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Multiple Functions of the Nonconserved N-Terminal Domain of Yeast TATA-Binding Protein


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Copyright2001 by the Genetics Society of America

Multiple Functions of the Nonconserved N-Terminal Domain

of Yeast TATA-Binding Protein

Mark Lee


and Kevin Struhl

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115 Manuscript received December 15, 2000

Accepted for publication January 26, 2001


The binding protein (TBP) is composed of a highly conserved core domain sufficient for TATA-element binding and preinitiation complex formation as well as a highly divergent N-terminal region that is dispensable for yeast cell viability.In vitro, removal of the N-terminal region domain enhances TBP-TATA association and TBP dimerization. Here, we examine the effects of truncation of the N-terminal region in the context of yeast TBP mutants with specific defects in DNA binding and in interactions with various proteins. For a subset of mutations that disrupt DNA binding and the response to transcriptional activators, removal of the N-terminal domain rescues their transcriptional defects. By contrast, deletion of the N-terminal region is lethal in combination with mutations on a limited surface of TBP. Although this surface is important for interactions with TFIIA and Brf1, TBP interactions with these two factors do not appear to be responsible for this dependence on the N-terminal region. Our results suggest that the N-terminal region of TBP has at least two distinct functionsin vivo. It inhibits the interaction of TBP with TATA elements, and it acts positively in combination with a specific region of the TBP core domain that presumably interacts with another protein(s).


HE TATA-binding protein (TBP) plays a central relative to full-length TBP (Horikoshiet al.1990; Lieb-ermanet al.1991), primarily by increasing the rate of role in eukaryotic transcription, being required for

TBP-TATA association (Kuddus and Schmidt 1993). accurate transcriptional initiation by all three nuclear

As a consequence, DNA binding by TBP mutants defec-RNA polymerases (Hernandez 1993; Struhl 1994;

tive for the TBP-TATA interaction can be restored by Burley andRoeder 1996). TBPs from a wide variety

removal of the N-terminal domain (Lee et al. 1992). of eukaryotes and archea have a highly conserved

180-Second, the yeast TBP core domain readily forms tran-residue C-terminal core domain (80% identical between

scriptionally inert dimers and higher order oligomers yeast and human) that is sufficient for TATA-element

in vitro(Katoet al.1994;Colemanet al.1995). Although binding and preinitiation complex formation. TBPs also

the physiological relevance of TBP dimerization is con-contain an N-terminal region that is very divergent

troversial (Jackson-Fisher et al. 1999; Geisberg and across species with respect to both length and sequence

Struhl 2000), the N-terminal domain inhibits oligo-and whose function is poorly understood. Human TBP

merization of full-length TBP, potentially enhancing the does not support yeast cell growth, but species-specific

probability that TBP is monomeric under physiologic difference maps to the C-terminal core domain, not the

conditions (Campbellet al.2000). Third, a peptide or N-terminal region (Cormacket al.1991;GillandTjian

a monoclonal antibody corresponding to a portion of 1991). Indeed, a single amino acid change within the

the N-terminal region selectively blocks TATA-depen-core domain enables human TBP to substitute for all

dent transcription by RNA polymerases II and III while of the essential activities of yeast TBPin vivo(Cormack

sparing RNA polymerase I and TATA-less promoter et al.1994).

transcription (Lescureet al. 1994). Fourth, yeast and The TBP core domain and full-length TBP behave

human NC2 are most effective in repressing transcrip-similarly in many biochemical assays, but there are

sev-tion in reacsev-tions reconstituted with TBP from the same eral differences that provide insight into the function of

species, and maximal repression requires the N-terminal the N-terminal domain. First, deletion of the N-terminal

region (Goppelt and Meisterernst 1996). Fifth, re-region results in enhanced binding and bending of DNA

moval of the N-terminal region of yeast TBP increases interactions with human TBP-associated factors (TAFs) and the formation of a hybrid TFIID complex (Zhou Corresponding author:Kevin Struhl, Department of Biological Chem- andBerk1995). Sixth, the N-terminal region of human istry and Molecular Pharmacology, Harvard Medical School, Boston,

TBP mediates cooperative binding with the small nu-MA 02115. E-mail: kevin@hms.harvard.edu

clear RNA activating protein (SNAP) complex to the

1Present address:Department of Medicine, Rm. S-101, Stanford

Uni-versity Medical Center, Stanford, CA 94305. U6 promoter and enhances U6 transcription (Mittal


and Hernandez 1997). Taken together, these results suggest a regulatory role for the N-terminal domain in governing the interactions of TBP with the TATA element, with other transcription factors, and with TBP itself. However, the physiological relevance of these bio-chemical properties of the TBP N-terminal region re-mains to be established.

In yeast cells, expression of the TBP core domain at physiological levels has minimal phenotypic conse-quence, indicating that the 63-residue N-terminal re-gion of TBP is dispensable for viability and the response to transcriptional activators (Cormacket al. 1991;Reddy andHahn1991). However, overexpression of the TBP

Figure1.—N-terminal truncation can rescue the transcrip-core domain inhibits cell growth, particularly on

nonfer-tional phenotypes of a subset of activation-deficient DNA-bind-mentable carbon sources (GillandTjian1991;Zhou ing mutants of yeast TBP.-Galactosidase activity of a Gal4-et al. 1991), and this toxicity is suppressed by concurrent dependentLacZreporter in wild-type and mutant TBP strains grown with galactose as the sole carbon source (inducing overexpression of Std1(Msn3) (Ganster et al. 1993).

conditions) is shown. Standard errors are given as error bars. Std1 directly associates with TBP, and deletion of the

Solid bars, full-length TBP derivatives; stippled bars, N-termi-N-terminal region qualitatively alters this interaction

nally truncated derivatives (⌬4-63). (Tillmanet al. 1995). Apart from these studies,

how-ever, relatively little is known about the function of the

TBP N-terminal regionin vivo. RESULTS

To examine the physiological role of the N-terminal

Deletion of the N-terminal region rescues the activa-region of yeast TBP, we deleted this activa-region in the

con-tion-deficient phenotype of a subset of DNA-binding text of a large number of yeast TBP mutants. Our results

mutants:Certain TBP mutants deficient in the response suggest that the N-terminal region of TBP has at least

to transcriptional activators contain mutations on the two distinct functionsin vivo. It inhibits the interaction

DNA-binding surface that dramatically reduce TATA-of TBP with TATA elements, and it functions in concert

element bindingin vitro(Kimet al. 1994;Arndtet al. with a specific surface of TBP that presumably interacts

1995; Leeand Struhl 1995). As removal of the N-ter-with another transcriptional regulatory protein.

minal region can restore TBP-TATA associationin vitro for some TBP mutants with DNA-binding defects (Lee et al. 1992), we examined the genetic properties of N-ter-MATERIALS AND METHODS

minally deleted versions of three TBP mutants deficient DNA molecules:TBP mutants used in this study have been for DNA binding and transcriptional activation (Lee described previously (CormackandStruhl 1993;Leeand

andStruhl1995). All three N-terminally deleted

deriv-Struhl1995, 1997). The N-terminally deleted derivatives in

atives support yeast cell growth at levels comparable to Table 1 derive from pBC83, aTRP1-marked centromeric

plas-mid with the 2.4-kb EcoRI-BamHI fragment containing the their full-length counterparts (Table 1). As previously yeastTBPgene with a deletion of residues 4–63 (Cormacket reported (Leeand Struhl1995), the F148L, N159L, al. 1991). The N-terminally deleted derivatives in Figure 2

and V161A derivatives are compromised for Gal4-depen-derive from pML3095, a derivative of pBC83 in which a FLAG

dent activation when compared to wild-type TBP (39, epitope was engineered at the N terminus of the TBP core

42, and 8% of wild-type activity, respectively; Figure 1). domain by subcloning of annealed oligonucleotides. Serial

deletions of the N-terminal region were generated by PCR Removal of the N-terminal region from wild-type TBP using the wild-typeTBPgene as template. results in a 40% decrease in Gal4-dependent activation,

Phenotypic analyses:TBP derivatives were assayed for their

in accord with previous results (Cormack et al. 1991; ability to support cell growth by spotting 104and 105cells on

ReddyandHahn1991). By contrast, N-terminal dele-glucose medium supplemented with casamino acids and

5-flu-oroorotic acid, using the plasmid shuffle assay and strain BY⌬2 tion confers increased transcriptional activation by the (Cormacket al. 1991); growth was monitored after 2–3 days N159L, V161A, and perhaps the F148L derivatives. incubation at 30⬚. S1 nuclease protection assays for measuring Deletion of the N-terminal region of TBP does not RNA levels and␤-galactosidase assays for determining

Gal4-affectHIS3TATA-element utilization:The results above dependent activation were performed as described elsewhere

and previous biochemical experiments indicate that the (Cormack and Struhl 1992; Lee and Struhl1995; Iyer

andStruhl1996). Intracellular levels of N-terminally deleted N-terminal region can act as an inhibitor of TBP func-TBPs were determined by Western blotting using monoclonal tion. For this reason, we examined whether the N-termi-antibody mAb58C9 (Santa Cruz Biotechnologies) against the nal region of TBP affects TATA-element utilization at FLAG epitope. To avoid the confounding effects of

homeo-theHIS3promoter in a manner similar to that of other static mechanisms on TBP levels, mutant TBP levels were

mea-general inhibitors of TBP function such as Mot1 (Col-sured in a strain containing hemagglutinin-tagged TBP (Lee



Viability of defined TBP mutants with and without the N-terminal domain

Viability as

TBP derivative Biochemical defect Full length TBP ⌬N terminus

Wild type (TBP⫹) None ⫹⫹⫹ ⫹⫹⫹

L114K DNA binding ⫹ ⫹

S118L DNA binding ⫹⫹⫹ ⫹⫹

N159L DNA binding ⫹⫹ ⫹⫹

V161A DNA binding ⫹⫹⫹ ⫹⫹⫹

F148L DNA binding ⫹⫹⫹ ⫹⫹⫹

D130A TFIIA interaction ⫹⫹⫹ ⫹⫹

R137A TFIIA interaction ⫹⫹⫹ ⫺

D130A, R137A TFIIA interaction ⫹⫹ ⫺

Y139A TFIIA interaction ⫹⫹⫹ ⫹⫹⫹

E186A TFIIB interaction ⫺ ⫺

E188A TFIIB interaction ⫹⫹⫹ ⫹⫹⫹

L189K TFIIB interaction ⫺ ⫺

L134A, E222A TFIIF, Pol II interaction ⫹⫹⫹ ⫹⫹

E108A, L134A, L189A, E222A TFIIB, TFIIF, Pol II interaction ⫹⫹ ⫹⫹

R137W TDS4 interaction ⫹⫹ ⫺

A140R TDS4 interaction ⫹⫹ ⫺

F152E TDS4 interaction ⫹⫹⫹ ⫺

F155S TDS4 interaction ⫹⫹⫹ ⫺

I160H TDS4 interaction ⫹ ⫺

G162Y TDS4 interaction ⫹⫹⫹ ⫹

R220A TDS4 interaction ⫹⫹ ⫹⫹

Y224K TDS4 interaction ⫹ ⫹

Y231V TDS4 interaction ⫹⫹ ⫹⫹

R238D TDS4 interaction ⫹⫹ ⫺

A135T Decreased Pol I, Pol II ⫹⫹ ⫺

K138W TFIIA? ⫹⫹ ⫺

(Moqtaderiet al. 1996). TheHIS3promoter contains tein-protein interactions with other components of the transcription apparatus (Lescureet al. 1994;Zhouand a noncanonical TATA-like element (TC) that is

responsi-ble for initiation from the⫹1 site and a consensus TATA Berk1995; Goppelt and Meisterernst 1996). Dele-tion of the N-terminal region has minimal effects on element (TR) that is responsible for initiation from the

⫹13 site (IyerandStruhl1995). Loss of Mot1, NC2, or growth and on transcription by all three nuclear RNA polymerases. Thus, if the N-terminal region mediates TAF130 results in a dramatic decrease in TC-dependent

transcription from the⫹1 site, but does not affect TR- physiologically important functions, such functions

must be also performed by another region of TBP or dependent transcription from the⫹13 site. In contrast,

deletion of the N-terminal region of TBP does not affect by another protein(s).

To search for such potential redundant functions, we the pattern of transcriptional initiation, and hence

TATA-element utilization, at theHIS3promoter region constructed N-terminally deleted versions of a panel of TBP mutants with specific defects for interactions with (Figure 2). In addition, the N-terminally deleted version

of TBP has minimal effects on transcription by RNA TFIIA (Stargell andStruhl1995; Leeand Struhl 1997), TFIIB (Kimet al. 1994;LeeandStruhl1997), polymerases I and III. Thus, by the criterion of

TATA-element utilization at theHIS3promoter, the N-termi- TFIIF, RNA polymerase II (LeeandStruhl1997), and the RNA polymerase III factor Brf1 (Cormack and nal region of TBP behaves differently from other

pro-teins that can function as inhibitors of TBP function. Struhl1993). Deletion of the N-terminal region from TBP mutants deficient for interaction with DNA, TFIIB, Mutations within the core domain of TBP render the

N-terminal domain essential for viability:In addition to TFIIF, and RNA polymerase II produces only modest changes in growth (Table 1). In contrast, N-terminal its negative effect on DNA binding, the N-terminal



Viability of N-terminally truncated TBP derivatives with and without an N-terminal FLAG epitope

Viability as

TBP Full-length ⌬N FLAG-⌬N

derivative TBP terminus terminus

Wild type (TBP⫹) ⫹⫹⫹ ⫹⫹⫹ ⫹⫹⫹

A135T ⫹⫹ ⫺ ⫹

K138W ⫹⫹ ⫺ ⫹⫹

R238D ⫹⫹ ⫺ ⫹

R137A ⫹⫹⫹ ⫺ ⫺

A140R ⫹⫹ ⫺ ⫺

F152E ⫹⫹⫹ ⫺ ⫺

F155S ⫹⫹ ⫺ ⫺

I160H ⫹ ⫺ ⫺

level achieved by N-terminally deleted wild-type TBP (Figure 3).

N-terminal-dependent mutations map to a limited sur-face of TBP and define a new TBP function:The muta-tions that confer dependence on the N-terminal domain lie in close proximity within the three-dimensional struc-ture of the TBP core domain (Figure 4). Specifically, the five positions define a limited surface on the convex face of TBP that lines the inner portion of the groove formed by helix H2, helix H2⬘, and the segments preced-ing strand S1 and connectpreced-ing helix H2 and strand S1⬘. Amino acid substitutions at neighboring positions

Figure 2.—Deletion of the N terminus of TBP does not

significantly alter Pol I, II, or III transcription in vivo. S1 where the side chains project away from this putative nuclease protection assays for determination ofHIS3, DED1, interaction surface do not yield this phenotype. For rRNA, and tRNAw transcription levels in yeast strains

sup-example, N159, I160, and V161 are adjacent residues; ported by either full-length or N-terminally deleted (⌬4-63)

but, unlike I160, the side chains of N159 and V161 TBP are shown. All bands in the right lane are⬍50% higher

project, away from the convex surface of TBP, and muta-in muta-intensity than muta-in the left lane and likely represent a

differ-ence in total RNA used for each assay. tions at these positions do not confer this phenotype. Despite the overlap of this surface with the regions previously implicated in interactions with TFIIA and and Brf1-interaction surfaces results in lethality. Al- Brf1, disruption of interaction with neither of these two though removal of the N-terminal domain does not factors appears to be responsible for this N-terminal destabilize wild-type TBP (Cormacket al. 1991;Reddy dependence. First, only a subset of the mutations that and Hahn1991;Ganster et al. 1993), it might cause disrupt either TFIIA or Brf1 interaction yield this pheno-protein instability of TBP derivatives with mutations

within the core domain. To address this possibility, FLAG-tagged versions of these inviable N-terminally de-leted TBP mutants were generated to facilitate detection of their protein levels in vivo. Unexpectedly, three of these mutants (A135T, K138W, and R238D) are viable in the context of this N-terminal FLAG epitope tag (Ta-ble 2). The ability of an unrelated peptide (i.e.,FLAG) to functionally substitute for the N terminus in these three mutants suggests that these mutants, in the ab-sence of the N terminus, are unstable or misfolded. The

Figure3.—Western blot analysis of inviable N-terminally remainder of the inviable N-terminally truncated TBP

truncated TBP mutants. Whole-cell extracts from yeast strains mutants, however, are inviable in the context of the supported by wild-type TBP and coexpressing the indicated FLAG epitope, and their in vivo protein levels (with TBP derivatives were analyzed with monoclonal antibody


Figure5.—Sequential truncation of the N terminus of TBP. Viability of TBP derivatives with successive deletions of the N-terminal domain was assessed by growth on medium con-taining 5-fluoroorotic acid (FOA) in a plasmid shuffle assay. R137A and A140R respectively affect the TFIIA- and Brf1-interaction surfaces.

the absence of a particular interaction(s) normally me-diated by the core domain of TBP, at least one function

Figure4.—TBP mutants with N-terminal dependence map

of the N-terminal region becomes essential for yeast cell to a discrete surface of TBP. Two views of an X-ray

crystallo-graphic structure of yeast TBP (based on coordinates from growth. To localize the region within the N terminus NCBI Entrez MMDB file 1TBP; Chasman et al. 1993) are that performs this function, we analyzed a series of suc-shown. Structure renditions were generated by Cn3D version cessive deletions within the N-terminal region in the 3.0 (NCBI). Residues given in green represent positions tested

context of two TBP mutants that require the N-terminal in this study in which full-length and N-terminally truncated

domain: R137A (TFIIA-interaction mutant) and A140R derivatives exhibited identical phenotypes. Residues given in

red indicate positions at which mutations conferred N-termi- (Brf1-interaction mutant). Remarkably, all but the final nal dependence. Top, view of TBP molecular saddle perpen- 10 amino acids of the N-terminal domain could be re-dicular to the intramolecular dyad axis. Bottom, view of the moved without affecting the viability of these two TBP convex surface of TBP molecular saddle along the

intramolec-mutants (Figure 5). This 10-amino-acid segment likely ular dyad axis, looking into the groove formed by helix H2,

encodes a specific function, as an unrelated sequence helix H2⬘, and the segments preceding strand S1 and

connect-ing helix H2 and strand S1⬘. (FLAG) could not be functionally substituted (Table 2).

DISCUSSION type (Table 1). Second, Y139A, which is 20–30 times


the N-terminal region from these DNA-binding mutants region of TBP performs a positive function. In one model, the N-terminal domain stabilizes the interaction of TBP can partially restore their activation competency.

This result provides evidence that the inhibitory effect between TBP and the factor that interacts with the sur-face of the core domain identified by virtue of the syn-of the TBP N-terminal domain on DNA binding, long

recognizedin vitro(Horikoshiet al. 1990;Lieberman thetic lethal effects described above. The role of the N-terminal region of human TBP in mediating coopera-et al. 1991;Leeet al. 1992;KuddusandSchmidt1993),

has physiological relevance. tive binding with the SNAP complex at the U6 promoter (MittalandHernandez1997) is a precedent for such More generally, our results indicate that the

N-termi-nal region of TBP has an autoinhibitory role in vivo. a model, although the SNAP complex and its target site (PSE) do not exist in yeast cells. In a second model, the In otherwise wild-type cells, loss of this autoinhibitory

function does not significantly affect cell growth or gen- apparent positive role of the N-terminal region might actually be a negative function that is redundant with eral transcriptional functions of TBP. In part, the

mini-mal phenotype caused by loss of the TBP N-terminal a distinct negative regulatory function that is mediated by the limited surface of the TBP core domain. In this region might be due to functional redundancy with

other negative regulators of TBP function such as NC2 view, synthetic lethality results from the simultaneous elimination of multiple negative regulators of TBP func-(Gadbois et al. 1997; Kim et al. 1997, 2000; Prelich

1997;Lemaireet al. 2000;Xieet al. 2000), Mot1 (Auble tion. In accord with this model, the region immediately adjacent to yeast TBP core domain is required both for et al. 1994, 1997;Collart1996;MadisonandWinston

1997), the N terminus of TAF145 (Kokuboet al. 1998), the synthetic lethal interactions observed here (Figure 5) and for the toxicity observed upon overexpression and the NOT complex (Collart and Struhl 1994;

Collart 1996). Nevertheless, we suspect that loss of of the core domain (Zhouet al. 1991). By either model, our results and previous observations (ZhouandBerk this autoregulatory function might result in the

genera-tion of a hyperfuncgenera-tional TBP, thereby explaining why 1995; Goppelt andMeisterernst 1996;Mittal and Hernandez1997) suggest that the evolutionarily diver-overexpression of the TBP core domain strongly inhibits

cell growth even in the presence of wild-type TBP (Gill gent N-terminal region coevolved with other transcrip-tional regulators to mediate certain species-specific andTjian1991;Zhouet al. 1991).

Functional redundancy between the N terminus and functions of TBP.

a surface of the TBP core domain: We examined the We thank Martin Schmidt for providing STD constructs, Laurie effect of N-terminal deletion in the context of TBP muta- Stargell for helpful discussions at the initial stages of this work, and Lisete Fernandes and Ada Garcia for assistance in the preparation of tions representing 25 unique positions with the core

this manuscript. We also thank Susanna Chou, Sukalyan Chatterjee, domain. Mutations at only 5 of those positions yield a

and Irene Wu for their discussions and critical reading of the manu-lethal phenotype when combined with the N-terminal

script. This work was supported by a predoctoral fellowship to M.L. deletion (excluding the mutants that are rescued by the from the Howard Hughes Medical Institute and by research grants presence of an N-terminal FLAG epitope). Strikingly, to K.S. from the National Institutes of Health (GM 30186 and GM

53720). these 5 positions define a limited surface of TBP that

lines the inner portion of the groove formed by helix H2, helix H2⬘, and the segments preceding strand S1

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Figure 1.—N-terminal truncation can rescue the transcrip-tional phenotypes of a subset of activation-deficient DNA-bind-ing mutants of yeast TBP.dependentgrown with galactose as the sole carbon source (inducingconditions) is shown
Figure 2.—Deletion of the N terminus of TBP does notsignificantly alter Pol I, II, or III transcriptionnuclease protection assays for determination ofrRNA, and tRNAported by either full-length or N-terminally deleted (TBP are shown


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