scholarly journals Structure of human TFIID and mechanism of TBP loading onto promoter DNA

Science ◽  
2018 ◽  
Vol 362 (6421) ◽  
pp. eaau8872 ◽  
Author(s):  
Avinash B. Patel ◽  
Robert K. Louder ◽  
Basil J. Greber ◽  
Sebastian Grünberg ◽  
Jie Luo ◽  
...  
Keyword(s):  
Core Promoter ◽  
Mechanistic Model ◽  
Tata Box ◽  
Molecular Architecture ◽  
Eukaryotic Transcription ◽  
General Transcription Factor ◽  
Specific Loading ◽  
Promoter Dna ◽  
Tata Box Binding Protein ◽  
Initial Binding

The general transcription factor IID (TFIID) is a critical component of the eukaryotic transcription preinitiation complex (PIC) and is responsible for recognizing the core promoter DNA and initiating PIC assembly. We used cryo–electron microscopy, chemical cross-linking mass spectrometry, and biochemical reconstitution to determine the complete molecular architecture of TFIID and define the conformational landscape of TFIID in the process of TATA box–binding protein (TBP) loading onto promoter DNA. Our structural analysis revealed five structural states of TFIID in the presence of TFIIA and promoter DNA, showing that the initial binding of TFIID to the downstream promoter positions the upstream DNA and facilitates scanning of TBP for a TATA box and the subsequent engagement of the promoter. Our findings provide a mechanistic model for the specific loading of TBP by TFIID onto the promoter.

scholarly journals Expression and nuclear localization of the TATA-box-binding protein during baculovirus infection

2014 ◽  
Vol 95 (6) ◽  
pp. 1396-1407 ◽  
Author(s):  
Daniela Mainz ◽  
Ilja Quadt ◽  
Andrea K. Stranzenbach ◽  
Daniel Voss ◽  
Linda A. Guarino ◽  
...  
Keyword(s):  
Binding Protein ◽  
Degradation Pathway ◽  
Tata Box ◽  
Viral Dna ◽  
Eukaryotic Transcription ◽  
Protein Levels ◽  
Baculovirus Infection ◽  
Rnap Ii ◽  
Tata Box Binding Protein ◽  
Nuclear Domains

The TATA-box-binding protein (TBP) plays a key role in initiating eukaryotic transcription and is used by many viruses for viral transcription. We previously reported increased TBP levels during infection with the baculovirus Autographa californica multicapsid nuclear polyhedrovirus (AcMNPV). The TBP antiserum used in that study, however, cross-reacted with a baculoviral protein. Here, we reported that increased amounts of nuclear TBP were detected upon infection of Spodoptera frugiperda and TN-368 cells with a TBP-specific antiserum. TBP levels increased until 72 h post-infection (p.i.), whilst tbp transcripts decreased by 16 h p.i., which suggested a virus-induced influence on the TBP protein levels. To address a potential modification of the TBP degradation pathway during infection, we investigated the possible role of viral ubiquitin. Infection studies with AcMNPV recombinants carrying a mutated viral ubiquitin gene revealed that the TBP increase during infection was not altered. In addition, pulse–chase experiments indicated a high TBP half-life of ~60 h in uninfected cells, suggesting that a virus-induced increase of TBP stability was unlikely. This increase in TBP correlated with a redistribution to nuclear domains resembling sites of viral DNA synthesis. Furthermore, we observed colocalization of TBP with host RNA polymerase (RNAP) II, but only until 8 h p.i., whilst TBP, but not RNAPII, was present in the enlarged replication domains late during infection. Thus, we suggested that AcMNPV adapted a mechanism to accumulate the highly stable cellular TBP at sites of viral DNA replication and transcription.

Core promoter elements recognized by transcription factor IIB

2006 ◽  
Vol 34 (6) ◽  
pp. 1051-1053 ◽  
Author(s):  
W. Deng ◽  
S.G.E. Roberts
Keyword(s):  
Transcription Factor ◽  
Rna Polymerase Ii ◽  
Core Promoter ◽  
Critical Role ◽  
Tata Box ◽  
Transcription Factor Iib ◽  
General Transcription Factor ◽  
Recognition Elements ◽  
Recognition Motifs ◽  
Definition Of

The general transcription factor TFIIB (transcription factor IIB) plays a critical role in the assembly of the RNA polymerase II pre-initiation complex. TFIIB can make sequence-specific DNA contacts both upstream and downstream of the TATA box. This has led to the definition of two core promoter BREs (TFIIB-recognition elements), one upstream [BREu (upstream BRE)] and one downstream of TATA box [BREd (downstream BRE)]. TFIIB–BREu and TFIIB–BREd contacts are mediated by two independent DNA-recognition motifs within the core domain of TFIIB. Both the BREu and the BREd modulate the transcriptional potency of a promoter. However, the net effect of the BREs on promoter activity is dependent on the specific blend of elements present within a core promoter.

scholarly journals Architecture of TAF11/TAF13/TBP complex suggests novel regulatory state in General Transcription Factor TFIID function

2017 ◽  
Author(s):  
Kapil Gupta ◽  
Aleksandra A. Watson ◽  
Tiago Baptista ◽  
Elisabeth Scheer ◽  
Anna L. Chambers ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Core Promoter ◽  
Supporting Cell ◽  
Tata Box ◽  
Integrative Approach ◽  
Regulatory State ◽  
Histone Fold ◽  
General Transcription Factor

AbstractGeneral transcription factor TFIID is a key component of RNA polymerase II transcription initiation. Human TFIID is a megadalton-sized complex comprising TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). TBP binds to core promoter DNA, recognizing the TATA-box. We identified a ternary complex formed by TBP and the histone fold (HF) domain-containing TFIID subunits TAF11 and TAF13. We demonstrate that TAF11/TAF13 competes for TBP binding with TATA-box DNA, and also with the N-terminal domain of TAF1 previously implicated in TATA-box mimicry. In an integrative approach combining crystal coordinates, biochemical analyses and data from cross-linking mass-spectrometry (CLMS), we determine the architecture of the TAF11/TAF13/TBP complex, revealing TAF11/TAF13 interaction with the DNA binding surface of TBP. We identify a highly conserved C-terminal TBP-binding domain (CTID) in TAF13 which is essential for supporting cell growth. Our results thus have implications for cellular TFIID assembly and suggest a novel regulatory state for TFIID function.

scholarly journals The gammaherpesviral TATA-box-binding protein directly interacts with the CTD of host RNA Pol II to direct late gene transcription

2020 ◽  
Author(s):  
Angelica F. Castañeda ◽  
Allison L. Didychuk ◽  
Robert K. Louder ◽  
Chloe O. McCollum ◽  
Zoe H. Davis ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Gene Transcription ◽  
Binding Protein ◽  
Tata Box ◽  
Late Gene ◽  
Rna Pol Ii ◽  
Eukaryotic Transcription ◽  
Pol Ii ◽  
Terminal Domain ◽  
Tata Box Binding Protein

ABSTRACTβ- and γ-herpesviruses include the oncogenic human viruses Kaposi’s sarcoma-associated virus (KSHV) and Epstein-Barr virus (EBV), and human cytomegalovirus (HCMV), which is a significant cause of congenital disease. Near the end of their replication cycle, these viruses transcribe their late genes in a manner distinct from host transcription. Late gene transcription requires six virally-encoded proteins, one of which is a functional mimic of host TATA-box-binding protein (TBP) that is also involved in recruitment of RNA polymerase II (Pol II) via unknown mechanisms. Here, we applied biochemical protein interaction studies together with electron microscopy-based imaging of a reconstituted human preinitiation complex to define the mechanism underlying Pol II recruitment. These data revealed that the herpesviral TBP, encoded by ORF24 in KSHV, makes a direct protein-protein contact with the C-terminal domain of host RNA polymerase II (Pol II), which is a unique feature that functionally distinguishes viral from cellular TBP. The interaction is mediated by the N-terminal domain (NTD) of ORF24 through a conserved motif that is shared in its β- and γ-herpesvirus homologs. Thus, these herpesviruses employ an unprecedented strategy in eukaryotic transcription, wherein promoter recognition and polymerase recruitment are facilitated by a single transcriptional activator with functionally distinct domains.SIGNIFICANCE STATEMENTThe β- and γ-herpesviruses mediate their late gene transcription through a set of viral transcriptional activators (vTAs). One of these vTAs, ORF24 in Kaposi’s sarcoma-associated herpesvirus (KSHV), is a mimic of host TATA-box-binding protein (TBP). We demonstrate that the N-terminal domain of ORF24 and its homologs from other β- and γ-herpesviruses directly bind the unstructured C-terminal domain (CTD) of RNA Pol II. This functionally distinguishes the viral TBP mimic from cellular TBP, which does not bind Pol II. Thus, herpesviruses encode a transcription factor that has the dual ability to directly interact with promoter DNA and the polymerase, a property which is unique in eukaryotic transcription and is conceptually akin to prokaryotic transcription factors.

scholarly journals Requirement for transcription factor IIA (TFIIA)-TFIID recruitment by an activator depends on promoter structure and template competition.

1997 ◽  
Vol 17 (11) ◽  
pp. 6624-6632 ◽  
Author(s):  
P M Lieberman ◽  
J Ozer ◽  
D B Gürsel
Keyword(s):  
Transcriptional Activation ◽  
Core Promoter ◽  
Initiation Site ◽  
Transcriptional Initiation ◽  
Barr Virus ◽  
Tata Element ◽  
Epstein Barr ◽  
Substitution Mutations ◽  
Promoter Dna ◽  
Tata Box Binding Protein

Different mechanisms of transcriptional activation may be required for distinct classes of promoters and cellular conditions. The Epstein-Barr virus (EBV)-encoded transcriptional activator Zta recruits the general transcription factors IID (TFIID) and IIA (TFIIA) to promoter DNA and induces a TATA box-binding protein (TBP)-associated factor-dependent footprint downstream of the transcriptional initiation site. In this study, we investigated the functional significance of TFIID-TFIIA (D-A complex) recruitment by Zta. Alanine substitution mutations in the Zta activation domain which eliminate the ability of Zta to stimulate the D-A complex were examined. These Zta mutants were defective in the ability to activate transcription from an EBV-derived promoter (BHLF1) but activated a highly responsive synthetic promoter (Z7E4T). Both the number of activator binding sites and the core promoter region contribute to the requirement for D-A complex recruitment. These functionally distinct core promoters had significant differences in affinity for TBP and TFIID binding. The D-A complex-recruiting activity of Zta was found to be important for promoter selection in the presence of a competitor template. Conditions which limit TFIID binding to the TATA element or compromise the ability of TFIIA to bind TBP required activator stimulation of the D-A complex. These results indicate that D-A complex recruitment is one of at least two activation pathways utilized by Zta and is the essential pathway for a subset of promoters and conditions which limit TFIID binding to the TATA element.

Basal and regulated transcription in Archaea

2001 ◽  
Vol 29 (4) ◽  
pp. 392-395 ◽  
Author(s):  
S. D. Bell ◽  
C. P. Magill ◽  
S. P. Jackson
Keyword(s):  
In Vitro Transcription ◽  
Tata Box ◽  
Basal Transcription ◽  
General Transcription Factors ◽  
General Transcription Factor ◽  
Promoter Recognition ◽  
Transcription In Vitro ◽  
Rnap Ii ◽  
Tata Box Binding Protein

The basal transcription machinery of Archaea is fundamentally related to the eucaryal RNA polymerase (RNAP) II apparatus. In addition to a 12-subunit RNAP, Archaea possess two general transcription factors, the activities of which are required for accurate and efficient in vitro transcription. These factors, TBP and TFB, are homologues of the eucaryal TATA-box binding protein and TFIIB respectively. Archaea also possess TFE, a homologue of the eucaryal RNAP II general transcription factor TFIIE. Although not absolutely required for transcription in vitro, TFE nonetheless plays a stimulatory role under conditions where promoter recognition by TBP is sub-optimal. The basal transcription apparatus of Archaea is closely related to that of Eucarya but archaeal transcriptional regulators resemble those of bacteria. The mode of action of two such regulators has been characterized to determine how these ‘bacterial-like’ regulators impinge on the ‘eucaryal-like’ basal machinery.

scholarly journals Global Role of TATA Box-Binding Protein Recruitment to Promoters in Mediating Gene Expression Profiles

2004 ◽  
Vol 24 (18) ◽  
pp. 8104-8112 ◽  
Author(s):  
Jonghwan Kim ◽  
Vishwanath R. Iyer
Keyword(s):  
Gene Expression ◽  
Binding Protein ◽  
Core Promoter ◽  
Expression Profiles ◽  
Rna Polymerase Iii ◽  
Gene Expression Profiles ◽  
Tata Box ◽  
Expression Levels ◽  
Tata Box Binding Protein

ABSTRACT The recruitment of TATA box-binding protein (TBP) to promoters is one of the rate-limiting steps during transcription initiation. However, the global importance of TBP recruitment in determining the absolute and changing levels of transcription across the genome is not known. We used a genomic approach to explore the relationship between TBP recruitment to promoters and global gene expression profiles in Saccharomyces cerevisiae. Our data indicate that first, RNA polymerase III promoters are the most prominent binding targets of TBP in vivo. Second, the steady-state transcript levels of genes throughout the genome are proportional to the occupancy of their promoters by TBP, and changes in the expression levels of these genes are closely correlated with changes in TBP recruitment to their promoters. Third, a consensus TATA element does not appear to be a major determinant of either TBP binding or gene expression throughout the genome. Our results indicate that the recruitment of TBP to promoters in vivo is of universal importance in determining gene expression levels in yeast, regardless of the nature of the core promoter or the type of activator or repressor that may mediate changes in transcription. The primary data reported here are available at http://www.iyerlab.org/tbp .

scholarly journals The TAFs of TFIID Bind and Rearrange the Topology of the TATA-Less RPS5 Promoter

2019 ◽  
Vol 20 (13) ◽  
pp. 3290 ◽  
Author(s):  
Sarah N. Le ◽  
Christopher R. Brown ◽  
Stacy Harvey ◽  
Hinrich Boeger ◽  
Hans Elmlund ◽  
...  
Keyword(s):  
Dna Binding ◽  
Core Promoter ◽  
Ribosomal Protein Gene ◽  
Dna Topology ◽  
Nucleosome Core ◽  
Sequence Elements ◽  
A Subunit ◽  
Promoter Dna ◽  
Tata Box Binding Protein ◽  
Tfiid Complex

The general transcription factor TFIID is a core promoter selectivity factor that recognizes DNA sequence elements and nucleates the assembly of a pre-initiation complex (PIC). The mechanism by which TFIID recognizes the promoter is poorly understood. The TATA-box binding protein (TBP) is a subunit of the multi-protein TFIID complex believed to be key in this process. We reconstituted transcription from highly purified components on a ribosomal protein gene (RPS5) and discovered that TFIIDΔTBP binds and rearranges the promoter DNA topology independent of TBP. TFIIDΔTBP binds ~200 bp of the promoter and changes the DNA topology to a larger extent than the nucleosome core particle. We show that TBP inhibits the DNA binding activities of TFIIDΔTBP and conclude that the complete TFIID complex may represent an auto-inhibited state. Furthermore, we show that the DNA binding activities of TFIIDΔTBP are required for assembly of a PIC poised to select the correct transcription start site (TSS).

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