CSL4/YNL232W Summary Help

Standard Name CSL4 1
Systematic Name YNL232W
Alias SKI4 2 , 3
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 an S1 RNA binding domain; has similarity to human hCsl4p (EXOSC1) (4, 5, 6, 7 and see Summary Paragraph)
Name Description Cep1 Synthetic Lethal 1
Chromosomal Location
ChrXIV:214923 to 215801 | ORF Map | GBrowse
Gbrowse
Gene Ontology Annotations All CSL4 GO evidence and references
  View Computational GO annotations for CSL4
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 4 genes
Resources
Classical genetics
null
reduction of function
repressible
unspecified
Large-scale survey
conditional
null
reduction of function
unspecified
Resources
145 total interaction(s) for 47 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 103
  • Affinity Capture-RNA: 2
  • Affinity Capture-Western: 13
  • Biochemical Activity: 1
  • Co-purification: 1
  • PCA: 1
  • Two-hybrid: 1

Genetic Interactions
  • Negative Genetic: 4
  • Phenotypic Suppression: 7
  • Positive Genetic: 1
  • Synthetic Lethality: 5
  • Synthetic Rescue: 6

Resources
Expression Summary
histogram
Resources
Length (a.a.) 292
Molecular Weight (Da) 31,583
Isoelectric Point (pI) 5.08
Localization
Phosphorylation PhosphoGRID | PhosphoPep Database
Structure
Homologs
sequence information
ChrXIV:214923 to 215801 | 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..879 214923..215801 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 SGDIDS000005176
SUMMARY PARAGRAPH for CSL4

The exosome complex possesses 3'-5' exonuclease and endoribonucleolytic activities that are essential for diverse ribonucleolytic processes in both the nucleus and the cytoplasm (8, 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 (8), 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 (6, 7).

CSL4 encodes a core subunit of the exosome and is predicted to contain an S1 RNA binding domain (4, 5 and references therein). Like most exosome components, Csl4p is highly conserved among eukaryotes, including humans (hCsl4p (EXOSC1)) (6 and references therein). CSL4 is an essential gene (1, 17), but cells depleted for Csl4p accumulate aberrant forms of rRNA (4, 14). The csl4 mutation was originally isolated in a screen for mutations that were synthetically lethal with null mutations in the chromatin remodeling factor Cbf1p (1). Another mutant allele, ski4-1, was independantly isolated in a screen for mutations that caused the superkiller phenotype, which includes an increase in the concentration of viral dsRNAs (2); this mutant was later shown to also have defects in 3' to 5' mRNA degradation (3).

Last updated: 2009-09-09 Contact SGD

References cited on this page View Complete Literature Guide for CSL4
1) Baker RE, et al.  (1998) Mutations synthetically lethal with cep1 target S. cerevisiae kinetochore components. Genetics 149(1):73-85
2) Toh-E A, et al.  (1978) Chromosomal superkiller mutants of Saccharomyces cerevisiae. J Bacteriol 136(3):1002-7
3) van Hoof A, et al.  (2000) Function of the ski4p (Csl4p) and Ski7p proteins in 3'-to-5' degradation of mRNA. Mol Cell Biol 20(21):8230-43
4) 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
5) 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
6) Liu Q, et al.  (2006) Reconstitution, activities, and structure of the eukaryotic RNA exosome. Cell 127(6):1223-37
7) 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
8) Mitchell P, et al.  (1997) The exosome: a conserved eukaryotic RNA processing complex containing multiple 3'-->5' exoribonucleases. Cell 91(4):457-66
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) 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
16) Schaeffer D, et al.  (2008) Determining in vivo activity of the yeast cytoplasmic exosome. Methods Enzymol 448:227-39
17) Capozzo C, et al.  (2000) Gene disruption and basic phenotypic analysis of nine novel yeast genes from chromosome XIV. Yeast 16(12):1089-97