TATA Binding Protein

---

The TATA Binding Protein (TBP) is a protein involved in eukaryotic transcription that binds to the TATA box on the DNA template. 

 

Role in Transcription Structure and DNA Interaction Structure DNA Interaction Regulation Role in Neurodegenerative Diseases

 

 

Role in Transcription

---

The TATA binding protein is essential for transcription initiation. The TBP is just one of the many general transcription factors that must be present for the polymerase to effectively transcribe a gene.  TBP is necessary for transcription involving all three forms of RNA polymerase (I,II,and III), however TBP is been best studied for its role in transcription involving polymerase II (Burley, 1996).^[1]  The TBP is a subunit of the TFIID transcription factor, and TBP brings the TFIID complex to the DNA by binding to the TATA box, . The binding of the TFIID unit is important for the recruitment and assembly of the pre-intitiation complex (Fig.1).  Once the TBP binds to the TATA box, the protein is able to bend the DNA and unwind the DNA strand.^[2] 

 

 

Structure and DNA Interaction

---

 

Structure

The TATA binding protein consists of two structural domains – the C-terminal domain and the N-terminal domain.  TBP is, for the most part, a symmetrical protein, however there is some asymmetry in the perpendicular axis dividing the two domains.  The two subdomains form a curved β-sheet.  On each side of the axis, two loops emanate from the S2 and S3 positions of the β-sheet.  Two smaller helices are also located at the ends of the molecule (Chasman et al., 1993 ).^[3]

 

Two helices make up the N-terminal domain and are situated on top of the β-sheet. The two domains are linked at the S1 and S1' positions.  Unlike the C-terminus, the N-terminus is not highly conserved (Burley). The upper portion of the molecule is responsible for binding various transcriptional machinery (Burley, 1996).^[4]

 

 

 

 

 

 

 

 

 

DNA Interaction

The TBP interacts with the DNA by at the TATA box. X-ray crystallography has shown that the highly conserved C-terminal 180-aminoacid domain binds with the TATA box promoter DNA with high affinity and a slow dissociation rate.^[5]  The underside of the 'saddle' binds to the minor groove and bends the DNA at an 80 degree angle.^[6]  It is quite strange that TBP would bind to the minor groove of the DNA since it offers less selectivity than the major groove.  The underside contains a curved, eight-stranded, antiparallel β-sheet.  This large, concave surface provides excellent contact with the minor groove and the eight base pairs of the TATA box. 

 

A string of lysine and arginine amino acids (which can be seen in dark blue on the image to the left) interact with the phosphate groups of the DNA (yellow and red). This provides a strong bond to the DNA (RCSB). 

 

The 5' end of the DNA strand enters the underside of the protein and two phenylalanine residue coming off of the C-terminal domain are inserted into the helix at the first T-A base pair step.  The DNA is kinked when two more phenylalanine residues insert at the last two base pairs of the box, which can be seen in the lower picture.  This results in the partial unwinding of the DNA helix.  The DNA is then shifted further into the protein, where the six central base pairs of the TATA box interact with the protein side chains.  A more recent study has suggested that the formation of hydrogen bonds with the central bases of the TATA box, also plays a role in the kinking of the DNA.^[7] Two asparagine amino acids responsible for forming hydrogen bonds can be seen in the middle of the protein (RCSB).

 

 

 

 

 

 

 

 

 

 

 

 

---

Video of TBD/DNA Interaction

 

 

 

 

 

 

Regulation

---

Due to TBP's high affinity to binding to the TATA box, there must be a mechanism to regulate TBP in order to turn of gene transcription.  Histones may play some role in limiting access to the TBP, however the more likely mechanism of regulation hinges on the ability of TBP for form a dimeric complex with other TBP.  TBP dimers result when the curved C-terminals of two TBP bind, kind of like a 'handshake' (Fig. 2).  When dimerized, the TPB are incapable of binding to the DNA.  The TBP dimer also helps prevent it from degrading within the cell.  Transcriptional activators (TFIIA) are responsible for disrupting the dimers, allowing the TBP to bind to the DNA.^[8]

 

There are also proteins involved in the regulation of TBP (Fig. 3):

 

• Mot1:  A protein, which posseses ATPase activity, and utilize the energy of ATP hydrolisis to remove the TBP from the TATA box.  Mot1 normally removes TBP from weak TATA or non-TATA sequence.  After the TBP has been removed, it is free to bind to a stronger TATA sequence.^[9]
• NC2: Binds the TBP/TATA complex and prevents the incorporation of TFIIA and/or TFIIB.^[10]
• NOT complex:  Binds the TBP/TATA complex and prevents the recruitment of the polymerase II holoenzyme.^[11]

 

 

 

Role in Neurodegenerative Diseases

---

Recent research has shown that TBP could be involved in the development of certain neurodegenerative diseases, specifically polyglutamine repeat diseases.  TBP contains a stretch of uninterrupted glutamine residues on the N-terminus which are necessary to aid the C-terminus in binding to the DNA.  However, when certain mutations arise in the gene that codes for TBP, it can results in polyglutamine expansion.  The allele coding for TBP contains CAG repeats, which code for the polyglutamine tract.  In normal individuals the number of CAG repeats ranges from 25-42, whith 38 repeats being the average (Reid et al., 2003).^[12]  But when the allele contain a mutation so that the number of CAG repeats increase (>43), the length of the polyglutamine tract expands.

 

Polyglutamine expansions has been linked with many neurodegenerative disease.  One disease that might directly be caused by a defective TBP is cerebellar ataxia (SCA17) (Nakamura et al., 2001).^[13]  When TBP contains a large polyglutamine tract, it increases the formation of aggregates (where proteins misfold and clump together).  When this occurs, there is less TBP available, which results in the down-regulation of transcription.^[14] The polyQ tract on TBP can also bind and sequester certain transcription factors, such asTFIIB, and further reduce transcription (fig. 4). It is thought that the insoluble aggregates themselves might exert cytotoxicity (Meyer et al., 2008).^[15]

 

A few studies have also reported that TBP may play a role in Huntington's disease (HD), a neurological disorder that is autosomal dominant, where specific neurodegeneration is caused by an extended polyglutamine stretch in the huntingtin protein.  One study compared the distribution of the TBP with that of the huntingtin protein in the brain of Huntington's disease and normal subject.  The study showed that seven different types of TBP aggregates were found in the diseased brain, compared to none in the normal brain (van Room-Mom et al., 2002).^[16]

 

TBP has also been linked to Alzheimer's Disease (AD) after finding the presence of insoluble TBP protein and TBP positive neurofibrillary tangles in AD brain (Reid et al., 2003).^[17]It has been suggested that the polyglutamine N-terminal fragment of TBP found in AD brain could occur due to the alternative splicing of the TBP encoding mRNA. This alternatively splicing gene, referred to as TBPex3, encodes a TBP N-terminal fragment that is of a similar length to that found in the AD brain.  The TBPex3 uses an alternative stop site that results in a reduction of exons, which leads to only 165 amino acids being translated, compared to the 339 amino acids found in normal TBP (fig. 5) (Reid et al, 2009).^[18]

 

 

 

 

---

 

Footnotes

1. Burley, Stephen K. "The TATA box binding protein." Current Opinion in Structural Biology. 6 (1996): 69-75 ▲
2. Pierce, Benjamin A. "Genetics: A Conceptual Approach." 2nd ed. New York: W.H. Freeman and Company, 2006 ▲
3. Chasman, D.I., et al. "Crystal structure of yeast TATA-binding protein and model for interaction with DNA." Proceedings of the National Academy of Science for the United States of America. 90 (1993): 8174-8178. ▲
4. Burley, Stephen K., "The TATA box binding protein." Current Opinion in Structural Biology. 6 (1996): 69-75 ▲
5. Pollard, Thomas, William Earnshaw. "Cell Biology". Saunders. Philadelphia, Pennsylvania. 1st ed. 2002. ▲
6. Karp, Gerald. "Cell and Molecular Biology" John Wiley & Sons, Inc. New York. 3rd Ed. 2002. ▲
7. Pardo, Leonardo, et al. "Binding Mechanism of TATA-Box Binding Proteins: DNA Kinking is Stabilized by Specific Hydrogen Bonds." Biophysical Journal. 78 (2000): 1988-96. ▲
8. Pugh, Franklin B., "Control of gene expression through regulation of the TATA-binding protein." Gene 255 (2000) 1-14. ▲
9. Pugh, Franklin B., "Control of gene expression through regulation of the TATA-binding protein." Gene 255 (2000) 1-14. ▲
10. Cang, Y., Auble, D.T., Prelich, G., "A new regulatory domain on the TATA-binding protein." EMBO J. 18 (1999) 6662-6671. ▲
11. Lee, T.I., Young, R.A.,"Regulation of gene expression by TBP-associated proteins." Genes Dev. 12 (1998)1398-1408. ▲
12. Reid et al., 2003 S.J. Reid, M.I. Rees, W.M. van Roon-Mom, A.L. Jones, M.E. MacDonald, G. Sutherland, M.J. During, R.L. Faull, M.J. Owen, M. Dragunow and R.G. Snell. "Molecular investigation of TBP allele length: a SCA17 cellular model and population study". Neurobiol. Dis. 13 (2003), pp. 37- 45. ▲
13. Nakamura et al., 2001 K. Nakamura, S.Y. Jeong, T. Uchihara, M. Anno, K. Nagashima, T. Nagashima, S. Ikeda Si, S. Tsuji and I. Kanazawa. "SCA17, a novel autosomal dominant cerebellar ataxia caused by an expanded polyglutamine in TATA-binding protein". Hum. Mol. Genet. 10 (2001), pp. 1441-1448. ▲
14. Van Room-Mom, W.M.C., et al. "TATA Binding Protein in Neurodegenerative Disease." Neuroscience. 133 (2005): 863-72. ▲
15. Meyer J. Friedman, Chuan-En Wang, Xiao-Jiang Li, and Shihua Li. "Polyglutamine Expansion Reduces the Association of TATA-binding Protein with DNA and Induces DNA Binding-independent Neurotoxicity." J Biol Chem. 2008 March 28; 283(13): 8283 - 8290. doi: 10.1074/jbc.M709674200. PMCID: PMC2276379 ▲
16. Van Roon-Mom, W.M., Reid, S.J., Jones, A.L., MacDonald, M.E., Faull, R.L., Snell, R.G., 2002. "Insoluble TATA-binding protein accumulation in Huntington's disease cortex." Brain Res. Mol. Brain Res. 109, 1-10. ▲
17. Reid et al., 2004 S.J. Reid, W.M. van Roon-Mom, P.C. Wood, M.I. Rees, M.J. Owen, R.L. Faull, M. Dragunow and R.G. Snell. "TBP, a polyglutamine tract containing protein, accumulates in Alzheimer's disease". Brain Res. Mol. Brain Res. 125 (2004), pp. 120-128. ▲
18. Reid, S.J., et al., "A splice variant of the TATA-box binding protein encoding the polyglutamine-containing N-terminal domain that accumulates in Alzheimer's disease". Brain Research. 1268 (2009) pp. 190-199. ▲