See More

Ribosomes are highly conserved large ribonucleoprotein (RNP) particles, consisting in yeast of a large 60S subunit and a small 40S subunit, that perform protein synthesis. Yeast ribosomes contain one copy each of four ribosomal RNAs (5S, 5.8S, 18S, and 25S; produced in two separate transcripts encoded within the rDNA repeat present as hundreds of copies on Chromosome 12) and 79 different ribosomal proteins (r-proteins), which are encoded by 137 different genes scattered about the genome, 59 of which are duplicated (6, 4). The 60S subunit contains 46 proteins and three RNA molecules: 25S RNA of 3392 nt, hydrogen bonded to the 5.8S RNA of 158 nt and associated with the 5S RNA of 121 nt. The 40S subunit has a single 18S RNA of 1798 nt and 33 proteins (7, 4). All yeast ribosomal proteins have a mammalian homolog (8).

In a rapidly growing yeast cell, 60% of total transcription is devoted to ribosomal RNA, and 50% of RNA polymerase II transcription and 90% of mRNA splicing are devoted to the production of mRNAs for r-proteins. Coordinate regulation of the rRNA genes and 137 r-protein genes is affected by nutritional cues and a number of signal transduction pathways that can abruptly induce or silence the ribosomal genes, whose transcripts have naturally short lifetimes, leading to major implications for the expression of other genes as well (9, 10, 11). The expression of some r-protein genes is influenced by Abf1p (12), and most are directly induced by binding of Rap1p to their promoters, which excludes nucleosomes and recruits Fhl1p and Ifh1p to drive transcription (13).

Ribosome assembly is a complex process, with different steps occurring in different parts of the cell. Ribosomal protein genes are transcribed in the nucleus, and the mRNA is transported to the cytoplasm for translation. The newly synthesized r-proteins then enter the nucleus and associate in the nucleolus with the two rRNA transcripts, one of which is methylated and pseudouridylated (view sites of modifications), and then cleaved into three individual rRNAs (18S, 5.8S, and 25S) as part of the assembly process (6). Separate ribosomal subunits are then transported from the nucleolus to the cytoplasm where they assemble into mature ribosomes before functioning in translation (14, 15). Blockage of subunit assembly, such as due to inhibition of rRNA synthesis or processing, results in degradation of newly synthesized r-proteins (16, 15). (For more information on the early steps of rRNA processing and small ribosomal subunit assembly, see the summary paragraph for the U3 snoRNA, encoded by snR17A and snR17B.)", "date_edited": "2007-02-14"}, "literature_overview": {"primary_count": 27, "additional_count": 61, "review_count": 11, "go_count": 1, "phenotype_count": 6, "disease_count": 1, "interaction_count": 64, "regulation_count": 5, "ptm_count": 3, "funComplement_count": 0, "htp_count": 43, "total_count": 201}, "disease_overview": {"manual_disease_terms": [{"annotation_type": "manually curated", "qualifiers": [null], "term": {"link": "/disease/DOID:1339", "display_name": "Diamond-Blackfan anemia"}, "evidence_codes": [{"display_name": "IGI", "link": "http://wiki.geneontology.org/index.php/Inferred_from_Genetic_Interaction_(IGI)"}, {"display_name": "ISS", "link": "http://wiki.geneontology.org/index.php/Inferred_from_Sequence_or_structural_Similarity_(ISS)"}]}], "htp_disease_terms": [], "computational_annotation_count": 0, "date_last_reviewed": "2024-05-06", "paragraph": "Yeast RPL2B is homologous to human RPL8 and has been used to study mutations associated with Diamond-Blackfan anemia"}, "ecnumbers": [], "URS_ID": null, "main_strain": "S288C", "regulation_overview": {"regulator_count": 16, "target_count": 0}, "reference_mapping": {"592544": 1, "588764": 2, "548623": 3, "397935": 4, "526423": 5, "592595": 6, "517471": 7, "556638": 8, "631529": 9, "554134": 10, "585697": 11, "608664": 12, "518051": 13, "592541": 14, "508692": 15, "508689": 16, "316136": 17}, "history": [{"category": "Name", "history_type": "LSP", "note": "Name: RPL2B", "date_created": "2000-05-19", "references": [{"id": 551590, "display_name": "SGD (2007)", "citation": "SGD (2007) Information without a citation in SGD ", "pubmed_id": null, "link": "/reference/S000073348", "year": 2007, "urls": []}]}, {"category": "Name", "history_type": "LSP", "note": "Name: RPL5A", "date_created": "2010-02-16", "references": []}, {"category": "Name", "history_type": "LSP", "note": "Name: LOT2", "date_created": "2010-02-16", "references": []}, {"category": "Name", "history_type": "LSP", "note": "Name: rp8", "date_created": "2010-02-16", "references": [{"id": 592544, "display_name": "Planta RJ and Mager WH (1998)", "citation": "Planta RJ and Mager WH (1998) The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae. Yeast 14(5):471-7", "pubmed_id": 9559554, "link": "/reference/S000058461", "year": 1998, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1002/(SICI)1097-0061(19980330)14:5<471::AID-YEA241>3.0.CO;2-U"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/9559554"}]}]}, {"category": "Name", "history_type": "LSP", "note": "Name: L5B", "date_created": "2010-02-16", "references": [{"id": 592544, "display_name": "Planta RJ and Mager WH (1998)", "citation": "Planta RJ and Mager WH (1998) The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae. Yeast 14(5):471-7", "pubmed_id": 9559554, "link": "/reference/S000058461", "year": 1998, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1002/(SICI)1097-0061(19980330)14:5<471::AID-YEA241>3.0.CO;2-U"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/9559554"}]}]}, {"category": "Name", "history_type": "LSP", "note": "Name: L2B", "date_created": "2010-02-16", "references": [{"id": 592544, "display_name": "Planta RJ and Mager WH (1998)", "citation": "Planta RJ and Mager WH (1998) The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae. Yeast 14(5):471-7", "pubmed_id": 9559554, "link": "/reference/S000058461", "year": 1998, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1002/(SICI)1097-0061(19980330)14:5<471::AID-YEA241>3.0.CO;2-U"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/9559554"}]}]}, {"category": "Name", "history_type": "LSP", "note": "Name: YL6", "date_created": "2010-02-16", "references": [{"id": 592544, "display_name": "Planta RJ and Mager WH (1998)", "citation": "Planta RJ and Mager WH (1998) The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae. Yeast 14(5):471-7", "pubmed_id": 9559554, "link": "/reference/S000058461", "year": 1998, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1002/(SICI)1097-0061(19980330)14:5<471::AID-YEA241>3.0.CO;2-U"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/9559554"}]}]}, {"category": "Name", "history_type": "LSP", "note": "Name: L2", "date_created": "2012-10-12", "references": [{"id": 397935, "display_name": "Jenner L, et al. (2012)", "citation": "Jenner L, et al. (2012) Crystal structure of the 80S yeast ribosome. Curr Opin Struct Biol 22(6):759-67", "pubmed_id": 22884264, "link": "/reference/S000150523", "year": 2012, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1016/j.sbi.2012.07.013"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/22884264"}]}]}, {"category": "Name", "history_type": "LSP", "note": "Name: uL2", "date_created": "2016-08-09", "references": [{"id": 316136, "display_name": "Ban N, et al. (2014)", "citation": "Ban N, et al. (2014) A new system for naming ribosomal proteins. Curr Opin Struct Biol 24:165-9", "pubmed_id": 24524803, "link": "/reference/S000182084", "year": 2014, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1016/j.sbi.2014.01.002"}, {"display_name": "PMC full text", "link": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4358319/"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/24524803"}]}]}, {"category": "Mapping", "history_type": "SEQUENCE", "note": "Mapping: Edition 14: The name RPL2B was previously used to refer to YDR012W, which is now called RPL4B and encodes ribosomal protein L4B", "date_created": "1997-10-20", "references": [{"id": 587084, "display_name": "Cherry JM, et al. (1997)", "citation": "Cherry JM, et al. (1997) Genetic and physical maps of Saccharomyces cerevisiae. Nature 387(6632 Suppl):67-73", "pubmed_id": 9169866, "link": "/reference/S000060841", "year": 1997, "urls": [{"display_name": "PMC full text", "link": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057085/"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/9169866"}]}]}], "complexes": []}; RPL2B Regulation | SGD

AboutBlogDownloadExploreHelpGet Data
Regulation Help

RPL2B / YIL018W Regulation

Transcriptional regulation information for a gene, including any predicted DNA binding site motifs (YeTFaSCo) for the gene's protein product, as well as any of its targets (genes it regulates) or regulators (genes that regulate it), based on experimental evidence. For genes with regulatory targets, shared GO Biological Process terms for these targets are listed.

    Domains and Classification

    Collection of domains associated with the protein based on various sources, including the protein coordinates for the domain, a domain Description, a Source and corresponding accession ID, and the number of S. cerevisiae genes that share the same domain.

    Increase the total number of rows showing on this page by using the pull-down located below the table, or use the page scroll at the table's top right to browse through its pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table.

    Gene Protein Coordinates Accession ID Description Source No. of Genes with Domain

    Targets

    This table lists putative transcriptional regulatory targets for the central gene represented on this page. These targets were identified based on the presence of predicted regulator binding sites or experimental regulator binding in the target promoter, and/or changes in the target gene’s transcript levels in regulator mutant strains. Data includes high-throughput techniques such as microarray, RNA-seq, and ChIP assays; information about the experiment and assay type, constructs, conditions, and strains, as well as a reference, are provided for each Regulator annotation.

    Manually Curated

    Increase the total number of rows displayed on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; to filter the table by a specific experiment type, type a keyword into the Filter box (for example, “microarray”); download this table as a .txt file using the Download button or click Analyze to further view and analyze the list of target genes using GO Term Finder, GO Slim Mapper, or SPELL.

    Target Direction Regulation of Happens During Evidence Strain Background Reference

     

    High-throughput

    Increase the total number of rows displayed on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; to filter the table by a specific experiment type, type a keyword into the Filter box (for example, “microarray”); download this table as a .txt file using the Download button or click Analyze to further view and analyze the list of target genes using GO Term Finder, GO Slim Mapper, or SPELL.

    Target Direction Regulation of Happens During Evidence Strain Background Reference

    Increase the total number of rows displayed on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; to filter the table by a specific experiment type, type a keyword into the Filter box (for example, “microarray”); download this table as a .txt file using the Download button or click Analyze to further view and analyze the list of target genes using GO Term Finder, GO Slim Mapper, or SPELL.

    Target Direction Regulation of Happens During Evidence Strain Background Reference

    Shared GO Processes Among Targets

    The shared GO processes listed in this table are based on the data presented in the Targets section above; shared GO terms, the number of target genes that share them, and the P-value are all indicated in the table.

    Increase the total number of rows displayed on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table; download this table as a .txt file using the Download button; after filtering the above table, the option to ”Recalculate With New Filter” will appear next to the Download button in this Shared GO Processes table.

    GO Term ID GO Term Number of genes P-Value

    Regulators

    This table lists genes that are putative regulators of the central gene represented on this page, based primarily on experiments showing that a regulator binds to the gene’s promoter or affects the gene’s transcription when the regulator is mutated. This includes data generated by high-throughput techniques such as microarray, RNA-seq, and ChIP assays; information about the experiment and assay type, constructs, conditions, and strains, as well as a reference, are provided for each Regulator annotation.

    Manually Curated

    Increase the total number of rows displayed on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; to filter the table by a specific experiment type, type a keyword into the Filter box (for example, “microarray”); download this table as a .txt file using the Download button or click Analyze to further view and analyze the list of target genes using GO Term Finder, GO Slim Mapper, or SPELL.

    Regulator Happens During Regulator Type Direction Regulation Of Happens During Evidence Strain Background Reference

     

    High-throughput

    Increase the total number of rows displayed on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; to filter the table by a specific experiment type, type a keyword into the Filter box (for example, “microarray”); download this table as a .txt file using the Download button or click Analyze to further view and analyze the list of target genes using GO Term Finder, GO Slim Mapper, or SPELL.

    Regulator Happens During Regulator Type Direction Regulation Of Happens During Evidence Strain Background Reference

    Increase the total number of rows displayed on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; to filter the table by a specific experiment type, type a keyword into the Filter box (for example, “microarray”); download this table as a .txt file using the Download button or click Analyze to further view and analyze the list of target genes using GO Term Finder, GO Slim Mapper, or SPELL.

    Regulator Happens During Regulator Type Direction Regulation Of Happens During Evidence Strain Background Reference

    Regulation Network

    This diagram displays targets (purple) and regulators (green) of the given gene (blue) based on the data presented in the Targets and Regulators tables and therefore includes high-throughput data generated by techniques such as microarray, RNA-seq, and ChIP assays. The arrows move in the direction of Regulator -> Target and include any regulatory relationships between genes other than the given gene.

    © Stanford University, Stanford, CA 94305.