Transcription factor IID mutants defective for interaction with transcription factor IIA

In vitro association between the Jun protein family and the general transcription factors, TBP and TFIIB

Transcriptional activator proteins interact with the general transcription factors TATA-binding protein (TBP), TFIIB and/or other TBP-associated factors (TAFs). Using affinity chromatography we demonstrate that members of the Jun family of transcriptional activators interact with both TBP and TFIIB in vitro. TBP binds to both the N-terminal activation domain and C-terminal bZIP regions of c-Jun, whereas TFIIB binds to only the c-Jun bZIP domain. This interaction requires the dimerization of the Jun protein. The ability of the N-terminal activation domains of c-Jun, JunB, JunD and v-Jun to interact with TBP in vitro correlates with their transcriptional activity in vivo. Domain mapping experiments indicate that c-Jun interacts with the conserved C-terminus of TBP. Studies using a set of TFIIB inframe deletion mutants demonstrate that C-terminal amino acids 178-201 and 238-316 play an important role in modulating the interaction between TFIIB and c-Jun. Although phosphorylation of the c-Jun N-terminal activation domain stimulates c-Jun transcriptional activity in vivo, it has no effect on the ability of c-Jun to interact with either TBP or TFIIB in vitro. These data suggest that the Jun family of activator proteins may activate transcription by interacting with the general transcription factors TBP and TFIIB.

Multiple regions of TBP participate in the response to transcriptional activators in vivo

We used mutant yeast and human TBP molecules with an altered DNA-binding specificity to examine the role of TBP in transcriptional activation in vivo. We show that yeast TBP is functionally equivalent to human TBP for response to numerous transcriptional activators in human cells, including those that do not function in yeast. Despite the extensive conservation of TBP, its ability to respond to transcriptional activators in vivo is curiously resistant to clustered sets of alanine substitution mutations in different regions of the protein, including those that disrupt DNA binding and basal transcription in vitro. Combined sets of these mutations, however, can attenuate the in vivo activity of TBP and can differentially affect response to different activation domains. Although the activity of TBP mutants in vivo did not correlate with DNA binding or basal transcription in vitro, it did correlate with binding in vitro to the largest subunit of TFIID, hTAFII250. Together, these data suggest that TBP utilizes multiple interactions across its surface to respond to RNA polymerase II transcriptional activators in vivo; some of these interactions appear to involve recruitment of TBP into TFIID, whereas others are involved in response to specific types of transcriptional activators.

Molecular cloning of the small (gamma) subunit of human TFIIA reveals functions critical for activated transcription

TFIIA is thought to play an important role in transcriptional regulation in higher eukaryotes, but its precise function is unclear. A human cDNA encoding a protein with 45% identity to the small subunit of yeast TFIIA has been isolated. TFIIA activity could be reconstituted by the mixing of recombinant large (alpha beta) and small (gamma) subunits. TFIIA-depleted HeLa nuclear extracts were used to demonstrate that TFIIA is essential for basal and activated transcription by several distinct classes of activators. Recombinant TFIIA functioned in transcriptional activation whether expressed as a dimer (alpha beta+gamma) or as a trimer (alpha+beta+gamma), which closely resembles the native form. Yeast TFIIA also functioned in transcriptional activation, and the human gamma subunit was functionally interchangeable with TOA2, its yeast homolog. Recombinant TFIIA mediated the stimulation of TFIID binding to the TATA region and downstream promoter sequences by the Zta transcriptional activator. Significantly, we found that TFIIA bound directly to Zta in an activation domain-dependent manner. One consequence of the TFIIA-mediated interaction between Zta and TFIID was the formation of a promoter-bound complex resistant to TATA oligonucleotide competition. These results demonstrate that TFIIA is an evolutionarily conserved general factor critical for activator-regulated transcription.

Reconstitution of human TFIIA activity from recombinant polypeptides: a role in TFIID-mediated transcription

Human TFIIA activity is composed of three subunits (alpha, beta, gamma). Here we report the isolation of a human cDNA clone encoding the gamma-subunit and the reconstitution of TFIIA activity from recombinant polypeptides (holo-TFIIA). Protein-protein interaction analysis established that the beta and gamma subunits of TFIIA interact with the TBP component of TFIID. The alpha-subunit is recruited into the complex by association with the gamma-subunit. Functional studies indicate that recombinant TFIIA stimulates basal TFIID-dependent transcription but is without effect on TBP-dependent transcription. Our studies indicate that TFIIA not only functions by physically removing negative components present in TFIID (antirepression), as demonstrated previously, but that it can stimulate basal transcription through components of the TFIID complex. Holo-TFIIA also stimulated activation of transcription in vitro as well as in vivo in transfected HeLa cells.

2.1 A resolution refined structure of a TATA box-binding protein (TBP)

The three-dimensional structure of a TATA box-binding protein (TBP2) from Arabidopsis thaliana has been refined at 2.1 A resolution. TBPs are general eukaryotic transcription factors that participate in initiation of RNA synthesis by all three eukaryotic RNA polymerases. The carboxy-terminal portion of TBP is a unique DNA-binding motif/protein fold, adopting a highly symmetric alpha/beta structure that resembles a molecular saddle with two stirrup-like loops. A ten-stranded, antiparallel beta-sheet provides a concave surface for recognizing class II nuclear gene promoters, while the four amphipathic alpha-helices on the convex surface are available for interaction with other transcription factors. The myriad interactions of TBP2 with components of the transcription machinery are discussed.

1.9 A resolution refined structure of TBP recognizing the minor groove of TATAAAAG

The three-dimensional structure of a TATA box-binding protein (TBP) from Arabidopsis thaliana complexed with a fourteen base pair oligonucleotide bearing the Adenovirus major late promoter TATA element has been refined at 1.9 A resolution, giving a final crystallographic R-factor of 19.4%. Binding of the monomeric, saddle-shaped alpha/beta protein induces an unprecedented conformational change in the DNA. A detailed structural and functional analysis of this unusual protein-DNA complex is presented, with particular emphasis on the mechanisms of DNA deformation, TATA element recognition, and preinitiation complex assembly.

The zinc finger region of the adenovirus E1A transactivating domain complexes with the TATA box binding protein

The 289R E1A protein of adenovirus transactivates a variety of viral and cellular promoters through protein-protein interactions. In earlier studies, mutational analyses of the E1A transactivating domain identified residues that are critical for transactivation and implied that the zinc finger region of the transactivating domain binds a transcription factor. Also, the E1A activation domain was found to bind to the TATA box binding protein (TBP) in vitro. Here, we tested the significance of the E1A-TBP interaction for E1A transactivation by analyzing the effects of conservative substitutions at each of the 49 residues of the E1A activation domain. Seven of the substitutions significantly diminished TBP binding in vitro. All of these were in the zinc finger region and were defective for transactivation in vivo. The perfect correlation between reduced TBP binding and transactivation argues strongly that a direct interaction between the E1A activation domain and TBP is critical to the mechanism of E1A activation. This genetic analysis leads us to further suggest that another factor, which is limiting, is also necessary for E1A-mediated transactivation.

NOT1(CDC39), NOT2(CDC36), NOT3, and NOT4 encode a global-negative regulator of transcription that differentially affects TATA-element utilization

The yeast HIS3 TR and TC TATA elements support basal transcription, but only TR can respond to transcriptional activators. Four genes, NOT1(CDC39), NOT2(CDC36), NOT3, NOT4, act as general negative regulators and preferentially affect TC-dependent transcription. Allele-specific suppression, a two-hybrid interaction, and biochemical confractionation suggest that NOT1 and NOT2 are nuclear proteins associated in a discrete, 500-kD complex. NOT4 interacts with NOT1 and NOT3 in the two-hybrid assay, and overexpression of NOT3 or NOT4 suppresses not1 and not2 mutations. Repression by the NOT proteins is not attributable to inhibition of transcriptional activators, does not involve the CYC8/TUP1 negative regulatory complex, and is distinct from repression by nucleosomes or by the SPT4, 5, 6 proteins that affect chromatin structure. We propose that the NOT protein inhibit the basic RNA polymerase II transcription machinery, possibly by affecting TFIID function.

Human cytomegalovirus IE86 protein interacts with promoter-bound TATA-binding protein via a specific region distinct from the autorepression domain

The major immediate-early gene of human cytomegalovirus encodes several isoforms of an immediate-early protein which has distinct transcriptional regulatory properties. The IE86 isoform autorepresses the major immediate-early promoter by directly binding the cis repression signal element located between the TATA box and the mRNA cap site. In addition to this activity, IE86 stimulates other viral and cellular promoters. One mechanism by which eukaryotic regulatory proteins are thought to stimulate transcription is by contacting one or more general transcription factors. We show that the IE86 protein physically interacts with the DNA-binding subunit (TATA-binding protein) human transcription factor IID via the TATA-binding protein-contacting domain in the N terminus of IE86. In a mobility shift assay, IE86 was also observed to stabilize the binding of TATA-binding protein to promoter DNA. The domains within IE86 responsible for mediating transactivation and repression functioned independently. These experiments thus demonstrate the elegant ability of human cytomegalovirus to join different protein domains to produce distinct multifunctional proteins.

Altered promoter binding of the TATA box-binding factor induced by the transcriptional activation domain of VP16 and suppressed by TFIIA

The acidic transcriptional activation domain of the Herpes simplex virus protein VP16 has been shown to bind directly to both the TATA box-binding factor TBP and the general initiation factor TFIIB. Using DNase I footprinting assays, we have shown here that the VP16 activation domain qualitatively alters binding of Saccharomyces cerevisiae TBP to a TATA sequence in DNA. The effect of VP16 on promoter binding by TBP was reduced by mutations in VP16 known to reduce transactivation and could not be overcome by increasing the amount of TBP used in the footprinting assays. However, the association of yeast TFIIA with TBP on the promoter reversed the VP16-mediated effect and restored normal binding of TBP to the promoter. We suggest that VP16 induces a conformational change in TBP which alters its binding to promoter DNA, and that this effect of VP16 is suppressed by TFIIA.

Isolation of a cDNA encoding the largest subunit of TFIIA reveals functions important for activated transcription

Transcription factor IIA has been shown to interact with the TATA-binding protein and to act early during preinitiation complex formation. The human factor is composed of three subunits (alpha, beta, gamma). A human cDNA clone encoding the largest subunit of TFIIA (alpha) was isolated. The recombinant alpha polypeptide, together with the beta and gamma subunits, was capable of reconstituting TFIIA activity. Studies using antibodies raised against recombinant alpha polypeptide demonstrate that TFIIA can be an integral component of the preinitiation complex. We demonstrate that TFIIA not only interacts with TBP but also can associate with the TFIID complex. Functional assays establish that TFIIA has no apparent role in basal transcription but plays an important role in activation of transcription. Interestingly, amino acid sequence analyses of the beta-subunit demonstrate these residues to be entirely contained within the carboxyl terminus of the cDNA clone encoding the alpha-subunit.

A single cDNA, hTFIIA/alpha, encodes both the p35 and p19 subunits of human TFIIA

TFIIA is a transcription factor that, by interacting with the TATA-binding subunit (TBP) of TFIID, modulates transcription initiation by RNA polymerase II in vitro. By use of a mobility shift assay, TFIIA was purified from HeLa cells as a complex of 35-, 19-, and 12-kD subunits. Oligonucleotides were used to isolate a human cDNA clone, hTFIIA/alpha, which encodes a 55-kD protein with homology to the product of the yeast gene TOA1. The open reading frame of hTFIIA/alpha contains peptide sequences obtained from both the p35 and p19 subunits of natural human TFIIA, and thus encodes these two subunits. Consistent with this, antiserum raised against the 55-kD hTFIIA/alpha-encoded protein reacted with both the p35 and p19 subunits of natural TFIIA, and the recombinant protein could functionally replace those subunits in a mobility shift assay with renatured p12. An efficient affinity purification for natural human TFIIA was suggested by the sequence of the hTFIIA/alpha protein and demonstrated biochemically. Finally, transcription from the adenovirus major late promoter was greatly reduced in nuclear extracts depleted with anti-TFIIA/alpha serum and was restored to original levels by the readdition of purified human TFIIA.

Regional codon randomization: defining a TATA-binding protein surface required for RNA polymerase III transcription

The TATA-binding protein (TBP) is required for transcription by all three nuclear RNA polymerases. TBP was subjected to regional codon randomization, a codon-based mutagenesis method that generates complex yet compact protein libraries. Analysis of 186 temperature-sensitive TBP mutants yielded 65 specifically defective in transcription by RNA polymerase III (Pol III). These mutants map to a limited TBP surface that may interact with Tds4, a component of the Pol III transcription factor TFIIIB. Strains that contain the Pol III-defective derivatives have increased amounts of messenger RNA, which suggests that competition among TBP-interacting factors for limiting quantities of TBP determines the ratio of Pol II and Pol III transcription in vivo.

Co-crystal structure of TBP recognizing the minor groove of a TATA element

The three-dimensional structure of a TATA-box binding polypeptide complexed with the TATA element of the adenovirus major late promoter has been determined by X-ray crystallography at 2.25 A resolution. Binding of the saddle-shaped protein induces a conformational change in the DNA, inducing sharp kinks at either end of the sequence TATAAAAG. Between the kinks, the right-handed double helix is smoothly curved and partially unwound, presenting a widened minor groove to TBP's concave, antiparallel beta-sheet. Side-chain/base interactions are restricted to the minor groove, and include hydrogen bonds, van der Waals contacts and phenylalanine-base stacking interactions.

Crystal structure of yeast TATA-binding protein and model for interaction with DNA

The C-terminal 179-aa region of yeast (Saccharomyces cerevisiae) TATA-binding protein (TBP), phylogenetically conserved and sufficient for many functions, formed crystals diffracting to 1.7-A resolution. The structure of the protein, determined by molecular replacement with coordinates from Arabidopsis TBP and refined to 2.6 A, differed from that in Arabidopsis slightly by an angle of about 12 degrees between two structurally nearly identical subdomains, indicative of a degree of conformational flexibility. A model for TBP-DNA interaction is proposed with the following important features: the long dimension of the protein follows the trajectory of the minor groove; two rows of basic residues conserved between the subdomains lie along the edges of the protein in proximity to the DNA phosphates; a band of hydrophobic residues runs down the middle of the groove; and amino acid residues whose mutation alters specificity for the second base of the TATA sequence are juxtaposed to that base.

Unusual charge configurations in transcription factors of the basic RNA polymerase II initiation complex

A systematic analysis of the primary sequences of the polymerase II initiation complex has revealed unusual charge features in the TFII family proteins. In particular, the proteins TFIIA alpha, TFIIE alpha, and TFIIF carry multiple charge clusters and hyper charge runs, sequence features occurring in < 4% of all (available) eukaryotic proteins. Possible implications for these charge structures are discussed in relation to the assembly and function of the polymerase II transcriptional complex.

Yeast transcription factors

Studies of yeast transcription factors have contributed greatly to understanding basic molecular mechanisms of eukaryotic gene regulation, largely due to powerful genetic approaches that are unavailable in other organisms. The broad outlines of these mechanisms are fairly well understood, and there is an increasing number of examples where detailed information is available.

An ATP-dependent inhibitor of TBP binding to DNA

An activity in yeast nuclear extracts (termed ADI) is described that inhibits the binding of the TATA-binding protein (TBP) to DNA in an ATP-dependent manner. The effect is reversible, ATP specific, rapid, and is not promoter specific. ADI is specific for TBP because three other protein-DNA complexes are not affected by ADI. The action of ADI is blocked by association of TFIIA with the TBP-DNA complex. ADI activity at the adenovirus major late promoter requires a segment of DNA upstream from the TATA sequence, suggesting that ADI recognizes aspects of both TBP and DNA. The evolutionarily conserved carboxy-terminal domain of TBP is sufficient for ADI recognition, and amino acids in the basic region of TBP are required for ADI action. ADI can repress transcription in vitro in an ATP-dependent manner. In the presence of ADI, both TFIIA and TBP are required to commit a template to transcription. A model of ADI action is proposed, and possible roles of ADI in the regulation of the transcription complex assembly are discussed.

Near-zero linking difference upon transcription factor IID binding to promoter DNA

Binding of yeast transcription factor IID (TFIID) to the adenoviral major late promoter in circular DNA molecules caused a linking number change of less than 0.1. TFIID on its own therefore fails to unwind DNA appreciably, or else it causes both unwinding and compensatory writhing. Highly purified, recombinant yeast TFIID relaxed supercoiled DNA, because of a contaminant of bacterial topoisomerase I. Relaxing activity of topoisomerase I was enhanced by the adenoviral major late promoter, suggesting an instability of the TATA sequence or a destabilizing effect on flanking DNA.

Near-zero linking difference upon transcription factor IID binding to promoter DNA

Binding of yeast transcription factor IID (TFIID) to the adenoviral major late promoter in circular DNA molecules caused a linking number change of less than 0.1. TFIID on its own therefore fails to unwind DNA appreciably, or else it causes both unwinding and compensatory writhing. Highly purified, recombinant yeast TFIID relaxed supercoiled DNA, because of a contaminant of bacterial topoisomerase I. Relaxing activity of topoisomerase I was enhanced by the adenoviral major late promoter, suggesting an instability of the TATA sequence or a destabilizing effect on flanking DNA.

Characterisation of the gene encoding an unusually divergent TATA-binding protein (TBP) from the extremely A+T-rich human malaria parasite Plasmodium falciparum

The intergenic regions of the human malaria parasite, Plasmodium falciparum, are extreme in their base composition, averaging approx. 90% A + T. As a first step to investigating whether transcription in this organism follows conventional models based largely on yeast, we have isolated and characterised the gene (TBP) encoding its TATA-binding protein (TBP). The gene is present as a single copy on chromosome 5 and is expressed as a 1.8-kb mRNA encoding a protein of 228 amino acids (aa) (26 164 Da). The inferred protein product has a bipartite structure consisting of a 45-aa species-specific N-terminal domain and a 183-aa C-terminal domain. In the latter, the malarial protein contains two directly repeated, but imperfectly homologous regions, each approx. 78 aa in length, together with a highly basic region located between them. These features are characteristic of all TBPs studied to date. Moreover, hydropathy plots suggest that the overall folding of this C-terminal domain is very similar to that of other TBPs. However, TBP from P. falciparum is much less closely related at the primary sequence level to the archetypal yeast homologue than are all other characterised TBPs (42% identity, compared to 76-93%, respectively). Despite this divergence of the primary sequence, most residues known to be involved in DNA binding are conserved. Those instances where sequence variation at generally conserved residues is observed may reflect functional differences that could ultimately be exploited by selective chemotherapy.

Mechanism of TATA-binding protein recruitment to a TATA-less class III promoter

The TATA-binding protein (TBP) is required for transcription by RNA polymerase III (pol III), even though many pol III templates, such as the adenovirus VA1 gene, lack a consensus TATA box. We show that TBP alone does not form a stable, productive interaction with VA1 DNA. However, it can be incorporated into an initiation complex if the other class III basal factors, TFIIIB and TFIIIC, are also present. TFIIIB can associate with the evolutionarily conserved C-terminal domain of TBP in the absence of DNA or TFIIIC, suggesting that TFIIIB exists in solution as a complex with TBP. The stable association of TBP with an essential component of the pol III transcription apparatus may account for the ability of TATA-less class III genes to recruit TBP.

A suppressor of TBP mutations encodes an RNA polymerase III transcription factor with homology to TFIIB

The TDS4 gene of S. cerevisiae was isolated as an allele-specific high copy suppressor of mutations within the basic region of the TATA-binding protein (TBP). The gene is essential for viability and encodes a 596 aa protein. The first 300 aa of the TDS4 protein exhibit significant sequence similarity to the RNA polymerase II transcription factor TFIIB. However, TDS4 is required for RNA polymerase III transcription in vivo and in vitro. Antibodies specific for TDS4 or TBP react with the TFIIIB complex, indicating that both proteins are components of the RNA polymerase III initiation complex. These findings suggest that the RNA polymerase II and III initiation mechanisms are extremely similar, and they explain how the TATA-binding protein can function in both systems.

How do eukaryotic activator proteins stimulate the rate of transcription by RNA polymerase II?

A large number of activator proteins have now been identified in higher and lower eukaryotes, which bind to the regulatory regions of protein-encoding genes and increase the rate at which they are transcribed by RNA polymerase II. The mechanism by which activators function is being intensively studied and some of the targets of transcriptional activation domains have now been identified. These studies have also revealed novel classes of regulatory factors, which were not anticipated by extrapolating from the principles obtained with prokaryotic promoters.

Advances in RNA polymerase II transcription

Multiple protein factors are necessary to mediate transcription by RNA polymerase II. Recently, a number of advances have been made in our understanding of how general transcription factors collectively modulate basal transcription in the context of different promoter environments and how this process is activated and repressed by accessory components.

Variants of the TATA-binding protein can distinguish subsets of RNA polymerase I, II, and III promoters

Transcription extracts prepared from yeast that are deficient in the TATA-binding protein (TBP or TFIID) are also impaired in specific promoter recognition by all three nuclear RNA polymerases (pol I, II, and III). Specific initiation can be rescued by the addition of purified recombinant TBP, demonstrating that pol I, II, and III all require this factor. A mutation of TBP has been identified that will function with pol I but not with pol II or III. Conversely, another mutation, which inactivates TATA element binding in vitro, will function with pol I and III promoters but is inactive for a pol II promoter. Thus, it is possible to identify TBP variants that will only function on different subsets of all nuclear promoters.

The TATA-binding protein is required for transcription by all three nuclear RNA polymerases in yeast cells

Using temperature- and proteolytically sensitive derivatives to inactivate the function of the yeast TATA-binding protein (TBP) in vivo, we investigated the requirement of TBP for transcription by the three nuclear RNA polymerases in yeast cells. TBP is required for RNA polymerase II (pol II) transcription from promoters containing conventional TATA elements as well as functionally distinct promoters that lack TATA-like sequences. TBP is also required for transcription of the U6 snRNA and two different tRNA genes mediated by RNA pol III as well as transcription of ribosomal RNA mediated by RNA pol I. For all promoters tested, transcription decreases rapidly and specifically upon inactivation of TBP, strongly suggesting that TBP is directly involved in the transcription process. These observations suggest that TBP is required for transcription of all nuclearly encoded genes in yeast, although distinct molecular mechanisms are probably involved for the three RNA polymerase transcription machineries.

Two different cDNAs encoding TFIID proteins of maize

Two different complementary DNAs (cDNAs) encoding maize TFIID proteins were isolated from a maize leaf cDNA. Both cDNA sequences reveal two types of TFIID, each encoding an open reading frame of 200 amino acids. The two cDNAs are 76% identical at the DNA level and their putative amino acid sequences differ at only three amino acids. Like TATA box binding proteins from other organisms they show a bipartite structure containing a specific N-terminal region and a highly conserved C-terminal domain expected to be necessary and sufficient for the essential TFIID functions in transcriptional initiation.