Structure of RNA Polymerase II

Of the three RNA polymerases, RNA polymerase II is the most extensively studied, and the yeast Saccharomyces cerevisiaie if, the most common model system. Yeast RNA polymerase II consists of 12 subunits, as shown in Table 11.2. The subunits are called RPBl through RPB12. RPB stands for RNA polymerase B because another nomenclature system refers to the polymerases as A, B, and C, instead of I, II, and III. 

The function of many of the subunits is not known. The core subunits, RBPl through RBP3, seem to play a role similar to their homologues in prokaryotic RNA polymerase. Five of them are present in all three RNA polymerases. RPBl has a repeated sequence of PTSPSYS in the C-terminal domain (CTD), which, as the name applies, is found at the G-terminal region of the protein. Threonine, serine, and tyrosine are all substrates for phosphorylation, which is important in the control of transcription initiation. 

Recent structural work on RNA polymerases from prokaryotes and eukaryotes has led to some exciting conclusions regarding their evolution. Extensive homology exists between the core regions of RNA polymerases from bacteria, yeast, and humans, leading researchers to speculate that RNA polymerase 

The described structural studies of yeast Pol II are directly relevant for the Pol II enzymes in higher organisms, since the Pol II subunits are very well conserved in sequence and function. Approximately half of the amino acid residues in the twelve Pol II subunits are identical between yeast and human sequences. Furthermore, most yeast subunits can functionally replace their human counterparts (Woychik, 1998). The human Rpb4/7 complex can also functionally replace its yeast counterpart (Khazak et al., 1995), indicating that the core-Rpb4/7 interface is conserved. 

JCore Sequence partially homologous in all RNA polymerases. Common shared by all eukaryotic RNA polymerases, Rpb4/7 Rpb4/7 heterodimer and its structural counterparts. Unclear It is unclear if A12.2 and Cll are true Rpb9 homologs. It appears that the C-terminal domain of the Pol II subunit Cll is functionally and structurally homologous to the Pol II transcript cleavage factor TFIIS. 

Pol II element and subelement Subunit Homology region Function (proposed if in parenthesis) 

Bridge Rpbl F Positioning of nascent base pair, stabilization of twist between bases 

Clamp Rpbl A, B, C, H in the template strand, maintenance of downstream end of the bubble, a-amanitin-binding, (translocation) Processivity, template strand binding, hybrid retention, bubble 

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Figure 37-9. The eukaryotic basal transcription complex. Formation of the basal transcription complex begins when TFIID binds to the TATA box. It directs the assembly of several other components by protein-DNA and protein-protein interactions. The entire complex spans DNA from position -30 to +30 relative to the initiation site (+1, marked by bent arrow). The atomic level, x-ray-derived structures of RNA polymerase II alone and ofTBP bound to TATA promoter DNA in the presence of either TFIIB or TFIIA have all been solved at 3 A resolution. The structure of TFIID complexes have been determined by electron microscopy at 30 A resolution. Thus, the molecular structures of the transcription machinery are beginning to be elucidated. Much of this structural information is consistent with the models presented here.

Polypeptide Structure of RNA Polymerase II from Various Eukaryotic... 

Nucleosomes core particles containing H2A only have 118 base pairs of DNA incorporated compared to the canonical nucleosomes protecting about 147 base pairs from micrococcal nuclease (Bao et al. 2004). These nucleosomes are more flexible in structure and might facilitate passage of RNA polymerase II. However, the function of this histone variant in mammalian cells is not fully understood. As... 

The yeast holoenzyme contains further proteins, known as mediators or SRB proteins (SRB, suppressor of RNA polymerase B). The mediators function as coactivators (see Section 1.4.4.2) and appear to integrate signals from transcriptional activators at promotors. A complete structural characterization of the holoenzyme has proven to be difficult, because some of the proteins accessory to the core enzyme are not permanently and are often only loosely associated with the core of RNA polymerase II. Clearly different forms of the RNA polymerase II holoenzyme exist in the living cell, each of slightly different composition and function. 

Capping at the 5 end of the pre-mRNA occurs immediately after incorporation of about 30 nucleotides in the primary transcript. The enzymes involved in capping become associated with the CTD of RNA polymerase II immediately after CTD hyperphosphorylation, at the transition from initiation to elongation. The 5 cap structure is required for the binding of the mRNA to the 40S subunit of the ribosome during the initiation of translation. Also, a stabilizing function for mRNA is ascribed to capping. 

Tomaletti, S., Reines, D., and Hanawalt, P.C. (1999) Structural characterization of RNA polymerase II complexes arrested by a cydobutane pyrimidine dimer in the transcribed strand of template DNA. J. Biol. Chem., 274, 24124-24130. 

A FIGURE 11-6 Schematic representation of the subunit structure of the E. coli RNA core polymerase and yeast nuclear RNA polymerases. All three yeast polymerases have five core subunits homologous to the p, p, two a. and co subunits of E. coli RNA polymerase. The largest subunit (RPB1) of RNA polymerase II also contains an essential C-terminal domain (CTD). RNA polymerases I and III contain the same two nonidentical a-like subunits, whereas RNA polymerase II contains two other nonidentical a-like subunits. All three polymerases share the same co-like subunit and four other common subunits. 

Cramer, P., et al. Architecture of RNA Polymerase II and Implications for the Transcription Mechanism. Sdmce 288, 640-649 (2000). [Good overview of RNA polymerase structure and function.]... 

Cagas, P. M., and Corden. J. L. (1995). Structural studies of a synthetic peptide derived from the carboxyl-terminal domain of RNA polymerase II. Proteins 21(2), 149-160. 

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