Gene transcriptions/TATA binding proteins

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, along with a variety of TBP-associated factors, make up the TFIID, a general transcription factor that in turn makes up part of the RNA polymerase II preinitiation complex.^[2] 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.

File:Tjian fig2 lg.gif

The diagram illustrates the approximate application and location of TBP during gene transcription. Credit: Robert Tjian.

Notations

Notation: let the symbol TBP represent the TATA binding protein, or TATA box binding protein.

Genetics

This is an image of Bob, the guinea pig. Credit: selbst.

This guinea pig has gorgeous long hair and was a prize winner at the Puyallup, WA fair. Credit: Christine from Washington State, USA.

Genetics involves the expression, transmission, and variation of inherited characteristics.

Def. a "branch of biology that deals with the transmission and variation of inherited characteristics, in particular chromosomes and DNA"^[3] is called genetics.

Gene transcriptions

DNA is a double helix of interlinked nucleotides surrounded by an epigenome. On the basis of biochemical signals, an enzyme, specifically a ribonucleic acid (RNA) polymerase, is chemically bonded to one of the strands (the template strand) of this double helix. The polymerase, once phosphorylated, begins to catalyze the formation of RNA using the template strand. Although the catalysis may have more than one beginning nucleotide (a start site) and more than one ending nucleotide (a stop site) along the DNA, each nucleotide sequence catalyzed that ultimately produces approximately the same RNA is part of a gene. The catalysis of each RNA representation from the template DNA is a transcription, specifically a gene transcription. The overall process is also referred to as gene transcription.

Theoretical DNA binding proteins

DNA melting

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.

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. It is interesting to note that this incompleteness allows DNA to be passively bent on binding.

Preinitiation complexes

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.^[4]^[5]

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.

Modulation of transcription

TBP has a long string of glutamines (Gs) 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.

Hypotheses

TBP initiates transcription of A1BG.

References

↑ RD Kornberg (2007). "The molecular basis of eukaryotic transcription". Proc. Natl. Acad. Sci. U.S.A. 104 (32): 12955–61. doi:10.1073/pnas.0704138104. PMID 17670940. PMC 1941834. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1941834/.
↑ TI Lee , RA Young (2000). "Transcription of eukaryotic protein-coding genes". Annu. Rev. Genet. 34: 77–137. doi:10.1146/annurev.genet.34.1.77. PMID 11092823.
↑ genetics. San Francisco, California: Wikimedia Foundation, Inc. April 16, 2014. https://en.wiktionary.org/wiki/genetics. Retrieved 2014-05-07.
↑ Hochheimer A, Tjian R (June 2003). "Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression". Genes Dev. 17 (11): 1309-20. doi:10.1101/gad.1099903. PMID 12782648.
↑ Pugh BF (September 2000). "Control of gene expression through regulation of the TATA-binding protein". Gene 255 (1): 1-14. PMID 10974559.

External links

[Kornberg-1] RD Kornberg (2007). "The molecular basis of eukaryotic transcription". Proc. Natl. Acad. Sci. U.S.A. 104 (32): 12955–61. doi:10.1073/pnas.0704138104. PMID 17670940. PMC 1941834. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1941834/.

[Lee-2] TI Lee , RA Young (2000). "Transcription of eukaryotic protein-coding genes". Annu. Rev. Genet. 34: 77–137. doi:10.1146/annurev.genet.34.1.77. PMID 11092823.

[GeneticsWikt-3] genetics. San Francisco, California: Wikimedia Foundation, Inc. April 16, 2014. https://en.wiktionary.org/wiki/genetics. Retrieved 2014-05-07.

[Hochheimer-4] Hochheimer A, Tjian R (June 2003). "Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression". Genes Dev. 17 (11): 1309-20. doi:10.1101/gad.1099903. PMID 12782648.

[Pugh-5] Pugh BF (September 2000). "Control of gene expression through regulation of the TATA-binding protein". Gene 255 (1): 1-14. PMID 10974559.

[1]

[2]

[3]

[4]

[5]