Eukaryotic Transcription Factor-Dna Complexes

Patikoglou, Georgia A.; Burley, S.K.

doi:10.1146/annurev.biophys.26.1.289

Cited by 128 publications

(106 citation statements)

References 156 publications

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“…Likewise, we find that TBP recognizes and binds to TATAAA or CATAAA with similar affinities and that the stability of TBP bound to the elements is identical. On a structural basis, the substitution of a cytosine for the thymine in position 1 of the TATAAA element should allow for TBP binding because no steric clashes exist in the minor groove between the exocyclic NH 2 group from the guanine and the adjacent side chains of TBP (40,41). Because we observe a 50-fold difference in expression level from these two elements in vivo, we examined higher ordered interactions to determine which factors play a critical role in modulating the output of gene expression on noncanonical elements.…”

Section: Discussionmentioning

confidence: 99%

“…This apparent lack of specificity of TBP for its cognate site is at least partially due to the fact that TBP binds to the minor groove of DNA (55)(56)(57)(58), which provides few functional groups to direct specificity of binding (41). Genetic and biochemical studies suggest that the cell has devised several means of increasing the specificity of TBP for TATA-containing promoters.…”

Section: Discussionmentioning

confidence: 99%

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The Stability of the TFIIA-TBP-DNA Complex Is Dependent on the Sequence of the TATAAA Element

Stewart¹,

Stargell²

2001

Journal of Biological Chemistry

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To determine the mechanistic differences between canonical and noncanonical TATA elements, we compared the functional activity of two sequences: TATAAA (canonical) and CATAAA (noncanonical). The TATAAA element can support high levels of transcription in vivo, whereas the CATAAA element is severely defective for this function. This dramatic functional difference is not likely to be due to a difference in TBP (TATA-binding protein) binding efficiency because protein-DNA complex studies in vitro indicate little difference between the two DNA sequences in the formation and stability of the TBP-DNA complex. In addition, the binding and stability of the TFIIB-TBP-DNA complex is similar for the two elements. In striking contrast, the TFIIA-TBP-DNA complex is significantly less stable on the CATAAA element when compared with the TATAAA element. A role for TFIIA in distinguishing between TATAAA and CATAAA in vivo was tested by fusing a subunit of TFIIA to TBP. We found that fusion of TFIIA to TBP dramatically increases transcription from CATAAA in yeast cells. Taken together, these results indicate that the stability of the TFIIA-TBP complex depends strongly on the sequence of the core promoter element and that the TFIIA-TBP complex plays an important function in recognizing optimal promoters in vivo.Initiation of mRNA synthesis by RNA polymerase II is the major step of regulation of eukaryotic gene expression and occurs at core promoters that typically consist of a TATA box and initiator element (1). The first step in promoter recognition is binding of TBP (TATA-binding protein) to the TATAAA element (reviewed in Ref.2). Recruitment of TBP is a ratelimiting step in transcriptional initiation in vivo at a majority of promoters (3-5), and promoter occupancy of TBP correlates very well with transcriptional activity (6, 7). The TBP-TATA interaction sets the stage for the nucleation of the remainder of the preinitiation complex, which includes TFIIA, TFIIB, TFIIE, TFIIF, TFIIH, TFIIJ, and RNA polymerase II (reviewed in Ref. 8). TFIIA and TFIIB have each been shown to make direct contacts with TBP and DNA and, in so doing, stabilize the TBP-DNA complex (reviewed in Ref. 9). In addition, TFIIA and TFIIB promoter occupancy is coordinated with that of TBP (10); thus interactions between the DNA, TBP, TFIIA, and TFIIB are likely to play an important role in a majority of promoters in vivo.Despite the apparent requirement of the TATAAA sequence in the initiation of RNA polymerase II transcription, many natural eukaryotic core promoters lack recognizable TATA elements but still require TBP for transcription initiation (11-13). This noncanonical or "TATA-less" subclass includes the promoters of several different types of genes, including the ubiquitously expressed "housekeeping" genes, developmentally regulated genes (growth factors and growth factor receptors), and many oncogenes (14 -16). In addition, several instances of multiple, yet functionally distinct elements driving the expression of a single gene have been described in y...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

The Stability of the TFIIA-TBP-DNA Complex Is Dependent on the Sequence of the TATAAA Element

Stewart¹,

Stargell²

2001

Journal of Biological Chemistry

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“…The most common DNA-protein binding motif involves interactions of R-helices of transcription factors and restriction enzymes with the major groove. 27 …”

Section: Methodsmentioning

confidence: 99%

Chemical Properties of Oxopropenyl Adducts of Purine and Pyrimidine Nucleosides and Their Reactivity toward Amino Acid Cross-Link Formation

2008

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N 2 -Oxopropenyldeoxyguanosine (2) forms in duplex DNA by modification of dG residues with base propenal or malondialdehyde. The pKa of 2 was estimated to be 6.9 from the pH dependence of its ring-closing to the pyrimidopurinone derivative 1. The acidity of 2 may be an important determinant of its miscoding properties and its reactivity to nucleophiles in DNA or protein. To test this hypothesis, analogous N-oxopropenyl derivatives of dA (4), dC (5), and N1-methyl-dG (6) were synthesized and their pKa's were determined by optical titration. The N-oxopropenyl derivatives of dA and dC both exhibited pKa's of 10.5, whereas the N-oxopropenyl derivative of N1-methyldG exhibited a pKa of 8.2. Cross-linking of 2, 4, 5, and 6 to N R -acetyl-lysine was explored at neutral pH. Adduct 2 did not react with N R -acetyl-lysine, whereas 4-6 readily formed cross-links. The structures of the cross-links were elucidated, and their stabilities were investigated. The results define the acidity of oxopropenyl deoxynucleosides and highlight its importance to their reactivity toward nucleophiles. This study also identifies the structures of a potential novel class of DNA-protein cross-links.

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“…1 For initiation by yeast Pol II, TBP binding to a TATA sequence present in most promoters nucleates stepwise assembly of a large complex containing TBP-associated factors (1), termed TFIID, as well as multiple general transcription factors and Pol II (reviewed in Refs. [2][3][4][5]. In an alternative, but not mutually exclusive, model of initiation, TFIID binding creates a platform for recruitment of a massive holoenzyme, consisting of Pol II, the SRB proteins, and other cofactors (like Gal11), as well as the general transcription factors, TFIIB, TFIIF, and TFIIH (reviewed in Refs.…”

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confidence: 99%

Purification and Enzymic Properties of Mot1 ATPase, a Regulator of Basal Transcription in the Yeast Saccharomyces cerevisiae

Adamkewicz

Mueller²,

Hansen

et al. 2000

Journal of Biological Chemistry

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The 1867-residue Mot1 protein is a member of a superfamily of ATPases, some of which are helicases, that interact with protein-nucleic acid assemblies. Mot1 is an essential regulator of RNA polymerase II-dependent transcription in vivo and dissociates TATA box-binding protein (TBP)-DNA complexes in vitro. Mot1-(His) 6 was purified to apparent homogeneity from yeast extracts. The preparation efficiently dissociated TBP⅐TATA complexes, suggesting that no other protein or cofactor is required. Mot1 behaved as a non-globular monomer in hydrodynamic studies, and no association was detected between differentially tagged co-expressed Mot1 constructs. ATPase activity was stimulated Transcription by all three eukaryotic RNA polymerases requires TBP.1 For initiation by yeast Pol II, TBP binding to a TATA sequence present in most promoters nucleates stepwise assembly of a large complex containing TBP-associated factors (1), termed TFIID, as well as multiple general transcription factors and Pol II (reviewed in Refs. 2-5). In an alternative, but not mutually exclusive, model of initiation, TFIID binding creates a platform for recruitment of a massive holoenzyme, consisting of Pol II, the SRB proteins, and other cofactors (like Gal11), as well as the general transcription factors, TFIIB, TFIIF, and TFIIH (reviewed in Refs. 6 -8). In both models, promoter binding by TBP is the rate-limiting step in initiation complex formation and thus provides a physiologically relevant target for transcriptional control by both positive (9, 10) and negative (11-14) regulatory factors.Factors that negatively regulate eukaryotic transcription utilize a wide variety of mechanisms, including quenching of activators, promoting assembly of chromatin, recruiting chromatin-binding proteins or histone-modifying enzymes, and interfering with the general transcription machinery itself. In addition, several proteins are thought to block Pol II transcription via interaction with TBP. Such regulators include Evenskipped (eve gene product), a Drosophila homeodomain protein (15, 16), and a general repressor, NC2 (or Dr1-DRAP1) (17-19). NC2 binds to TBP⅐DNA complexes and prevents the association of TFIIA and TFIIB, possibly by altering conformation of the .Another kind of negative regulator of TBP action was first identified both genetically and biochemically in the yeast Saccharomyces cerevisiae. A TBP-targeted repressing activity, termed ADI for "ATP-dependent inhibitor" of TATA binding, was detected in yeast nuclear extracts (25). ADI removed TBP from the TATA element of the adenovirus major late promoter (AdMLP) in an ATP-dependent manner. TFIIA, and to some extent TFIIB, inhibited ADI activity by competing for binding to TBP or by stabilizing the TBP⅐DNA complex, or both (25). It was subsequently found that ADI corresponded to the product of the MOT1 gene (26). The MOT1 locus had been previously identified by temperature-sensitive mutations that increased basal expression of many Pol II-specific genes (27, 28).The MOT1 gene was isolated by complementat...

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Eukaryotic Transcription Factor-Dna Complexes

Cited by 128 publications

References 156 publications

The Stability of the TFIIA-TBP-DNA Complex Is Dependent on the Sequence of the TATAAA Element

The Stability of the TFIIA-TBP-DNA Complex Is Dependent on the Sequence of the TATAAA Element

Chemical Properties of Oxopropenyl Adducts of Purine and Pyrimidine Nucleosides and Their Reactivity toward Amino Acid Cross-Link Formation

Purification and Enzymic Properties of Mot1 ATPase, a Regulator of Basal Transcription in the Yeast Saccharomyces cerevisiae

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