Polyamines alter sequence-specific DNA-protein interactions.
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Journal: 1995/July - Nucleic Acids Research
ISSN: 0305-1048
PUBMED: 7784186
Abstract:
The polyamines are abundant biogenic cations implicated in many biological processes. Despite a plethora of evidence on polyamine-induced DNA conformational changes, no thorough study of their effects on the activities of sequence-specific DNA binding proteins has been performed. We describe the in vitro effects of polyamines on the activities of purified, representative DNA-binding proteins, and on complex protein mixtures. Polyamines at physiological concentrations enhance the binding of several proteins to DNA (e.g. USF, TFE3, Ig/EBP, NF-IL6, YY1 and ICP-4, a herpes simplex virus gene regulator), but inhibit others (e.g. Oct-1). The degree of enhancement correlates with cationic charge; divalent putrescine is ineffective whereas tetravalent spermine is more potent than trivalent spermidine. Polyamine effects on USF and ICP-4 result from increased rate of complex formation rather than a decreased rate of dissociation. DNAse I footprint analysis indicated that polyamines do not alter DNA-protein contacts. Polyamines also facilitate formation of complexes involving binding of more than one protein on a DNA fragment.
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Nucleic Acids Res 23(10): 1800-1809
PMID: 7784186

Polyamines alter sequence-specific DNA-protein interactions.

Abstract

The polyamines are abundant biogenic cations implicated in many biological processes. Despite a plethora of evidence on polyamine-induced DNA conformational changes, no thorough study of their effects on the activities of sequence-specific DNA binding proteins has been performed. We describe the in vitro effects of polyamines on the activities of purified, representative DNA-binding proteins, and on complex protein mixtures. Polyamines at physiological concentrations enhance the binding of several proteins to DNA (e.g. USF, TFE3, Ig/EBP, NF-IL6, YY1 and ICP-4, a herpes simplex virus gene regulator), but inhibit others (e.g. Oct-1). The degree of enhancement correlates with cationic charge; divalent putrescine is ineffective whereas tetravalent spermine is more potent than trivalent spermidine. Polyamine effects on USF and ICP-4 result from increased rate of complex formation rather than a decreased rate of dissociation. DNAse I footprint analysis indicated that polyamines do not alter DNA-protein contacts. Polyamines also facilitate formation of complexes involving binding of more than one protein on a DNA fragment.

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Selected References

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  • Tabor CW, Tabor H. 1,4-Diaminobutane (putrescine), spermidine, and spermine. Annu Rev Biochem. 1976;45:285–306. [PubMed] [Google Scholar]
  • Tabor CW, Tabor H. Polyamines. Annu Rev Biochem. 1984;53:749–790. [PubMed] [Google Scholar]
  • Pegg AE. Polyamine metabolism and its importance in neoplastic growth and a target for chemotherapy. Cancer Res. 1988 Feb 15;48(4):759–774. [PubMed] [Google Scholar]
  • Bacchi CJ, Nathan HC, Hutner SH, McCann PP, Sjoerdsma A. Polyamine metabolism: a potential therapeutic target in trypanosomes. Science. 1980 Oct 17;210(4467):332–334. [PubMed] [Google Scholar]
  • Steglich C, Scheffler IE. An ornithine decarboxylase-deficient mutant of Chinese hamster ovary cells. J Biol Chem. 1982 Apr 25;257(8):4603–4609. [PubMed] [Google Scholar]
  • Tabor H, Hafner EW, Tabor CW. Construction of an Escherichia coli strain unable to synthesize putrescine, spermidine, or cadaverine: characterization of two genes controlling lysine decarboxylase. J Bacteriol. 1980 Dec;144(3):952–956.[PMC free article] [PubMed] [Google Scholar]
  • Tabor H, Tabor CW, Cohn MS, Hafner EW. Streptomycin resistance (rpsL) produces an absolute requirement for polyamines for growth of an Escherichia coli strain unable to synthesize putrescine and spermidine [delta(speA-speB) delta specC]. J Bacteriol. 1981 Aug;147(2):702–704.[PMC free article] [PubMed] [Google Scholar]
  • Whitney PA, Morris DR. Polyamine auxotrophs of Saccharomyces cerevisiae. J Bacteriol. 1978 Apr;134(1):214–220.[PMC free article] [PubMed] [Google Scholar]
  • Braunlin WH, Strick TJ, Record MT., Jr Equilibrium dialysis studies of polyamine binding to DNA. Biopolymers. 1982 Jul;21(7):1301–1314. [PubMed] [Google Scholar]
  • Gessner RV, Frederick CA, Quigley GJ, Rich A, Wang AH. The molecular structure of the left-handed Z-DNA double helix at 1.0-A atomic resolution. Geometry, conformation, and ionic interactions of d(CGCGCG). J Biol Chem. 1989 May 15;264(14):7921–7935. [PubMed] [Google Scholar]
  • Williams LD, Frederick CA, Ughetto G, Rich A. Ternary interactions of spermine with DNA: 4'-epiadriamycin and other DNA: anthracycline complexes. Nucleic Acids Res. 1990 Sep 25;18(18):5533–5541.[PMC free article] [PubMed] [Google Scholar]
  • Fratini AV, Kopka ML, Drew HR, Dickerson RE. Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG. J Biol Chem. 1982 Dec 25;257(24):14686–14707. [PubMed] [Google Scholar]
  • Feuerstein BG, Pattabiraman N, Marton LJ. Spermine-DNA interactions: a theoretical study. Proc Natl Acad Sci U S A. 1986 Aug;83(16):5948–5952.[PMC free article] [PubMed] [Google Scholar]
  • Feuerstein BG, Pattabiraman N, Marton LJ. Molecular mechanics of the interactions of spermine with DNA: DNA bending as a result of ligand binding. Nucleic Acids Res. 1990 Mar 11;18(5):1271–1282.[PMC free article] [PubMed] [Google Scholar]
  • Behe M, Felsenfeld G. Effects of methylation on a synthetic polynucleotide: the B--Z transition in poly(dG-m5dC).poly(dG-m5dC). Proc Natl Acad Sci U S A. 1981 Mar;78(3):1619–1623.[PMC free article] [PubMed] [Google Scholar]
  • Thomas TJ, Messner RP. Structural specificity of polyamines in left-handed Z-DNA formation. Immunological and spectroscopic studies. J Mol Biol. 1988 May 20;201(2):463–467. [PubMed] [Google Scholar]
  • Thomas TJ, Gunnia UB, Thomas T. Polyamine-induced B-DNA to Z-DNA conformational transition of a plasmid DNA with (dG-dC)n insert. J Biol Chem. 1991 Apr 5;266(10):6137–6141. [PubMed] [Google Scholar]
  • Feuerstein BG, Williams LD, Basu HS, Marton LJ. Implications and concepts of polyamine-nucleic acid interactions. J Cell Biochem. 1991 May;46(1):37–47. [PubMed] [Google Scholar]
  • Gosule LC, Schellman JA. Compact form of DNA induced by spermidine. Nature. 1976 Jan 29;259(5541):333–335. [PubMed] [Google Scholar]
  • Chattoraj DK, Gosule LC, Schellman A. DNA condensation with polyamines. II. Electron microscopic studies. J Mol Biol. 1978 May 25;121(3):327–337. [PubMed] [Google Scholar]
  • Widom J, Baldwin RL. Cation-induced toroidal condensation of DNA studies with Co3+(NH3)6. J Mol Biol. 1980 Dec 25;144(4):431–453. [PubMed] [Google Scholar]
  • Widom J, Baldwin RL. Monomolecular condensation of lambda-DNA induced by cobalt hexamine. Biopolymers. 1983 Jun;22(6):1595–1620. [PubMed] [Google Scholar]
  • Wilson RW, Bloomfield VA. Counterion-induced condesation of deoxyribonucleic acid. a light-scattering study. Biochemistry. 1979 May 29;18(11):2192–2196. [PubMed] [Google Scholar]
  • Smirnov IV, Dimitrov SI, Makarov VL. Polyamine-DNA interactions. Condensation of chromatin and naked DNA. J Biomol Struct Dyn. 1988 Apr;5(5):1149–1161. [PubMed] [Google Scholar]
  • Fredericq E, Hacha R, Colson P, Houssier C. Condensation and precipitation of chromatin by multivalent cations. J Biomol Struct Dyn. 1991 Feb;8(4):847–865. [PubMed] [Google Scholar]
  • Feuerstein BG, Pattabiraman N, Marton LJ. Molecular dynamics of spermine-DNA interactions: sequence specificity and DNA bending for a simple ligand. Nucleic Acids Res. 1989 Sep 12;17(17):6883–6892.[PMC free article] [PubMed] [Google Scholar]
  • Geiger LE, Morris DR. Stimulation of deoxyribonucleic acid replication fork movement by spermidine analogs in polyamine-deficient Escherichia coli. J Bacteriol. 1980 Mar;141(3):1192–1198.[PMC free article] [PubMed] [Google Scholar]
  • Mikhailov VS, Androsova IM. Effect of spermine on interaction of DNA polymerase alpha from the loach (Misgurnus fossilis) eggs with DNA. Biochim Biophys Acta. 1984 Oct 5;783(1):6–14. [PubMed] [Google Scholar]
  • Shimamura S, Hibasami H, Kano U, Watanabe S, Suzuki S, Nakashima K. Modulation by polyamines of DNA-dependent DNA polymerase activity from human serum. Int J Biochem. 1990;22(5):545–549. [PubMed] [Google Scholar]
  • Pingoud A, Urbanke C, Alves J, Ehbrecht HJ, Zabeau M, Gualerzi C. Effect of polyamines and basic proteins on cleavage of DNA by restriction endonucleases. Biochemistry. 1984 Nov 20;23(24):5697–5703. [PubMed] [Google Scholar]
  • Sabbah M, Le Ricousse S, Redeuilh G, Baulieu EE. Estrogen receptor-induced bending of the Xenopus vitellogenin A2 gene hormone response element. Biochem Biophys Res Commun. 1992 Jun 30;185(3):944–952. [PubMed] [Google Scholar]
  • Gibson W, Roizman B. Compartmentalization of spermine and spermidine in the herpes simplex virion. Proc Natl Acad Sci U S A. 1971 Nov;68(11):2818–2821.[PMC free article] [PubMed] [Google Scholar]
  • Cohen SS, McCormick FP. Polyamines and virus multiplication. Adv Virus Res. 1979;24:331–387. [PubMed] [Google Scholar]
  • Yao F, Courtney RJ. Association of a major transcriptional regulatory protein, ICP4, of herpes simplex virus type 1 with the plasma membrane of virus-infected cells. J Virol. 1991 Mar;65(3):1516–1524.[PMC free article] [PubMed] [Google Scholar]
  • Gelman IH, Silverstein S. Dissection of immediate-early gene promoters from herpes simplex virus: sequences that respond to the virus transcriptional activators. J Virol. 1987 Oct;61(10):3167–3172.[PMC free article] [PubMed] [Google Scholar]
  • Gerster T, Roeder RG. A herpesvirus trans-activating protein interacts with transcription factor OTF-1 and other cellular proteins. Proc Natl Acad Sci U S A. 1988 Sep;85(17):6347–6351.[PMC free article] [PubMed] [Google Scholar]
  • apRhys CM, Ciufo DM, O'Neill EA, Kelly TJ, Hayward GS. Overlapping octamer and TAATGARAT motifs in the VF65-response elements in herpes simplex virus immediate-early promoters represent independent binding sites for cellular nuclear factor III. J Virol. 1989 Jun;63(6):2798–2812.[PMC free article] [PubMed] [Google Scholar]
  • Peterson CL, Calame K. Proteins binding to site C2 (muE3) in the immunoglobulin heavy-chain enhancer exist in multiple oligomeric forms. Mol Cell Biol. 1989 Feb;9(2):776–786.[PMC free article] [PubMed] [Google Scholar]
  • Papavassiliou AG, Silverstein SJ. Interaction of cell and virus proteins with DNA sequences encompassing the promoter/regulatory and leader regions of the herpes simplex virus thymidine kinase gene. J Biol Chem. 1990 Jun 5;265(16):9402–9412. [PubMed] [Google Scholar]
  • Smith DB, Johnson KS. Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase. Gene. 1988 Jul 15;67(1):31–40. [PubMed] [Google Scholar]
  • Descombes P, Chojkier M, Lichtsteiner S, Falvey E, Schibler U. LAP, a novel member of the C/EBP gene family, encodes a liver-enriched transcriptional activator protein. Genes Dev. 1990 Sep;4(9):1541–1551. [PubMed] [Google Scholar]
  • Shrivastava A, Saleque S, Kalpana GV, Artandi S, Goff SP, Calame K. Inhibition of transcriptional regulator Yin-Yang-1 by association with c-Myc. Science. 1993 Dec 17;262(5141):1889–1892. [PubMed] [Google Scholar]
  • Dignam JD, Lebovitz RM, Roeder RG. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 1983 Mar 11;11(5):1475–1489.[PMC free article] [PubMed] [Google Scholar]
  • Ejercito PM, Kieff ED, Roizman B. Characterization of herpes simplex virus strains differing in their effects on social behaviour of infected cells. J Gen Virol. 1968 May;2(3):357–364. [PubMed] [Google Scholar]
  • Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976 May 7;72:248–254. [PubMed] [Google Scholar]
  • Strauss F, Varshavsky A. A protein binds to a satellite DNA repeat at three specific sites that would be brought into mutual proximity by DNA folding in the nucleosome. Cell. 1984 Jul;37(3):889–901. [PubMed] [Google Scholar]
  • Ferré-D'Amaré AR, Pognonec P, Roeder RG, Burley SK. Structure and function of the b/HLH/Z domain of USF. EMBO J. 1994 Jan 1;13(1):180–189.[PMC free article] [PubMed] [Google Scholar]
  • Kattar-Cooley P, Wilcox KW. Characterization of the DNA-binding properties of herpes simplex virus regulatory protein ICP4. J Virol. 1989 Feb;63(2):696–704.[PMC free article] [PubMed] [Google Scholar]
  • Kadonaga JT, Carner KR, Masiarz FR, Tjian R. Isolation of cDNA encoding transcription factor Sp1 and functional analysis of the DNA binding domain. Cell. 1987 Dec 24;51(6):1079–1090. [PubMed] [Google Scholar]
  • Towbin H, Staehelin T, Gordon J. Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications. Proc Natl Acad Sci U S A. 1979 Sep;76(9):4350–4354.[PMC free article] [PubMed] [Google Scholar]
  • Thomas T, Kiang DT. A twenty-two-fold increase in the relative affinity of estrogen receptor to poly (dA-dC).poly (dG-dT) in the presence of polyamines. Nucleic Acids Res. 1988 May 25;16(10):4705–4720.[PMC free article] [PubMed] [Google Scholar]
  • Artandi SE, Cooper C, Shrivastava A, Calame K. The basic helix-loop-helix-zipper domain of TFE3 mediates enhancer-promoter interaction. Mol Cell Biol. 1994 Dec;14(12):7704–7716.[PMC free article] [PubMed] [Google Scholar]
  • Faber SW, Wilcox KW. Association of the herpes simplex virus regulatory protein ICP4 with specific nucleotide sequences in DNA. Nucleic Acids Res. 1986 Aug 11;14(15):6067–6083.[PMC free article] [PubMed] [Google Scholar]
  • DiDonato JA, Spitzner JR, Muller MT. A predictive model for DNA recognition by the herpes simplex virus protein ICP4. J Mol Biol. 1991 Jun 5;219(3):451–470. [PubMed] [Google Scholar]
  • Muller MT. Binding of the herpes simplex virus immediate-early gene product ICP4 to its own transcription start site. J Virol. 1987 Mar;61(3):858–865.[PMC free article] [PubMed] [Google Scholar]
  • Roberts MS, Boundy A, O'Hare P, Pizzorno MC, Ciufo DM, Hayward GS. Direct correlation between a negative autoregulatory response element at the cap site of the herpes simplex virus type 1 IE175 (alpha 4) promoter and a specific binding site for the IE175 (ICP4) protein. J Virol. 1988 Nov;62(11):4307–4320.[PMC free article] [PubMed] [Google Scholar]
  • DeLuca NA, Schaffer PA. Physical and functional domains of the herpes simplex virus transcriptional regulatory protein ICP4. J Virol. 1988 Mar;62(3):732–743.[PMC free article] [PubMed] [Google Scholar]
  • Wei TF, Bujalowski W, Lohman TM. Cooperative binding of polyamines induces the Escherichia coli single-strand binding protein-DNA binding mode transitions. Biochemistry. 1992 Jul 7;31(26):6166–6174. [PubMed] [Google Scholar]
  • Lohman TM, Bujalowski W, Overman LB. E. coli single strand binding protein: a new look at helix-destabilizing proteins. Trends Biochem Sci. 1988 Jul;13(7):250–255. [PubMed] [Google Scholar]
  • Gregor PD, Sawadogo M, Roeder RG. The adenovirus major late transcription factor USF is a member of the helix-loop-helix group of regulatory proteins and binds to DNA as a dimer. Genes Dev. 1990 Oct;4(10):1730–1740. [PubMed] [Google Scholar]
  • Beckmann H, Su LK, Kadesch T. TFE3: a helix-loop-helix protein that activates transcription through the immunoglobulin enhancer muE3 motif. Genes Dev. 1990 Feb;4(2):167–179. [PubMed] [Google Scholar]
  • Roman C, Matera AG, Cooper C, Artandi S, Blain S, Ward DC, Calame K. mTFE3, an X-linked transcriptional activator containing basic helix-loop-helix and zipper domains, utilizes the zipper to stabilize both DNA binding and multimerization. Mol Cell Biol. 1992 Feb;12(2):817–827.[PMC free article] [PubMed] [Google Scholar]
  • Shi Y, Seto E, Chang LS, Shenk T. Transcriptional repression by YY1, a human GLI-Krüppel-related protein, and relief of repression by adenovirus E1A protein. Cell. 1991 Oct 18;67(2):377–388. [PubMed] [Google Scholar]
  • Parslow TG, Jones SD, Bond B, Yamamoto KR. The immunoglobulin octanucleotide: independent activity and selective interaction with enhancers. Science. 1987 Mar 20;235(4795):1498–1501. [PubMed] [Google Scholar]
  • Beckmann H, Kadesch T. The leucine zipper of TFE3 dictates helix-loop-helix dimerization specificity. Genes Dev. 1991 Jun;5(6):1057–1066. [PubMed] [Google Scholar]
  • Vinson CR, Hai T, Boyd SM. Dimerization specificity of the leucine zipper-containing bZIP motif on DNA binding: prediction and rational design. Genes Dev. 1993 Jun;7(6):1047–1058. [PubMed] [Google Scholar]
  • Conaway RC, Conaway JW. General initiation factors for RNA polymerase II. Annu Rev Biochem. 1993;62:161–190. [PubMed] [Google Scholar]
  • Berg OG, Winter RB, von Hippel PH. Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry. 1981 Nov 24;20(24):6929–6948. [PubMed] [Google Scholar]
  • Bloomfield VA. Condensation of DNA by multivalent cations: considerations on mechanism. Biopolymers. 1991 Nov;31(13):1471–1481. [PubMed] [Google Scholar]
  • Billett MA, Hall TJ. Cations and the accessibility of chromatin to nucleases. Nucleic Acids Res. 1979 Jun 25;6(8):2929–2945.[PMC free article] [PubMed] [Google Scholar]
  • Krasnow MA, Cozzarelli NR. Catenation of DNA rings by topoisomerases. Mechanism of control by spermidine. J Biol Chem. 1982 Mar 10;257(5):2687–2693. [PubMed] [Google Scholar]
  • 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 Jun;12(6):2503–2512.[PMC free article] [PubMed] [Google Scholar]
  • Porschke D. Structure and dynamics of double helices in solution: modes of DNA bending. J Biomol Struct Dyn. 1986 Dec;4(3):373–389. [PubMed] [Google Scholar]
  • Marquet R, Wyart A, Houssier C. Influence of DNA length on spermine-induced condensation. Importance of the bending and stiffening of DNA. Biochim Biophys Acta. 1987 Aug 25;909(3):165–172. [PubMed] [Google Scholar]
  • Stimac E, Morris DR. Messenger RNAs coding for enzymes of polyamine biosynthesis are induced during the G0-G1 transition but not during traverse of the normal G1 phase. J Cell Physiol. 1987 Dec;133(3):590–594. [PubMed] [Google Scholar]
  • Auvinen M, Paasinen A, Andersson LC, Hölttä E. Ornithine decarboxylase activity is critical for cell transformation. Nature. 1992 Nov 26;360(6402):355–358. [PubMed] [Google Scholar]
  • Bannister AJ, Kouzarides T. Basic peptides enhance protein/DNA interaction in vitro. Nucleic Acids Res. 1992 Jul 11;20(13):3523–3523.[PMC free article] [PubMed] [Google Scholar]
Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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Abstract
The polyamines are abundant biogenic cations implicated in many biological processes. Despite a plethora of evidence on polyamine-induced DNA conformational changes, no thorough study of their effects on the activities of sequence-specific DNA binding proteins has been performed. We describe the in vitro effects of polyamines on the activities of purified, representative DNA-binding proteins, and on complex protein mixtures. Polyamines at physiological concentrations enhance the binding of several proteins to DNA (e.g. USF, TFE3, Ig/EBP, NF-IL6, YY1 and ICP-4, a herpes simplex virus gene regulator), but inhibit others (e.g. Oct-1). The degree of enhancement correlates with cationic charge; divalent putrescine is ineffective whereas tetravalent spermine is more potent than trivalent spermidine. Polyamine effects on USF and ICP-4 result from increased rate of complex formation rather than a decreased rate of dissociation. DNAse I footprint analysis indicated that polyamines do not alter DNA-protein contacts. Polyamines also facilitate formation of complexes involving binding of more than one protein on a DNA fragment.
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