| Nucleic Acids Research | Pages |
Biochemical and genetic characterization of the dominant positive element driving transcription ofthe yeast TBP-encoding gene, SPT15
Introduction
Materials And Methods
Gel shift analyses
Chemical interference assays
Site-directed mutagenesis
[beta]-galactosidase and genomic footprinting assays
Purification of PED binding activity
Immunoblot analysis
UV crosslinking
Results
An abundant, sequence specific DNA binding factor present in yeast WCE can bind to the PED element in vitro
Chemical interference assays identify the close contacts between PEDBF and the nucleotides comprising the PED element of the TBP-encoding gene
Mutation of PED sequences involved in making close contacts with PEDBF results in decreased TBP gene 5[prime]-flanking sequence-driven reporter gene activity in vivo
In vivo and in vitro DNA binding assays indicate that mutant PED alleles drive TBP gene transcription less efficiently because PEDBF binds these sequences more weakly
Genomic footprinting
DNA binding-competition assays
Purification and characterization of PEDBF
Immunological analyses indicate that PEDBF is Abf1p
Biochemical assays show that Abf1p binds indistinguishably to PED and ABF1 sites in vitro
Discussion
Abf1p as a global regulator of macromolecular biosynthetic events
Acknowledgements
References
Biochemical and genetic characterization of the dominant positive element driving transcription ofthe yeast TBP-encoding gene, SPT15
ABSTRACT
INTRODUCTION
The TATA-box binding protein, TBP, is required for transcription by all three nuclear DNA dependent RNA polymerases (-5) and is the only such shared transcription factor subunit. Moreover, a large body of published data suggests that the levels of TBP are limiting in vivo (6-8). For these reasons it is important to understand the regulatory mechanisms which control the expression of the TBP encoding gene. We previously found that transcription of the TBP encoding gene is subject to both positive and negative control and here we examine in detail one of the cis-elements, which we termed PED (for positive element distal) (9). Two features of the PED cis-element drove us to examine it in more detail. First, our deletion mutagenesis studies suggested that PED plays a dominant role in the regulation of TBP gene transcription. Second, when the PED element was placed in either one or multiple copies upstream of a heterologous promoter, it failed to drive high level transcription in vivo. Taken together, these results suggested that PED plays an important role in transcription of the TBP-encoding gene, perhaps through a non-classical mechanism.
To date, the 5[prime]-flanking sequences of four non-yeast TBP-encoding genes have been cloned and sequenced (10-16) and the apparent cis-regulatory elements of two of these promoters have been characterized in some detail (11,17). Analyses of the proteins binding to Acanthamoeba castellani TBP gene cis-elements have resulted in the identification and subsequent cloning of a trans-acting factor, termed TBPF (18). BLAST searches of the yeast genome with either the TBPF amino acid sequence or the DNA site bound by TBPF failed to identify any significant matches. In the case of the human TBP-encoding gene, a sequence which matches the consensus site for an Ets-family transcription factor was recently shown to be an important positive element for human TBP gene expression (17). Again, computer based analyses of yeast TBP-gene 5[prime]-flanking sequences failed to identify a comparable sequence to that found in the human gene. The A.castellani TBPF factor does not resemble an Ets family protein by similar sequence analysis. These results suggest that neither TBPF nor Ets proteins are evolutionarily conserved factors utilized to modulate TBP gene transcription in all eukaryotes. Clearly additional work is needed in order to uncover such conserved features of regulation of the TBP-encoding genes.
In the present report, we describe a detailed characterization of the PED element, which resides between the TBP gene 5[prime]-flanking sequences -147 and -128. Furthermore, we have identified, purified and sequenced the factor which interacts with the PED sequence element. This amino acid sequence information indicates that the PED binding factor (PEDBF) is the previously characterized transcription and replication factor, Abf1p.
MATERIALS AND METHODS
Gel shift analyses
Gel shift assays were performed in a total volume of 20 µl using a 32P-labeled DNA probe generated by annealing complementary 26 bp oligos comprising the PED element. The sequences ofthese oligos are: TCGAGCCGTAAATAGTTATCTTCCAC andTCGAGTGGAAGATAACTATTTACGGC; bolded sequences correspond to XhoI sites. Annealed oligos were labeled as previously described (19,20). Typical probe specific activity was [ge]5000 c.p.m./fmol DNA and 20 fmol of labeled DNA (~100 000 c.p.m.) was used in each assay. Binding reactions were incubated at room temperature for 20 min and protein-DNA complexes were separated from unbound DNA as previously described (19).
In some experiments a double-stranded oligo termed PEP (TBP positive element proximal) was used as a non-specific competitor, the sequence of which is: TCGAGGGGAAAAGAAAAAAATTTTC (9). A double-stranded ABF1 consensus oligo was also used, the sequence of which is: TCGAGATCACTTATCACGAC. In the antibody gel shift experiments, DNA binding assays were conducted as detailed above except either non-immune or anti-Abf1p IgGs were added as indicated in the figure legends. IgGs were pre-incubated with extract at room temperature for 15 min prior to addition of binding buffer and probe.
Chemical interference assays
To generate fragments for chemical interference DNA binding assays, duplex oligos comprising the PED element described above were ligated into XhoI digested pBluescript II KS+ (Stratagene). Digestion of these constructs with BamHI and KpnI restriction endonucleases generated fragments which could be singly end-labeled on either strand at the BamHI site (20). Specific activities of the labeled PED probes averaged 2000 c.p.m./fmol DNA. These end-labeled probes were partially reacted with either DMS or DEPC and used in chemical interference assays as described (21,22).
Site-directed mutagenesis
Site-directed mutagenesis was performed using plasmid pTW-1076 as template as described previously (9). Oligos complementary to TBP promoter sequences from -147 to -128 were used for mutagenesis (Fig.
[beta]-galactosidase and genomic footprinting assays
[beta]-galactosidase assays were performed exactly as described previously (9). DMS genomic footprinting was performed as described (9).
Purification of PED binding activity
The protease deficient yeast strain BJ5457 (23) (MATa ura3-52 trp1 lys2-801 his3[Delta]200 pep4::HIS3 prb1[Delta]1.6R can1 Gal+) was used for PEDBF purification (details available upon request). Whole cell extract (WCE) was prepared as described previously (24). WCE [1.3 × 108 U of ABF1 DNA binding/SA 14.35 U/µg protein (1 U of binding activity is the amount of protein required to shift 1 fmol of labeled probe in the EMSA assay)] was subjected to standard heparin-Sepharose chromatography (recovered 3 × 107 U; SA 17.3 U/µg) and DEAE Sepharose chromatography (recovered2.6 × 107 U; SA 128 U/µg) prior to two cycles of chromatography on a PED-DNA affinity column (second pass recovered 1.4 × 106 U; SA 23 000 U/µg protein). The PED-DNA affinity column was generated as described (25) using an oligo containing PED sequences fused to oligo dA, of sequence TGAAGCCGTAAATAGTTATCTTCCAA(dA)18.
Immunoblot analysis
Proteins/extracts were fractionated via SDS-PAGE using a 6% polyacrylamide gel, transferred to PVDF membranes (Millipore) and subsequently blocked and incubated with either anti-Abf1p or preimmune antibodies as described by Francesconi and Eisenberg (26).
UV crosslinking
Binding/crosslinking reactions were performed in a final volume of 50 µl. After incubation at room temperature, the reaction mixtures were then transferred to a 96-well microtiter plate. Crosslinking was induced by placing a UV lamp (Fisher model UVGL-25) directly over the dish held on ice. After 1 h of irradiation, 50 µl of SDS sample buffer was added to each well and the reactions were denatured by heating to 75°C. Crosslinked proteins were separated from free DNA by electrophoresis on a 7.5% polyacrylamide SDS-PAGE (0.15 cm×11 cm × 50 cm).
RESULTS
An abundant, sequence specific DNA binding factor present in yeast WCE can bind to the PED element in vitro
As we described previously, the PED element is a positive-acting element important for transcription activity which is occupied in vivo as evidenced by genomic footprinting (9). We conducted gel shift or EMSA assays with yeast WCE protein and a double-stranded oligonucleotide fragment which contains the PED element to test whether yeast proteins specifically bound to this DNA in vitro. As shown in Figure
| Figure 1. (A) Detection of an abundant factor in yeast WCE capable of specifically binding to 32P-labeled PED sequences. Autoradiograph of a gel shift analysis of PEDBF. An aliquot of 50 ng of yeast WCE protein was used. Free 32P-PED probe and the PEDBF + 32P-PED DNA complex separated by native gel electrophoresis are labeled at the left with arrows. The presence of competitor DNAs is as listed at the top of the gel; lane 1, probe alone; lane 2, no competitor + WCE; lanes 3, 4 and 5, +WCE, display binding reactions which contained a 5-, 25- or 100-fold molar excess of a non-specific competitor DNA, NS (PEP element sequences, see Materials and Methods); lanes 6, 7 and 8 +WCE, display binding reactions which contained a 5-, 25- or 100-fold molar excess of PED DNA (S). (B) Chemical interference assays define PED residues recognized by PEDBF. Autoradiograph of a sequencing gel run to separate the cleaved products of binding reactions containing yeast WCE proteins and 32P-end-labeled (UPPER or LOWER strand) PED sequences that had been reacted with the indicated chemical (either DMS or DEPC). Bound (B) and free (F) DNAs are indicated. Guanine (G) and adenine (A) residues which interfere with PEDBF binding are indicated with asterisks. The results of this analysis are summarized underneath the autoradiogram. |
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| Figure 2. (A) Mutant alleles that were generated to functionally dissect the PED element. The sequence of PED WT (-149 to -126) and mutated forms of PED used in this study are shown. The designation given to these PED alleles is listed on the right (ie. WT, #1, #2, etc.). Underlined sequences denote the bases changed in each construct while bracketed gaps in the sequence represent sequences deleted. Below the sequences are indicated the three regions of PED. (B) In vivo analysis of wild-type and mutant PED function. (Left) lacZ reporter gene expression. [beta]-galactosidase expression levels of spt15::lacZ constructs bearing the various PED mutations as depicted in Figure 2A. Units of [beta]-galactosidase activity are given as [Delta]A420 nm/[(A600)(ml cells used)(min)]*1000. n = 15 (independent determinations). The standard error is shown by error bars. (Right) Mutations in PED regions #1 or #2 are unable to drive sufficient TBP gene transcription to support cell growth. Photographs of yeast plates after inoculation with yeast strains containing wild-type and mutant alleles of the TBP encoding gene. In the center column, marked CONSTRUCT, is listed the TBP-PED allele used to drive TBP gene transcription on the test plasmid (A). The control column (-FOA) depicts the growth of each strain on selective media prior to selection on 5-FOA. The + 5-FOA column depicts the growth of each strain after 7 days at 30°C on selective media supplemented with 5-FOA. These cells have all lost the URA3-marked WT TBP covering plasmid. |
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Chemical interference assays identify the close contacts between PEDBF and the nucleotides comprising the PED element of the TBP-encoding gene
We next employed chemical interference assays to characterize the essential DNA bases required for PEDBF binding to PED. To map these contacts we used dimethyl sulfate [DMS; G reactivity (major groove) > A reactivity (minor groove)] and diethyl pyrocarbonate (DEPC; A reactivity > G reactivity).
In lanes 1-4 of Figure
A summary of the chemical interference results is shown at the bottom of Figure
Mutation of PED sequences involved in making close contacts with PEDBF results in decreased TBP gene 5[prime]-flanking sequence-driven reporter gene activity in vivo
To directly corroborate the results of the interference assays with functional genetic studies we introduced mutations into each of the three PED regions and tested the ability of these mutant alleles to drive transcription in vivo. Shown in Figure 2A are the mutations we constructed. All of the PED mutations shown, #1 through TVN PED1-3 as listed top to bottom (Fig.
In order to rigorously assess the effect of our family of mutations on TBP gene activity, two different constructs were generated for each mutant. In the first, a fusion of the mutated TBP genes was made to the bacterial reporter gene lacZ. The second type of construct utilized the TBP ORF as the reporter gene in place of lacZ. This second class of constructs was used in the background of a strain containing a complete gene deletion of the TBP-encoding ORF (spt15[Delta]1::TRP1; 27) in order to test whether these mutations in the episomal gene would decrease TBP protein levels to the point where viability of the strain was compromised.
Shown in Figure
To further address the role PED plays in TBP expression, these same wild-type and mutant PED alleles were fused to the TBP ORF carried on the HIS3-marked single copy plasmid pRS413 (27,28). These TBP expression plasmids were tested for their ability to drive sufficient TBP gene expression to support growth using the plasmid shuffle technique (29). Figure
Based upon these two complementary reporter expression assays, we conclude that the integrity of both regions #1 and #2 of the PED element is absolutely critical for TBP gene expression in vivo while region #3 of the PED element also contributes to expression significantly. Further, mutation of the PEP element, the other TBP gene positive cis element (9), is much less deleterious to TBP gene expression than is mutation of the PED element.
In vivo and in vitro DNA binding assays indicate that mutant PED alleles drive TBP gene transcription less efficiently because PEDBF binds these sequences more weakly
Mutant alleles of the TBP-encoding genes bearing mutations in PED sequences could result in lower levels of TBP gene expression because they interact less efficiently with PEDBF. We examined binding to PED using two sensitive and complementary DNA binding assays. First, we measured the occupancy of the PED element in vivo via genomic footprinting using our collection of WT and mutant PEDs, and secondly we used gel shift DNA binding assays to compare the competitive strengths of WT and mutant forms of PED for binding of PEDBF to a 32P-labeled WT PED probe.
| Figure 3. Biochemical analysis of PED mutants. (A) Genomic footprinting. Autoradiograph of genomic footprinting reactions of the TBP-encoding gene using DMS as a cleavage reagent. Purified plasmids containing the cognate mutations were also treated with DMS to serve as DMS reactivity controls (denoted as N) for the DMS reactivity of the genomic DMS reacted in vivo (G). Reactive G residues of the PED element are marked as follows by arrows: filled black arrows denote G residue -145, open arrows denote G residue -138, and grey arrows denote G residues created by mutation of PED to TVN PED. Other relevant regions of the footprint are labeled (i.e. PEP and TATA) and bracketed. Lanes 1 and 2, reactions for wild-type TBP gene; lanes 3 and 4, reactions for transversion mutation in regions #1 through #3 of PED (TVN PED); lanes 5 and 6, reactions for transversion mutation of PEP (TBP gene sequences -108 to -88) (TVN PEP); lanes 7 and 8, reactions for a mutation in region #1 of PED; lanes 9 and 10, reactions for a mutation in region #2 of PED; lanes 11 and 12, reactions for a mutation in region #3 of PED. The relevant PED and PEP sequences analyzed in this genomic footprinting experiment are shown below the autoradiogram. The triangles above the sequences represent the highly DMS-reactive residues scored by footprinting. Underlined sequences indicate the nucleotides mutated (see also Fig. 2A). (B) Quantitation of cis-element occupancy in WT and mutant TBP genes. The autoradiogram shown in (A) along with three additional replicates of this experiment were scanned using an E-C Apparatus model EC910 densitometer. Areas under the curves were integrated using Hoeffer GS370 v3.0 software and percent PED cis-element occupancy (i.e. % protection) was calculated as follows. The formula used was: [1-(([Gen. G-138 or G-145]/[Gen. G-165])/([Nak. G-138 or G-145]/[Nak. G-165]))]*100. (C) Relative competitive DNA binding strengths of PED wild-type and mutant sequences. Autoradiograph of a gel shift competition DNA binding assay which shows only that portion of the gel containing the PEDBF . DNA complex. Wild-type PED fragment was used as labeled probe and 100 ng of WCE was used for the binding reactions that were gel-fractionated in lanes 2-17. Lane 1 contained probe alone while various `cold' competitor DNAs (see Figs 3 and 4) were used as follows: lane 2, no competitor; lanes 3, 4 and 5, 5-, 25- and 100-fold molar excesses of wild-type PED; lane 6, 100-fold excess of PED mutant [Delta]1+[Delta]2; lane 7, 100-fold excess of PED mutant [Delta]3; lane 8, 100-fold excess of PED mutant TVN PED 1-3; lane 9, 100-fold excess of PED mutant #1; lane 10, 100-fold molar excess of PED mutant #2; lanes 11, 12 and 13, 5-, 25- and 100-fold molar excess of PED mutant #3; lane 14, 100-fold molar excess PED mutant #1+#2; lane 15, 100-fold molar excess PED mutant #1+#3; lane 16, 100-fold molar excess PED mutant #2+#3; lane 17, 100-fold molar excess PED mutant #1+#2+#3. |
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Genomic footprinting
The results of our genomic footprinting experiment are presented in Figure
Further support that PED plays the dominant positive role in TBP gene transcription comes from an analysis of the constructs carrying either a transversion of the PEP element (TVN PEP) or a mutation in PED region #3 (MUT #3). Both of these mutant constructs retained significant promoter activity (~25 and ~50% of WT, respectively; Fig.
DNA binding-competition assays
We performed EMSA assays using yeast WCE protein, wild-type PED sequence as the labeled probe, and various mutant forms of the PED element as competitors to test their relative affinities for PEDBF. The results of these assays are presented in Figure
Purification and characterization of PEDBF
The overall scheme which we developed for the purification of PEDBF is outlined in Figure
| Figure 4. Purification and immunological characterization of PEDBF. (A) Purification of PEDBF. Shown at the top of the figure is a flowchart of the chromatographic steps used to purify PEDBF. In the middle portion of the figure is an autoradiograph of a gel shift assay of 1 µl aliquots of each fraction eluted from the second pass over the PED DNA affinity column (see above). Lane 1, 32P-PED Probe alone (-); lane 2, assay of the pooled input fraction applied to the second pass DNA affinity column (I); lane 3, assay of the breakthrough fraction (B); lane 4, assay of the 100 mM NaCl wash step (W); lanes 5-29, assay of the column fractions obtained following NaCl gradient elution of the second DNA affinity column. The approximate magnitude of the NaCl gradient is shown by the inclined plane (100-1000 mM NaCl) above lanes 5-29. Free PED probe and the PED.PEDBF complexes are indicated by the labeling and arrows. At the bottom of the figure is a photograph of a silver stained analytical SDS-PAGE analysis of selected fractions assayed in the gel shift above. Aliquots of 200 µl of the input (I), lane 1; breakthrough (B), lane 2; and second pass affinity pooled peak fractions (P), lane 3 were precipitated with TCA and fractionated on a denaturing 6.5% SDS polyacrylamide gel. The mobility of protein standards (Sigma high molecular weight standard mixture) run in a parallel lane of this gel are indicated at the left side of the gel. The arrow to the right of the gel indicates the 120 kDa PEDBF polypeptide. (B) Immunoblotting shows that PEDBF is Abf1p. Increasing amounts of PED affinity purified PEDBF [(Affinity Pure Abf1p) lanes 2-4, ~10, 25 and 50 ng and WCE protein (WCE) lanes 5-7, ~32.5, 65 and 130 µg] were fractionated by SDS-PAGE (6% polyacrylamide, the dye front was purposely run off the gel) along with 50 ng of pure Abf1p (control), lane 1. Fractionated proteins were blotted and duplicate sets of these samples were probed with either anti-Abf1p IgG or non-immune IgG as indicated. The mobility of prestained molecular weight standards (GIBCO BENCHMARK Protein Ladders, prestained standards) is indicated at the left of each blot. (C) EMSA IgG-induced inhibition assays confirm that PEDBF is Abf1p. Standard EMSA assays were performed except 2 µg of IgG were pre-incubated with the WCE added to eight identical 32P-PED DNA binding assays. These assays contained a mixture of non-immune and anti-Abf1p IgG (indicated by the + in the insert). The reaction in lane 2 contained 2 µg non-immune IgG while the reaction fractionated in lane 9 contained 2 µg of anti-Abf1 IgG. The lanes between, lanes 3-8, contained the amounts of anti-Abf1p IgG shown on the ordinate of the plot. The reaction fractionated in lane 1 was a control reaction in which no IgG was added in the binding reaction. Following EMSA, the gel was exposed to X-ray film (insert) and the amount of Abf1p-DNA complex quantitated using a BioRad PhosphorImager and software and is plotted as a function of anti-Abf1p IgG present in the assay. |
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Shown in the middle portion of Figure
The entire preparation of second pass DNA-affinity purified PEDBF was subjected to preparative SDS-PAGE, transferred to a PVDF membrane, stained with Ponceau S, the 120 kDa protein excised, proteolyzed and the resulting peptides were fractionated by HPLC (Harvard University Microchemistry Facility). Two of the peptides derived from this digest were sequenced by mass spectrometry and Blast searches of the GenBank database indicated that both were derived from the same previously cloned and sequenced yeast protein. This protein, Abf1p, is the protein product of ABF1 (ARS binding factor 1; GenBank accession no Z228111x1). The two peptides LDFVTDDLEYHLANTHPDDTNDK and EVENLHQNNDDDVDDVMVDVDVESQYNK comprise Abf1p amino acids 134-156 and 660-687, respectively.
Immunological analyses indicate that PEDBF is Abf1p
The fact that PEDBF was Abf1p was confirmed by immunological experiments. The first was to show that PED DNA-affinity chromatography purified protein specifically reacted with anti-Abf1p antibodies. The second experiment was an anti-Abf1p IgG-induced inhibition EMSA DNA binding assay. The results of these two experiments are presented in Figure
Biochemical assays show that Abf1p binds indistinguishably to PED and ABF1 sites in vitro
We were surprised by the discovery that PEDBF was Abf1p since our own previous computer analyses had failed to indicate that the PED element was similar to the Abf1p binding site. With the exception of two examples of variant cis-elements, both of which bind Abf1p very poorly in vitro (RPL2A and RPL45; 33,34), all previous descriptions of Abf1p binding sites have matched the consensus sequence shown at the top of Figure
| Figure 5. Abf1p binds equally well to a consensus ABF1 site and the non-consensus PED-variant ABF1 site. (A) Gel shift competition analyses. An alignment of the TBP gene PED element to the consensus ABF1 sequence is shown at the top of the figure. The PED element (residues -146 to -132) was aligned with the 13 nt long consensus ABF1 site; N = and nucleotide, R = G or A, and B = any nucleotide except C. Underlined sequences denote the two sets of invariant residues of the consensus ABF1 site (C3 and A11, C12, G13). Asterisks indicate PED residues which match the ABF1 consensus site. Using 32P-labeled PED as a probe and yeast WCE as a source for PEDBF, the relative affinities of PEDBF for PED and ABF1 sites was determined using a competition DNA binding assay. Equivalent increasing amounts of unlabeled PED or ABF1 DNA (0-100-fold molar excesses) were added to the binding reactions. Bound and free 32P-PED probe was separated via non-denaturing gel electrophoresis, and these two populations of DNA were quantitated using a phosphorimager. The results of these assays are depicted (graph and insert of gel). Use of PED competitor is depicted with the filled triangles while the ABF1 competition curve is indicated with the open circles. (B) UV crosslinking of PEDBF to PED and ABF1 sequences. Autoradiograph of results of gel shift and SDS-PAGE gel. WCE (1 µg) or 0.1 ng of affinity-purified PEDBF were used in each assay. 25- and/or 100-fold molar excesses of `cold' competitors were used as depicted at the top of lanes. Prior to crosslinking, 1 µl of each sample was loaded onto a gel shift gel (shown; labeled Gel Shift) while the remaining sample was crosslinked. Crosslinked reactions were heated with SDS sample buffer as described in Materials and Methods and were fractionated on a 7.5% polyacrylamide SDS-PAGE. Uncrosslinked (labeled Gel Shift) and crosslinked (labeled SDS-PAGE) protein-DNA complexes are indicated by the arrows. The apparent lack of competition of crosslinking seen in lane 19 is an anomaly; numerous additional though not exact replicates of this experiment showed the expected efficient competition of crosslinking (data not shown). (C) Off-rate measurements of Abf1p bound to ABF1 and PED sites. Autoradiographs and graphs of off-rate measurements. Abf1p-DNA complexes were formed in 10×-scaled-up binding reactions by incubation at 37°C for 20 min. At time zero a 100-fold excess of the competitor DNA listed (+PED or +ABF) was added to the reactions and at the indicated times 20 µl aliquots of the 10× reactions were removed and immediately applied to a standard EMSA gel that already had a voltage potential of 100 V applied. |
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In order to directly assess the inter-relationships of PED and ABF1 sites, we performed a series of experiments to examine the relative affinity of Abf1p for PED and a consensus ABF1 site. We utilized three types of experiments for this purpose, a DNA binding competition assay, a UV crosslinking DNA competition experiment and measurements of the off-rates of dissociation of Abf1p from both ABF1 and the TBP gene-PED site.
The results of the gel shift competition DNA-binding experiment which utilized 32P-labeled PED as a probe and WCE protein as the source of Abf1p are presented in Figure
Results of our UV-crosslinking experiment using both 32P-labeled PED and 32P-labeled ABF1 sequences as probes are presented in Figure
In Figure
Table 1. Saccharomyces cerevisiae genes involved in transcription which contain Abf1p binding sites within 500 bp upstream of their ATGs
DISCUSSION
In this study we have conducted a detailed analysis of a positive acting cis-element, termed PED, which we had previously crudely characterized. Through a series of genetic and biochemical experiments we have determined that appropriate PED cis/trans function is essential for high level TBP gene transcription. Indeed, PED integrity is crucial for driving sufficient TBP gene transcription to support cell growth. Using several types of DNA binding analyses coupled with various protein purification and immunological techniques, we have identified, purified, characterized and sequenced the trans-acting factor which binds to the PED element and determined that this protein factor is Abf1p.
Abf1p as a global regulator of macromolecular biosynthetic events
Our hope when we initiated our dissection of the cis- and trans-acting factors which control TBP gene expression was to identify a transcription factor(s) that was responsible for the global control of yeast macromolecular biosynthesis. We reasoned that given the central role of TBP in transcription that the regulatory network(s) which converged on the TBP-encoding gene might also participate directly in controlling expression of other proteins involved in the processes of transcription, replication and translation. Abf1p appears to fit this criterion since ABF1 consensus sites have been found not only in replication origins, hence the name ARS binding factor, but ABF1 sites have also been described upstream of genes encoding subunits of the translational machinery, subunits of all three nuclear DNA-dependent RNA polymerases and many other genes.
We scanned the yeast genome to identify all genes which contain a consensus Abf1p binding site within the 1000 nucleotides of DNA upstream of the initiator ATG codon of the relevant ORF. In Table 1 we present a list of a subset of these genes, those which encode proteins involved in transcription that contain consensus ABF1 sites. These genes include those encoding DNA-dependent RNA polymerase subunits, TAFs, and general factors involved in transcription by all three nuclear RNA polymerases. Several of these genes have previously been reported to contain Abf1p binding sites (33,35), corroborating our search parameters. Three genes involved in transcription were found to contain the PED-variant Abf1p site. These genes are RPB11, SRB4 and SRB7. The fact that ABF1 consensus and PED-variant ABF1 sites frequently occur in the regulatory regions of these genes suggests that Abf1p could very well play a central and global role in regulating transcription by acting as a master switch to modulate the levels of these many mRNAs. Based upon similar reasoning, since genes encoding replication and translation proteins also contain ABF1 sites, other macromolecular biosynthetic reactions such as DNA and protein synthesis could similarly be regulated. That Abf1p is also apparently involved in modulating rDNA transcription by RNA polymerase I (38) provides further support for this hypothesis.
Our previous computer-based sequence analyses were unable to uncover any large regions of sequence similarity between the 5[prime]-flanking region of the gene encoding Saccharomyces cerevisiae TBP and the 5[prime]-flanking regions of genes encoding TBP in other organisms. However, armed with the knowledge that Abf1p binds to the PED element in the gene encoding TBP in S.cerevisiae, we directly searched for Abf1p binding sites in the 5[prime]-flanking regions of genes encoding TBP in other organisms. Interestingly we found ABF1 sites in the promoters of the TBP-encoding genes of Schizosaccharomyces pombe (10) and Drosophila melanogaster (39). It is not yet clear if these organisms contain an activity which binds specifically to an ABF1 site. However, this finding does raise the intriguing possibility that not only is Abf1p responsible for modulating the expression of the multitude of genes in S.cerevisiae which encode components of the general transcription machinery, but that this regulatory network could be conserved among other disparate eukaryotic organisms. These considerations suggest that the Abf1p regulatory system described herein could be both ancient and important to cellular function in many different eukaryotic organisms. Additional experimentation will be required to address this idea.
ACKNOWLEDGEMENTS
We would like to thank Dr Shlomo Eisenberg for providing pure Abf1p and antibodies, our colleagues in the laboratory for their constructive criticisms, support and advice throughout the course of this work, and Drs S. Johnston, J. Segall and M. Groudine for their critical comments on our manuscript. This work was supported by a grant from the NIH (GM52461).
REFERENCES
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