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Volumn 260, Issue 2, 1996, Pages 196-206

On the connection between inherent DNA flexure and preferred binding of hydroxymethyluracil-containing DNA by the type II DNA-binding protein TF1

Author keywords

DNA flexibility; DNA protein interactions; Hydroxymethyluracil; Phage SPO1; Transcription factor 1

Indexed keywords

DNA BINDING PROTEIN; TRANSCRIPTION FACTOR;

EID: 0030581143     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0392     Document Type: Article
Times cited : (38)

References (53)
  • 1
    • 0028343504 scopus 로고
    • Determinants of affinity and mode of DNA binding at the carboxy terminus of the bacteriophage SPO1-encoded type II DNA-binding protein, TF1
    • Andera, L. & Geiduschek, E. P. (1994). Determinants of affinity and mode of DNA binding at the carboxy terminus of the bacteriophage SPO1-encoded type II DNA-binding protein, TF1. J. Bacterial 176, 1364-1373.
    • (1994) J. Bacterial , vol.176 , pp. 1364-1373
    • Andera, L.1    Geiduschek, E.P.2
  • 2
    • 0009520268 scopus 로고
    • Interrelations of secondary structure stability and DNA-binding affinity in the bacteriophage SPO1-encoded type II DNA-binding protein TF1
    • Andera, L., Spangler, C. J., Galeone, A., Mayol, L. & Geiduschek, E. P. (1994). Interrelations of secondary structure stability and DNA-binding affinity in the bacteriophage SPO1-encoded type II DNA-binding protein TF1. J. Mol. Biol. 236, 139-150.
    • (1994) J. Mol. Biol. , vol.236 , pp. 139-150
    • Andera, L.1    Spangler, C.J.2    Galeone, A.3    Mayol, L.4    Geiduschek, E.P.5
  • 3
    • 0028136642 scopus 로고
    • DNA-binding parameters of the HU protein of Escherichia coli to cruciform DNA
    • Bonnefoy, E., Takahashi, M. & Rouvière-Yaniv, J. (1994). DNA-binding parameters of the HU protein of Escherichia coli to cruciform DNA. J. Mol. Biol. 242, 116-129.
    • (1994) J. Mol. Biol. , vol.242 , pp. 116-129
    • Bonnefoy, E.1    Takahashi, M.2    Rouvière-Yaniv, J.3
  • 5
    • 0028927786 scopus 로고
    • Old phage, new insights: Two recently recognised mechanisms of transcriptional regulation in bacteriophage T4 development
    • Brody, E. M., Kassavetis, G. A., Ouhammouch, M., Sanders, G. M., Tinker, R. L. & Geiduschek, E. P. (1995). Old phage, new insights: two recently recognised mechanisms of transcriptional regulation in bacteriophage T4 development. FEMS Microbiol. Letters, 128, 1-8.
    • (1995) FEMS Microbiol. Letters , vol.128 , pp. 1-8
    • Brody, E.M.1    Kassavetis, G.A.2    Ouhammouch, M.3    Sanders, G.M.4    Tinker, R.L.5    Geiduschek, E.P.6
  • 6
    • 0022914418 scopus 로고
    • Principles of sequence-dependent flexure of DNA
    • Calladine, C. R. & Drew, H. R. (1986). Principles of sequence-dependent flexure of DNA. J. Mol. Biol. 192, 907-918.
    • (1986) J. Mol. Biol. , vol.192 , pp. 907-918
    • Calladine, C.R.1    Drew, H.R.2
  • 7
    • 0028901705 scopus 로고
    • HU protein of Escherichia coli binds specifically to DNA that contains single-strand breaks or gaps
    • 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, 10291-10296.
    • (1995) J. Biol. Chem. , vol.270 , pp. 10291-10296
    • Castaing, B.1    Zelwer, C.2    Laval, J.3    Boiteux, S.4
  • 8
    • 0023042678 scopus 로고
    • Activity of a phage-modified RNA polymerase at hybrid promoters: Effects of substituting thymine for hydroxymethyluracil in a phage SPO1 middle promoter
    • Choy, H. A., Romeo, J. M. & Geiduschek, E. P. (1986). Activity of a phage-modified RNA polymerase at hybrid promoters: effects of substituting thymine for hydroxymethyluracil in a phage SPO1 middle promoter. J. Mol. Biol. 191, 59-73.
    • (1986) J. Mol. Biol. , vol.191 , pp. 59-73
    • Choy, H.A.1    Romeo, J.M.2    Geiduschek, E.P.3
  • 10
  • 11
    • 0001344298 scopus 로고
    • G(syn)·A(anti) mismatch formation in DNA dodecamers at acidic pH: PH-dependent conformational transition of G-A mispairs detected by proton NMR
    • Gao, X. & Patel, D. J. (1988). G(syn)·A(anti) mismatch formation in DNA dodecamers at acidic pH: pH-dependent conformational transition of G-A mispairs detected by proton NMR. J. Am. Chem. Soc. 110, 5178-5182.
    • (1988) J. Am. Chem. Soc. , vol.110 , pp. 5178-5182
    • Gao, X.1    Patel, D.J.2
  • 12
    • 0028225644 scopus 로고
    • The crystal structure of C-C-A-T-T-A-A-T-G-G. Implications for bending of B-DNA at T-A steps
    • Goodsell, D. S., Kaczor-Grzeskoviak, M. & Dickerson, R. E. (1994). The crystal structure of C-C-A-T-T-A-A-T-G-G. Implications for bending of B-DNA at T-A steps. J. Mol. Biol. 239, 79-96.
    • (1994) J. Mol. Biol. , vol.239 , pp. 79-96
    • Goodsell, D.S.1    Kaczor-Grzeskoviak, M.2    Dickerson, R.E.3
  • 14
    • 0027370073 scopus 로고
    • Characterization of a set of integration host factor mutants deficient for DNA binding
    • Granston, A. E. & Nash, H. A. (1993). Characterization of a set of integration host factor mutants deficient for DNA binding. J. Mol. Biol. 234, 45-59.
    • (1993) J. Mol. Biol. , vol.234 , pp. 45-59
    • Granston, A.E.1    Nash, H.A.2
  • 15
    • 0022065259 scopus 로고
    • Site-specific DNA binding by the bacteriophage SPO1-encoded type II DNA-binding protein
    • Greene, J. R. & Geiduschek, E. P. (1985). Site-specific DNA binding by the bacteriophage SPO1-encoded type II DNA-binding protein. EMBO J. 4, 1345-1349.
    • (1985) EMBO J. , vol.4 , pp. 1345-1349
    • Greene, J.R.1    Geiduschek, E.P.2
  • 16
    • 0030581147 scopus 로고    scopus 로고
    • Localized DNA flexibility contributes to target site selection by DNA-bending proteins
    • Grove, A., Galeone, A., Mayol, L. & Geiduschek, E. P. (1996). Localized DNA flexibility contributes to target site selection by DNA-bending proteins. J. Mol. Biol. 260, 120-125.
    • (1996) J. Mol. Biol. , vol.260 , pp. 120-125
    • Grove, A.1    Galeone, A.2    Mayol, L.3    Geiduschek, E.P.4
  • 18
    • 0025190888 scopus 로고
    • Reduced DNA flexibility in complexes with a type II DNA binding protein
    • Hard, T. & Kearns, D. R. (1990). Reduced DNA flexibility in complexes with a type II DNA binding protein. Biochemistry, 29, 959-965.
    • (1990) Biochemistry , vol.29 , pp. 959-965
    • Hard, T.1    Kearns, D.R.2
  • 19
    • 0024508994 scopus 로고
    • Fluorescence studies of a single tyrosine in a type II DNA binding protein
    • Hard, T., Hsu, V., Geiduschek, E. P., Appelt, K. & Kearns, D. (1989a). Fluorescence studies of a single tyrosine in a type II DNA binding protein. Biochemistry, 28, 396-406.
    • (1989) Biochemistry , vol.28 , pp. 396-406
    • Hard, T.1    Hsu, V.2    Geiduschek, E.P.3    Appelt, K.4    Kearns, D.5
  • 20
    • 0024539550 scopus 로고
    • A type II DNA-binding protein genetically engineered for fluorescence spectroscopy: The "arm" of Transcription Factor 1 binds in the DNA grooves
    • Hard, T., Sayre, M. H., Geiduschek, E. P. & Kearns, D. R. (1989b). A type II DNA-binding protein genetically engineered for fluorescence spectroscopy: the "arm" of Transcription Factor 1 binds in the DNA grooves. Biochemistry, 28, 2813-2819.
    • (1989) Biochemistry , vol.28 , pp. 2813-2819
    • Hard, T.1    Sayre, M.H.2    Geiduschek, E.P.3    Kearns, D.R.4
  • 21
    • 0026665954 scopus 로고
    • Kinetic analysis of yeast TFIID-TATA box complex formation sugests a multi-step pathway
    • Hoopes, B. C., LeBlanc, J. F. & Hawley, D. K. (1992). Kinetic analysis of yeast TFIID-TATA box complex formation sugests a multi-step pathway. J. Biol. Chem. 267, 11539-11547.
    • (1992) J. Biol. Chem. , vol.267 , pp. 11539-11547
    • Hoopes, B.C.1    LeBlanc, J.F.2    Hawley, D.K.3
  • 22
    • 0028000411 scopus 로고
    • Proton and nitrogen NMR sequence-specific assignments and secondary structure determination of the Bacillus subtilis SPO1-encoded transcription factor 1
    • Jia, X., Reisman, J. M., Hsu, V. L., Geiduschek, E. P., Parello, J. & Kearns, D. R. (1994). Proton and nitrogen NMR sequence-specific assignments and secondary structure determination of the Bacillus subtilis SPO1-encoded transcription factor 1. Biochemistry, 33, 8842-8852.
    • (1994) Biochemistry , vol.33 , pp. 8842-8852
    • Jia, X.1    Reisman, J.M.2    Hsu, V.L.3    Geiduschek, E.P.4    Parello, J.5    Kearns, D.R.6
  • 23
    • 0017349150 scopus 로고
    • Specificity of the weak binding between the phage SPO1 transcription-inhibitory protein, TF1, and SPO1 DNA
    • Johnson, G. G. & Geiduschek, E. P. (1977). Specificity of the weak binding between the phage SPO1 transcription-inhibitory protein, TF1, and SPO1 DNA. Biochemistry, 16, 1473-1485.
    • (1977) Biochemistry , vol.16 , pp. 1473-1485
    • Johnson, G.G.1    Geiduschek, E.P.2
  • 24
    • 0028820166 scopus 로고
    • DNA twist, flexibility and transcription of the osmoregulated proll promoter of Salmonella typhimurium
    • Jordi, B. J. A. M., Owen-Hughes, T., Hulton, C. S. J. & Higgins, C. F. (1995). DNA twist, flexibility and transcription of the osmoregulated proll promoter of Salmonella typhimurium. EMBO J. 14, 5690-5700.
    • (1995) EMBO J. , Issue.14 , pp. 5690-5700
    • Jordi, B.J.A.M.1    Owen-Hughes, T.2    Hulton, C.S.J.3    Higgins, C.F.4
  • 25
    • 0028289189 scopus 로고
    • Detection of localized DNA flexibility
    • Kahn, J. D., Yun, E. & Crothers, D. M. (1994). Detection of localized DNA flexibility. Nature, 368, 163-166.
    • (1994) Nature , vol.368 , pp. 163-166
    • Kahn, J.D.1    Yun, E.2    Crothers, D.M.3
  • 26
    • 0026685334 scopus 로고
    • Chromatins of low-protein content: Special features of their compaction and condensation
    • Kellenberger, E. & Arnold-Schulz-Gahmen, B. (1992). Chromatins of low-protein content: special features of their compaction and condensation. FEMS Microbiol. Letters, 100, 361-370.
    • (1992) FEMS Microbiol. Letters , vol.100 , pp. 361-370
    • Kellenberger, E.1    Arnold-Schulz-Gahmen, B.2
  • 27
    • 0027483012 scopus 로고
    • Co-crystal structure of TBP recognizing the minor groove of a TATA element
    • Kim, J. L., Nikolov, D. B. & Burley, S. K. (1993). Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature, 365, 520-527.
    • (1993) Nature , vol.365 , pp. 520-527
    • Kim, J.L.1    Nikolov, D.B.2    Burley, S.K.3
  • 28
    • 0027504913 scopus 로고
    • Crystal structure of a yeast TBP/TATA-box complex
    • Kim, Y., Geiger, J. H., Hahn, S. & Sigler, P. B. (1993). Crystal structure of a yeast TBP/TATA-box complex. Nature, 365, 512-520.
    • (1993) Nature , vol.365 , pp. 512-520
    • Kim, Y.1    Geiger, J.H.2    Hahn, S.3    Sigler, P.B.4
  • 29
    • 0022477409 scopus 로고
    • DNA bending at adenine·thymine tracts
    • Koo, H. S., Wu, H. M. & Crothers, D. M. (1986). DNA bending at adenine·thymine tracts. Nature, 320, 501-506.
    • (1986) Nature , vol.320 , pp. 501-506
    • Koo, H.S.1    Wu, H.M.2    Crothers, D.M.3
  • 30
    • 0019332568 scopus 로고
    • Transcription of cloned DNA from Bacillus subtilis phage SPO1. Requirement for hydroxymethyluracil-containing DNA by phage-modified RNA polymerase
    • Lee, G., Hannett, N. M., Korman, A. & Pero, J. (1980). Transcription of cloned DNA from Bacillus subtilis phage SPO1. Requirement for hydroxymethyluracil-containing DNA by phage-modified RNA polymerase. J. Mol. Biol. 139, 407-422.
    • (1980) J. Mol. Biol. , vol.139 , pp. 407-422
    • Lee, G.1    Hannett, N.M.2    Korman, A.3    Pero, J.4
  • 31
    • 0022885153 scopus 로고
    • The DNA binding domain and bending angle of E. coli CAP protein
    • Liu-Johnson, H.-N., Gartenberg, M. R. & Crothers, D. M. (1986). The DNA binding domain and bending angle of E. coli CAP protein. Cell, 47, 995-1005.
    • (1986) Cell , vol.47 , pp. 995-1005
    • Liu-Johnson, H.-N.1    Gartenberg, M.R.2    Crothers, D.M.3
  • 32
    • 0019442506 scopus 로고
    • Cascades of sigma factors
    • Losick, R. & Pero, J. (1981). Cascades of sigma factors. Cell, 25, 581-584.
    • (1981) Cell , vol.25 , pp. 581-584
    • Losick, R.1    Pero, J.2
  • 33
    • 0027257707 scopus 로고
    • Structures of base pairs with 5-(hydroxymethyl)-2′-deoxyuridine in DNA determined by NMR spectroscopy
    • Mellac, S., Fazakerley, G. V. & Sowers, L. C. (1993). Structures of base pairs with 5-(hydroxymethyl)-2′-deoxyuridine in DNA determined by NMR spectroscopy. Biochemistry, 32, 7779-7786.
    • (1993) Biochemistry , vol.32 , pp. 7779-7786
    • Mellac, S.1    Fazakerley, G.V.2    Sowers, L.C.3
  • 34
    • 0027327311 scopus 로고
    • Genetic and biochemical analysis of the integration host factor of Escherichia coli
    • Mengeritsky, G., Goldenberg, D., Mendelson, I., Giladi, H. & Oppenheim, A. B. (1993). Genetic and biochemical analysis of the integration host factor of Escherichia coli. J. Mol. Biol. 231, 646-657.
    • (1993) J. Mol. Biol. , vol.231 , pp. 646-657
    • Mengeritsky, G.1    Goldenberg, D.2    Mendelson, I.3    Giladi, H.4    Oppenheim, A.B.5
  • 35
    • 0000525413 scopus 로고
    • Torsion and bending of nucleic acids studied by subnanosecond time-resolved fluorescence depolariztion of intercalated dyes
    • Millar, D. P., Robbins, R. J. & Zewail, A. H. (1982). Torsion and bending of nucleic acids studied by subnanosecond time-resolved fluorescence depolariztion of intercalated dyes. J. Chem. Phys. 76, 2080-2094.
    • (1982) J. Chem. Phys. , vol.76 , pp. 2080-2094
    • Millar, D.P.1    Robbins, R.J.2    Zewail, A.H.3
  • 36
    • 0002480960 scopus 로고    scopus 로고
    • The E. coli HU and IHF proteins: Accessory factors for complex protein-DNA assemblies
    • Lin, E. C. C. & Lynch, A. S., eds, in the press
    • Nash, H. A. (1996). The E. coli HU and IHF proteins: accessory factors for complex protein-DNA assemblies. In Regulation of Gene Expression in Escherichia coli (Lin, E. C. C. & Lynch, A. S., eds), in the press.
    • (1996) Regulation of Gene Expression in Escherichia Coli
    • Nash, H.A.1
  • 37
    • 0026682657 scopus 로고
    • Transcription factors: Structural families and principles of DNA recognition
    • Pabo, C. O. & Sauer, R. T. (1992). Transcription factors: structural families and principles of DNA recognition. Annu. Rev. Biochem. 61, 1053-1095.
    • (1992) Annu. Rev. Biochem. , vol.61 , pp. 1053-1095
    • Pabo, C.O.1    Sauer, R.T.2
  • 38
    • 0027997526 scopus 로고
    • DNA lesions. A thermodynamic perspective
    • Plum, G. E. & Breslauer, K. J. (1994). DNA lesions. A thermodynamic perspective. Ann. N. Y. Acad. Sci. 726, 45-57.
    • (1994) Ann. N. Y. Acad. Sci. , vol.726 , pp. 45-57
    • Plum, G.E.1    Breslauer, K.J.2
  • 40
    • 0026624859 scopus 로고
    • Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G
    • Quintana, J. R., Grzeskowiak, K., Yanagi, K. & Dickerson, R. E. (1992). Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G. J. Mol. Biol. 225, 379-395.
    • (1992) J. Mol. Biol. , vol.225 , pp. 379-395
    • Quintana, J.R.1    Grzeskowiak, K.2    Yanagi, K.3    Dickerson, R.E.4
  • 42
    • 0022448111 scopus 로고
    • The phage SPO1-specific RNA polymerase, E.gp28, recognizes its cognate promoters in thymine-containing DNA
    • Romeo, J. M., Greene, J. R., Richards, S. H. & Geiduschek, E. P. (1986). The phage SPO1-specific RNA polymerase, E.gp28, recognizes its cognate promoters in thymine-containing DNA. Virology, 153, 46-52.
    • (1986) Virology , vol.153 , pp. 46-52
    • Romeo, J.M.1    Greene, J.R.2    Richards, S.H.3    Geiduschek, E.P.4
  • 43
    • 0028027303 scopus 로고
    • An arcane role of DNA in transcription activation
    • Ryu, S., Garges, S. & Adhya, S. (1994). An arcane role of DNA in transcription activation. Proc. Natl Acad. Sci. USA, 91, 8582-8586.
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 8582-8586
    • Ryu, S.1    Garges, S.2    Adhya, S.3
  • 44
    • 0024456709 scopus 로고
    • Asymmetry and polarity of nucleosomes in chicken erythrocyte chromatin
    • Satchwell, S. C. & Travers, A. A. (1989). Asymmetry and polarity of nucleosomes in chicken erythrocyte chromatin. EMBO J. 8, 229-238.
    • (1989) EMBO J. , vol.8 , pp. 229-238
    • Satchwell, S.C.1    Travers, A.A.2
  • 45
    • 0023820681 scopus 로고
    • TF1, the bacteriophage SPO1-encoded type II DNA-binding protein, is essential for viral multiplication
    • Sayre, M. H. & Geiduschek, E. P. (1988). TF1, the bacteriophage SPO1-encoded type II DNA-binding protein, is essential for viral multiplication. J. Virol. 62, 3455-3462.
    • (1988) J. Virol. , vol.62 , pp. 3455-3462
    • Sayre, M.H.1    Geiduschek, E.P.2
  • 46
    • 0025607896 scopus 로고
    • Effects of mutations at amino acid 61 in the arm of TF1 on its DNA-binding properties
    • Sayre, M. H. & Geiduschek, E. P. (1990). Effects of mutations at amino acid 61 in the arm of TF1 on its DNA-binding properties. J. Mol. Biol. 216, 819-833.
    • (1990) J. Mol. Biol. , vol.216 , pp. 819-833
    • Sayre, M.H.1    Geiduschek, E.P.2
  • 48
    • 0025144957 scopus 로고
    • Effects of DNA sequence and histone-histone interactions on nucleosome placement
    • Shrader, T. E. & Crothers, D. M. (1990). Effects of DNA sequence and histone-histone interactions on nucleosome placement. J. Mol. Biol. 216, 69-84.
    • (1990) J. Mol. Biol. , vol.216 , pp. 69-84
    • Shrader, T.E.1    Crothers, D.M.2
  • 49
    • 0021286693 scopus 로고
    • 3-Å resolution structure of a protein with histone-like properties in prokaryotes
    • Tanaka, I., Appelt, K., Dijk, J., White, S. W. & Wilson, K. S. (1984). 3-Å resolution structure of a protein with histone-like properties in prokaryotes. Nature, 310, 376-381.
    • (1984) Nature , vol.310 , pp. 376-381
    • Tanaka, I.1    Appelt, K.2    Dijk, J.3    White, S.W.4    Wilson, K.S.5
  • 50
    • 0002524447 scopus 로고
    • Bending of DNA in nucleoprotein complexes
    • Cozzarelli, N. R. & Wang, J. C., eds, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
    • Travers, A. A. & Klug, A. (1990). Bending of DNA in nucleoprotein complexes. In DNA Topology and its Biological Effects (Cozzarelli, N. R. & Wang, J. C., eds), pp. 57-106, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
    • (1990) DNA Topology and its Biological Effects , pp. 57-106
    • Travers, A.A.1    Klug, A.2
  • 51
    • 0028785254 scopus 로고
    • The solution structure of the human ETS1-DNA complex reveals a novel mode of binding and true side chain intercalation
    • Werner, M. H., Clore, G. M., Fisher, C. L., Fisher, R. J., Trinh, L., Shiloach, J. & Gronenborn, A. M. (1995). The solution structure of the human ETS1-DNA complex reveals a novel mode of binding and true side chain intercalation. Cell, 83, 761-771.
    • (1995) Cell , vol.83 , pp. 761-771
    • Werner, M.H.1    Clore, G.M.2    Fisher, C.L.3    Fisher, R.J.4    Trinh, L.5    Shiloach, J.6    Gronenborn, A.M.7
  • 53
    • 0012046407 scopus 로고    scopus 로고
    • DNA structure implications for chromatin structure and function
    • IRL Press, in the press
    • Wolffe, A. P. & Drew, H. R. (1996). DNA structure implications for chromatin structure and function. In Frontiers in Molecular Biology, IRL Press, in the press.
    • (1996) Frontiers in Molecular Biology
    • Wolffe, A.P.1    Drew, H.R.2


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