SKI6/YGR195W Summary Help

Standard Name SKI6 1, 2
Systematic Name YGR195W
Alias ECM20 3 , RRP41 4
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; has similarity to E. coli RNase PH and to human hRrp41p (EXOSC4) (1, 4, 5, 6, 7, 8 and see Summary Paragraph)
Name Description SuperKIller 2
Chromosomal Location
ChrVII:888882 to 889622 | ORF Map | GBrowse
Gbrowse
Gene Ontology Annotations All SKI6 GO evidence and references
  View Computational GO annotations for SKI6
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Mutant phenotypes All SKI6 Phenotype evidence and references
Classical genetics
conditional
null
reduction of function
repressible
unspecified
Large-scale survey
conditional
null
repressible
unspecified
Resources
interactions All SKI6 Interaction evidence and references
154 total interaction(s) for 40 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 100
  • Affinity Capture-RNA: 1
  • Affinity Capture-Western: 27
  • Co-fractionation: 1
  • Co-purification: 1
  • PCA: 2
  • Reconstituted Complex: 1
  • Two-hybrid: 7
Genetic Interactions
  • Negative Genetic: 2
  • Phenotypic Enhancement: 3
  • Phenotypic Suppression: 1
  • Positive Genetic: 4
  • Synthetic Rescue: 4
Resources
Expression Summary
histogram
Resources
Protein Information All SKI6 Protein evidence and references
Localization
Phosphorylation PhosphoGRID | PhosphoPep Database
Structure
Homologs
sequence information
ChrVII:888882 to 889622 | 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..741 888882..889622 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 SGDIDS000003427
SUMMARY PARAGRAPH for SKI6

The exosome complex possesses 3'-5' exonuclease and endoribonucleolytic activities that are essential for diverse ribonucleolytic processes in both the nucleus and the cytoplasm (4, 9, 10). The nuclear exosome is associated with the TRAMP complex and is involved in RNA catabolic processes including RNA surveillance (11, 12 and references therein), pre-mRNA turnover (13) and the production of mature 3' ends for snoRNAs, snRNAs and rRNAs (9, 14 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 (15) as well as the degradation of aberrant mRNAs (16 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) (10).

Although the exosome was originally described as a "complex of exonucleases," with multiple subunits proposed to have RNase activity (4), 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 (7, 8).

SKI6 encodes a core subunit of the exosome (4, 6, 1, 5). Like most exosome components, Ski6p is highly conserved among eukaryotes, including humans (hRrp41p (EXOSC4)) (7 and references therein). Although Ski6p has similarity to the RNase PH class of RNases (5, and references therein) and actually. SKI6 is an essential gene (17, 1), but cells depleted for Ski6p accumulate unspliced pre-mRNAs (13) and aberrant forms of rRNA (4, 14, 1), while a temperature sensitive mutant accumulates aberrant forms of snoRNA, snRNA (9) and displays defects in 3' to 5' mRNA degradation at restrictive temperature (15). ski6 was originally isolated in a screen for mutations that caused ski6 was originally isolated in a screen for mutations that caused the superkiller phenotype, which includes an increase in the concentration of viral dsRNAs (2).

Last updated: 2009-09-09

References cited on this page View Complete Literature Guide for SKI6
1) Benard L, et al.  (1998) Ski6p is a homolog of RNA-processing enzymes that affects translation of non-poly(A) mRNAs and 60S ribosomal subunit biogenesis. Mol Cell Biol 18(5):2688-96
2) Ridley SP, et al.  (1984) Superkiller mutations in Saccharomyces cerevisiae suppress exclusion of M2 double-stranded RNA by L-A-HN and confer cold sensitivity in the presence of M and L-A-HN. Mol Cell Biol 4(4):761-70
3) Lussier M, et al.  (1997) Large scale identification of genes involved in cell surface biosynthesis and architecture in Saccharomyces cerevisiae. Genetics 147(2):435-50
4) Mitchell P, et al.  (1997) The exosome: a conserved eukaryotic RNA processing complex containing multiple 3'-->5' exoribonucleases. Cell 91(4):457-66
5) 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
6) 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
7) Liu Q, et al.  (2006) Reconstitution, activities, and structure of the eukaryotic RNA exosome. Cell 127(6):1223-37
8) 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
9) 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
10) 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
11) Vanacova S, et al.  (2005) A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol 3(6):e189
12) LaCava J, et al.  (2005) RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121(5):713-24
13) Bousquet-Antonelli C, et al.  (2000) Identification of a regulated pathway for nuclear pre-mRNA turnover. Cell 102(6):765-75
14) Allmang C, et al.  (2000) Degradation of ribosomal RNA precursors by the exosome. Nucleic Acids Res 28(8):1684-91
15) Anderson JS and Parker RP  (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
16) Schaeffer D, et al.  (2008) Determining in vivo activity of the yeast cytoplasmic exosome. Methods Enzymol 448:227-39
17) Rodriguez-Pena JM, et al.  (1998) The deletion of six ORFs of unknown function from Saccharomyces cerevisiae chromosome VII reveals two essential genes: YGR195w and YGR198w. Yeast 14(9):853-60