TFIIS binding

Jaws Rpbl/9jaw Rpbl G TFIIS binding, (interaction with downstream DNA during initiation and... 

TFIIS binding, (NTP entry, RNA exit during backtracking and arrest) TFIIS binding, crevice opening triggers conformational changes... 

Fig. 5. Structure-based alignment of the sequences of the water-soluble Rieske fragment from bovine heart bci complex (ISF), the water-soluble Rieske fragment from spinach b f complex (RFS), and of the Rieske domain of naphthalene dioxygenase (NDO) and of the metal binding loops of rubredoxin (RXN) and transcriptional factor TFIIS (TFI). The numbering of the j3 strands is the same for the ISF and RFS. The metal binding ligands are highlighted the asterisks indicate those residues that are fully conserved between the three Rieske proteins.

The general topology of rubredoxins is also observed in the general zinc-ribbon motif in RNA polymerases or in transcription factors (59). The first published zinc-ribbon structure was that of the nucleic-acid binding domain of human transcriptional elongation factor TFIIS (PDB file ITFI) 40). These zinc binding domains and rubredoxins... 

In any case, the ability of USF and TFII-I to recognize both E box and Inr-like elements clearly has interesting implications for the potential role of a member of this transcription factor family in oocyte-specific gene expression. Namely, it is possible that a USF-related factor could be involved in oocyte-specific expression of both the c-mos and ZP genes via interaction with Inr and E box elements, respectively. Identification and characterization of the oocyte factors that bind to these sequences will obviously be needed to test this possibility. 

After TFIIIA binds, proteins TFIIIC and then TFII-IB also bind. Although promoters of classes 2 and 3 do not require TFIIIA, all three classes depend upon TFIIIB and TFIIIC.484 The TATA-binding protein TBF is one of three components present in TFIIIB, which may be regarded as the true initiation factor.47 485 Both TFIIIA and TFIIIC can be described as assembly factors 47 A silkworm RNA pol III has been reported to require a transcription factor consisting of RNA 486... 

Cis-acting elements constitute only part of the puzzle of eukaryotic gene expression. Transcription factors that bind to these elements also are required. For example, RNA polymerase II is guided to the start site by a set of transcription factors known collectively as TFII (TF stands for transcription factor, and II refers to RNA polymerase II). Individual TFII factors are called TFIIA, TFIIB, and so on. Initiation begins with the binding of TFIID to the TATA box (Figure 28.19). 

A prototypical RNA pol II-dependent eukaryotic promoter. Three classes of transcription factors are schematically represented the TFII auxiliary factors (TFIIF, TFIIJ, TFIIH, etc.), TBP with its associated factors (TAFs), and various transcriptional regulatory factors which bind to DNA sequences called response elements (RE). See Chapter 24 for more information about TBP and the RNA pol II holoenzyme. 

Fig. 14.7. Transcription apparatus. The TATA-binding protein (TBP), a component of TFIID, binds to the TATA box. Transcription factors TFII A and B bind to TBP. RNA polymerase binds, then TFII E, F, and H bind. This complex can transcribe at a basal level. Some coactivator proteins are present as a component of TFIID, and these can bind to other regulatory DNA binding proteins (called specific transcription factors or transcriptional activators).

TBP serves a critical role as an enucleating center for the assembly of the minimal molecular apparatus (the basal transcription assembly) required for transcription by RNA polymerase II. After TBP binds the TATA box, other TFII proteins and RNA polymerase II join the supramolecular complex to render it transcriptionally competent. In addition to enabling the assembly of the apparatus through its ability to recognize and bind the TATA box, TBP binds this asymmetric sequence in one orientation that points the RNA polymerase in the right direction, thereby defining the strand of DNA that "will serve as the template. 

Because the Pol II core alone is sufficient to maintain the transcription bubble and the DNA-RNA hybrid during RNA chain elongation, there must be exposed elements on the enzyme surface that keep the nucleic acid strands apart. Protein elements are needed to separate the DNA strands downstream of the active site and to separate the RNA from the DNA template strand at the upstream end of the hybrid. On the basis of their location with respect to nucleic acids, several Pol II structural elements are predicted to maintain the bubble and the hybrid. These proposals are currently tested by site-directed mutagenesis. Separation of the DNA strands at the downstream edge of the bubble may be attributed to binding of the DNA template strand by switch regions 1 and 2 and to blocking of the path of the nontemplate strand by fork loop 2. In the Pol II-TFIIS complex structure, fork loop 2 is ordered and restricts the cleft to a diameter of 15 A, consistent with the proposal that this loop removes the DNA nontemplate strand from the template strand before the active site. 

There are, however, minor differences on the enzymes surfaces caused by amino acid insertions and deletions. These differences are most likely responsible for conferring specificity toward the interaction with factors specific for Pol I, II, and III. In addition to the 12 subunits that are either identical or homologous, Pol I contains two specific subunits, A34.5 and A49, and Pol III contains a subcomplex of three specific subunits, called C82, C34, and C31, in yeast. The location of the two Pol I—specific subunits has been determined by electron microscopy and immunolabeling (Bischler et al., 2002). The Pol I subunit A49 binds to the top of the clamp, and subunit A34.5 is located near the jaws. The location of the specific C82/C34/C31 complex of Pol III can be inferred from subunit-subunit interaction studies (Ferri et al., 2000 Flores et al., 1999). These studies indicate that the specific subcomplex is located between the largest polymerase subunit and the Rpb4/7 complex counterpart C17/C25. The Cll subunit of Pol III contains a C-terminal domain that apparently corresponds structurally and functionally to domain III of TFIIS (Chedin et al., 1998 Kettenberger et al., 2003), which inserts into the polymerase pore. Thus, in Pol III, the RNA cleavage stimulatory activity is incorporated into a polymerase subunit, in contrast to Pol II, where it is provided by the additional factor TFIIS. 

Note Abbreviations used CTD, carboxy-terminal domain RNAPII, RNA polymerase II TAP, TBP-associated factor TBP, TATA-binding proteins TFII, transcription factor for RNAPII. 

Although TBP is utilized by both Pol II and Pol III, TFIID is the specific complex for Pol n recognition of a promoter. Other transcription factors (e.g., IFllA) bind to the IFllD promoter complex and cover increasing segments of DNA. In addition to TFIIA, these include TFIIE, TFIIF, TFTIH, and TFIU. Most of the TFII factors... 

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