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Adaptability and Specificity in DNA Binding by trp Repressor

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Part of the book series: Nucleic Acids and Molecular Biology ((NUCLEIC,volume 8))

Abstract

Cellular processes such as growth and differentiation are controlled by transcription factors that regulate gene expression by binding to specific DNA sites. Our present understanding of the mechanisms of repression and activation (gene regulation) has evolved from extensive studies on these sequence-specific DNA binding proteins and their DNA targets. A central question in these studies concerns how the protein distinguishes its target site(s) from an enormous background of nonspecific sites. Many regulatory proteins must recognize several closely related but nonidentical sites, or must be able to interact or combine with other factors or subunits that confer new DNA specificities. An emerging picture for the recognition process involves the mutual adjustment, or adaptation, of molecular surfaces to provide the required level of energetic interaction for specific recognition.

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References

  • Bass, S, Sugiono P, Arvidson DN, Gunsalus RP, Youderian P (1987) DNA specificity determinants of E. coli tryptophan repressor binding. Genes Dev 1:565–572

    Article  PubMed  CAS  Google Scholar 

  • Bass S, Sorrells V, Youderian P (1988) Mutant trp repressors with new DNA-binding specificities. Science 242:240–245

    Article  PubMed  CAS  Google Scholar 

  • Benhar I, Engelberg-Kulka H (1993) Frameshifting in the expression of the E. coli trpR gene occurs by the bypassing of a segment of its coding sequence. Cell 72:121–130

    Article  PubMed  CAS  Google Scholar 

  • Bowie JU, Sauer RT (1989) Equilibrium dissociation and unfolding of the arc repressor dimer. Biochemistry 28:7139–7143

    Article  PubMed  CAS  Google Scholar 

  • Calladine CR, Drew HR (1986) Principles of sequence-dependent flexure of DNA. J Mol Biol 192:907–918

    Article  PubMed  CAS  Google Scholar 

  • Carey J (1988) Gel retardation at low pH resolves trp repressor-DNA complexes for quantitative study. Proc Natl Acad Sci USA 85:975–979

    Article  PubMed  CAS  Google Scholar 

  • Carey J (1989) trp repressor arms contribute binding energy without occupying unique locations on DNA. J Biol Chem 264:1941–1945

    PubMed  CAS  Google Scholar 

  • Carey J, Lewis DEA, Lavoie TA, Yang J (1991) How does trp repressor recognize its operator? J Biol Chem 266:24509–24513

    PubMed  CAS  Google Scholar 

  • Carey J, Combatti N, Lewis DEA, Lawson CL (1993) Cocrystals of E. coli trp repressor bound to an alternative operator DNA sequence. J Mol Biol 234:496–498

    Article  PubMed  CAS  Google Scholar 

  • Cooper SR (ed) (1992) Crown compounds: toward future applications. VCH, New York

    Google Scholar 

  • Dickerson RE (1983) Base sequence and helix structure variation in B and A DNA. J Mol Biol 166:419–441

    Article  PubMed  CAS  Google Scholar 

  • Ellenberger TE, Brandi CJ, Struhl K, Harrison SC (1992) The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted α-helices: crystal structure of the protein-DNA complex. Cell 71:1223–1237

    Article  PubMed  CAS  Google Scholar 

  • Gunsalus RP, Yanofsky C (1980) Nucleotide sequence and expression of E. coli trpR, the structural gene for the trp aporepressor. Proc Natl Acad Sci USA 77:7117–7121

    Article  PubMed  CAS  Google Scholar 

  • Haran TE, Joachimiak A, Sigler PB (1992) The DNA target of the trp repressor. EMBO J 11:3021–3030

    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 

  • Hunter C (1993) Sequence-dependent DNA structure. J Mol Biol 230:1025–1054

    Article  PubMed  CAS  Google Scholar 

  • Hunter WN, D’Estaintot BL, Kennard O (1989) Structural variation in d(CTCTAGAG). Implications for protein-DNA interactions. Biochemistry 28:2444–2451

    Article  PubMed  CAS  Google Scholar 

  • Jin L, Yang J, Carey J (1993) Thermodynamics of ligand binding to trp repressor. Biochemistry 32:7302–7309

    Article  PubMed  CAS  Google Scholar 

  • Joachimiak A, Kelley RL, Gunsalus RP, Yanofsky C, Sigler PB (1983) Purification and characterization of trp aporepressor. Proc Natl Acad Sci USA 80:668–672

    Article  PubMed  CAS  Google Scholar 

  • Johnson PF, McKnight SL (1989) Eukaryotic transcriptional regulatory proteins. Annu Rec Biochem 58:799–839

    Article  CAS  Google Scholar 

  • Kelley RL, Yanofsky C (1982) Mutational studies with the trp repressor of E. coli support the helix-turn-helix model of repressor recognition of operator DNA. Proc Natl Acad Sci USA 79:3120–3124

    Article  PubMed  CAS  Google Scholar 

  • Kennard O, Hunter WN (1991) Single-crystal X-ray diffraction studies of oligonucleotides and oligonucleotide drug complexes. Angew Chem Int Ed Engl 30:1254–1277

    Article  Google Scholar 

  • Kim J, Tzamarias D, Ellenberger T, Harrison SC, Struhl K (1993) Adaptability at the protein-DNA interface is an important aspect of sequence recognition by bZip proteins. Proc Natl Acad Sci USA 90:4513–4517

    Article  PubMed  CAS  Google Scholar 

  • Kumamoto AA, Miller WG, Gunsalus RP (1987) Eschericia coli tryptophan repressor binds multiple sites within the aroH and trp operators. Genes Dev 1:556–564

    Article  PubMed  CAS  Google Scholar 

  • Kyba EP, Helgeson RC, Madan K, Gokel GW, Tarnowski TL, Moore SS, Cram DJ (1977) Host-guest complexation. 1. Concept and illustration. J Am Chem Soc 99:2564–2569

    Article  CAS  Google Scholar 

  • Lawson CL, Carey J (1993) Tandem binding in crystals of a trp repressor/operator half-site complex. Nature 366:178–182

    Article  PubMed  CAS  Google Scholar 

  • Lawson CL, Sigler PB (1988) The structure of trp pseudorepressor at 1.65 Å shows why indole propionate acts as a trp “inducer”. Nature 333:869–871

    Article  PubMed  CAS  Google Scholar 

  • Lawson CL, Zhang RG, Schevitz RW, Otwinowski Z, Joachimiak A, Sigler PB (1988) Flexibility of the DNA-binding domains of trp repressor. Proteins 3:18–31

    Article  PubMed  CAS  Google Scholar 

  • Lefevre J-F, Lane AN, Jardetzky O (1987) Solution structure of the trp operator of Escherichia coli determined by NMR. Biochemistry 26:5076–5090

    Article  PubMed  CAS  Google Scholar 

  • Lesser DR, Kurpiewski MR, Jen-Jacobson L (1990) The energetic basis of specificity in the EcoRI endonuclease-DNA interaction. Science 250:776–786

    Article  PubMed  CAS  Google Scholar 

  • Lewis DEA, Carey J (1993) Analysis of trp repressor-DNA interactions using gel electrophoresis. Electrophoresis 14:713–719

    Article  PubMed  CAS  Google Scholar 

  • Liu Y-C, Matthews KS (1993) Dependence of trp repressor-operator affinity, stoichiometry, and apparent cooperativity on DNA sequence and size. J Biol Chem 268:23239–23249

    PubMed  CAS  Google Scholar 

  • Marmorstein RQ, Sigler PB (1989) Structure and mechanism of the trp repressor/operator system. In: Eckstein F, Lilley DMJ (eds) Nucleic Acids and Molecular Biology, vol 3. Springer, Berlin Heidelberg New York

    Google Scholar 

  • McKnight SL, Yamamoto KR (eds) (1992) Transcriptional regulation, vol 1. Cold Spring Harbor Laboratory Press, New York

    Google Scholar 

  • Mossing MC, Record MT (1985) Thermodynamic origins of specificity in the lac repressor-operator interaction. J Mol Biol 186:295–305

    Article  PubMed  CAS  Google Scholar 

  • O’Neil KT, Hoess RH, Degrado WF (1990) Design of DNA-binding peptides based on the leucine zipper motif. Science 249:774–778

    Article  PubMed  Google Scholar 

  • O’Neil KT, Shuman JD, Ampe C, Degrado WF (1991) DNA-induced increase in the α-helical content of C/EBP and GCN4. Biochemistry 30:9030–9034

    Article  PubMed  Google Scholar 

  • Otwinowski Z, Schevitz RW, Zhang R-G, Lawson CL, Joachimiak A, Marmorstein RQ, Luisi B, Sigler PB (1988) The crystal structure of the trp repressor/operator complex at atomic resolution. Nature 335:321–329

    Article  PubMed  CAS  Google Scholar 

  • Schevitz RW, Otwinowski Z, Joachimiak A, Lawson CL, Sigler PB (1985) The three-dimensional structure of trp repressor. Nature 317:782–786

    Article  PubMed  CAS  Google Scholar 

  • Shakked Z, Guzikevich-Guerstein G, Frolow, F, Rabinovich D, Joachimiak A, Sigler PB (1994) Determinants of repressor/operator recognition from the structure of the trp operator binding site. Nature 268:469–473

    Article  Google Scholar 

  • Seeman NC, Rosenberg JM, Rich A (1976) Sequence-specific recognition of double-helical nucleic acids by proteins. Proc Natl Acad Sci USA 73:804–808

    Article  PubMed  CAS  Google Scholar 

  • Sellers JW, Vincent AC, Struhl K (1990) Mutations that define the optimal half-site for binding yeast GCN4 activator protein and identify an ATF/CREB-like repressor that recognizes similar DNA sites. Mol Cell Biol 10:5077–5086

    PubMed  CAS  Google Scholar 

  • Staacke D, Walter B, Kisters-Woicke B, von Wilcken-Bergman B, Muller-Hill B (1990) How trp repressor binds to its operator. EMBO J 9:1963–1967

    PubMed  CAS  Google Scholar 

  • Steitz TA (1990) Structural studies of protein-nucleic acid interaction: the sources of sequence-specific binding. Q Rev Biophys 23:205–280

    Article  PubMed  CAS  Google Scholar 

  • Talanian RV, McKnight JC, Kim PS (1990) Sequence-specific DNA binding by a short peptide dimer. Science 249:769–771

    Article  PubMed  CAS  Google Scholar 

  • Vogtle F, Weber E (eds) (1985) Host guest complex chemistry. Macrocycles: synthesis, structures, applications. Springer, Berlin Heidelberg New York

    Google Scholar 

  • von Hippel PH, Berg OG (1986) On the specificity of DNA-protein interactions. Proc Natl Acad Sci USA 83:1608–1612

    Article  Google Scholar 

  • Weiss MA, Ellenberger T, Wobbe CR, Lee JP, Harrison SC, Struhl K (1990) Folding transition in the DNA-binding domain of GCN4 on specific binding to DNA. Nature 347:575–578

    Article  PubMed  CAS  Google Scholar 

  • Zhang RG, Joachimiak A, Lawson CL, Schevitz RW, Otwinowski Z, Sigler PB (1987) The crystal structure of trp aporepressor at 1.8Å shows how binding tryptophan enhances DNA affinity. Nature 327:591–597

    Article  PubMed  CAS  Google Scholar 

  • Zhao D, Arrowsmith CH, Jia X, Jardetzky O (1993) The refined solution structures of the E. coli trp holo and aporepressor. J Mol Biol 229:735–746

    Article  PubMed  CAS  Google Scholar 

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© 1994 Springer-Verlag Berlin Heidelberg

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Lavoie, T.A., Carey, J. (1994). Adaptability and Specificity in DNA Binding by trp Repressor. In: Eckstein, F., Lilley, D.M.J. (eds) Nucleic Acids and Molecular Biology. Nucleic Acids and Molecular Biology, vol 8. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-78666-2_10

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  • DOI: https://doi.org/10.1007/978-3-642-78666-2_10

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-78668-6

  • Online ISBN: 978-3-642-78666-2

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