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Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
Received 25 March 2003/ Returned for modification 30 April 2003/ Accepted 22 July 2003
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ABSTRACT |
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 Top Abstract IntroductionMaterials and MethodsResultsDiscussionReferences |
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INTRODUCTION |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionReferences |
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TBP is unique among basal factors in that it is the only known basal factor that is involved in transcription by all three eukaryotic nuclear RNA polymerases—Pol I, Pol II, and Pol III—from promoters with and without a TATA box (10). Consistent with its central role in transcription, TBP contains a highly conserved and structured 180-amino-acid C-terminal core domain, illustrated in Fig. 1A and called TBPCORE. On TATA-box-containing Pol II and Pol III promoters, TBPCORE binds the TATA box and unwinds the DNA to form an unusually bent TBPCORE-TATA box complex (11, 13, 14, 20). The TBP-induced bent DNA structure plays an important role in the assembly of the correct preinitiation complex. In addition to the conserved TBPCORE, TBP also contains an N-terminal region that is highly divergent in both sequence and length among different species.
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In contrast to the general involvement of TBP in nuclear transcription, TFIIB is restricted to Pol II transcription; two human TFIIB-related proteins, Brf1 (BRF/TFIIIB90) and Brf2 (BRFU/TFIIIB50), are involved in human Pol III transcription, as illustrated in Fig. 1B and C (26, 37). Brf1 promotes transcription from the gene-internal Pol III promoters in humans and yeast, whereas the human Brf2 protein, for which there is no known yeast homolog, is involved in transcription from Pol III promoters with gene-external promoter elements, such as the human U6 small nuclear RNA (snRNA) gene promoter, for which there are no known counterparts in yeast (27, 32). The basal elements of the evolutionarily restricted human U6 snRNA promoter are a proximal sequence element (PSE), which recruits a protein complex called SNAPC/PTF (25, 26, 38), and a TATA box, which recruits TBP; SNAPC and TBP bind cooperatively on the human U6 promoter DNA (19).
To date, TFIIB, Brf1, and Brf2 constitute the human TFIIB protein family (Fig. 1B). TFIIB contains an N-terminal region with a structured zinc ribbon (8, 41) and a structured C-terminal core domain (TFIIBCORE) (1, 21, 35). TFIIBCORE binds cooperatively to the second stirrup region of the saddle-shaped TBPCORE on the TATA box, and the N-terminal region of TFIIB recruits a Pol II/TFIIF complex to the promoter (22). Brf1 and Brf2 contain (i) N-terminal conserved TFIIB-like zinc ribbon and core domains and (ii) unrelated C-terminal regions (26).
Unlike TFIIB, Brf1 largely utilizes its unique C-terminal region to recognize and form a stable complex with TBP (6, 36), although a weak association between the N-terminal region of Brf1 and TBP exists (12, 23). Consistent with these findings, a Brf1 contact surface of TBP differs from the TFIIB contact surface and overlaps the IDB surface; this surface is involved in transcription from Brf1-dependent Pol III promoters (6, 28, 40). Interestingly, Brf2 shares features with both TFIIB and Brf1 in its interaction with TBP. On the one hand, Brf2 behaves like TFIIB because they both utilize the conserved TFIIB core domain for association with TBP (5) and recognize the second stirrup region of TBP similarly to initiate transcription from Pol III and Pol II promoters, respectively (40). On the other hand, Brf2 and Brf1 recognize a shared residue on the IDB surface of TBP (5, 6, 28). Nevertheless, although full-length human TBP TATA box recognition is inhibited by the TBP IDB surface (39) and stimulated by TFIIB and Brf2 (5, 17, 22, 40), the specific role, if any, of the IDB surface and its function in TBP interaction with the TFIIB family proteins are unknown.
Here we have analyzed the effect of an extensive set of human TBP IDB surface mutations on recruitment of the human TFIIB family proteins to the TATA box. We show that the complete IDB surface is involved in recruitment of all three TFIIB family proteins, although surprisingly, the role is different for each TFIIB family member. Indeed, remarkably, even though the IDB surface and TFIIB contact surface of TBP are located on opposite sides of the TBPCORE (Fig. 1A), they both promote TBP association with TFIIB and cooperate to form the wild-type TFIIB-TBP-TATA box complex. These results reveal the versatility of the human TBP and TFIIB family proteins in the assembly of Pol II and Pol III promoter preinitiation complexes.
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MATERIALS AND METHODS |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionReferences |
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Protein preparations were done as described previously, with the GST moiety of the GST fusion protein removed by proteolysis (27, 39). Importantly, the purified TBP proteins were not normalized by any activity assay, such as for DNA-binding activity or transcriptional activity, but rather by determination of molecular quantity by Coomassie staining after sodium dodecyl sulfate-polyacrylamide gel electrophoresis and by immunoblot analysis with the N-terminal-specific monoclonal antibody SL30 (24) for full-length wild-type and mutant TBP molecules and with a C-terminal polyclonal TBP antibody (Geneka Biotechnology) for full-length and N-terminally truncated TBP molecules (39). To ensure the accuracy of protein purification and normalization procedures, we examined each normalized mutant TBP molecule by transcription from a set of four promoters in vitro, and each exhibited the wild-type level of activity for transcription from at least one of the four promoters (40), excluding the possibility that inactive samples are due to denatured TBP molecules. Preparation of SNAPC synthesized in baculovirus was done as described previously (9).
DNA probe preparation and electrophoretic mobility retardation assay. DNA probe preparation and electrophoretic mobility retardation assays were performed as described previously (39). DNA probes for electrophoretic mobility retardation assays were generated by PCR amplification of the human U6 (positions -70 to -14) and AdML (positions -38 to -17) promoter regions by use of 5'-32P-labeled universal (USP) and reverse (RSP) sequencing primers as described previously (39). The sequences of the human U6 promoter region (positions -70 to -14) and the AdML promoter region (positions -38 to -17) are tatgcttaccgtaacttgaaagtatttcgatttcttggcttTATATAtcttgtggaa and gggggcTATAAAAGggggtggg, respectively, with the TATA boxes indicated by uppercase letters. All the binding reactions were performed at 30°C for 30 min. For the TBP-TFIIB family protein binding reactions, the amount of TBP protein used for each probe preparation was that determined to provide optimal formation of the unbent TBP-TATA box complex (TBPFL complex). In general, 4 to 20 ng (4.4 to 22 nM) of TBP and 50,000 cpm (0.2 to 1 nM) of 32P-labeled DNA probes were used. The formation of the TBPFL complex in these studies is consistent with the maximum levels of TBP-TATA box complex formation reported previously (3, 30). The amount of the TFIIB family proteins used was that determined to provide maximum cooperative binding with TBP. By use of Coomassie staining after polyacrylamide gel electrophoresis and comparison to bovine serum albumin titration, we estimate that the molar ratios of TFIIB, Brf2, and Brf1 over TBP are roughly 60:1, 12:1, and 2.5:1, respectively. Compared to the TBPFL complex, the significantly increased formation of the TFIIB-TBP-TATA box complex indicates that a large fraction of active TBP molecules do not bind to DNA in the binding reaction of TBP alone with DNA, which is consistent with the view of the intrinsically weak DNA-binding activity for full-length human TBP (3, 30). For the TBP-SNAPC binding reactions, the amounts of the wild-type TBP and SNAPC proteins used were those determined to provide maximum cooperative binding.
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RESULTS |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionReferences |
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Selective effects of IDB surface mutations of human TBP on interaction with the human TFIIB family proteins. We examined the effects of amino acid substitution of residues (i) in the center, (ii) on the border, and (iii) outside of the IDB surface (39) in full-length human TBP on TBP interaction with TFIIB, Brf2, and Brf1. (Note that, in this report, we use the word "interaction" to denote "action on each other," which may be direct or indirect, and use the word "contact" to denote "physical touching.") As shown in Fig. 2, we assayed TBP interaction with TFIIB (panel A), Brf2 (panel B), and Brf1 (panel C) on TATA-box-containing DNA by electrophoretic mobility retardation assays. For each assay, the even-numbered lanes contain the added TFIIB family member. Simple examination of the three panels in Fig. 2 reveals the strikingly selective effects of IDB surface mutations on TFIIB family member interaction with the TBP-TATA box complex, because the odd-numbered lanes lacking TFIIB family protein generate the same pattern in each panel, as they are identical samples, and the even-numbered lanes generate very different patterns, thus producing the very different overall look for each panel in the figure.
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As described previously, mutations on the IDB surface of TBP led to the formation of an abundant and bent TBP-TATA box complex that we refer to as the TBPFL* complex (Fig. 2, compare lanes 9, 11, 13, 15, 17, and 19 to lanes 3 and 21) (39). The TBPFL* complex has been demonstrated previously to be TATA box specific (39). Surprisingly, each of the four central IDB mutations exhibits the same effect upon association with a TFIIB family member, but the effect differs for each TFIIB family member. With TFIIB, all the mutations on the IDB surface led to formation of the same robust complex of non-wild-type mobility (Fig. 2A, compare lanes 10, 12, 14, 16, 18, and 20 to lanes 4 and 22; see arrowhead). These TBP mutant TFIIB-TBP-TATA box complexes possess a faster electrophoretic mobility than the wild-type TFIIB-TBP-TATA box complex. In addition, both the radical and alanine mutations on the IDB surface led to formation of the mutant TFIIB-TBP-TATA box complex, with the same altered electrophoretic mobility (data not shown).
With Brf2 and Brf1, the central set of four IDB mutations displayed deleterious effects, albeit different effects for each of these two proteins. They prevented Brf2-TBP-TATA box complex formation without affecting TBPFL* complex formation (Fig. 2B, compare lanes 14, 16, 18, and 20 with lanes 13, 15, 17, and 19, respectively). In stark contrast, however, Brf1 had a large effect on activated DNA binding caused by the IDB mutations: it greatly inhibited TBPFL* complex formation by these IDB-defective mutants (Fig. 2C, compare lanes 14, 16, 18, and 20 with lanes 13, 15, 17, and 19, respectively).
Mutations on the border of the IDB surface showed selective effects on TBP association with Brf2 and Brf1. The R205E mutation had little, if any, effect on Brf2 and Brf1 complex formation (Fig. 2B and C, compare lanes 10 to lanes 4 and 22), whereas the V240D mutation prevented Brf2 and Brf1 association with the TBP-TATA box complex (compare lanes 11 and 12). In conclusion, the IDB surface is differentially involved in the recruitment of the TFIIB family of proteins to TATA-box-containing DNA in the assembly of the preinitiation complex.
The effects of mutations on the IDB surface of human TBP on interaction with the human TFIIB family of proteins were observed for both the Pol III human U6 promoter TATA box (Fig. 2) and the Pol II adenovirus major late (AdML) promoter TATA box (data not shown), indicating that the human TBP IDB surface interacts with the TFIIB family of proteins similarly for these two TATA-box-containing Pol II and Pol III promoters. These two TATA boxes possess very different flanking sequences (see Materials and Methods). Thus, the role of the human TBP IDB surface in recruitment of the TFIIB family of proteins is probably independent of specific TATA-box-flanking sequences.
Mutations on the IDB surface of human TBP do not affect its interaction with the human snRNA promoter-specific factor SNAPC. In contrast to human TBP interaction with TFIIB family members, the IDB surface mutations have little, if any, effect on cooperative binding with another basal transcription factor, SNAPC, as shown in Fig. 3. As described previously, SNAPC alone binds to the human U6 promoter PSE to form a SNAPC-DNA complex (lane 2) of low abundance (19). TBP binds to the U6 TATA box to form both the unbent TBPFL and the bent TBPFL* complexes (lane 3) (39). As reported previously, with the higher TBP concentrations used in this assay, for unknown reasons TBP forms two TBPFL*-like complexes (40). As expected, TBP bound to U6 promoter DNA cooperatively with SNAPC and led to formation of the SNAPC-TBP-TATA box complex, with increased abundance and slightly retarded electrophoretic mobility compared to those of the SNAPC-DNA complex (compare lane 4 to lanes 2 and 3) (19). In contrast to its effects on interactions with the TFIIB family proteins, the R188E mutation in the center of the IDB surface did not show any evident effect on TBP interaction with SNAPC, as did the non-IDB surface mutation K181E (compare lanes 4, 6, and 8). Thus, of the two human U6 promoter TBP-interacting proteins Brf2 and SNAPC, only Brf2 interacts with the IDB surface of TBP, indicating that the IDB-defective effects on TFIIB family member interaction with TBP on DNA are not universal among basal transcription factors.
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The N-terminal region of human TFIIB is not essential for interaction with the IDB surface of human TBP. The locations of the known human TFIIBCORE contact and IDB surfaces of TBP—on opposite sides of TBP (Fig. 1A)—suggest that the IDB surface cannot directly contact the TFIIBCORE. Full-length TFIIB, however, was used in the experiments shown in Fig. 2A and 4A, and thus the TFIIB N terminus (e.g., the zinc ribbon [Fig. 1B]) could be involved. Therefore, we asked whether the N-terminal region of TFIIB influences TFIIB interaction with the IDB surface of TBP.
Figure 5 shows full-length TFIIB and TFIIBCORE interaction with the IDB surface of TBP on the AdML promoter. Interestingly, the TFIIBCORE displayed the same altered mobility effect on the TFIIB-TBP-TATA box complex with the full-length IDB-defective R188E mutant TBP molecule as the full-length TFIIB molecule did (compare lanes 5 and 8 with lanes 6 and 9). This result indicates that the N-terminal region of TFIIB has no evident influence on the interaction of TFIIB with the IDB surface of TBP (compare lanes 5 and 6, and compare lanes 8 and 9). Combined with the TBP N-terminal deletion analysis shown in Fig. 4, these results suggest that the effect of the IDB surface on TBP interaction with TFIIB is an intrinsic property of the TBPCORE and TFIIBCORE and probably does not result from direct contact between the IDB surface of TBP and TFIIB. Thus, the human TBP IDB surface is involved in interaction with, but does not directly contact, human TFIIB.
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As shown in Fig. 6, wild-type TBP bound to DNA to form an unbent TBPFL complex of low affinity (lane 3), and addition of TFIIB retarded this complex to an abundant and bent wild-type TFIIB-TBP-TATA box complex (lane 4; the nature of the unbent or bent DNA conformation in all of the complexes described for Fig. 6 was determined with DNA-bending probes [39; data not shown]). The IDB-defective R188E TBP mutation led to formation of an abundant and bent TBPFL* complex (lane 5), and addition of TFIIB retarded this complex to an abundant and bent mutant TFIIB-TBPR188E-TATA box complex with an altered electrophoretic mobility (lane 6; see arrowhead). The second-stirrup-region E284R TBP mutation, which has been shown to contact TFIIB in vitro (3, 21, 29, 35) and in vivo (31), resulted in formation of both unbent TBPFL and bent TBPFL* complexes of low affinity (lane 7) compared to the wild-type unbent TBPFL complex and the R188E bent TBPFL* complex, respectively (compare lane 7 to lanes 3 and 5). The addition of TFIIB retarded both the TBPFL and TBPFL* complexes to an abundant and bent mutant TFIIB-TBPE284R-TATA box complex (lane 8) with the same altered mobility as the mutant TFIIB-TBPR188E-TATA box complex (compare lane 8 to lanes 6 and 4; see arrowhead). Remarkably, the combined TBPR188E+E284R mutant retained the bent TBPFL* complex formation property of the TBPR188E mutant (compare lanes 5 and 9), but, unlike either of the single mutants, was unaffected by TFIIB in our assay (compare lanes 9 and 10, and compare lane 10 to lanes 6 and 8). Thus, unexpectedly, TFIIB completely failed to associate with the TBP-TATA box complex only when there were mutations on both the prototypical second-stirrup TFIIB contact surface and the IDB surface of TBP.
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DISCUSSION |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionReferences |
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We found that mutations on the IDB surface of human TBP display selective effects on TBP interaction with each human TFIIB family protein. Importantly, our results reflect the activities of human TBP. It is currently unknown whether the DNA binding and TFIIB family interaction properties of the human TBP IDB surface have been conserved in yeast, in which TBP has been more extensively analyzed.
Diverse roles of the IDB surface of human TBP in recruitment of the human TFIIB family proteins. The results of the mutations of the IDB surface of human TBP on interaction with the human TFIIB family proteins are striking. Essentially, the four central IDB mutations demonstrate the same specific, yet different, defect pattern for each interaction with TFIIB, Brf2, and Brf1 (Fig. 2). With TFIIB, they induce formation of a non-wild-type altered-mobility TFIIB-TBP-TATA box complex; with Brf2, they inhibit its association with the TBP-TATA box complex; and with Brf1, they permit inhibition of the activated TBP binding to the TATA box. These activities, especially the responses of TFIIB and Brf1 to the IDB mutations, are surprising. The IDB mutations could influence the DNA-binding affinity or specificity of TBP or could affect TFIIB family member interaction with DNA. Discrimination among these and other explanations will require further analysis.
Whatever the case, these results suggest that for the assembly of preinitiation complexes, as key polymerase-specific bridging factors between TBP and Pol II or Pol III, TFIIB, Brf2, and Brf1 differentially interact with a specific surface of a shared target in the transcriptional apparatus, namely the TBP IDB surface. Thus, during evolution, the TFIIB family members maintained their association with the highly conserved TBP molecule but altered the ways in which they interact with it, perhaps, in this way, enhancing the variety of regulatory strategies in different promoter contexts.
In contrast to its diverse effects on interaction with the human TFIIB family members, the central IDB mutation R188E had no evident effect on cooperative interaction with the human Pol II and Pol III snRNA promoter-specific factor SNAPC (Fig. 3). Therefore, not all basal transcription factors use the IDB surface in cooperative binding with TBP on TATA-box-containing DNA. Interestingly, the IDB surface overlaps with the Pol II-specific TFIIA contact surface of TBP (3, 7, 29); it will be interesting to determine the role, if any, of the TBP IDB surface in its interaction with Pol II-specific basal factors such as TFIIA.
In addition to its independent function on the human Pol II U1 and Pol III U6 snRNA promoters and its interaction with basal factors such as SNAPC and TFIIA, in human cells TBP also exists in many different types of stable multisubunit complexes, including the Pol II-specific TFIID and B-TFIID complexes and the Pol III-specific TFIIIB complex (16, 22, 26, 33). The human TFIIIB complex includes TBP, Brf1, and the general human Pol III factor B" (Bdp1) and is required for transcription from human Pol III TATA-less promoters (26). Thus, the TBP-Brf1 interaction and the role of the IDB surface in this interaction likely reflect a natural mechanism of TBP function within the Pol III TFIIIB complex. In contrast, TBP, Brf2, and Bdp1, which are required for U6 snRNA gene transcription, can be viewed either as a loosely associated TFIIIB complex or as individual free basal transcription factors for transcription from human Pol III TATA-box-containing promoters (26, 27). In either case, the role of the IDB surface of TBP in interaction with Brf2 probably reflects a role in the assembly of the human Pol III TATA-box-containing preinitiation complex. For Pol II transcription from promoters directing the synthesis of mRNA transcripts, the IDB surface may also play a role within the TFIID complex, because the N-terminal region (2, 15, 34) and the HMG-like region (17a) of the largest TBP-associated factor, TAF1, interacts with a surface of TBP overlapping the IDB surface. It will be interesting to determine whether the IDB surface plays a specific role in TFIID function in addition to a role in TFIIB recruitment.
Two surfaces of human TBP are involved in TFIIB recruitment. Although crystallographic studies have demonstrated that TFIIBCORE contacts the second stirrup region of TBPCORE (21, 35), we found that the entire IDB surface of TBP affects full-length TBP interaction with full-length TFIIB (Fig. 2). The fact that the N-terminal regions of TBP and TFIIB are not required for this effect (Fig. 4 and 5) surprisingly suggests that the interaction between the IDB surface of TBP and TFIIB is indirect. Interestingly, mutations of both the IDB surface and the second stirrup region of TBP individually led to formation of the same aberrant-mobility TFIIB-TBP-TATA box complex. The formation of mutant TFIIB-TBP-TATA box complexes with the same altered electrophoretic mobility is unlikely, owing to dissociation of the wild-type TFIIB-TBP-TATA box complex during electrophoresis, because dissociation of a complex during electrophoresis will result in smeared or absent bands. In our case, the unique electrophoretic mobility of the altered-mobility complex is specifically induced by mutations of the IDB and the second stirrup surfaces of human TBP (Fig. 6). We conclude that these mutant complexes may possess a distinct conformation. Our previous studies (39) demonstrated that the DNA-bending angle of the IDB-defective R188E mutant TFIIB-TBPR188E-TATA box complex is greater than that of the wild-type TFIIB-TBP-TATA box complex. This difference, however, would make the TFIIB-TBPR188E-TATA box complex migrate more slowly, not faster, as we observed. Thus, there is probably a nonbending angle effect that alters the mobility. Importantly, the combined mutations in the IDB and second stirrup TFIIB contact surfaces prevented TBP interaction with TFIIB (Fig. 6), indicating that these two surfaces of TBP cooperate for TBP interaction with TFIIB in ways that are not revealed by crystallographic studies (11, 20, 21, 35).
In conclusion, we have revealed a role for the IDB surface of free human TBP in promoting its interaction with the three human TFIIB family members. Thus, the IDB surface plays both negative (for DNA binding) (39) and positive (for TFIIB family protein interaction) (this study) roles in initiation complex formation, illustrating how a single surface of a regulatory molecule can play opposing regulatory roles. The interaction with the TFIIB family members illustrates how a family of trans factors can target the same autoinhibitory surface of a key regulator to assemble different preinitiation complexes. The many modes of intermolecular interaction regulated by the IDB surface reveal a diverse range of regulatory mechanisms provided by a small surface of a key regulator of transcription.
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ACKNOWLEDGMENTS |
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These studies were supported by Public Health Service grant CA13106.
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FOOTNOTES |
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