RRP6/YOR001W Summary Help

Standard Name RRP6 1
Systematic Name YOR001W
Feature Type ORF, Verified
Description Nuclear exosome exonuclease component; has 3'-5' exonuclease activity that is regulated by Lrp1p; involved in RNA processing, maturation, surveillance, degradation, tethering, and export; role in sn/snoRNAs precursor degradation; forms a stable heterodimer with Lrp1p; has similarity to E. coli RNase D and to human PM-Sc1 100 (EXOSC10); mutant displays reduced transcription elongation in the G-less-based (1, 2, 3, 4, 5, 6, 7, 8, 9, 10 and see Summary Paragraph)
Name Description Ribosomal RNA Processing 1
Chromosomal Location
ChrXV:326832 to 329033 | ORF Map | GBrowse
Gbrowse
Gene Ontology Annotations All RRP6 GO evidence and references
  View Computational GO annotations for RRP6
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 2 genes
Resources
Classical genetics
conditional
null
reduction of function
unspecified
Large-scale survey
null
overexpression
repressible
Resources
530 total interaction(s) for 302 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 116
  • Affinity Capture-RNA: 3
  • Affinity Capture-Western: 18
  • Biochemical Activity: 1
  • Co-crystal Structure: 1
  • Reconstituted Complex: 6
  • Two-hybrid: 2

Genetic Interactions
  • Dosage Growth Defect: 2
  • Dosage Lethality: 1
  • Dosage Rescue: 11
  • Negative Genetic: 205
  • Phenotypic Enhancement: 26
  • Phenotypic Suppression: 16
  • Positive Genetic: 58
  • Synthetic Growth Defect: 32
  • Synthetic Lethality: 9
  • Synthetic Rescue: 23

Resources
Expression Summary
histogram
Resources
Length (a.a.) 733
Molecular Weight (Da) 84,038
Isoelectric Point (pI) 7.14
Localization
Phosphorylation PhosphoGRID | PhosphoPep Database
Structure
Homologs
sequence information
ChrXV:326832 to 329033 | ORF Map | GBrowse
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..2202 326832..329033 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 | E.C. | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000005527
SUMMARY PARAGRAPH for RRP6

The exosome complex possesses 3'-5' exonuclease and endoribonucleolytic activities that are essential for diverse ribonucleolytic processes in both the nucleus and the cytoplasm (11, 12, 13). The nuclear exosome is associated with the TRAMP complex and is involved in RNA catabolic processes including RNA surveillance (14, 15 and references therein), pre-mRNA turnover (4) and the production of mature 3' ends for snoRNAs, snRNAs and rRNAs (12, 16 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 (17) as well as the degradation of aberrant mRNAs (18 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) (13).

Although the exosome was originally described as a "complex of exonucleases," with multiple subunits proposed to have RNase activity (11), 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 (19, 20).

Rrp6p is a 3'-5' exonuclease that is a subunit of the nuclear exosome (2, 21). In addition to its involvement in processes mediated by the nuclear exosome, Rrp6p also performs the final trimming step in the maturation of pre-5.8S rRNA and certain pre-snoRNAs that have already been processed by the core exosome (1, 22). Rrp6p exonucleatic activity requires two divalent metal ions (Mn2+ and Zn2+), similar to other exonucleases in the DEDD family, of which Rrp6p is a member (23 and references therein). Other DEDD exonucleases include the Rrp6p homologs bacterial RNase D and human PM-Scl 100/EXOSC10 (1).

Null mutations in rrp6 result in slow growth at normal temperatures and inviability at 37 degrees C (1, 16), while point mutations in the catalytic domain lead to cold-sensitivity (1). Other rrp6 mutant phenotypes include 5-fluorouracil sensitivity (24), accumulation of processing intermediates and polyadenylated forms of rRNAs, snRNAs, and snoRNAs (22, 5, 25, 12), impaired mRNA surveillance/degradation/export, and defects in UV-induced DNA repair (26, 5 and references therein).

Last updated: 2009-09-09 Contact SGD

References cited on this page View Complete Literature Guide for RRP6
1) Briggs MW, et al.  (1998) Rrp6p, the yeast homologue of the human PM-Scl 100-kDa autoantigen, is essential for efficient 5.8 S rRNA 3' end formation. J Biol Chem 273(21):13255-63
2) Burkard KT and Butler JS  (2000) A nuclear 3'-5' exonuclease involved in mRNA degradation interacts with Poly(A) polymerase and the hnRNA protein Npl3p. Mol Cell Biol 20(2):604-16
3) Hilleren P, et al.  (2001) Quality control of mRNA 3'-end processing is linked to the nuclear exosome. Nature 413(6855):538-42
4) Bousquet-Antonelli C, et al.  (2000) Identification of a regulated pathway for nuclear pre-mRNA turnover. Cell 102(6):765-75
5) Hieronymus H, et al.  (2004) Genome-wide mRNA surveillance is coupled to mRNA export. Genes Dev 18(21):2652-62
6) Vodala S, et al.  (2008) The nuclear exosome and adenylation regulate posttranscriptional tethering of yeast GAL genes to the nuclear periphery. Mol Cell 31(1):104-13
7) Tous C, et al.  (2011) A novel assay identifies transcript elongation roles for the Nup84 complex and RNA processing factors. EMBO J 30(10):1953-64
8) Gudipati RK, et al.  (2012) Extensive degradation of RNA precursors by the exosome in wild-type cells. Mol Cell 48(3):409-21
9) Feigenbutz M, et al.  (2013) Assembly of the yeast exoribonuclease rrp6 with its associated cofactor rrp47 occurs in the nucleus and is critical for the controlled expression of rrp47. J Biol Chem 288(22):15959-70
10) Dedic E, et al.  (2014) Structural analysis of the yeast exosome Rrp6p-Rrp47p complex by small-angle X-ray scattering. Biochem Biophys Res Commun 450(1):634-40
11) Mitchell P, et al.  (1997) The exosome: a conserved eukaryotic RNA processing complex containing multiple 3'-->5' exoribonucleases. Cell 91(4):457-66
12) 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
13) 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
14) Vanacova S, et al.  (2005) A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol 3(6):e189
15) LaCava J, et al.  (2005) RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121(5):713-24
16) Allmang C, et al.  (2000) Degradation of ribosomal RNA precursors by the exosome. Nucleic Acids Res 28(8):1684-91
17) 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
18) Schaeffer D, et al.  (2008) Determining in vivo activity of the yeast cytoplasmic exosome. Methods Enzymol 448:227-39
19) Liu Q, et al.  (2006) Reconstitution, activities, and structure of the eukaryotic RNA exosome. Cell 127(6):1223-37
20) 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
21) 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
22) Allmang C, et al.  (1999) Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J 18(19):5399-410
23) Midtgaard SF, et al.  (2006) Structure of the nuclear exosome component Rrp6p reveals an interplay between the active site and the HRDC domain. Proc Natl Acad Sci U S A 103(32):11898-903
24) Fang F, et al.  (2004) 5-fluorouracil enhances exosome-dependent accumulation of polyadenylated rRNAs. Mol Cell Biol 24(24):10766-76
25) Kuai L, et al.  (2004) Polyadenylation of rRNA in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 101(23):8581-6
26) Mitchell P, et al.  (2003) Rrp47p is an exosome-associated protein required for the 3' processing of stable RNAs. Mol Cell Biol 23(19):6982-92