Most of the genes encoding subunits of RNA polymerase II are essential (4 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 (14). Also not required for catalytic activity, Rpb9p is involved in selection of the transcription initiation site and control of fidelity (22; 25). 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 (29). 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 (4 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 (8 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 (11, 16). 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 (8, 16). 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 (16). 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 (26). Thus the CTD plays essential roles in the coordinate regulation of gene expression, mRNA production, and the export of mRNAs to the cytoplasm.", "date_edited": "2010-04-29"}, "literature_overview": {"primary_count": 104, "additional_count": 282, "review_count": 58, "go_count": 9, "phenotype_count": 5, "disease_count": 0, "interaction_count": 158, "regulation_count": 2, "ptm_count": 4, "funComplement_count": 0, "htp_count": 16, "total_count": 575}, "disease_overview": {"manual_disease_terms": [], "htp_disease_terms": [], "computational_annotation_count": 0, "date_last_reviewed": null}, "ecnumbers": [], "URS_ID": null, "main_strain": "S288C", "genetic_position": -17.0, "regulation_overview": {"regulator_count": 2, "target_count": 0, "paragraph": {"text": "RPB3 promoter is bound by Fkh1p; RPB3 transcription is regulated by Gcr1p", "date_edited": "2023-11-16", "references": [{"id": 371969, "display_name": "Ostrow AZ, et al. (2014)", "citation": "Ostrow AZ, et al. (2014) Fkh1 and Fkh2 bind multiple chromosomal elements in the S. cerevisiae genome with distinct specificities and cell cycle dynamics. PLoS One 9(2):e87647", "pubmed_id": 24504085, "link": "/reference/S000156933", "year": 2014, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1371/journal.pone.0087647"}, {"display_name": "PMC full text", "link": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3913637/"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/24504085"}]}, {"id": 502259, "display_name": "Hu Z, et al. (2007)", "citation": "Hu Z, et al. (2007) Genetic reconstruction of a functional transcriptional regulatory network. Nat Genet 39(5):683-7", "pubmed_id": 17417638, "link": "/reference/S000122436", "year": 2007, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1038/ng2012"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/17417638"}]}]}}, "reference_mapping": {"552023": 1, "622412": 2, "642215": 3, "594866": 4, "592304": 5, "533862": 6, "592915": 7, "470582": 8, "464821": 9, "585697": 10, "551031": 11, "460342": 12, "492848": 13, "529034": 14, "575677": 15, "464818": 16, "463212": 17, "460333": 18, "465581": 19, "643847": 20, "541014": 21, "638694": 22, "463201": 23, "460367": 24, "473258": 25, "463008": 26, "511123": 27, "543040": 28, "611672": 29, "466275": 30, "468765": 31, "616185": 32, "532715": 33, "644466": 34, "628168": 35}, "history": [{"category": "Name", "history_type": "LSP", "note": "Name: B44", "date_created": "2010-02-16", "references": [{"id": 464821, "display_name": "Sentenac A (1985)", "citation": "Sentenac A (1985) Eukaryotic RNA polymerases. CRC Crit Rev Biochem 18(1):31-90", "pubmed_id": 3893883, "link": "/reference/S000132482", "year": 1985, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.3109/10409238509082539"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/3893883"}]}]}, {"category": "Name", "history_type": "LSP", "note": "Name: RPB3", "date_created": "2000-05-19", "references": [{"id": 552023, "display_name": "Mortimer RK, et al. (1989)", "citation": "Mortimer RK, et al. (1989) Genetic map of Saccharomyces cerevisiae, edition 10. Yeast 5(5):321-403", "pubmed_id": 2678811, "link": "/reference/S000073208", "year": 1989, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1002/yea.320050503"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/2678811"}]}, {"id": 622412, "display_name": "Kolodziej P and Young RA (1989)", "citation": "Kolodziej P and Young RA (1989) RNA polymerase II subunit RPB3 is an essential component of the mRNA transcription apparatus. Mol Cell Biol 9(12):5387-94", "pubmed_id": 2685562, "link": "/reference/S000048315", "year": 1989, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1128/mcb.9.12.5387-5394.1989"}, {"display_name": "PMC full text", "link": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC363706/"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/2685562"}]}, {"id": 642215, "display_name": "Nonet M, et al. (1987)", "citation": "Nonet M, et al. (1987) Eucaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis. Mol Cell Biol 7(5):1602-11", "pubmed_id": 3299050, "link": "/reference/S000041638", "year": 1987, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1128/mcb.7.5.1602-1611.1987"}, {"display_name": "PMC full text", "link": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC365259/"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/3299050"}]}]}], "complexes": [{"format_name": "CPX-2662", "display_name": "DNA-directed RNA polymerase II complex"}]}, tabs: {"id": 1268954, "protein_tab": true, "interaction_tab": true, "summary_tab": true, "go_tab": true, "sequence_section": true, "expression_tab": true, "phenotype_tab": true, "literature_tab": true, "wiki_tab": false, "regulation_tab": true, "sequence_tab": true, "history_tab": true, "homology_tab": true, "disease_tab": false} };
RPB3 / YIL021W Overview
Sequence
The S. cerevisiae Reference Genome sequence is derived from laboratory strain S288C. Download DNA or protein sequence, view genomic context and coordinates. Click "Sequence Details" to view all sequence information for this locus, including that for other strains.
Analyze Sequence
S288C only
BLASTN | BLASTP | Design Primers | Restriction Fragment Map | Restriction Fragment Sizes | Six-Frame Translation
S288C vs. other species
BLASTN vs. fungi | BLASTP at NCBI | BLASTP vs. fungi
S288C vs. other strains
Protein
Basic sequence-derived (length, molecular weight, isoelectric point) and experimentally-determined (median abundance, median absolute deviation) protein information. Click "Protein Details" for further information about the protein such as half-life, abundance, domains, domains shared with other proteins, protein sequence retrieval for various strains, physico-chemical properties, protein modification sites, and external identifiers for the protein.
- Summary
- Rpb3p is 318 amino acids long, of average half-life, moderate in abundance; sumoylated on K9, phosphorylated on S2 and T250, acetylated on 8 lysines
- Length (a.a.)
- 318
- Mol. Weight (Da)
- 35274.8
- Isoelectric Point
- 4.27
- Median Abundance (molecules/cell)
- 9093 +/- 2484
- Half-life (hr)
- 10.8
Alleles
Curated mutant alleles for the specified gene, listed alphabetically. Click on the allele name to open the allele page. Click "SGD search" to view all alleles in search results.
View all RPB3 alleles in SGD search
Gene Ontology
GO Annotations consist of four mandatory components: a gene product, a term from one of the three Gene Ontology (GO) controlled vocabularies (Molecular Function, Biological Process, and Cellular Component), a reference, and an evidence code. SGD has manually curated and high-throughput GO Annotations, both derived from the literature, as well as computational, or predicted, annotations. Click "Gene Ontology Details" to view all GO information and evidence for this locus as well as biological processes it shares with other genes.
- Summary
- Subunit of the RNA polymerase II core complex that contributes to RNA polymerase II activity; involved in transcription and termination of transcription by RNA polymerase II; localized to the nucleoplasm
View computational annotations
Molecular Function
- Manually Curated
- contributes to DNA-directed RNA polymerase activity (IDA)
- contributes to RNA-directed RNA polymerase activity (IDA)
- enables zinc ion binding (RCA)
Biological Process
- Manually Curated
- involved in termination of RNA polymerase II transcription (IMP)
- involved in transcription by RNA polymerase II (IMP)
Cellular Component
- Manually Curated
- located in nucleoplasm (IDA)
- part of RNA polymerase II, core complex (IDA)
Complex
Macromolecular complex annotations are imported from the Complex Portal. These annotations have been derived from physical molecular interaction evidence extracted from the literature and cross-referenced in the entry, or by curator inference from information on homologs in closely related species or by inference from scientific background.
Phenotype
Phenotype annotations for a gene are curated single mutant phenotypes that require an observable (e.g., "cell shape"), a qualifier (e.g., "abnormal"), a mutant type (e.g., null), strain background, and a reference. In addition, annotations are classified as classical genetics or high-throughput (e.g., large scale survey, systematic mutation set). Whenever possible, allele information and additional details are provided. Click "Phenotype Details" to view all phenotype annotations and evidence for this locus as well as phenotypes it shares with other genes.
- Summary
- Essential gene in reference strain S288C; repressible alleles confer sensitivity to hydroxyurea and to UV; conditional alleles confer sensitivity to heat; overexpression confers resistance to rapamycin
Classical Genetics
- null
- overexpression
- reduction of function
- conditional
Large-scale Survey
Interaction
Interaction annotations are curated by BioGRID and include physical or genetic interactions observed between at least two genes. An interaction annotation is composed of the interaction type, name of the interactor, assay type (e.g., Two-Hybrid), annotation type (e.g., manual or high-throughput), and a reference, as well as other experimental details. Click "Interaction Details" to view all interaction annotations and evidence for this locus, including an interaction visualization.
- Summary
- Rpb3p interacts physically with proteins involved in transcription; RPB3 interacts genetically with genes involved in transcription
1593 total interactions for 911 unique genes
Physical Interactions
- Affinity Capture-MS: 960
- Affinity Capture-RNA: 13
- Affinity Capture-Western: 144
- Biochemical Activity: 1
- Co-crystal Structure: 4
- Co-fractionation: 2
- Co-localization: 6
- Co-purification: 18
- PCA: 4
- Protein-RNA: 4
- Proximity Label-MS: 1
- Reconstituted Complex: 24
- Two-hybrid: 2
Genetic Interactions
- Dosage Rescue: 1
- Negative Genetic: 324
- Phenotypic Suppression: 4
- Positive Genetic: 68
- Synthetic Growth Defect: 3
- Synthetic Haploinsufficiency: 2
- Synthetic Lethality: 6
- Synthetic Rescue: 2
Regulation
The number of putative Regulators (genes that regulate it) and Targets (genes it regulates) for the given locus, based on experimental evidence. This evidence includes data generated through high-throughput techniques. Click "Regulation Details" to view all regulation annotations, shared GO enrichment among regulation Targets, and a regulator/target diagram for the locus.
- Regulators
- 2
- Targets
- 0
Expression
Expression data are derived from records contained in the Gene Expression Omnibus (GEO), and are first log2 transformed and normalized. Referenced datasets may contain one or more condition(s), and as a result there may be a greater number of conditions than datasets represented in a single clickable histogram bar. The histogram division at 0.0 separates the down-regulated (green) conditions and datasets from those that are up-regulated (red). Click "Expression Details" to view all expression annotations and details for this locus, including a visualization of genes that share a similar expression pattern.
Summary Paragraph
A summary of the locus, written by SGD Biocurators following a thorough review of the literature. Links to gene names and curated GO terms are included within the Summary Paragraphs.
Last Updated: 2010-04-29
Literature
All manually curated literature for the specified gene, organized into topics according to their relevance to the gene (Primary Literature, Additional Literature, or Review). Click "Literature Details" to view all literature information for this locus, including shared literature between genes.