Yeast RNA polymerase II subunits

Tan Q, et al. Activation mutants in yeast RNA polymerase II subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria. Genes Dev. 2000 14 339-348. 

Polymerase Family Yeast RNA polymerase II subunit A 1K83 Cys 2 Cys 6 Cys 2 His2b ... 

Wooddell, C. I., and Burgess, R. R. (2000). Topology of yeast RNA polymerase II subunits in transcription elongation complexes studied by photoaffinity crosslinking [in process citation]. Biochemistry 39(44), 13405-13421. 

A FIGURE 11-5 Comparison of three-dimensional structures of bacterial and eukaryotic RNA polymerases. These C trace models are based on x-ray crystallographic analysis of RNA polymerase from the bacterium T aquaticus and RNA polymerase II from S. cerevisiae. (a) The five subunits of the bacterial enzyme are distinguished by color. Only the N-terminal domains of the a subunits are included in this model, (b) Ten of the twelve subunits constituting yeast RNA polymerase II are shown in this model. 

The carboxyl end of the largest subunit of RNA polymerase II (RPBI) contains a stretch of seven amino acids that Is nearly precisely repeated multiple times. Neither RNA polymerase I nor III contains these repeating units. This hep-tapeptlde repeat, with a consensus sequence of Tyr-Ser-Pro-Thr-Ser-Pro-Ser, Is known as the carboxyl-terminal domain (CTD). Yeast RNA polymerase II contains 26 or more repeats, the mammalian enzyme has 52 repeats, and an Intermediate number of repeats occur In RNA polymerase II from nearly all other eukaryotes. The CTD Is critical for viability, and at least 10 copies of the repeat must be present for yeast to survive. 

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. 

Khazak, V., Sadhale, P. P., Woychik, N. A., Brent, R., and Golemis, E. A. (1995). Human RNA polymerase II subunit hsRPB7 functions in yeast and influences stress survival and cell morphology. Mol. Biol. Cell 6(7), 759-775. 

RNA polymerase II can be isolated from the cell in various forms. From yeast and from metazooans, holoenzyme forms of RNA polymerase have been purified that are composed of the core of RNA polymerase II and other accessory transcription factors, suggesting that a preassembled transcription apparatus can be assembled at the promotor in one step. These holoenzymes are formed from the core of RNA polymerase associated to a variable degree with the general transcription factors and with one or more other subunit complexes called mediators or coactivators. 

The core of the RNA polymerase II is a functional unit composed of 12 subunits. The structure of the core of RNA Pol II from yeast has been resolved, providing a comprehensive model of template- and mRNA-binding as well as of the location of the active site of nucleotide incorporation (Cramer et al., 2001). 

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. 

Larkin, R. M., and Guilfoyle, T. J. (1998). Two small subunits in Arabidopsis RNA polymerase II are related to yeast RPB4 and RPB7 and interact with one another. J. Biol. Chem. 273(10), 5631-5637. 

Sakurai, H., Mitsuzawa, H., Kimura, M., and Ishihama, A. (1999). The Rpb4 subunit of fission yeast Schizosaccharomyces pombe RNA polymerase II is essential for cell viability and similar in structure to the corresponding subunits of higher eukaryotes. Mol. Cell. Biol. 19(11), 7511-7518. 

The molecular weights of RNA polymerase II polypeptides (x 10 ) are reported for yeast (Dezelee et al., 1976), Drosophila (Kramer and Bautz, 1981), mouse myeloma plasmacytoma (Boeder, 1976), and calf thymus (Hodo and Blatti, 1977 Dahmus, 1981 , ). The boxed polypeptides are thought to be common of polymerases I, II, and III (Huet et aL, 1982). The three largest subunits of the mouse polymerase are labeled IIo, Ha, and IIb (Schwartz and Boeder, 1975). A multisubunit polymerase only contains one of these polypeptides lU and IIb are thought to be related by proteolytic cleavage. 

Eukaryotic RNA polymerases are less well-characterized than the bacterial enzyme. Biochemical studies have so far identified three distinct nuclear RNA polymerase activities in eukaryotic cell extracts prepared from both yeast and human cells. These RNA polymerases, referred to as RNA pol I, RNA pol II, and RNA pol HI, each contain a large number of subunits, some of which appeared to be shared between the different RNA polymerase subtypes. As shown in Table 24.1, RNA pol I transcribes ribosomal RNA genes, RNA pol II transcribes the majority of protein-coding genes, into mRNA, and RNA pol III transcribes tRNA, small nuclear RNAs (snRNAs), and ribosomal 5S genes. Note also that the mitochondrial genome is transcribed by a nuclear-encoded mitochondrial RNA polymerase. The yeast mitochondrial RNA polymerase holoenzyme consists of a 140-kd catalytic subunit and a 43-kd promoter-recognition protein similar to the bacterial s factor. 

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