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• W2000901433 abstract "The transcription factor TFIID is a multimeric protein complex containing the TATA box-binding polypeptide (TBP) and TBP-associated factors. We have previously reported that the N-terminal regions of dTAFⅡ62 and dTAFⅡ42 have sequence similarities with histones H4 and H3. Here, we demonstrate that the histone-homologous regions of dTAFⅡ62 and dTAFⅡ42 form a heteromeric complex both in vitro and in a yeast two-hybrid system. Neither dTAFⅡ62 nor dTAFⅡ42 forms a homomeric complex, in agreement with a nucleosomal histone character. Moreover, circular dichroism measurements show that the heteromeric complex is dominated by α-helical secondary structure. These results strongly suggest the existence of a histone-like surface on TFIID. The transcription factor TFIID is a multimeric protein complex containing the TATA box-binding polypeptide (TBP) and TBP-associated factors. We have previously reported that the N-terminal regions of dTAFⅡ62 and dTAFⅡ42 have sequence similarities with histones H4 and H3. Here, we demonstrate that the histone-homologous regions of dTAFⅡ62 and dTAFⅡ42 form a heteromeric complex both in vitro and in a yeast two-hybrid system. Neither dTAFⅡ62 nor dTAFⅡ42 forms a homomeric complex, in agreement with a nucleosomal histone character. Moreover, circular dichroism measurements show that the heteromeric complex is dominated by α-helical secondary structure. These results strongly suggest the existence of a histone-like surface on TFIID. The transcription factor TFIID plays a central role in the assembly of the basic transcriptional machinery into a preinitiation complex (for review, see (1.Roeder R.G. Trends Biochem. Sci. 1991; 16: 402-408Abstract Full Text PDF PubMed Scopus (350) Google Scholar)). TFIID binds to the core promoter and thus provides a foundation for association of the other initiation factors and RNA polymerase II. Biochemical studies of eukaryotic transcriptional activation demonstrate both physical and functional interactions of activators with TFIID that in turn facilitate preinitiation complex assembly and function (for review, see (1.Roeder R.G. Trends Biochem. Sci. 1991; 16: 402-408Abstract Full Text PDF PubMed Scopus (350) Google Scholar)). TFIID is a multimeric protein complex, comprising the TATA box-binding protein (TBP) 1The abbreviations used are: TBPTATA box-binding proteinTAFTBP-associated factorbpbase pair(s)GSTglutathione S-transferaseNTAnitriloacetateaaamino acids. and numerous tightly associated factors called TAFs (for review, see (2.Tjian R. Sci. Am. 1995; 272: 54-61Crossref PubMed Scopus (26) Google Scholar) and (3.Burley, S. K., Roeder, R. G. (1996) Annu. Rev. Biochem., in pressGoogle Scholar)). To date, nine TAF subunits of Drosophila TFIID (dTAFⅡ230, −150, −110, −85, −62, −42, −28α, −28β, and −22) have been cloned (reviewed in (3.Burley, S. K., Roeder, R. G. (1996) Annu. Rev. Biochem., in pressGoogle Scholar)). In addition, several homologs have been isolated from both human (hTAF) and yeast (yTAF), suggesting that TAF-mediated activation pathways are conserved from yeast to man (reviewed in (3.Burley, S. K., Roeder, R. G. (1996) Annu. Rev. Biochem., in pressGoogle Scholar)). TATA box-binding protein TBP-associated factor base pair(s) glutathione S-transferase nitriloacetate amino acids. A central question in eukaryotic transcriptional regulation is how TFIID gains access to a chromatin template and how stable association is maintained within the chromosome. A potentially relevant finding is that the N-terminal regions of the dTAFⅡ62 and dTAFⅡ42 proteins have sequence similarities with the C-terminal core domain of histones H4 and H3, respectively(4.Kokubo T. Gong D.W. Wootton J.C. Horikoshi M. Roeder R.G. Nakatani Y. Nature. 1994; 367: 484-487Crossref PubMed Scopus (106) Google Scholar). More recently, it has been shown that the histone-like regions are well conserved in both the yeast (5.Poon D. Bai Y. Campbell A.M. Bjorklund S. Kim Y.J. Zhou S. Kornberg R.D. Weil P.A. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 8224-8228Crossref PubMed Scopus (118) Google Scholar) 2M. Swanson and Y. Nakatani, unpublished observations. and human (6.Weinzierl R.O. Ruppert S. Dynlacht B.D. Tanese N. Tjian R. EMBO J. 1993; 12: 5303-5309Crossref PubMed Scopus (67) Google Scholar, 7.Hisatake K. Ohta T. Takada R. Guermah M. Horikoshi M. Nakatani Y. Roeder R.G. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 8195-8199Crossref PubMed Scopus (70) Google Scholar, 8.Klemm R.D. Goodrich J.A. Zhou S. Tjian R. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 5788-5792Crossref PubMed Scopus (106) Google Scholar, 9.Lu H. Levine A.J. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 5154-5158Crossref PubMed Scopus (282) Google Scholar) counterparts to dTAFⅡ62 and dTAFⅡ42. The nucleosome core consists of 146 bp of DNA wrapped around an octameric complex of two copies of each of histones H2A, H2B, H3, and H4. Despite a low sequence similarity, all histones contain a long helix flanked on either side by a loop segment and short helix, termed the “histone fold” (reviewed in (10.Arents G. Moudrianakis E.N. Proc. Natl. Acad. Sci. U. S. A. 1993; 90: 10489-10493Crossref PubMed Scopus (313) Google Scholar, 11.Ramakrishnan V. Curr. Opin. Struct. Biol. 1994; 4: 44-50Crossref Scopus (26) Google Scholar, 12.Arents G. Moudrianakis E.N. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 11170-11174Crossref PubMed Scopus (291) Google Scholar)). The histone fold is involved in formation of the stable H2A-H2B and H3-H4 heterodimers. H3-H4 dimers further associate to form the (H3-H4)2 tetramer. The (H3-H4)2 tetramer alone is responsible for organizing the core 120 bp of DNA into the arrangement found in the octameric complex(13.Hayes J.J. Clark D.J. Wolffe A.P. Proc. Natl. Acad. Sci. U. S. A. 1991; 88: 6829-6833Crossref PubMed Scopus (229) Google Scholar). Recently, numerous proteins potentially containing the histone fold have been identified by data base search(14.Baxevanis A.D. Arents G. Moudrianakis E.N. Landsman D. Nucleic Acids Res. 1995; 23: 2685-2691Crossref PubMed Scopus (181) Google Scholar). This group includes TAFⅡ62 and TAFⅡ42, plus many DNA-binding proteins and multimeric proteins. The data base search also identified transcription initiation factor TFIIB as a protein that has the histone fold. However, both NMR (15.Bagby S. Kim S. Maldonado E. Tong K.I. Reinberg D. Ikura M. Cell. 1995; 82: 857-867Abstract Full Text PDF PubMed Scopus (117) Google Scholar) and x-ray crystallography (16.Nikolov D.B. Chen H. Halay E.D. Usheva A.A. Hisatake K. Lee D.K. Roeder R.G. Burley S.K. Nature. 1995; 377: 119-128Crossref PubMed Scopus (484) Google Scholar) show that TFIIB does not have the histone fold. Thus, it is crucial to confirm the prediction using biochemical and physical techniques. To investigate the significance of the sequence similarities between dTAFⅡ62-dTAFⅡ42 and histones H4-H3, we have tested the ability of the histone-like regions in dTAFⅡ62 and dTAFⅡ42 to form a stable heteromeric complex. Here, we demonstrate that the histone-homologous regions of dTAFⅡ62 and dTAFⅡ42 form a heteromeric complex both in vitro and in a yeast two-hybrid system. We further demonstrate that this heteromeric complex, like the H3-H4 complex, is predominantly α-helical. The results described here strongly suggest that TFIID has a histone-like surface. To make a glutathione S-transferase (GST)-tagged dTAFⅡ62 expression plasmid, DNA encoding dTAFⅡ62 residues 1-91 (4.Kokubo T. Gong D.W. Wootton J.C. Horikoshi M. Roeder R.G. Nakatani Y. Nature. 1994; 367: 484-487Crossref PubMed Scopus (106) Google Scholar) was amplified by polymerase chain reaction as an EcoRI-BamHI fragment and subcloned into pGEX2 (Pharmacia Biotech Inc.). To create a histidine (His)-tagged dTAFⅡ42 expression plasmid, DNA encoding dTAFⅡ42 residues 1-100 (4.Kokubo T. Gong D.W. Wootton J.C. Horikoshi M. Roeder R.G. Nakatani Y. Nature. 1994; 367: 484-487Crossref PubMed Scopus (106) Google Scholar) was amplified by polymerase chain reaction as an NdeI-EcoRI fragment and subcloned into pET15e(17.Yamashita S. Wada K. Horikoshi M. Gong D.W. Kokubo T. Hisatake K. Yokotani N. Malik S. Roeder R.G. Nakatani Y. Proc. Natl. Acad. Sci. U. S. A. 1992; 89: 2839-2843Crossref PubMed Scopus (31) Google Scholar). For yeast two-hybrid plasmids, both dTAFⅡ62 (amino acids 1-91) and dTAFⅡ42 (amino acids 1-100) were amplified as NcoI-BamHI fragments and subcloned into both pAS1-CYH2 and pACTII. 3S. J. Elledge, unpublished data. Note that a stop codon was created just after the TAF sequence in all constructs. GST-tagged dTAFⅡ62 and His-tagged dTAFⅡ42 were expressed in Escherichia coli BL21(DE3) and BL21 cells, respectively, according to a standard protocol(17.Yamashita S. Wada K. Horikoshi M. Gong D.W. Kokubo T. Hisatake K. Yokotani N. Malik S. Roeder R.G. Nakatani Y. Proc. Natl. Acad. Sci. U. S. A. 1992; 89: 2839-2843Crossref PubMed Scopus (31) Google Scholar). After harvesting the bacteria, all procedures were carried out at 4°C. Bacterial pellets were resuspended into [1,25] culture volume of buffer B (20 mM Hepes-KOH, pH 7.5, 5 mM MgCl2, 10% glycerol, 10 mM β-mercaptoethanol, 1 mM phenylmethylsulfonyl fluoride) containing 0.5 M KCl and 6 M guanidine HCl and rotated for 60 min. After centrifugation at 50,000 rpm for 30 min, the supernatants were analyzed by SDS-polyacrylamide gel electrophoresis to estimate the concentrations of the recombinant proteins. Extracts were mixed in an equimolar ratio and dialyzed against buffer B containing 0.5 M KCl and 1 M guanidine HCl for 12 h. Dialysis was continued for another 12 h in buffer B containing 0.1 M KCl and 0.1 M guanidine HCl. After centrifugation at 12,000 rpm for 10 min, the supernatant was used for interaction experiments. The supernatant was incubated with [1,20] bed volume of either Ni2⁺-NTA-agarose (Qiagen) or glutathione-Sepharose (Pharmacia) for 30 min with rotation and washed with the same buffer 5 times. Protein was eluted from Ni2⁺-NTA and glutathione matrices with the same buffer containing 100 mM imidazole or 20 mM glutathione (pH 7.5), respectively. For CD measurements, both His- and GST-tags were removed from the dTAFⅡ62-dTAFⅡ42 complex in the following manner. The complex was immobilized on glutathione-Sepharose as described above and was equilibrated with digestion buffer containing 20 mM Tris-HCl (pH 8.3), 0.15 M KCl, 2.5 mM CaCl2, and 10% glycerol. Cleavage was carried out in 1 bed volume of the same buffer containing thrombin (10 units/ml). The supernatant was dialyzed against buffer B containing 0.5 M KCl. For further purification, 50 μl of the sample was applied to Superose 12 (25-ml bed volume) and chromatographed with the same buffer. The peak fractions (>98% purity) were used for CD measurements. CD measurements were performed at 25°C using a Jasco J700 spectropolarimeter. The spectra are presented as the average of eight scans in units of mean residue ellipticity (θ). The concentration of the protein was 15.7 μM in 20 mM sodium phosphate (pH 7.0). Protein concentration was determined by measuring absorbance at 280 nm and using a calculated extinction coefficient. The protein was denatured by the addition of guanidine hydrochloride to a concentration of 6 M. Protein secondary structure was estimated using the software supplied with the Jasco J700 spectropolarimeter. Plasmids for the yeast two-hybrid system were transformed into Saccharomyces cerevisiae strain Y190 in various combinations as shown in Table 1. β-Galactosidase activity was measured as described(18.Gill G. Ptashne M. Cell. 1987; 51: 121-126Abstract Full Text PDF PubMed Scopus (181) Google Scholar).Tabled 1 Based on the similarities between dTAFⅡ62 and dTAFⅡ42, and histones H4 and H3, intermolecular interactions between the histone-like regions in dTAFⅡ62 and dTAFⅡ42 were examined. dTAFⅡ62 (aa 1-91) and dTAFⅡ42 (aa 1-100) were expressed independently in E. coli as His- and GST-tagged proteins, respectively (Fig. 1A). Since both recombinant polypeptides are highly insoluble (data not shown), they were solubilized by disrupting E. coli in buffer containing 6 M guanidine. The two extracts were mixed at an equimolar ratio of recombinant polypeptides and co-renatured by dialyzing against buffer containing 0.1 M guanidine (Fig. 1B, lane 1). Complexes were purified by Ni2⁺-NTA agarose chromatography followed by glutathione-Sepharose chromatography (lanes 2 and 3). GST-dTAFⅡ62 (aa 1-91) and His-dTAFⅡ42 (aa 1-100) proteins co-purified through these chromatographic steps. Similar results were obtained by glutathione-Sepharose chromatography followed by Ni2⁺-NTA-agarose chromatography (lanes 4 and 5). In contrast, no specific protein was observed after the second chromatography step in controls including single extract (lanes 6-11). The far-UV (250-200 nm) CD spectrum of the dTAFⅡ62 (aa 1-91)-dTAFⅡ42 (aa 1-100) heterocomplex is shown in Fig. 2. The overall shape of the spectrum, with minima in the mean residue ellipticity at 208 and 222 nm, is characteristic of polypeptides dominated by α-helical secondary structure. In support of this, we used manufacturer-supplied software to obtain the following estimates for the secondary structure: 41.4% α-helix, 8.4% β-strand, 15.8% turn, and 34.4% random. The interaction between the histone-like regions was further analyzed in a yeast two-hybrid system. dTAFⅡ62 (aa 1-91) and dTAFⅡ42 (aa 1-100) were fused to either the GAL4 DNA-binding domain or activation domain. Yeast bearing an integrated GAL1-lacZ fusion were transformed with different combinations of plasmids (Table 1). The lacZ reporter gene is expressed in a manner dependent on the interaction of dTAFⅡ62 and dTAFⅡ42. Neither dTAFⅡ62 nor dTAFⅡ42 displayed significant activity when tested for self-interaction. We therefore conclude that dTAFⅡ62 and dTAFⅡ42 form only heteromeric complexes. It is noteworthy that dTAFⅡ62 and dTAFⅡ42 inhibited yeast growth (doubling time, >10 h) only when they were transformed together. Overexpression of acidic activators also inhibits yeast growth(19.Berger S.L. Pina B. Silverman N. Marcus G.A. Agapite J. Regier J.L. Triezenberg S.J. Guarente L. Cell. 1992; 70: 251-265Abstract Full Text PDF PubMed Scopus (356) Google Scholar). The growth inhibition may thus be caused by exceptionally strong interactions between dTAFⅡ62 and dTAFⅡ42, resulting in overproduction of the GAL4 DNA-binding domain-activation domain complex. Alternatively, the heteromeric dTAFⅡ62-dTAFⅡ42 complex may titrate yeast factors important for growth. In summary, we have demonstrated that the N-terminal regions of dTAFⅡ62 and dTAFⅡ42, similar in sequence to nucleosome core histones H4 and H3, form a heteromeric complex both in vitro and in a yeast two-hybrid system. Like histones H3 and H4, neither dTAFⅡ62 nor dTAFⅡ42 forms a homomeric complex, and CD measurements suggest that the heteromeric dTAFⅡ62-dTAFⅡ42 complex is dominated by α-helical secondary structure. In some promoters, including the adenovirus major late and human gfa promoters(20.Horikoshi M. Wang C.K. Fujii H. Cromlish J.A. Weil P.A. Roeder R.G. Proc. Natl. Acad. Sci. U. S. A. 1989; 86: 4843-4847Crossref PubMed Scopus (58) Google Scholar, 21.Nakajima N. Horikoshi M. Roeder R.G. Mol. Cell. Biol. 1988; 8: 4028-4040Crossref PubMed Scopus (297) Google Scholar, 22.Nakatani Y. Horikoshi M. Brenner M. Yamamoto T. Besnard F. Roeder R.G. Freese E. Nature. 1990; 348: 86-88Crossref PubMed Scopus (81) Google Scholar), the TFIID footprint extends from the TATA box through to 35 bp downstream from the initiation site, whereas the TBP footprint extends only over the TATA box region. These results indicate that one or more TAFs contribute to the downstream interaction. Recent studies with recombinant TAFs demonstrated that dTAFⅡ150 alone can bind to the initiator element(23.Verrijzer C.P. Yokomori K. Chen J.L. Tjian R. Science. 1994; 264: 933-941Crossref PubMed Scopus (178) Google Scholar). Moreover, the dTAFⅡ150-TBP complex gives a footprint from the TATA box through to 35 bp downstream from the initiation site(23.Verrijzer C.P. Yokomori K. Chen J.L. Tjian R. Science. 1994; 264: 933-941Crossref PubMed Scopus (178) Google Scholar, 24.Verrijzer C.P. Chen J.L. Yokomori K. Tjian R. Cell. 1995; 81: 1115-1125Abstract Full Text PDF PubMed Scopus (257) Google Scholar), like native TFIID. However, the dTAFⅡ150-TBP complex does not produce DNase I-hypersensitive sites as observed for native TFIID(24.Verrijzer C.P. Chen J.L. Yokomori K. Tjian R. Cell. 1995; 81: 1115-1125Abstract Full Text PDF PubMed Scopus (257) Google Scholar). Thus, it is likely that other TAFs are also involved in the downstream interaction. We predict that the histone-like region in dTAFⅡ62-dTAFⅡ42 is bound to the downstream sequence because, similar to histone core, TFIID produces DNase I-hypersensitive sites about every 10 bp. The important question is whether the dTAFⅡ62-dTAFⅡ42 complex is a heterodimer or heterotetramer in the TFIID complex; the N-terminal histone-like regions of dTAFⅡ62-dTAFⅡ42 do form heterotetramers under physiological conditions, 4X. Xie and S. K. Burley, personal communication. suggesting that these TAFs could be present as a tetramer in the TFIID complex. The downstream interaction plays an important role in both basal and activated transcription. TFIID binds to the downstream region in a DNA sequence-dependent fashion, at least in the human gfa promoter, contributing to both stable TFIID binding and effective transcription in vitro(22.Nakatani Y. Horikoshi M. Brenner M. Yamamoto T. Besnard F. Roeder R.G. Freese E. Nature. 1990; 348: 86-88Crossref PubMed Scopus (81) Google Scholar, 25.Nakatani Y. Brenner M. Freese E. Proc. Natl. Acad. Sci. U. S. A. 1990; 87: 4289-4293Crossref PubMed Scopus (40) Google Scholar). In contrast, in the adenovirus E4 promoter, TFIID does not bind to the downstream region and produces very low basal transcription activity. Importantly, activators induce the downstream interaction and facilitate preinitiation complex formation(26.Horikoshi M. Carey M.F. Kakidani H. Roeder R.G. Cell. 1988; 54: 665-669Abstract Full Text PDF PubMed Scopus (186) Google Scholar, 27.Horikoshi M. Hai T. Lin Y.S. Green M.R. Roeder R.G. Cell. 1988; 54: 1033-1042Abstract Full Text PDF PubMed Scopus (268) Google Scholar). Furthermore, the histone-like domains may have a more critical role in a natural chromatin environment, e.g. stimulation of the displacement of nucleosomal histones near the transcription start site and/or maintenance of histone exclusion from the transcription start site. Y. N. is grateful to A. S. Levine and B. H. Howard for their support and encouragement. We thank M. Swanson, D. Pruss, and A. P. Wolffe for helpful discussion and critical comments, S. J. Elledge for yeast two-hybrid plasmids, and M. L. Lanigan for editing the manuscript." @default.
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• W2000901433 title "The Histone Folds in Transcription Factor TFIID" @default.
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