RRP4/YHR069C Summary Help

Standard Name RRP4 1
Systematic Name YHR069C
Feature Type ORF, Verified
Description Exosome non-catalytic core component; involved in 3'-5' RNA processing and degradation in both the nucleus and the cytoplasm; predicted to contain RNA binding domains; has similarity to human hRrp4p (EXOSC2) (2, 3, 4, 5, 6 and see Summary Paragraph)
Name Description Ribosomal RNA Processing 1
Chromosomal Location
ChrVIII:234658 to 233579 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Gbrowse
Gene Ontology Annotations All RRP4 GO evidence and references
  View Computational GO annotations for RRP4
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 2 genes
Resources
Classical genetics
conditional
null
repressible
Large-scale survey
conditional
null
Resources
125 total interaction(s) for 46 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 83
  • Affinity Capture-RNA: 1
  • Affinity Capture-Western: 9
  • Co-purification: 1
  • PCA: 2
  • Reconstituted Complex: 1
  • Two-hybrid: 5

Genetic Interactions
  • Dosage Rescue: 1
  • Negative Genetic: 11
  • Phenotypic Enhancement: 2
  • Phenotypic Suppression: 1
  • Positive Genetic: 5
  • Synthetic Lethality: 3

Resources
Expression Summary
histogram
Resources
Length (a.a.) 359
Molecular Weight (Da) 39,427
Isoelectric Point (pI) 6.19
Localization
Phosphorylation PhosphoGRID | PhosphoPep Database
Structure
Homologs
sequence information
ChrVIII:234658 to 233579 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
SGD ORF map
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Relative
Coordinates
Chromosomal
Coordinates
Most Recent Updates
Coordinates Sequence
CDS 1..1080 234658..233579 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 SGDIDS000001111
SUMMARY PARAGRAPH for RRP4

The exosome complex possesses 3'-5' exonuclease and endoribonucleolytic activities that are essential for diverse ribonucleolytic processes in both the nucleus and the cytoplasm (3, 7, 8). The nuclear exosome is associated with the TRAMP complex and is involved in RNA catabolic processes including RNA surveillance (9, 10 and references therein), pre-mRNA turnover (11) and the production of mature 3' ends for snoRNAs, snRNAs and rRNAs (7, 12 and references therein). The cytoplasmic exosome is associated with Ski7p and the SKI complex and is involved in RNA catabolic processes that include both the routine turnover of normal mRNA (13) as well as the degradation of aberrant mRNAs (14 and references therein). The 10-subunit core exosome complex (Csl4p, Rrp4p, Rrp40p, Ski6p, Rrp42p, Rrp43p, Rrp45p, Rrp46p, Mtr3p, Dis3p) is the same in both locations, but the nuclear exosome contains an additional subunit (Rrp6p) and two additional accessory factors (Lrp1p, Mpp6p) (8).

Although the exosome was originally described as a "complex of exonucleases," with multiple subunits proposed to have RNase activity (3), later work has shown that this mechanism is unlikely in yeast. With the exception of Ski6p, none of the yeast subunits that show homology to E. coli RNase PH retain the active site residues seen in the bacterial or archael enzymes. Further research has also demonstrated that most, if not all, detectable enzymatic activity resides in the Dis3p and Rrp6p subunits (5, 6).

RRP4 encodes a core subunit of the exosome amd is predicted to contain both S1 and KH RNA binding domains (3, 2, 4, 15 and references therein). Like most exosome components, Rrp4p is highly conserved among eukaryotes, including humans (hRrp4p (EXOSC2)) (5 and references therein). RRP4 is an essential gene, but both temperature sensitive mutant cells (at restrictive temperature) and cells depleted for Rrp4p accumulate aberrant forms of rRNA (3, 1, 12). The same temperature sensitive mutant also accumulates aberrant forms of snoRNA and snRNA (7) and displays defects in 3' to 5' mRNA degradation (13).

Last updated: 2009-09-09 Contact SGD

References cited on this page View Complete Literature Guide for RRP4
1) Mitchell P, et al.  (1996) The 3' end of yeast 5.8S rRNA is generated by an exonuclease processing mechanism. Genes Dev 10(4):502-13
2) Allmang C, et al.  (1999) The yeast exosome and human PM-Scl are related complexes of 3' --> 5' exonucleases. Genes Dev 13(16):2148-58
3) Mitchell P, et al.  (1997) The exosome: a conserved eukaryotic RNA processing complex containing multiple 3'-->5' exoribonucleases. Cell 91(4):457-66
4) Synowsky SA, et al.  (2006) Probing genuine strong interactions and post-translational modifications in the heterogeneous yeast exosome protein complex. Mol Cell Proteomics 5(9):1581-92
5) Liu Q, et al.  (2006) Reconstitution, activities, and structure of the eukaryotic RNA exosome. Cell 127(6):1223-37
6) Dziembowski A, et al.  (2007) A single subunit, Dis3, is essentially responsible for yeast exosome core activity. Nat Struct Mol Biol 14(1):15-22
7) van Hoof A, et al.  (2000) Yeast exosome mutants accumulate 3'-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs. Mol Cell Biol 20(2):441-52
8) Synowsky SA, et al.  (2009) Comparative multiplexed mass spectrometric analyses of endogenously expressed yeast nuclear and cytoplasmic exosomes. J Mol Biol 385(4):1300-13
9) Vanacova S, et al.  (2005) A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol 3(6):e189
10) LaCava J, et al.  (2005) RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121(5):713-24
11) Bousquet-Antonelli C, et al.  (2000) Identification of a regulated pathway for nuclear pre-mRNA turnover. Cell 102(6):765-75
12) Allmang C, et al.  (2000) Degradation of ribosomal RNA precursors by the exosome. Nucleic Acids Res 28(8):1684-91
13) Jacobs JS, et al.  (1998) The 3' to 5' degradation of yeast mRNAs is a general mechanism for mRNA turnover that requires the SKI2 DEVH box protein and 3' to 5' exonucleases of the exosome complex. EMBO J 17(5):1497-506
14) Schaeffer D, et al.  (2008) Determining in vivo activity of the yeast cytoplasmic exosome. Methods Enzymol 448:227-39
15) Schaeffer D, et al.  (2009) The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities. Nat Struct Mol Biol 16(1):56-62