RPB9/YGL070C Summary Help

Standard Name RPB9 1, 2
Systematic Name YGL070C
Alias SSU73 3
Feature Type ORF, Verified
Description RNA polymerase II subunit B12.6; contacts DNA; mutations affect transcription start site selection and fidelity of transcription (4, 5, 6, 7, 8 and see Summary Paragraph)
Also known as: SHI 9
Name Description RNA Polymerase B 1
Gene Product Alias B12.6 10
Chromosomal Location
ChrVII:374827 to 374459 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Gene Ontology Annotations All RPB9 GO evidence and references
  View Computational GO annotations for RPB9
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 6 genes
Classical genetics
Large-scale survey
192 total interaction(s) for 76 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 94
  • Affinity Capture-Western: 11
  • Co-crystal Structure: 3
  • Co-purification: 10
  • PCA: 4
  • Two-hybrid: 5

Genetic Interactions
  • Dosage Rescue: 3
  • Negative Genetic: 1
  • Phenotypic Enhancement: 6
  • Phenotypic Suppression: 1
  • Synthetic Growth Defect: 21
  • Synthetic Haploinsufficiency: 1
  • Synthetic Lethality: 27
  • Synthetic Rescue: 5

Expression Summary
Length (a.a.) 122
Molecular Weight (Da) 14,288
Isoelectric Point (pI) 7.53
Phosphorylation PhosphoGRID | PhosphoPep Database
sequence information
ChrVII:374827 to 374459 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..369 374827..374459 2011-02-03 1996-07-31
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
External Links All Associated Seq | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000003038

Nuclear transcription in S. cerevisiae is performed by three multisubunit nuclear RNA polymerases (RNAPs) that are conserved in all eukaryotes (10, 11 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 (12). 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 (13), four of the five snRNAs (U1, U2, U4, and U5; 14), the RNase MRP RNA encoded by NME1 (12), and the telomerase RNA encoded by TLC1 (15). RNA polymerase III produces the 5S rRNA, all nuclear tRNAs, the U6 snRNA (16), the snR52 snoRNA (13), the RNase P RNA encoded by RPR1 (12), and the 7SL RNA component of the signal recognition particle encoded by SCR1 (12).

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 17). 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 18, 19, 20, and 21).

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 22). 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 23).

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 (24). 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 25, 11, and 26). For tables showing the correspondence between the subunits of the three nuclear RNA polymerases in S. cerevisiae see Cramer et al. 2008 (26) and Werner et al. 2009 (25); to see the correspondence with those of Archaea and bacteria see Cramer 2002 (11).

About RNA polymerase II

In S. cerevisiae, the RNA polymerase II core enzyme (RNAP II) is composed of twelve subunits. RPO21, RPB2, RPB3, RPB4, RPB7, RPB9, and RPB11 encode subunits unique to RNAP II, while RPB5, RPO26, RPB8, RPC10, and RPB10 encode shared subunits (11). A subcomplex composed of Rpb4p and Rpb7p (Rpb4/7) is substoichiometric in some growth conditions and easily dissociated during purification (27, 28). Purified enzyme composed of the remaining 10 subunits is capable of polymerizing RNA in vitro, but does not recognize or initiate at promoter sequences (29, 27). The structure of the core enzyme has been determined, with and without the Rpb4/7 subcomplex, and provides insight into the specific roles of the subunits within the complex (30, 31, 11 and references therein).

Most of the genes encoding subunits of RNA polymerase II are essential (5 and references therein). However null mutations in rpb4 or rpb9 are not essential in standard laboratory conditions, but become so when cells are subjected to stresses such as reduced or elevated temperature or absence of nutrients such as inositol. While not required for catalytic activity, Rpb4p as part of the Rpb4/7 subcomplex is required for response to heat or cold stress, recovery from stationary phase, and sporulation, and is also thought to be involved in response to transcriptional activators, mRNA export during heat stress, and regulation of transcription coupled repair (32). Also not required for catalytic activity, Rpb9p is involved in selection of the transcription initiation site and control of fidelity (4; 8). Partial truncations of the carboxyl terminal domain (CTD) of the largest subunit RPO21, or conditional mutations in one of the essential subunits, may also produce the combined phenotype of cold sensitivity, heat sensitivity and inositol auxotrophy. This combination of phenotypes appears to be due to sensitivity of specific genes, such as INO1, to reduction in the function or quantity of RNAP II (33). Mutations in core subunits such as RPO21, RPB2, or RPB3 often affect the basic functions of core enzyme assembly and catalytic properties of initiation, elongation, or termination, as well as the association of the core enzyme with the other complexes required for RNAP II function in vivo (5 and references therein).

In yeast, as in other eukaryotes, fully competent RNA polymerase II activity in vivo requires the association of the full core enzyme with several other complexes, including the general transcription factors (GTFs) TFIID, TFIIB, TFIIF, TFIIE, and TFIIH. Some of the GTFs bind directly to DNA to identify the promoter sequence and recruit the remaining GTFs and RNAP II to the promoter to form the preinitiation complex (PIC). In addition, Mediator, a large modular complex, is required for RNAP II to respond to gene-specific activators. Some of these factors travel with RNAP II along the transcription unit. When purified together, RNAP II and Mediator are sometimes referred to as "holoenzyme", though it appears that multiple "holoenzymes" have been purified with slightly varied subunit composition depending on the purification method, which may reflect the modular nature of Mediator as well as the need to respond to different regulatory signals (34 and references therein).

The largest subunit RPO21 contains a repetitive carboxyl terminal domain (CTD), unique to type II RNA polymerases, composed of numerous copies of the seven-amino-acid sequence YSPTSPS. Though the number of repeats varies between the largest subunits of different species, deletion of the entire CTD is invariably lethal even though it is not required in vitro for catalytic activity (29, 35). The CTD undergoes cycles of phosphorylation and dephosphorylation, especially on serines 2 and 5. Its phosphorylation state regulates interactions of the core enzyme with other protein complexes such as the GTFs, Mediator, and chromatin remodelling enzymes, thus regulating both initiation and elongation in vivo (34, 35). During production of the primary transcript, the phosphorylation state of the CTD changes to allow the transcribing polymerase to associate with the capping, splicing, polyadenylation, and mRNA export machinery (35). These associations are required for normal processing of pre-mRNAs to generate mRNAs and to export them to the cytoplasm, as well as for normal termination of transcription by RNAP II (36). Thus the CTD plays essential roles in the coordinate regulation of gene expression, mRNA production, and the export of mRNAs to the cytoplasm.

Last updated: 2010-02-04 Contact SGD

References cited on this page View Complete Literature Guide for RPB9
1) Nonet M, et al.  (1987) Eucaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis. Mol Cell Biol 7(5):1602-11
2) Woychik NA, et al.  (1991) Yeast RNA polymerase II subunit RPB9 is essential for growth at temperature extremes. J Biol Chem 266(28):19053-5
3) Sun ZW, et al.  (1996) Functional interaction between TFIIB and the Rpb9 (Ssu73) subunit of RNA polymerase II in Saccharomyces cerevisiae. Nucleic Acids Res 24(13):2560-6
4) Hull MW, et al.  (1995) RNA polymerase II subunit RPB9 is required for accurate start site selection. Genes Dev 9(4):481-90
5) Archambault J and Friesen JD  (1993) Genetics of eukaryotic RNA polymerases I, II, and III. Microbiol Rev 57(3):703-24
6) Hampsey M  (1998) Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol Mol Biol Rev 62(2):465-503
7) Cramer P, et al.  (2000) Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288(5466):640-9
8) Walmacq C, et al.  (2009) Rpb9 Subunit Controls Transcription Fidelity by Delaying NTP Sequestration in RNA Polymerase II. J Biol Chem 284(29):19601-12
9) Furter-Graves EM, et al.  (1994) Role of a small RNA pol II subunit in TATA to transcription start site spacing. Nucleic Acids Res 22(23):4932-6
10) Sentenac A  (1985) Eukaryotic RNA polymerases. CRC Crit Rev Biochem 18(1):31-90
11) Cramer P  (2002) Multisubunit RNA polymerases. Curr Opin Struct Biol 12(1):89-97
12) Dieci G, et al.  (2007) The expanding RNA polymerase III transcriptome. Trends Genet 23(12):614-22
13) Moqtaderi Z and Struhl K  (2004) Genome-wide occupancy profile of the RNA polymerase III machinery in Saccharomyces cerevisiae reveals loci with incomplete transcription complexes. Mol Cell Biol 24(10):4118-27
14) Xue D, et al.  (2000) U snRNP assembly in yeast involves the La protein. EMBO J 19(7):1650-60
15) Chapon C, et al.  (1997) Polyadenylation of telomerase RNA in budding yeast. RNA 3(11):1337-51
16) Eschenlauer JB, et al.  (1993) Architecture of a yeast U6 RNA gene promoter. Mol Cell Biol 13(5):3015-26
17) Warner JR  (1999) The economics of ribosome biosynthesis in yeast. Trends Biochem Sci 24(11):437-40
18) Grummt I  (2003) Life on a planet of its own: regulation of RNA polymerase I transcription in the nucleolus. Genes Dev 17(14):1691-702
19) Willis IM, et al.  (2004) Signaling repression of transcription by RNA polymerase III in yeast. Prog Nucleic Acid Res Mol Biol 77:323-53
20) Mayer C and Grummt I  (2006) Ribosome biogenesis and cell growth: mTOR coordinates transcription by all three classes of nuclear RNA polymerases. Oncogene 25(48):6384-91
21) Xiao L and Grove A  (2009) Coordination of Ribosomal Protein and Ribosomal RNA Gene Expression in Response to TOR Signaling. Curr Genomics 10(3):198-205
22) Shaw P and Doonan J  (2005) The nucleolus. Playing by different rules? Cell Cycle 4(1):102-5
23) McFarlane RJ and Whitehall SK  (2009) tRNA genes in eukaryotic genome organization and reorganization. Cell Cycle 8(19):3102-6
24) Kuhn CD, et al.  (2007) Functional architecture of RNA polymerase I. Cell 131(7):1260-72
25) Werner M, et al.  (2009) Structure-function analysis of RNA polymerases I and III. Curr Opin Struct Biol 19(6):740-5
26) Cramer P, et al.  (2008) Structure of eukaryotic RNA polymerases. Annu Rev Biophys 37():337-52
27) Edwards AM, et al.  (1991) Two dissociable subunits of yeast RNA polymerase II stimulate the initiation of transcription at a promoter in vitro. J Biol Chem 266(1):71-5
28) Choder M and Young RA  (1993) A portion of RNA polymerase II molecules has a component essential for stress responses and stress survival. Mol Cell Biol 13(11):6984-91
29) Christie KR, et al.  (1994) Purified yeast RNA polymerase II reads through intrinsic blocks to elongation in response to the yeast TFIIS analogue, P37. J Biol Chem 269(2):936-43
30) Meyer PA, et al.  (2009) Structure of the 12-subunit RNA polymerase II refined with the aid of anomalous diffraction data. J Biol Chem 284(19):12933-9
31) Armache KJ, et al.  (2005) Structures of complete RNA polymerase II and its subcomplex, Rpb4/7. J Biol Chem 280(8):7131-4
32) Sampath V and Sadhale P  (2005) Rpb4 and Rpb7: a sub-complex integral to multi-subunit RNA polymerases performs a multitude of functions. IUBMB Life 57(2):93-102
33) Archambault J, et al.  (1996) Underproduction of the largest subunit of RNA polymerase II causes temperature sensitivity, slow growth, and inositol auxotrophy in Saccharomyces cerevisiae. Genetics 142(3):737-47
34) Woychik NA and Hampsey M  (2002) The RNA polymerase II machinery: structure illuminates function. Cell 108(4):453-63
35) Phatnani HP and Greenleaf AL  (2006) Phosphorylation and functions of the RNA polymerase II CTD. Genes Dev 20(21):2922-36
36) Proudfoot NJ, et al.  (2002) Integrating mRNA processing with transcription. Cell 108(4):501-12