RPL11B/YGR085C Summary Help

Standard Name RPL11B 1
Systematic Name YGR085C
Feature Type ORF, Verified
Description Ribosomal 60S subunit protein L11B; expressed at half the level of Rpl11Ap; involved in ribosomal assembly; depletion causes degradation of 60S proteins and RNA; homologous to mammalian ribosomal protein L11 and bacterial L5; RPL11B has a paralog, RPL11A, that arose from the whole genome duplication (2, 3, 4, 5, 6, 7 and see Summary Paragraph)
Name Description Ribosomal Protein of the Large subunit
Gene Product Alias L11B 3 , L16A 2 , L5 7 , YL22 3 , rp39B 3
Chromosomal Location
ChrVII:648907 to 648383 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Gbrowse
Genetic position: 56 cM
Gene Ontology Annotations All RPL11B GO evidence and references
  View Computational GO annotations for RPL11B
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 12 genes
Resources
Classical genetics
null
Large-scale survey
null
Resources
160 total interaction(s) for 140 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 119
  • Affinity Capture-RNA: 3
  • Affinity Capture-Western: 5
  • Co-purification: 3
  • Two-hybrid: 3

Genetic Interactions
  • Negative Genetic: 21
  • Positive Genetic: 3
  • Synthetic Growth Defect: 1
  • Synthetic Lethality: 2

Resources
Expression Summary
histogram
Resources
Length (a.a.) 174
Molecular Weight (Da) 19,750
Isoelectric Point (pI) 10.73
Localization
Phosphorylation PhosphoGRID | PhosphoPep Database
Structure
Homologs
sequence information
ChrVII:648907 to 648383 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
SGD ORF map
Genetic position: 56 cM
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Relative
Coordinates
Chromosomal
Coordinates
Most Recent Updates
Coordinates Sequence
CDS 1..525 648907..648383 2011-02-03 1996-07-31
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
Resources
External Links All Associated Seq | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000003317
SUMMARY PARAGRAPH for RPL11B

About yeast ribosomes...

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 (8, 7). 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 (9, 7). All yeast ribosomal proteins have a mammalian homolog (1).

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 (10, 11, 12). The expression of some r-protein genes is influenced by Abf1p (13), and most are directly induced by binding of Rap1p to their promoters, which excludes nucleosomes and recruits Fhl1p and Ifh1p to drive transcription (14).

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 (8). Separate ribosomal subunits are then transported from the nucleolus to the cytoplasm where they assemble into mature ribosomes before functioning in translation (15, 16). Blockage of subunit assembly, such as due to inhibition of rRNA synthesis or processing, results in degradation of newly synthesized r-proteins (17, 16). (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.)

Last updated: 2014-06-20 Contact SGD

References cited on this page View Complete Literature Guide for RPL11B
1) Mager WH, et al.  (1997) A new nomenclature for the cytoplasmic ribosomal proteins of Saccharomyces cerevisiae. Nucleic Acids Res 25(24):4872-5
2) Rotenberg MO, et al.  (1988) Depletion of Saccharomyces cerevisiae ribosomal protein L16 causes a decrease in 60S ribosomal subunits and formation of half-mer polyribosomes. Genes Dev 2(2):160-72
3) Planta RJ and Mager WH  (1998) The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae. Yeast 14(5):471-7
4) Miyoshi K, et al.  (2002) Normal assembly of 60 S ribosomal subunits is required for the signaling in response to a secretory defect in Saccharomyces cerevisiae. J Biol Chem 277(21):18334-9
5) Lecompte O, et al.  (2002) Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale. Nucleic Acids Res 30(24):5382-90
6) Byrne KP and Wolfe KH  (2005) The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res 15(10):1456-61
7) Jenner L, et al.  (2012) Crystal structure of the 80S yeast ribosome. Curr Opin Struct Biol 22(6):759-67
8) Venema J and Tollervey D  (1999) Ribosome synthesis in Saccharomyces cerevisiae. Annu Rev Genet 33:261-311
9) Verschoor A, et al.  (1998) Three-dimensional structure of the yeast ribosome. Nucleic Acids Res 26(2):655-61
10) Li B, et al.  (1999) Transcriptional elements involved in the repression of ribosomal protein synthesis. Mol Cell Biol 19(8):5393-404
11) Zhao Y, et al.  (2003) Autoregulation in the biosynthesis of ribosomes. Mol Cell Biol 23(2):699-707
12) Warner JR  (1999) The economics of ribosome biosynthesis in yeast. Trends Biochem Sci 24(11):437-40
13) Mager WH and Planta RJ  (1990) Multifunctional DNA-binding proteins mediate concerted transcription activation of yeast ribosomal protein genes. Biochim Biophys Acta 1050(1-3):351-5
14) Zhao Y, et al.  (2006) Fine-structure analysis of ribosomal protein gene transcription. Mol Cell Biol 26(13):4853-62
15) Moritz M, et al.  (1990) Depletion of yeast ribosomal proteins L16 or rp59 disrupts ribosome assembly. J Cell Biol 111(6 Pt 1):2261-74
16) Milgrom E, et al.  (2007) Loss of vacuolar proton-translocating ATPase activity in yeast results in chronic oxidative stress. J Biol Chem 282(10):7125-36
17) Wang S, et al.  (2007) Influence of Substrate Conformation on the Deglycosylation of Ribonuclease B by Recombinant Yeast Peptide:N-glycanase. Acta Biochim Biophys Sin (Shanghai) 39(1):8-14