DNA by site-directed mutagenesis. Biochem J 242:645–653

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Giladi H, Igarashi K, Ishihama A, Oppenheim AB (1992) Stimulation of the phage lambda pL promoter by integration host factor requires the carboxy terminus of the a-subunit of RNA polymerase. J Mol Biol 227:985–990

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Goodrich JA, Schwartz ML, McClure WR (1990) 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 18:4993–5000

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Grosschedl R, Giese K, Pagel J (1994) HMG domain proteins: architectural elements in the assembly of nucleoprotein structures. Trends Genet 10:94–100

    Article  PubMed  CAS  Google Scholar 

  • Harrison SC (1991) A structural taxonomy of DNA-binding domains. Nature 353:715–719

    Article  PubMed  CAS  Google Scholar 

  • Harrison SC, Aggarwal AK (1990) DNA recognition by proteins with the helix-turn-helix motif. Annu Rev Biochem 59:933–969

    Article  PubMed  CAS  Google Scholar 

  • Heltzel A, Lee IW, Totis PA, Summers AO (1990) Activator-dependent preinduction binding of sigma-70 RNA polymerase at the metal-regulated mer promoter. Biochemistry 29:9572–9584

    Article  PubMed  CAS  Google Scholar 

  • Hilchey SP, Koodelka GB (1997) DNA-based loss of specificity mutations. J Bioc Chem (in press)

    Google Scholar 

  • Hochschild A, Irwin N, Ptashne M (1983) Repressor structure and the mechanism of positive control. Cell 32:319–325

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Joung JK, Le L, Hochschild A (1993) Synergistic activation of transcription by Escherichia coli cAMP receptor protein. Proc Natl Acad Sci USA 90:3083–3087

    Article  PubMed  CAS  Google Scholar 

  • Joung JK, Koepp DM, Hochschild A (1994) Synergistic activation of transcription by bacteriophage lambda cl protein and E. coli cAMP receptor protein. Science 265:1863–1866

    Article  PubMed  CAS  Google Scholar 

  • Kolb A, Igarashi K, Ishihama A, Lavigne M, Buckle M, Buc H (1993) E. coli RNA polymerase, deleted in the C-terminal part of its α-subunit, interacts differently with the cAMP-CRP complex at the lacP1 and at the galP1 promoter. Nucleic Acids Res 21:319–326

    Article  PubMed  CAS  Google Scholar 

  • Koudelka GB (1991) Bending of synthetic bacteriophage 434 operators by bacteriophage 434 proteins. Nucleic Acids Res 19:4115–4119

    Article  PubMed  CAS  Google Scholar 

  • Koudelka GB (1993) Indirect effects of DNA sequence on 434 repressor-DNA interactions. In: Eckstein F, Lilley DMJ (eds) Nucleic acids and molecular biology, vol 7. Springer, Berlin Heidelberg New York, pp 16–27

    Google Scholar 

  • Koudelka GB, Carlson P (1992) DNA twisting and the effects of non-contacted bases on affinity of 434 operator for 434 repressor. Nature 355:89–91

    Article  PubMed  CAS  Google Scholar 

  • Koudelka GB, Harrison SC, Ptashne M (1987) Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and Cro. Nature 326:886–888

    Article  PubMed  CAS  Google Scholar 

  • Koudelka GB, Harbury PH, Harrison SC, Ptashne M (1988) DNA twisting and the affinity of bacteriophage 434 operator for bacteriophage 434 repressor. Proc Natl Acad Sci USA 85:4633–4637

    Article  PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Kuldell N, Hochschild A (1994) Amino acid substitutions in the —35 recognition motif of sigma 70 that result in defect in phage lambda repressor-stimulated transcription. J Bacteriol 176:2991–2298

    PubMed  CAS  Google Scholar 

  • Lavigne M, Kolb A, Buc H (1992) Transcription activation by cAMP receptor protein (CRP) at the Escherichia coli gal PI promoter. Crucial role for the spacing between the CRP binding site and the —10 region. Biochemistry 31:9647–9656

    Article  PubMed  CAS  Google Scholar 

  • Lavigne M, Kolb A, Yeramian E, Buc H (1994) CRP fixes the rotational orientation of covalently closed DNA molecules. EMBO J 13:4983–4990

    PubMed  CAS  Google Scholar 

  • Li M, Moyle H, Susskind MM (1994) Target of the transcriptional activation function of phage lambda cl protein. Science 263:75–77

    Article  PubMed  CAS  Google Scholar 

  • Lund PA, Ford SJ, Brown NL (1986) Transcriptional regulation of the mercury-resistance genes of transposon Tn501. J Gen Microbiol 132:465–480

    PubMed  CAS  Google Scholar 

  • Misra TK (1992) Bacterial resistances to inorganic mercury salts and organomercurials. Plasmid 27:4–16

    Article  PubMed  CAS  Google Scholar 

  • Ni’Bhriain NN, Silver S, Foster TJ (1983) Tn5 insertion mutations in the mercuric ion resistance genes derived from plasmid R100. J Bacteriol 155:690–703

    PubMed  Google Scholar 

  • Niu W, Zhou Y, Dong Q, Ebright YW, Ebright RH (1994) Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP). I. Saturation and alanine-scanning mutagenesis. J Mol Biol 243:595–602

    Article  PubMed  CAS  Google Scholar 

  • Oberto J, Drlica K, Rouvière-Yaniv J (1994) Histones, HMG, HU, IHF: Même combat. Biochimie 76:901–908

    Article  PubMed  CAS  Google Scholar 

  • O’Halloran TV, Frantz B, Shin MK, Ralston DM, Wright JG (1989) The MerR heavy metal receptor mediates positive activation in a topologically novel transcription complex. Cell 56:119–129

    Article  PubMed  Google Scholar 

  • Pagel JM, Hatfield GW (1991) Integration host factor-mediated expression of the ilvGMEDA operon of Escherichia coli. J Biol Chem 266:1985–1996

    PubMed  CAS  Google Scholar 

  • Parekh BS, Hatfield GW (1996) Transcriptional activation by protein-induced DNA bending: evidence for a DNA structural transmission model. Proc Natl Acad Sci USA 93:1173–1177

    Article  PubMed  CAS  Google Scholar 

  • Parkhill J, Brown NL (1990) Site-specific insertion and deletion mutants in the mer promoter-operator region of Tn501; the nineteen base-pair spacer is essential for normal induction of the promoter by MerR. Nucleic Acids Res 18:5157–5162

    Article  PubMed  CAS  Google Scholar 

  • Poteete A, Ptashne M (1982) Control of transcription by bacteriophage P22 repressor. J Mol Biol 157:21–48

    Article  PubMed  CAS  Google Scholar 

  • Ptashne M (1986) A genetic switch. Blackwell, Palo Alto

    Google Scholar 

  • Ross W, Gosink KK, Salomon J, Igarashi K, Zou C, Ishihama A, Severinov K, Gourse RL (1993) A third recognition element in bacterial promoters: DNA binding by the a subunit of RNA polymerase. Science 262:1407–1413

    Article  PubMed  CAS  Google Scholar 

  • Sauer RT, Yocum RR, Doolittle RF, Lewis M, Pabo CO (1982) Homology among DNA-binding proteins suggests use of a conserved supersecondary structure. Nature 298:447–451

    Article  PubMed  CAS  Google Scholar 

  • Schmid MB (1990) More than just “histone-like” proteins. Cell 63:451–453

    Article  PubMed  CAS  Google Scholar 

  • Schroder I, Wolin CD, Cavicchioli R, Gunsalus RP (1994) Phosphorylation and dephosphorylation of the NarQ, NarX, and NarL proteins of the nitrate-dependent two-component regulatory system of Escherichia coli. J Bacteriol 176:4985–4992

    PubMed  CAS  Google Scholar 

  • Schultz SC, Shield GC, Steitz TA (1991) Crystal structure of a CAP-DNA complex. The DNA is bent by 90 degrees. Science 253:1001–1007

    Article  PubMed  CAS  Google Scholar 

  • Tang H, Severinov K, Goldfarb A, Fenyo D, Chait B, Ebright RH (1994) Location, structure, and function of the target of a transcriptional activator protein. Genes Dev 8:3058–3067

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Wharton RP (1986) Determinants of 434 repressor binding specificity Thesis. Harvard University Cambridge

    Google Scholar 

  • Williams RM, Rhodius VA, Bell AI, Kolb A, Busby SJ (1996) Orientation of functional activating regions in the Escherichia coli CRP protein during transcription activation at class II promoters. Nucleic Acids Res 24:1112–1118

    Article  PubMed  CAS  Google Scholar 

  • Woody ST, Fong RS-C, Gussin GN (1993) Effects of a single base-pair deletion in the bacteriophage lambda PRM promoter. Repression of PRM by repressor bound at OR2 and by RNA polymerase bound at PR J Mol Biol 229:37–51

    Article  PubMed  CAS  Google Scholar 

  • Wu L, Koudelka GB (1993) Sequence-dependent differences in DNA structure influence the affinity of P22 operator for P22 repressor. J Biol Chem 268:18975–18981

    PubMed  CAS  Google Scholar 

  • Wu L, Vertino A, Koudelka GB (1992) Non-contacted bases affect the affinity of synthetic P22 operators for P22 repressor. J Biol Chem 267:9134–9135

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Zhang X, Ebright RH (1990) Identification of a contact between arginine-180 of the catabolite gene activator protein (CAP) and base pair 5 of the DNA site in the CAP-DNA complex. Proc Natl Acad Sci USA 87:4717–4721

    Article  PubMed  CAS  Google Scholar 

  • Zhou Y, Zhang X, Ebright RH (1993) Identification of the activating region of catabolite gene activator protein (CAP): isolation and characterization of mutants of CAP specifically defective in transcription activation. Proc Natl Acad Sci USA 90:6081–6085

    Article  PubMed  CAS  Google Scholar 

  • Zhou Y, Merkel TJ, Ebright RH (1994a) Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP). II. Role at class I and class II CAP-dependent promoters. J Mol Biol 243:603–610

    Article  PubMed  CAS  Google Scholar 

  • Zhou Y, Pendergrast PS, Bell A, Williams R, Busby S, Ebright RH (1994b) The functional subunit of a dimeric transcription activator protein depends on promoter architecture. EMBO J 13:4549–4557

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Zulianello L, van Ulsen P, van de Putte P, Goosen N (1995) Participation of the flank regions of the integration host factor protein in the specificity and stability of DNA binding. J Biol Chem 270:17902–17907

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Biological Sciences, State University of New York at Buffalo, 14260, Buffalo, New York, USA

    S. Hilchey, J. Xu & G. B. Koudelka

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  1. S. Hilchey
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  2. J. Xu
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  3. G. B. Koudelka
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  1. Max-Planck-Institut für Experimentelle Medizin, Hermann-Rein-Straße 3, 37075, Göttingen, Germany

    Fritz Eckstein

  2. Biochemistry Department, University of Dundee, DD1 4HN, Dundee, UK

    David M. J. Lilley

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Hilchey, S., Xu, J., Koudelka, G.B. (1997). Indirect Effects of DNA Sequence on Transcriptional Activation by Prokaryotic DNA Binding Proteins. In: Eckstein, F., Lilley, D.M.J. (eds) Mechanisms of Transcription. Nucleic Acids and Molecular Biology, vol 11. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-60691-5_9

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  • DOI: https://doi.org/10.1007/978-3-642-60691-5_9

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