Comparative overview of RNA polymerase II and III transcription cycles, with focus on RNA polymerase III termination and reinitiation

Abstract

In eukaryotes, RNA polymerase (RNAP) III transcribes hundreds of genes for tRNAs and 5S rRNA, among others, which share similar promoters and stable transcription initiation complexes (TIC), which support rapid RNAP III recycling. In contrast, RNAP II transcribes a large number of genes with highly variable promoters and interacting factors, which exert fine regulatory control over TIC lability and modifications of RNAP II at different transitional points in the transcription cycle. We review data that illustrate a relatively smooth continuity of RNAP III initiation-elongation-termination and reinitiation toward its function to produce high levels of tRNAs and other RNAs that support growth and development.

Keywords: BREd; BREu; DPE; Inr; MTE; Motif 10 element; RNA polymerase III; TAF; TFIID-associated factors; TFIIIB; TFIIIC; downstream B recognition element; downstream promoter element; facilitated recycling; facilitated reinitiation; initiator element; polymerase recycling; term; terminator; transcription reinitiation; upstream B recognition element.

Figure 1. Schematic comparison of the promoter elements and transcription factor recruitment systems for RNAP II and III. (A) RNAP II. Some of the core promoter elements are shown as part of a composite promoter for RNAP II (see text). It should be noted that more elements are known than are shown here, and that the promoters of different genes contain variable combinations of the different elements; the consensus sequences are for metazoans. TBP and other TAFs constitute TFIID. Different TAFs interact with different core promoter elements, as indicated by the double-sided arrows. It should also be noted that TFIID is not required by all genes, at least in yeast, in which another TBP containing complex, SAGA, can take the place of TFIID. RNAP II is recruited largely via interaction with TFIIB, as indicated by the thick double-sided arrow. (B) RNAP III. Schematic of the tRNA gene, type 2 RNAP III promoter. While there are hundreds of tRNA genes of variable sequence, they all share the A and B box promoter elements, the consensus sequences of which were highly conserved through eukaryotic evolution, and the terminator element. Different subunits of TFIIIB and TFIIIC interact with the elements, as indicated by the double-sided arrows. The proximal TFIIIC subunits (Tfc1, Tfc4) comprise the τA module of TFIIIC, which binds to the A box promoter element, whereas the distal subunits (Tfc3, Tfc6) comprise τB binds with high affinity to the B box.^, A major function of TFIIIC τA is to place TFIIIB upstream of the initiation site, where a TATA box is rarely present in S. cerevisiae tRNA genes, but is much more frequently found in S. pombe and human tRNA genes (in the latter, it has recently been shown to be flanked by BREu and BREd elements).^,

Figure 2. RNAP III is equipped for streamlined initiation and reinitiation of stable complexes. (A and B) Comparison of RNAP II and III promoter complexes. (A) Schematic showing RNAP II and its dissociable initiation factors, TFsII A, B, D, E, F and H. During elongation, RNAP II initiation factors dissociate from the promoter complex (see text). (B) Schematic of RNAP III and initiation factors. RNAP III contains its integral subunits C53/C37 (TFIIF like), C31/C34/C82 (TFIIE like) and C11 (TFIIS like). C53/C37 and C11 also function during reinitiation, elongation and termination as well. After initiation, TFIIIB remains bound to the promoter. In the case of RNAP II, the interaction between RNAP II and TFIIB plays major role in recruitment of RNAP II, while for RNAP III, it is the interaction between Brf1 and the TFIIE-like subunit C34. (C and D) RNAP II and III maintained similar peripheral architecture while diverging functionally during evolution. (C) A schematic based on electron microscopic structure of RNAP III (EMDB accession no: EMD-1802).^, Electron densities corresponding to the RNAP III specific subunits C53/C37 and C34/C83/C31 are show in pink and blue, respectively, while RNAP III core is gray and the stalk is green. The N-terminal domain of C11 is shown in yellow. (D) Schematic of 12 subunit RNAP II based on crystal structure (PDB ID:1Y1Y). RNAP II core is shown in gray, RPB9 subunit in yellow and stalk in green. TFIIF dimerization domain is shown in pink (based on crystal structure of human TFIIF; PDB ID:1F3U) and TFIIE complex in blue.

Figure 3. Schematic models of reinitiation in conditions of limiting (in vitro reactions monitoring facilitated reinitiation) or excess RNAP III (presumed in vivo conditions, see text). Under limiting RNAP III concentrations (upper panel), RNAP III recruitment to the TFIIIIB-DNA complex is slower (as compared with when RNAP III is available in excess). Under limiting conditions, the terminating RNAP III is the only source of enzyme for reinitiation. In this case, proximity may drive the chance to reconnect with the initiation complex, which may be augmented by C53/C37-mediated pausing at the terminator. Lack of such a pause may explain the observed effect of C11 and C53/C37 on reinitiation in vitro. When RNAP III is present in excess (lower panel), multiple polymerases occupy the gene simultaneously. In addition, free polymerases in solution may compete with the terminating RNAP III for the initiation complexes.