In vitro fluorescence studies of transcription factor IIB-DNA interaction

• Authors: Andrzej Górecki , Małgorzata Figiel , Marta Dziedzicka-Wasylewska
• Languages of publication: EN

Abstracts

EN

General transcription factor TFIIB is one of the basal constituents of the preinitiation complex of eukaryotic RNA polymerase II, acting as a bridge between the preinitiation complex and the polymerase, and binding promoter DNA in an asymmetric manner, thereby defining the direction of the transcription. Methods of fluorescence spectroscopy together with circular dichroism spectroscopy were used to observe conformational changes in the structure of recombinant human TFIIB after binding to specific DNA sequence. To facilitate the exploration of the structural changes, several site-directed mutations have been introduced altering the fluorescence properties of the protein. Our observations showed that binding of specific DNA sequences changed the protein structure and dynamics, and TFIIB may exist in two conformational states, which can be described by a different microenvironment of W52. Fluorescence studies using both intrinsic and exogenous fluorophores showed that these changes significantly depended on the recognition sequence and concerned various regions of the protein, including those interacting with other transcription factors and RNA polymerase II. DNA binding can cause rearrangements in regions of proteins interacting with the polymerase in a manner dependent on the recognized sequences, and therefore, influence the gene expression.

Keywords

EN

transcription factors; TF2B; TFIIB; fluorescence spectroscopy; fluorescence quenching; site directed mutagenesis

• Publisher: Polish Biochemical Society
• Journal: Acta Biochimica Polonica
• Year: 2015
• Volume: 62
• Issue: 3
• Pages: 413-421

Dates

published

2015

received

2015-03-14

revised

2015-04-20

accepted

2015-05-20

(unknown)

2015-08-18

Contributors

author

Andrzej Górecki

• Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland

author

Małgorzata Figiel

• Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland

author

Marta Dziedzicka-Wasylewska

• Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland

References

• Agostini I et al. (1999) The HIV-1 Vpr co-activator induces a conformational change in TFIIB. FEBS Lett 450: 235-239.
• Bagby S et al. (1995) Solution structure of the C-terminal core domain of human TFIIB: similarity to cyclin A and interaction with TATA-binding protein. Cell 82: 857-867.
• Bangur CS et al. (1999) An interaction between the N-terminal region and the core domain of yeast TFIIB promotes the formation of TATA-binding protein-TFIIB-DNA complexes. J Biol Chem 274: 23203-23209.
• Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72: 248-254.
• Chen HT et al. (2000) Structure of a (Cys3His) zinc ribbon, a ubiquitous motif in archaeal and eucaryal transcription. Protein Sci 9: 1743-1752.
• Crowe JS et al. (1991) Improved cloning efficiency of polymerase chain reaction (PCR) products after proteinase K digestion. Nucleic Acids Res 19: 184.
• Deng W, Roberts SG (2005) A core promoter element downstream of the TATA box that is recognized by TFIIB. Genes Develop 19: 2418-2423.
• Deng W, Roberts SG (2007) TFIIB and the regulation of transcription by RNA polymerase II. Chromosoma 116: 417-429.
• Elsby LM et al. (2006) Assembly of transcription factor IIB at a promoter in vivo requires contact with RNA polymerase II. EMBO Reports 7: 898-903.
• Elsby LM, Roberts SG (2004) The role of TFIIB conformation in transcriptional regulation. Biochemi Soc Trans 32: 1098-1099.
• Fairley JA et al. (2002) Core promoter-dependent TFIIB conformation and a role for TFIIB conformation in transcription start site selection. Mol Cell Biol 22: 6697-6705.
• Fic E, Górecki A, Wasylewski Z (2007) Fluorescence quenching studies of conformational changes induced by cAMP and DNA binding to heterodimer of cyclic AMP receptor protein from Escherichia coli. Protein J 26: 457-466.
• Grossmann JG et al. (2001) Molecular shapes of transcription factors TFIIB and VP16 in solution: implications for recognition. Biochemistry 40: 6267-6274.
• Ha I, Lane WS, Reinberg D (1991) Cloning of a human gene encoding the general transcription initiation factor IIB. Nature 352: 689-695.
• Hawkes NA, Evans R, Roberts SG (2000) The conformation of the transcription factor TFIIB modulates the response to transcriptional activators in vivo. Curr Biol: CB 10: 273-276.
• Hawkes NA, Roberts SG (1999) The role of human TFIIB in transcription start site selection in vitro and in vivo. J Biol Chem 274: 14337-14343.
• Hayashi F et al. (1998) Human general transcription factor TFIIB: conformational variability and interaction with VP16 activation domain. Biochemistry 37: 7941-7951.
• Kostrewa D et al. (2009) RNA polymerase II-TFIIB structure and mechanism of transcription initiation. Nature 462: 323-330.
• Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227: 680-685.
• Lagrange T et al. (1998) New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB. Genes Develop 12: 34-44.
• Lakowicz JR (2006) Principles of Fluorescence Spectroscopy. Springer, New York.
• Lee S, Hahn S (1995) Model for binding of transcription factor TFIIB to the TBP-DNA complex. Nature 376: 609-612.
• Malik S, Lee DK, Roeder RG (1993) Potential RNA polymerase II-induced interactions of transcription factor TFIIB. Mol Cell Biol 13: 6253-6259.
• Nikolov DB et al. (1995) Crystal structure of a TFIIB-TBP-TATA-element ternary complex. Nature 377: 119-128.
• Reese JC (2003) Basal transcription factors. Curr Opin Genet Ddevel 13: 114-118.
• Roberts SG, Green MR (1994) Activator-induced conformational change in general transcription factor TFIIB. Nature 371: 717-720.
• Sievers F et al. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7: 539.
• Thompson NE et al. (2009) Minimal promoter systems reveal the importance of conserved residues in the B-finger of human transcription factor IIB. J Biol Chem 284: 24754-24766.
• Thomsen J et al. (2001) The basal transcription factors TBP and TFB from the mesophilic archaeon Methanosarcina mazeii: structure and conformational changes upon interaction with stress-gene promoters. J Mol Biol 309: 589-603.
• Tran K, Gralla JD (2008) Control of the timing of promoter escape and RNA catalysis by the transcription factor IIb fingertip. J Biol Chem 283: 15665-15671.
• Tsai FT, Sigler PB (2000) Structural basis of preinitiation complex assembly on human pol II promoters. EMBO J 19: 25-36.
• Wu WH, Hampsey M (1999) An activation-specific role for transcription factor TFIIB in vivo. Proc Natl Acad Sci USA 96: 2764-2769.
• Zhang DY et al. (2000) Intramolecular interaction of yeast TFIIB in transcription control. Nucleic Acids Res 28: 1913-1920.
• Zheng L et al. (2004) FRET evidence for a conformational change in TFIIB upon TBP-DNA binding. Eur J Biochem 271: 792-800.

Identifiers

DOI

10.18388/abp.2015_1034