RRP40/YOL142W Summary Help

Standard Name RRP40 1
Systematic Name YOL142W
Alias MTR14 2
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 both S1 and KH RNA binding domains; has similarity to human hRrp40p (EXOSC3) (1, 3, 4, 5 and see Summary Paragraph)
Name Description Ribosomal RNA Processing 1
Chromosomal Location
ChrXV:55558 to 56280 | ORF Map | GBrowse
Gbrowse
Gene Ontology Annotations All RRP40 GO evidence and references
  View Computational GO annotations for RRP40
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 9 genes
Resources
Classical genetics
repressible
Large-scale survey
null
repressible
Resources
73 total interaction(s) for 18 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 67
  • Affinity Capture-Western: 4
  • Co-purification: 1
  • Reconstituted Complex: 1

Resources
Expression Summary
histogram
Resources
Length (a.a.) 240
Molecular Weight (Da) 26,556
Isoelectric Point (pI) 5.39
Localization
Phosphorylation PhosphoGRID | PhosphoPep Database
Structure
Homologs
sequence information
ChrXV:55558 to 56280 | ORF Map | GBrowse
SGD ORF map
Last Update Coordinates: 2011-02-03 | Sequence: 2011-02-03
Subfeature details
Relative
Coordinates
Chromosomal
Coordinates
Most Recent Updates
Coordinates Sequence
CDS 1..723 55558..56280 2011-02-03 2011-02-03
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 SGDIDS000005502
SUMMARY PARAGRAPH for RRP40

The exosome complex possesses 3'-5' exonuclease and endoribonucleolytic activities that are essential for diverse ribonucleolytic processes in both the nucleus and the cytoplasm (6, 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 (6), 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 (4, 5).

RRP40 encodes a core subunit of the exosome (1, 3). Like most exosome components, Rrp40p is highly conserved among eukaryotes, including humans hRrp40p (EXOSC3) (4 and references therein). The Rrp40p sequence is predicted to contain both S1 and KH RNA binding domains (15 and references therein), however RNA binding activity of isolated Rrp40p is weak and detectable only in some experimental conditions (16, 17). Rrp40p has been definitively demonstrated to bind manganese (17). RRP40 is an essential gene, but cells depleted for Rrp40p accumulate aberrant forms of rRNA (1, 12).

Last updated: 2009-09-09 Contact SGD

References cited on this page View Complete Literature Guide for RRP40
1) 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
2) Smith SB, et al.  (2011) Pronounced and extensive microtubule defects in a Saccharomyces cerevisiae DIS3 mutant. Yeast 28(11):755-69
3) 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
4) Liu Q, et al.  (2006) Reconstitution, activities, and structure of the eukaryotic RNA exosome. Cell 127(6):1223-37
5) 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
6) Mitchell P, et al.  (1997) The exosome: a conserved eukaryotic RNA processing complex containing multiple 3'-->5' exoribonucleases. Cell 91(4):457-66
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
16) Luz JS, et al.  (2007) Analysis of the Saccharomyces cerevisiae exosome architecture and of the RNA binding activity of Rrp40p. Biochimie 89(5):686-91
17) Oddone A, et al.  (2007) Structural and biochemical characterization of the yeast exosome component Rrp40. EMBO Rep 8(1):63-9