SUMMARY PARAGRAPH for RET1
Nuclear transcription in S. cerevisiae is performed by three multisubunit nuclear RNA polymerases (RNAPs) that are conserved in all eukaryotes (7, 8 and references therein). The roles of these three RNA polymerases are generally conserved across eukaryotes, particularly with respect to production of rRNAs, mRNAs, and tRNAs, though production of other small RNAs is somewhat variable between RNAP II and RNAP III in different species (9). In S. cerevisiae, RNA polymerase I transcribes rDNA to produce the 35S primary rRNA transcript that is processed to produce three of the four mature ribosomal rRNAs: 25S, 18S, and 5.8S. RNA polymerase II produces all nuclear mRNAs, all of the snoRNAs except snR52 (10), four of the five snRNAs (U1, U2, U4, and U5; 11), the RNase MRP RNA encoded by NME1 (9), and the telomerase RNA encoded by TLC1 (12). RNA polymerase III produces the 5S rRNA, all nuclear tRNAs, the U6 snRNA (13), the snR52 snoRNA (10), the RNase P RNA encoded by RPR1 (9), and the 7SL RNA component of the signal recognition particle encoded by SCR1 (9).
Coordinate regulation of these three RNA polymerases is essential, since in rapidly growing yeast cells, much of the transcriptional output of the cell is devoted to the production of ribosomes. About 60% of total cellular transcription is devoted to transcription by RNAP I of the rRNA genes, which comprise about 10% of the entire genome. While mRNAs generally only comprise 5% of total cellular RNA and the 137 ribosomal protein (RP) genes represent only 2% of the genome, it is estimated that 50% of RNAP II transcription occurs on RP genes. RNAP II is also responsible for production of the majority of the snoRNAs, which are collectively involved in maturation of the ribosome. RNAP III plays a similarly important role in production of ribosomes and the process of translation, producing both the 5S rRNA and all nuclear tRNAs, which constitute about 15% of total cellular RNA (reviewed in 14). The TOR pathway is a major factor in this coordinate regulation as it regulates the activity of all three nuclear RNAPs in response to nutrient availability and growth conditions (reviewed in 15, 16, 17, and 18).
In addition to producing the majority of cellular RNA, RNAP I and RNAP III may also play roles in nuclear architecture and genome organization. RNAP I activity may be involved in organizing the rDNA repeats into the nucleolus (reviewed in 19). Active tRNA genes transcribed by RNAP III appear to act as chromatin boundary elements that affect both transcription and DNA replication. Additionally, recombination between dispersed tRNA genes may be a source of genetic instability and evolutionary change (reviewed in 20).
Five genes (RPB5, RPO26, RPB8, RPB10, and RPC10) encode subunits common to all three of the nuclear RNA polymerases. Two genes (RPC40 and RPC19) encode subunits present in both RNAP I and RNAP III; RPB3 and RPB11 encode the corresponding RNAP II subunits. Five more subunits are encoded by a separate gene for each polymerase, but are considered functional equivalents of each other. Thus there are twelve subunits that are conserved in all three of the nuclear RNA polymerases, eleven of which correspond to subunits of Archaeal RNAPs, and five of which also correspond to the subunits of E. coli RNAP. In each, ten of these comprise the enzyme cores, while Rpb4/7 (RNAP II), Rpa14/43 (RNAP I), and Rpc17/25 (RNAP III) form heterodimers which associate with this core and have roles in initiation (21). RNAPs I and III also have two subunits which are homologous to the subunits of the TFIIF general initiation factor for RNAP II, and RNAP III has three additional unique subunits (reviewed in 22, 8, and 23). For tables showing the correspondence between the subunits of the three nuclear RNA polymerases in S. cerevisiae see Cramer et al. 2008 (23) and Werner et al. 2009 (22); to see the correspondence with those of Archaea and bacteria see Cramer 2002 (8).
About RNA polymerase III
In S. cerevisiae, the RNA polymerase III enzyme is composed of seventeen subunits, all of which are essential. RPB5, RPO26, RPB8, RPC10, RPB10, RPC40, and RPC19 encode subunits shared with one or both of the other two nuclear RNA polymerases. RPC53 and RPC37 encode subunits with counterparts in RNAP I, and RPO31, RET1, RPC25, RPC17, and RPC11 encode subunits with counterparts in both RNA polymerases I and II. RPC82, RPC34, and RPC31 encode subunits unique to RNAP III and homologous to a detachable subassembly of human RNAP III implicated in response to specific transcription factors (reviewed in 24, 25, 23, and 22).
In contrast to RNAP I and II promoters, most RNAP III promoters are internal to the expressed sequence of the RNA being transcribed, though there are some exceptions such as the well studied U6 snRNA (encoded by snR6). These internal promoters can be divided into classes based on their organization. Class 1 genes are represented by the 5S rRNA genes, present within the intragenic spacer of the 37S rDNA, and are the only genes which require the specific DNA-binding initiation factor TFIIIA (encoded by PZF1), the archetype zinc finger protein, which then recruits TFIIIC. Class 2 genes comprise the tRNA genes, and others with similar promoter structures, containing internal box A and box B sequence elements which are recognized directly by the six subunit DNA-binding initiation factor TFIIIC (encoded by TFC1, TFC3, TFC4, TFC6, TFC7, and TFC8). In both classes, TFIIIC recruits TFIIIB, which does not bind to DNA by itself despite the fact that it contains the TATA-binding protein TBP (encoded by SPT15), as well as two other subunits (BDP1 and BRF1). Once bound to DNA, TFIIIB brings RNAP III to the promoter and helps initiate transcription (reviewed in 24, 26, and 22). RNAP III transcription is regulated by at least two nutrient-sensing signal transduction pathways, RAS and TOR. Both of these work through Maf1p, which is evolutionarily conserved from yeast to humans, and which represses RNAP III activity when yeast cells experience stress or unfavorable growth conditions (reviewed in 27).
Last updated: 2010-04-29 
