A Nonconserved Surface of the TFIIB Zinc Ribbon Domain Plays a Direct Role in RNA Polymerase II Recruitment

Tubon, Thomas C.; Tansey, William P.; Herr, Winship

doi:10.1128/mcb.24.7.2863-2874.2004

Cited by 23 publications

(21 citation statements)

References 66 publications

(90 reference statements)

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“…The TFIIB, Brf1, and Brf2 zinc ribbon domains (but not the B finger regions) are highly conserved (14,34,38), and so are the Pol II and Pol III dock regions (see references 7), a finding consistent with the Brf1 and Brf2 zinc ribbons associating with Pol III in much the same way as the TFIIB zinc ribbon associates with Pol II. Nevertheless, the specific amino acids involved in the interactions may be different; indeed, it is striking that, for example, the yeast TFIIB N-terminal region fails to recruit human Pol II to the adenovirus 2 major late promoter, even though both the yeast and human TFIIB N-terminal regions can recruit yeast Pol II to this promoter (39). Similarly, subtle differences within the zinc ribbons of TFIIB, Brf1, and Brf2, as well as the lack of an obvious B finger in Brf1 and Brf2, may contribute to specific recruitment of the correct RNA polymerase.…”

Section: Discussionmentioning

confidence: 99%

Structure-Function Analysis of the Human TFIIB-Related Factor II Protein Reveals an Essential Role for the C-Terminal Domain in RNA Polymerase III Transcription

Saxena

Schramm

et al. 2005

Molecular and Cellular Biology

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The transcription factors TFIIB, Brf1, and Brf2 share related N-terminal zinc ribbon and core domains. TFIIB bridges RNA polymerase II (Pol II) with the promoter-bound preinitiation complex, whereas Brf1 and Brf2 are involved, as part of activities also containing TBP and Bdp1 and referred to here as Brf1-TFIIIB and Brf2-TFIIIB, in the recruitment of Pol III. Brf1-TFIIIB recruits Pol III to type 1 and 2 promoters and Brf2-TFIIIB to type 3 promoters such as the human U6 promoter. Brf1 and Brf2 both have a C-terminal extension absent in TFIIB, but their C-terminal extensions are unrelated. In yeast Brf1, the C-terminal extension interacts with the TBP/TATA box complex and contributes to the recruitment of Bdp1. Here we have tested truncated Brf2, as well as Brf2/TFIIB chimeric proteins for U6 transcription and for assembly of U6 preinitiation complexes. Our results characterize functions of various human Brf2 domains and reveal that the C-terminal domain is required for efficient association of the protein with U6 promoter-bound TBP and SNAP c , a type 3 promoter-specific transcription factor, and for efficient recruitment of Bdp1. This in turn suggests that the C-terminal extensions in Brf1 and Brf2 are crucial to specific recruitment of Pol III over Pol II.In eukaryotes, the job of transcribing nuclear genes is divided among three different RNA polymerases: RNA polymerase I (Pol I), RNA Pol II, and RNA Pol III. A common step in transcription initiation by all three eukaryotic RNA polymerases is the recruitment of the polymerase to the proper promoters by a specific factor or complex. This transcription factor serves as a bridge between promoter-bound factors that nucleate preinitiation complex assembly and the RNA polymerase enzyme itself. For Pol II and Pol III transcription, the factors that accomplish this task are TFIIB and TFIIIB, respectively.Although TFIIB is a single polypeptide, the TFIIIB activity is minimally composed of three polypeptides (see references 11 and 33 for reviews). In human cells, two forms of the TFIIIB complex have been characterized thus far: Brf1-TFIIIB, which functions on type 1 and 2 Pol III promoters, and Brf2-TFIIIB, which functions on type 3 Pol III promoters such as the human U6 small nuclear RNA (snRNA) promoter. Brf1-TFIIIB and Brf2-TFIIIB both contain the TATA-box binding protein TBP and the SANT domain protein Bdp1. They differ by the presence of different members of a family of TFIIB-related factors: Brf1 in Brf1-TFIIIB and Brf2 in Brf2-TFIIIB.TFIIB, Brf1, and Brf2 each contain a Zn ribbon domain at their N terminus, followed by a core domain consisting of two imperfect repeats. In this region, human Brf2 is 20% identical with human TFIIB and 18% identical with human Brf1. In addition, Brf1 and Brf2 contain a C-terminal extension. In Brf1, this C-terminal segment contains two regions called homology domains II and III, which are conserved among yeast and human proteins. Moreover, a third region called homology domain I is conserved among several different yeast species (25...

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Section: Discussionmentioning

confidence: 99%

Structure-Function Analysis of the Human TFIIB-Related Factor II Protein Reveals an Essential Role for the C-Terminal Domain in RNA Polymerase III Transcription

Saxena

Schramm

et al. 2005

Molecular and Cellular Biology

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“…S5). Other investigators have reported activity with yeast-human chimeric TFIIB proteins in complex systems (24,46). To determine if the nature of the nonconserved residues at the tip of the B-finger plays a role in the activity of TFIIB in the MLP MMP system, we made a chimeric protein and tested it in the MLP MMP system.…”

Section: Mutational Analysis Across the B-finger: Effects In Minimal mentioning

confidence: 99%

“…Given the presumed role of the B-finger in transcription initiation and the high conservation of amino acid sequence among species, it is surprising that other investigators have reported some in vitro transcriptional activity in HeLa cell NE using deletion mutants that lack part or all of the human TFIIB B-finger (24,25) and in a defined transcription system that lacks all of the archaeal B-finger region (26). No systematic study has addressed the role of the individual residues of the B-finger in a defined transcription system.…”

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confidence: 99%

Minimal Promoter Systems Reveal the Importance of Conserved Residues in the B-finger of Human Transcription Factor IIB

Thompson

Glaser

Foley

et al. 2009

Journal of Biological Chemistry

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The "B-finger" of transcription factor IIB (TFIIB) is highly conserved and believed to play a role in the initiation process. We performed alanine substitutions across the B-finger of human TFIIB, made change-of-charge mutations in selected residues, and substituted the B-finger sequence from other organisms. Mutant proteins were examined in two minimal promoter systems (containing only RNA polymerase II, TATAbinding protein, and TFIIB) and in a complex system, using TFIIB-immunodepleted HeLa cell nuclear extract (NE). Mutations in conserved residues located on the sides of the B-finger had the greatest effect on activity in both minimal promoter systems, with mutations in residues Glu-51 and Arg-66 eliminating activity. The double change-of-charge mutant (E51R: R66E) did not show activity in either minimal promoter system. Mutations in the nonconserved residues at the tip of the B-finger did not significantly affect activity. However, all of the mutations in the B-finger showed at least 25% activity in the HeLa cell NE. Chimeric proteins, containing B-finger sequences from species with conserved residues on the side of the B-finger, showed wild-type activity in a minimal promoter system and in the HeLa cell NE. However, chimeric proteins whose sequence showed divergence on the sides of the B-finger had reduced activity. Transcription factor IIF (TFIIF) partially restored activity of the inactive mutants in the minimal promoter system, suggesting that TFIIF in HeLa cell NE helps to rescue the inactive mutations by interacting with either the B-finger or another component of the initiation complex that is influenced by the B-finger.The RNA polymerase II (RNAP II) 2 initiation complex is extremely complicated and, thus, very difficult to meaningfully dissect. Genes that are transcribed into mRNA by RNAP II generally require five general transcription factors (TFs), designated TFIIB, TFIID, TFIIE, TFIIF, and TFIIH (reviewed in Refs. 1-5). However, arguments have been made to include the "elongation" factor TFIIS (6) and the mediator complex (7) in the list of "general" transcription factors. RNAP II and most of the TFs are multimeric protein complexes. If all proteins contained in the yeast (Saccharomyces cerevisiae) RNAP II initiation complex were considered, the count of ϳ60 polypeptides would have a mass of ϳ3 MDa (8). The high resolution crystal structure of yeast RNAP II has provided invaluable insight into the topology of the RNAP II transcription initiation complex (9). Furthermore, the crystal structures of bacterial RNAP (10, 11) and RNAP from an archaeal organism (12) establish that RNAP from all three domains of life (Bacteria, Archaea, and Eukarya) show high conservation of overall structure. However, many mechanistic details of the transcription process have yet to be determined.TFIIB functions as a single polypeptide with a two-domain structure. The C-terminal domain of TFIIB (cTFIIB) contains an imperfect direct repeat motif. The co-crystal structure of cTFIIB with the DNA-bound TATA-binding protein ...

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“…A second motif is folded by association with a zinc atom (2). This binds a docking domain on RNA polymerase II (3) and recruits the enzyme to promoters to catalyze transcription initiation (4). A third motif is unstructured in solution but folds into a finger-like structure when bound to RNA polymerase (3).…”

Section: Tfiibmentioning

confidence: 99%

Control of the Timing of Promoter Escape and RNA Catalysis by the Transcription Factor IIB Fingertip

Tran

Gralla

2008

Journal of Biological Chemistry

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Transcription factor IIB (TFIIB) recruits RNA polymerase II to promoters and inserts a finger domain into its active site, with unknown consequences. Here we show that that the tip of this finger is important for two transcription initiation functions. First, TFIIB acts as a catalytic cofactor for initial RNA bond formation. It does so via a pair of fingertip aspartates that can bind magnesium, placing TFIIB within a family of proteins that insert finger domains to alter the catalytic functions of RNA polymerase. Second, the TFIIB fingertip mediates the timing of the release of TFIIB that is associated with appropriate promoter escape. These initiation requirements may assist in RNA quality control by minimizing functional synthesis when RNA polymerase becomes inappropriately associated with the genome without having been recruited there by TFIIB. TFIIB2 is a single-subunit protein that plays a central role in transcription by RNA polymerase II. It consists of three motifs with distinct structures and functions. The C terminus is composed of two cyclin repeats and is responsible for bringing TFIIB to promoters. It does so primarily by recognizing promoter-bound TATA-binding protein but also interacts with DNA sequences that flank the TATA box (1). A second motif is folded by association with a zinc atom (2). This binds a docking domain on RNA polymerase II (3) and recruits the enzyme to promoters to catalyze transcription initiation (4). A third motif is unstructured in solution but folds into a finger-like structure when bound to RNA polymerase (3). A number of functions have been suggested for this finger, mostly involving the escape by the recruited RNA polymerase (discussed below).TFIIB is unique among the general transcription factors in that it recycles during continuous transcription, i.e. TFIIF travels with the elongating RNA polymerase, and TATA-binding protein, TFIIH, and TFIIE largely remain bound to the promoter (5). Thus there can be a pioneer round of transcription that forms a scaffold upon which reinitiation can occur without requiring the reassembly of all factors from free solution. This allows transcription to occur at a facilitated rate (6). For each round of initiation, a new RNA polymerase must wait for the prior RNA polymerase to escape. This requires the recycling of TFIIB (7) by binding to the scaffold to recruit the next RNA polymerase. These initial steps of transcription initiation, involving initial bond formation, production of small RNAs, and disruption of contacts to the promoter, are collectively termed "escape" (8 -10).The finger domain of TFIIB has been proposed to play multiple roles in promoter escape. Both chemical probing (3) and structural studies (11) have shown that the finger penetrates the main channel of RNA polymerase II to approach the active site of the enzyme. From this location it could influence these early steps by interacting with the template DNA, the newly synthesized RNA, the catalytic center of the RNA polymerase, and perhaps TFIIF or other general transcr...

show abstract

A Nonconserved Surface of the TFIIB Zinc Ribbon Domain Plays a Direct Role in RNA Polymerase II Recruitment

Cited by 23 publications

References 66 publications

Structure-Function Analysis of the Human TFIIB-Related Factor II Protein Reveals an Essential Role for the C-Terminal Domain in RNA Polymerase III Transcription

Structure-Function Analysis of the Human TFIIB-Related Factor II Protein Reveals an Essential Role for the C-Terminal Domain in RNA Polymerase III Transcription

Minimal Promoter Systems Reveal the Importance of Conserved Residues in the B-finger of Human Transcription Factor IIB

Control of the Timing of Promoter Escape and RNA Catalysis by the Transcription Factor IIB Fingertip

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