Biology:TATA-binding protein

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Short description: Protein-coding gene in the species Homo sapiens


A representation of the 3D structure of the protein myoglobin showing turquoise α-helices.
Generic protein structure example
TBP
PDB 1ngm EBI.jpg
crystal structure of a yeast brf1-tbp-dna ternary complex
Identifiers
SymbolTBP
PfamPF00352
Pfam clanCL0407
InterProIPR000814
PROSITEPDOC00303
SCOP21tbp / SCOPe / SUPFAM

The TATA-binding protein (TBP) is a general transcription factor that binds specifically to a DNA sequence called the TATA box. This DNA sequence is found about 30 base pairs upstream of the transcription start site in some eukaryotic gene promoters.[1]

TBP gene family

TBP is a member of a small gene family of TBP-related factors.[2] The first TBP-related factor (TRF/TRF1) was identified in the fruit fly Drosophila, but appears to be fly or insect-specific. Subsequently TBPL1/TRF2 was found in the genomes of many metazoans, whereas vertebrate genomes encode a third vertebrate family member, TBPL2/TRF3. In specific cell types or on specific promoters TBP can be replaced by one of these TBP-related factors, some of which interact with the TATA box similarly to TBP.

Role as transcription factor

TBP is a subunit of the eukaryotic general transcription factor TFIID. TFIID is the first protein to bind to DNA during the formation of the transcription preinitiation complex of RNA polymerase II (RNA Pol II).[3] As one of the few proteins in the preinitiation complex that binds DNA in a sequence-specific manner, it helps position RNA polymerase II over the transcription start site of the gene. However, it is estimated that only 10–20% of human promoters have TATA boxes - the majority of human promoters are TATA-less housekeeping gene promoters - so TBP is probably not the only protein involved in positioning RNA polymerase II.. The binding of TBP to these promoters is facilitated by housekeeping gene regulators.[4][5] Interestingly, transcription initiates within a narrow region at around 30 bp downstream of TATA box on TATA-containing promoters,[6] while transcription start sites of TATA-less promoters are dispersed within a 200 bp region.[7][5]

Binding of TFIID to the TATA box in the promoter region of the gene initiates the recruitment of other factors required for RNA Pol II to begin transcription. Some of the other recruited transcription factors include TFIIA, TFIIB, and TFIIF. Each of these transcription factors contains several protein subunits.

TBP is also important for transcription by RNA polymerase I and RNA polymerase III, and is therefore involved in transcription initiation by all three RNA polymerases.[8]

TBP is involved in DNA melting (double strand separation) by bending the DNA by 80° (the AT-rich sequence to which it binds facilitates easy melting). The TBP is an unusual protein in that it binds the minor groove using a β sheet.

Another distinctive feature of TBP is a long string of glutamines in the N-terminus of the protein. This region modulates the DNA binding activity of the C-terminus, and modulation of DNA-binding affects the rate of transcription complex formation and initiation of transcription. Mutations that expand the number of CAG repeats encoding this polyglutamine tract, and thus increase the length of the polyglutamine string, are associated with spinocerebellar ataxia 17, a neurodegenerative disorder classified as a polyglutamine disease.[9]

DNA-protein interactions

When TBP binds to a TATA box within the DNA, it distorts the DNA by inserting amino acid side-chains between base pairs, partially unwinding the helix, and doubly kinking it. The distortion is accomplished through a great amount of surface contact between the protein and DNA. TBP binds with the negatively charged phosphates in the DNA backbone through positively charged lysine and arginine amino acid residues. The sharp bend in the DNA is produced through projection of four bulky phenylalanine residues into the minor groove. As the DNA bends, its contact with TBP increases, thus enhancing the DNA-protein interaction.

The strain imposed on the DNA through this interaction initiates melting, or separation, of the strands. Because this region of DNA is rich in adenine and thymine residues, which base-pair through only two hydrogen bonds, the DNA strands are more easily separated. Separation of the two strands exposes the bases and allows RNA polymerase II to begin transcription of the gene.

TBP's C-terminus composes of a helicoidal shape that (incompletely) complements the T-A-T-A region of DNA. This incompleteness allows DNA to be passively bent on binding.

For information on the use of TBP in cells see: RNA polymerase I, RNA polymerase II, and RNA polymerase III.

Protein–protein interactions

TATA-binding protein has been shown to interact with:


Complex assembly

The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box.[47][48] In the presence of a TATA-less promoter, TBP binds with the help of TBP-associated factors (TAFs).[49][50] TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins.[51]

Structure

The C-terminal core of TBP (~180 residues) is highly conserved and contains two 88-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins .[52] By contrast, the N-terminal region varies in both length and sequence.

References

  1. ↑ "The molecular basis of eukaryotic transcription". Proc. Natl. Acad. Sci. U.S.A. 104 (32): 12955–61. 2007. doi:10.1073/pnas.0704138104. PMID 17670940. Bibcode: 2007PNAS..10412955K. 
  2. ↑ "TBP-related factors: a paradigm of diversity in transcription initiation". Cell & Bioscience 1 (1): 23. 1 January 2011. doi:10.1186/2045-3701-1-23. PMID 21711503. 
  3. ↑ "Transcription of eukaryotic protein-coding genes". Annual Review of Genetics 34: 77–137. 2000. doi:10.1146/annurev.genet.34.1.77. PMID 11092823. 
  4. ↑ "The NSL complex regulates housekeeping genes in Drosophila". PLOS Genetics 8 (6): e1002736. 2012. doi:10.1371/journal.pgen.1002736. PMID 22723752. 
  5. ↑ 5.0 5.1 "The NSL complex-mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise". Genes & Development 33 (7–8): 452–465. February 2019. doi:10.1101/gad.321489.118. PMID 30819819. 
  6. ↑ "Genome-wide analysis of mammalian promoter architecture and evolution". Nature Genetics 38 (6): 626–35. June 2006. doi:10.1038/ng1789. PMID 16645617. 
  7. ↑ "A paired-end sequencing strategy to map the complex landscape of transcription initiation". Nature Methods 7 (7): 521–7. July 2010. doi:10.1038/nmeth.1464. PMID 20495556. 
  8. ↑ "Conservation between the RNA polymerase I, II, and III transcription initiation machineries". Molecular Cell 45 (4): 439–46. February 2012. doi:10.1016/j.molcel.2012.01.023. PMID 22365827. 
  9. ↑ "Entrez Gene: TBP TATA box binding protein". https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=6908. 
  10. ↑ "Alternatively spliced hBRF variants function at different RNA polymerase III promoters". EMBO J. 19 (15): 4134–43. August 2000. doi:10.1093/emboj/19.15.4134. PMID 10921893. 
  11. ↑ "Structure and function of a human transcription factor TFIIIB subunit that is evolutionarily conserved and contains both TFIIB- and high-mobility-group protein 2-related domains". Proc. Natl. Acad. Sci. U.S.A. 92 (15): 7026–30. July 1995. doi:10.1073/pnas.92.15.7026. PMID 7624363. Bibcode: 1995PNAS...92.7026W. 
  12. ↑ 12.0 12.1 12.2 12.3 "BRCA1 is a component of the RNA polymerase II holoenzyme". Proc. Natl. Acad. Sci. U.S.A. 94 (11): 5605–10. May 1997. doi:10.1073/pnas.94.11.5605. PMID 9159119. Bibcode: 1997PNAS...94.5605S. 
  13. ↑ "Cloning and biochemical characterization of TAF-172, a human homolog of yeast Mot1". Mol. Cell. Biol. 18 (3): 1701–10. March 1998. doi:10.1128/MCB.18.3.1701. PMID 9488487. 
  14. ↑ "c-Fos-induced activation of a TATA-box-containing promoter involves direct contact with TATA-box-binding protein". Mol. Cell. Biol. 14 (9): 6021–9. September 1994. doi:10.1128/MCB.14.9.6021. PMID 8065335. 
  15. ↑ "In vitro association between the Jun protein family and the general transcription factors, TBP and TFIIB". Biochem. J. 305 (3): 967–74. February 1995. doi:10.1042/bj3050967. PMID 7848298. 
  16. ↑ "Multiprotein bridging factor-1 (MBF-1) is a cofactor for nuclear receptors that regulate lipid metabolism". Mol. Endocrinol. 16 (6): 1367–77. June 2002. doi:10.1210/mend.16.6.0843. PMID 12040021. 
  17. ↑ "Interaction between endothelial differentiation-related factor-1 and calmodulin in vitro and in vivo". J. Biol. Chem. 275 (31): 24047–51. August 2000. doi:10.1074/jbc.M001928200. PMID 10816571. 
  18. ↑ "The role of human MBF1 as a transcriptional coactivator". J. Biol. Chem. 274 (48): 34196–202. November 1999. doi:10.1074/jbc.274.48.34196. PMID 10567391. 
  19. ↑ 19.0 19.1 "Protein–protein interactions in eukaryotic transcription initiation: structure of the preinitiation complex". Proc. Natl. Acad. Sci. U.S.A. 93 (3): 1119–24. February 1996. doi:10.1073/pnas.93.3.1119. PMID 8577725. Bibcode: 1996PNAS...93.1119T. 
  20. ↑ "Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms". Science 303 (5660): 983–8. February 2004. doi:10.1126/science.1090838. PMID 14963322. Bibcode: 2004Sci...303..983B. 
  21. ↑ "Human general transcription factor TFIIA: characterization of a cDNA encoding the small subunit and requirement for basal and activated transcription". Proc. Natl. Acad. Sci. U.S.A. 92 (8): 3313–7. April 1995. doi:10.1073/pnas.92.8.3313. PMID 7724559. Bibcode: 1995PNAS...92.3313D. 
  22. ↑ "Transcription factor IIA derepresses TATA-binding protein (TBP)-associated factor inhibition of TBP-DNA binding". J. Biol. Chem. 273 (23): 14293–300. June 1998. doi:10.1074/jbc.273.23.14293. PMID 9603936. 
  23. ↑ "Reconstitution of human TFIIA activity from recombinant polypeptides: a role in TFIID-mediated transcription". Genes Dev. 8 (19): 2336–48. October 1994. doi:10.1101/gad.8.19.2336. PMID 7958900. 
  24. ↑ "Human TAFII250 interacts with RAP74: implications for RNA polymerase II initiation". Genes Dev. 9 (22): 2747–55. November 1995. doi:10.1101/gad.9.22.2747. PMID 7590250. 
  25. ↑ "A dynamic model for PC4 coactivator function in RNA polymerase II transcription". Proc. Natl. Acad. Sci. U.S.A. 95 (5): 2192–7. March 1998. doi:10.1073/pnas.95.5.2192. PMID 9482861. Bibcode: 1998PNAS...95.2192M. 
  26. ↑ "Repression of p53-mediated transcription by MDM2: a dual mechanism". Genes Dev. 11 (15): 1974–86. August 1997. doi:10.1101/gad.11.15.1974. PMID 9271120. 
  27. ↑ "The MDM2 C-terminal region binds to TAFII250 and is required for MDM2 regulation of the cyclin A promoter". J. Biol. Chem. 272 (49): 30651–61. December 1997. doi:10.1074/jbc.272.49.30651. PMID 9388200. 
  28. ↑ "Transcriptional autorepression of Msx1 gene is mediated by interactions of Msx1 protein with a multi-protein transcriptional complex containing TATA-binding protein, Sp1 and cAMP-response-element-binding protein-binding protein (CBP/p300)". Biochem. J. 339 (3): 751–8. May 1999. doi:10.1042/0264-6021:3390751. PMID 10215616. 
  29. ↑ "Heterodimerization of Msx and Dlx homeoproteins results in functional antagonism". Mol. Cell. Biol. 17 (5): 2920–32. May 1997. doi:10.1128/mcb.17.5.2920. PMID 9111364. 
  30. ↑ "A role for the Msx-1 homeodomain in transcriptional regulation: residues in the N-terminal arm mediate TATA binding protein interaction and transcriptional repression". Proc. Natl. Acad. Sci. U.S.A. 93 (5): 1764–9. March 1996. doi:10.1073/pnas.93.5.1764. PMID 8700832. Bibcode: 1996PNAS...93.1764Z. 
  31. ↑ 31.0 31.1 31.2 31.3 31.4 31.5 31.6 31.7 "CCAAT binding NF-Y-TBP interactions: NF-YB and NF-YC require short domains adjacent to their histone fold motifs for association with TBP basic residues". Nucleic Acids Res. 25 (11): 2174–81. June 1997. doi:10.1093/nar/25.11.2174. PMID 9153318. 
  32. ↑ "Wild-type p53 binds to the TATA-binding protein and represses transcription". Proc. Natl. Acad. Sci. U.S.A. 89 (24): 12028–32. December 1992. doi:10.1073/pnas.89.24.12028. PMID 1465435. Bibcode: 1992PNAS...8912028S. 
  33. ↑ 33.0 33.1 "Pax-6 interactions with TATA-box-binding protein and retinoblastoma protein". Invest. Ophthalmol. Vis. Sci. 40 (7): 1343–50. June 1999. PMID 10359315. 
  34. ↑ "The POU domains of the Oct1 and Oct2 transcription factors mediate specific interaction with TBP". Nucleic Acids Res. 22 (9): 1655–62. May 1994. doi:10.1093/nar/22.9.1655. PMID 8202368. 
  35. ↑ "Involvement of TFIID and USA components in transcriptional activation of the human immunodeficiency virus promoter by NF-kappaB and Sp1". Mol. Cell. Biol. 18 (6): 3234–44. June 1998. doi:10.1128/mcb.18.6.3234. PMID 9584164. 
  36. ↑ "Interaction of the COOH-terminal transactivation domain of p65 NF-kappa B with TATA-binding protein, transcription factor IIB, and coactivators". J. Biol. Chem. 270 (13): 7219–26. March 1995. doi:10.1074/jbc.270.13.7219. PMID 7706261. 
  37. ↑ "Interactions between the retinoid X receptor and a conserved region of the TATA-binding protein mediate hormone-dependent transactivation". Proc. Natl. Acad. Sci. U.S.A. 92 (18): 8288–92. August 1995. doi:10.1073/pnas.92.18.8288. PMID 7667283. Bibcode: 1995PNAS...92.8288S. 
  38. ↑ "Rb inhibits the intrinsic kinase activity of TATA-binding protein-associated factor TAFII250". Mol. Cell. Biol. 19 (1): 846–54. January 1999. doi:10.1128/MCB.19.1.846. PMID 9858607. 
  39. ↑ 39.0 39.1 39.2 39.3 "Cloning and expression of human TAFII250: a TBP-associated factor implicated in cell-cycle regulation". Nature 362 (6416): 175–9. March 1993. doi:10.1038/362175a0. PMID 7680771. Bibcode: 1993Natur.362..175R. 
  40. ↑ "Functional analysis of the human TAFII250 N-terminal kinase domain". Mol. Cell 1 (6): 905–11. May 1998. doi:10.1016/S1097-2765(00)80089-1. PMID 9660973. 
  41. ↑ 41.0 41.1 41.2 "The intracellular localisation of TAF7L, a paralogue of transcription factor TFIID subunit TAF7, is developmentally regulated during male germ-cell differentiation". J. Cell Sci. 116 (Pt 9): 1847–58. May 2003. doi:10.1242/jcs.00391. PMID 12665565. 
  42. ↑ "Specific interactions and potential functions of human TAFII100". J. Biol. Chem. 272 (10): 6714–21. March 1997. doi:10.1074/jbc.272.10.6714. PMID 9045704. 
  43. ↑ "Human STAGA complex is a chromatin-acetylating transcription coactivator that interacts with pre-mRNA splicing and DNA damage-binding factors in vivo". Mol. Cell. Biol. 21 (20): 6782–95. October 2001. doi:10.1128/MCB.21.20.6782-6795.2001. PMID 11564863. 
  44. ↑ 44.0 44.1 "Cloning and characterization of hTAFII18, hTAFII20 and hTAFII28: three subunits of the human transcription factor TFIID". EMBO J. 14 (7): 1520–31. April 1995. doi:10.1002/j.1460-2075.1995.tb07138.x. PMID 7729427. 
  45. ↑ "Human TAF(II28) promotes transcriptional stimulation by activation function 2 of the retinoid X receptors". EMBO J. 15 (12): 3093–104. June 1996. doi:10.1002/j.1460-2075.1996.tb00672.x. PMID 8670810. 
  46. ↑ "Cloning and characterization of human TAF20/15. Multiple interactions suggest a central role in TFIID complex formation". J. Biol. Chem. 271 (30): 18194–202. July 1996. doi:10.1074/jbc.271.30.18194. PMID 8663456. 
  47. ↑ "Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression". Genes & Development 17 (11): 1309–20. June 2003. doi:10.1101/gad.1099903. PMID 12782648. 
  48. ↑ "Control of gene expression through regulation of the TATA-binding protein". Gene 255 (1): 1–14. September 2000. doi:10.1016/s0378-1119(00)00288-2. PMID 10974559. 
  49. ↑ Weaver, Robert Franklin (2012-01-01). Molecular biology. McGraw-Hill. ISBN 9780073525327. OCLC 789601172. 
  50. ↑ "Structure of promoter-bound TFIID and model of human pre-initiation complex assembly". Nature 531 (7596): 604–9. March 2016. doi:10.1038/nature17394. PMID 27007846. Bibcode: 2016Natur.531..604L. 
  51. ↑ "The genetics of TBP and TBP-related factors". Trends in Biochemical Sciences 28 (7): 391–8. July 2003. doi:10.1016/S0968-0004(03)00117-8. PMID 12878007. 
  52. ↑ "Crystal structure of TFIID TATA-box binding protein". Nature 360 (6399): 40–6. November 1992. doi:10.1038/360040a0. PMID 1436073. Bibcode: 1992Natur.360...40N. 

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