RNA polymerase II C-terminal domain

Legagneux, V., Morange, M., Bensaude, O. (1990). Heat-shock and related stress enhance RNA polymerase II C-terminal-domain kinase activity in HeLa cell extracts. Eur. J. Biochemistry 193, 121-126. 

Bienkiewicz, E. A., Moon Woody, A., and Woody, R. W. (2000). Conformation of the RNA polymerase II C-terminal domain Circular dichroism of long and short fragments./. Mol. Biol. 297, 119-133. 

Lunde BM, Reichow SL, Kim M, Suh H, Keeper TC, Yang F, Mutschler H, Buratowski S, Meinhart A, Varani G (2010) Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain. Nat Struct Mol Biol 17(10) 195-1201. doi 10.1038/nsmb.l893... 

Phosphorylation of HSF substantially enhances the transcriptional activity of HS gene expression which may be up to 100-fold of basal levels after HSFl binds to the promoter element. Heat shock will increase the C-terminal-domain-kinase activity in cell extracts, and this action may enhance the activity of RNA polymerase II that is bound to HS genes (Legagneux et al., 1990). Whether this kinase activity also affects HSFl phosphorylation is not known, but increased HS gene expression appears to occur as long as HSFl is bound to the promoter region. The CTD kinase complex contains multiple proteins, and it is quite possible that one or more of these proteins is also regulated by stress. 

The large subimit of RNA polymerase II plays an important role at the beginning of the transcription process. The large subimit of the mammalian enzyme contains 52 copies of the heptamer sequence YSPTSPS in the C-terminal domain (CTD) at which phosphorylation occurs. Phosphorylation occurs extensively on the Ser-residues of the CTD, to a lesser degree at the Thr-residues, and, very rarely, at the Tyr-residues. Two forms of RNA polymerase II can be isolated from cellular extracts a underphosphory-lated form and a hyper-phosphorylated form. The isoforms fulfill different functions RNA polymerase found in the initiation complex tends to display little or no phosphorylation at the C-terminus of the large subunit, while RNA polymerase II active in elongation is hyperphosphorylated in this region of the protein. 

Fig. 1.32. Phosphorylation of the C-terminal domain of RNA polymerase II and the beginning of transcription. The transition from the initiation complex to actual begin of transcription is regulated via phosphorylation of the C-terminal domain (CTD) of RNA polymerase II. In the above model it is assumed that initially a complex is formed between TFIID and a holoenzyme of RNA polymerase consisting of RNA polymerase II and associated factors (mediators, SRB proteins) and the basal transcription factors. Phosphorylation of the C-terminal domain effects the dissociation of the RNA polymerase from the initation complex and the transition to the elongation phase. A protein kinase, which is part of TFIIH, is responsible for the phosphorylation. The nature of the signal that induces phosphorylation of RNA polymerase II remains unknown. SRB suppressor of RNA polymerase B. After Koleske and Young (1995).

TBP TATA box binding protein, TAF TATA box binding protein associated factor, SRB suppressor of RNA polymerase B, CTD C-terminal domain of RNA polymerase II, PC positive cofactor, NC negative cofactor, HMG high mobihty group proteins, UAS upstream activating sequence. 

Mediators include proteins which are components of various forms of the holoenzyme of RNA polymerase II and interact with the C-terminal domain (CTD review Bjor-klimd and Kim, 1996). Mediators include, among others, the SRB protein see 1.4.2.3). 

S ATP -I- [DNA-directed eukaryotic RNA polymerase II subunit Ila] (<4> distinct from other protein phosphokinases, transfers about 20 phosphates to the heptapeptide repeats Pro-Thr-Ser-Pro-Ser-Tyr-Ser in C-terminal domain of MW 220000 subunit of RNA-polymerase II [7] <4> substrates are RNA-polymerase II subunits of wheat germ, soy bean, pea and human [7] phosphorylates predominantly Ser-residues [1-3,5,7] <1> kinase CTDKl almost exclusively phosphorylates Ser-residues [5] <1> kinase CTDK2 phosphorylates to a lesser extent Thr-resi-dues [1] <3-5> phosphorylates to a lesser extent Thr-residues [1,5,7] <1> phosphorylates Ser- and Thr-residues equally [6] <1,3,5> phosphorylates not Tyr-residues [1,6] <1> kinase CTDKl 33 mol phosphate per mol IIA-subunit [5] <1> kinase CTDK2 40-50 mol phosphate per mol IIA-subunit, i.e. 1 phosphate per heptapeptide repeat [5] <4> no substrate is GTP [7] <2,4> no substrates are CTP and UTP [3,7] <2> no substrates are dTTP and AMP-PNP [3] <4> no substrates are bovine serum albumin and calf thymus histone [7] <5> no substrate is phosvitin... 

Baskaran, R. Escobar, S.R. Wang, J.Y. Nuclear c-Abl is a COOH-terminal repeated domain (CTD)-tyrosine (CTD)-tyrosine kinase-specific for the mammalian RNA polymerase II possible role in transcription elongation. Cell Growth Differ., 10, 387-396 (1999)... 

Peterson, C.L., Kruger, W., and Herskowitz, I., 1991, A functional interaction between the C-terminal domain of RNA polymerase II and the negative regulator SIN1. Cell 64 1135-1143. 

KimYJ,Bjorklund S,Li Y, SayreMH,Ko-rnberg RD. 1994. A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 77 599-608... 

An alternative or additional explanation for the observed role of Pinl/Essl in cell cycle control is provided by the strong link that exists in particular between Essl and gene transcription. Essl interacts with the regulatory C-terminal domain of RNA polymerase II (CTD) in vitro and in vivo (Morris et al., 1999). CTD consists of many repeats of the heptapeptide sequence YSPTSPS, which can be heavily phosphorylated. Five out of six multicopy suppressors of ts mutants of essl are involved in transcription the sixth suppressor is the major cytoplasmic cyclophilin CypA (Arevalo-Rodriguez et al., 2000 Wu et al., 2000). 

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. 

Subunits that are similar in conformation to those in the bacterial enzyme are shown in the same colors. The C-terminal domain of the large subunit RPBl was not observed in the crystal structure, but it is known to extend from the position marked with a red arrow. (RPB is the abbreviation for "RNA polymerase 6," which is an alternative way of referring to RNA polymerase II.) [Part (a) based on crystal structures from G. Zhang et at,1999, Ce//98 811. 

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. 

Lu H., Zawel L., Fisher L., Egly J.-M., Reinberg D. (1992) Human general transcription factor IIH phosphorylates the C-terminal domain of RNA polymerase II. Nature 358 641. 

Other "footprinting" techniques, e.g., observing cleavage of the DNA by hydroxyl radicals generated by reduction of IT2O2 by Fe(II) (Fig. 5-50), have also been employed. If was shovm that RNA polymerase binds to both the -10 and -35 sequences and also to sequences further upstream. The subunit associates with the DNA, principally the transcribed strand, along a region from about the -25 to the +12 position relative to the transcription start site. The a subunits bind to an UP element from —40 to -60 via their C-terminal domains (CTDs). See Fig. 28-4B. ... 

TFIID (which contains the TATA-box binding protein, TBP) binds to the TATA box. TFIIA and TFIIB then bind, followed by recruitment of RNA polymerase II and TFIIF. TFIIH and TFIIE then bind to form the preinitiation complex (PIC). Kinases phosphorylate the C-terminal domain of Pol II, leading to the open complex in which the DNA strands are separated. RNA is produced during elongation as Pol II and TFIIF leave the promoter and the other general transcription factors behind. Pol II dissociates during the termination phase, and the CTD is dephosphorylated. Pol II/TFIIF is then recycled to bind to another promoter. 

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. 

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. 

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