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2003 | 50 | 4 | 909-920
Article title

Effects of distortions by A-tracts of promoter B-DNA spacer region on the kinetics of open complex formation by Escherichia coli RNA polymerase.

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EN
Abstracts
EN
A-tracts in DNA due to their structural morphology distinctly different from the canonical B-DNA form play an important role in specific recognition of bacterial upstream promoter elements by the carboxyl terminal domain of RNA polymerase α subunit and, in turn, in the process of transcription initiation. They are only rarely found in the spacer promoter regions separating the -35 and -10 recognition hexamers. At present, the nature of the protein-DNA contacts formed between RNA polymerase and promoter DNA in transcription initiation can only be inferred from low resolution structural data and mutational and crosslinking experiments. To probe these contacts further, we constructed derivatives of a model Pa promoter bearing in the spacer region one or two An (n = 5 or 6) tracts, in phase with the DNA helical repeat, and studied the effects of thereby induced perturbation of promoter DNA structure on the kinetics of open complex (RPo) formation in vitro by Escherichia coli RNA polymerase. We found that the overall second-order rate constant ka of RPo formation, relative to that at the control promoter, was strongly reduced by one to two orders of magnitude only when the A-tracts were located in the nontemplate strand. A particularly strong 30-fold down effect on ka was exerted by nontemplate A-tracts in the -10 extended promoter region, where an involvement of nontemplate TG (-14, -15) sequence in a specific interaction with region 3 of σ-subunit is postulated. A-tracts in the latter location caused also 3-fold slower isomerization of the first closed transcription complex into the intermediate one that precedes formation of RPo, and led to two-fold faster dissociation of the latter. All these findings are discussed in relation to recent structural and kinetic models of RPo formation.
Publisher

Year
Volume
50
Issue
4
Pages
909-920
Physical description
Dates
published
2003
received
2003-08-11
revised
2003-10-15
accepted
2003-12-03
Contributors
  • Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
  • Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
  • Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
References
  • Bertrand-Burggraf E, Lefévre JF, Daune M. (1984) A new experimental approach for studying the association between RNA polymerase and the tet promoter of pBR322. Nucleic Acids Res.; 12: 1697-706.
  • Boutonnet N, Hui X, Zakrzewska K. (1993) Looking into the grooves of DNA. Biopolymers.; 33: 479-90.
  • Burgess RR, Jendrisak JJ. (1975) A procedure for the rapid, large-scale purification of Escherichia coli DNA-dependent RNA polymerase involving Polymin P precipitation and DNA-cellulose chromatography. Biochemistry.; 14: 4634-8.
  • Chamberlin M, Kingston R, Gilman M, Wiggs J, deVera A. (1983) Isolation of bacterial and bacteriophage RNA polymerases and their use in synthesis of RNA in vitro. Methods Enzymol.; 101: 540-68.
  • Chen H, Tang H, Ebright RH. (2003) Functional interaction between RNA polymerase alpha subunit C-terminal domain and sigma70 with UP-element- and activator-dependent transcription. Mol Cell.; 11: 1621-33.
  • Estrem ST, Ross W, Gaal T, Chen ZW, Niu W, Ebright RH. (1999) Bacterial promoter architecture: subsite structure of UP elements and interaction with the carboxy-terminal domain of the RNA polymerase α subunit. Genes Dev.; 13: 2134-47.
  • Fenton MS, Lee SJ, Graala JD. (2000) Escherichia coli promoter opening and Escherichia coli promoter opening and -10 recognition: mutational analysis of σ70. EMBO J.; 19: 1130-7.
  • Gorin AA, Zhurkin VB, Olson W. (1995) B-DNA twisting correlates with base-pair morphology. J Mol Biol.; 247: 34-48.
  • Hsu L. (2002) Promoter clearance and escape in prokaryotes. Biochim Biophys Acta.; 1577: 191-207.
  • Kolasa IK. (2001) Influence of An·Tn DNA bending sequences on Escherichia coli promoter strength in vitro. Ph.D. Thesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland (in Polish).
  • Kolasa IK, Łozńnski T, Wierzchowski KL. (2002) Effect of An tracts within the UP element proximal subsite of a model promoter on kinetics of open complex formation by Escherichia coli RNA polymerase. Acta Biochim Polon.; 49: 659-69.
  • Luscombe NM, Thornton JM. (2002) Protein-DNA interaction: amino-acid conservation and the effects of mutations on binding specificity. J Mol Biol.; 320: 991-1009.
  • Łozńnski T, Wierzchowski KL. (1996) Effect of reversed orientation and length of An·Tn DNA bending sequences in the -35 and spacer domains of a consensus-like Escherichia coli promoter on its strength in vivo and gross structure of the open complex in vitro. Acta Biochim Polon.; 43: 265-80.
  • Łozńnski T, Adrych-Rożek K, Markiewicz WT, Wierzchowski KL. (1991) Effect of DNA bending in various regions of the consensus-like Escherichia coli promoter on its strength in vivo and structure of the open complexin vitro. Nucleic Acids Res.; 19: 2947-53.
  • MacDonald D, Herbert K, Zhang X, Pologruto T, Lu P. (2001) Solution structure of an A-tract DNA bend. J Mol Biol.; 306: 1081-98.
  • Mecsas J, Cowing DW, Gross CA. (1991) Development of RNA polymerase-promoter contacts during open complex formation. J Mol Biol.; 220: 585-97.
  • Mekler V, Kortkhonija K, Mukhopadhyay J, Knight J, Revyakin A, Kapanidis AN, Niu W, Ebright YW, Levy R, Ebright RH. (2002) Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell.; 108: 599-614.
  • Misra VK, Draper DE. (1999) The interpretation of Mg2+ binding isotherms for nucleic acids using Poisson-Boltzmann theory. J Mol Biol.; 294: 1135-47.
  • Murakami KS, Masuda S, Campbell E, Muzzin O, Darst SA. (2002) Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science.; 296: 1285-90.
  • Naryshkin N, Revyakin A, Kim Y, Mekler V, Ebright RH. (2000) Structural organization of the RNA polymerase-promotor open complex. Cell.; 101: 601-11.
  • Nelson HCM, Finch JT, Luisi BF, Klug A. (1987) The structure of an oligo(dA)·oligo(dT) tract and its biological implications. Nature (London).; 330: 221-6.
  • Noel RJ, Reznikoff WS. (2000) Structural studies of lacUV5-RNA polymerase interactions in vitro. J Biol Chem.; 275: 7708-12.
  • Roe JH, Burgess RR, Record MT Jr. (1984) Kinetics and mechanism of the interaction of Escherichia coli RNA polymerase with the λPR promoter. J Mol Biol.; 176: 495-521.
  • Roe JH, Burgess RR, Record MT Jr. (1985) Temperature dependence of the rate constants of the Escherichia coli RNA polymerase-λPR promoter interaction. Assignment of the kinetic steps corresponding to protein conformational change and DNA opening. J Mol Biol.; 184: 441-53.
  • Ross W, Ernst A, Gourse RL. (2001) Fine structure of E. coli RNA polymerase-promoter interactions: α subunit binding to the UP element minor groove. Genes Dev.; 15: 491-506.
  • Ross W, Schneider DA, Paul BJ, Mertens A, Gourse RL. (2003) An intersubunit contact stimulating transcription initiation by E. coli RNA polymerase: interaction of the α C-terminal domain and sigma region 4. Genes Dev.; 17: 1293-307.
  • Rudakova EA, Ivanovskaya MG, Kozlov MV, Khorotonenko MV, Oretskaya TS, Nikiforov VG. (2000) Probing of contacts of oligonucleotide phosphate groups from the non-template strand of lacUV5 promoter with RNA polymerase of E. coli by regioselective crosslinking. Biokhimija.; 65: 753-64.
  • Saecker RM, Tsodikov OV, McQuade KL, Schlax PE Jr, Capp MW, Record MT Jr. (2002) Kinetic studies and structural models of the association of E. coli σ70 RNA polymerase with the λPR promoter: large scale conformational changes in forming the kinetically significant intermediates. J Mol Biol.; 319: 649-71.
  • Sanderson A, Mitchell JE, Minchin SD, Busby JW. (2003) Substitutions in Escherichia coli RNA polymerase σ70 factor that affect recognition of extended -10 elements at promoters. FEBS Lett.; 544: 199-205.
  • Schickor P, Metzger W, Werel W, Lederer H, Heumann H. (1990) Topography of intermediates in transcription initiation of E. coli. EMBO J.; 9: 2215-20.
  • Studitsky VM, Brodolin KL, Liu Y, Mirzabekov AD. (2001) Topography of lacUV5 initiation complexes. Nucleic Acids Res.; 29: 854-61.
  • Suh WC, Leirmo S, Record MT Jr. (1992) Role of Mg2+ in the mechanism of formation and dissociation of open complexes between Escherichia coli RNA polymerase and the λPR promoter: Kinetic evidence for a second open complex requiring Mg2+. Biochemistry.; 31: 7815-25.
  • Travers AA. (1987) Structure and function of E. coli promoter DNA. CRC Crit Rev Biochem.; 22: 181-219.
  • Tsodikov OV, Record MT Jr. (1999) General method of analysis of kinetic equations for multistep reversible mechanisms in the single-exponential regime: Application to kinetics of open complex formation between Eσ70 RNA polymerase and λPR promoter DNA. Biophys J.; 76: 1320-9.
  • Yarbrough LR, Schlageck JG, Baughman M. (1979) Synthesis and properties of fluorescent nucleotide substrates for DNA-dependent RNA polymerases. J Biol Chem.; 254: 12069-73.
  • Yasuno K, Yamazaki T, Tanaka Y, Kodama TS, Matsugami A, Katahira M, Ishihama A, Kyogoku Y. (2001) Interaction of the C-terminal domain of the E. coli polymerase α subunit with the UP element: recognizing the backbone structure in the minor groove surface. J Mol Biol.; 306: 213-25.
Document Type
Publication order reference
Identifiers
YADDA identifier
bwmeta1.element.bwnjournal-article-abpv50i4p909kz
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