RRP43/YCR035C Summary Help

Standard Name RRP43 1
Systematic Name YCR035C
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 hRrp43p (OIP2, EXOSC8); protein abundance increases in response to DNA replication stress (1, 2, 3, 4, 5, 6 and see Summary Paragraph)
Name Description Ribosomal RNA Processing 1
Chromosomal Location
ChrIII:193018 to 191834 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Gbrowse
Gene Ontology Annotations All RRP43 GO evidence and references
  View Computational GO annotations for RRP43
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 4 genes
Resources
Classical genetics
conditional
repressible
Large-scale survey
null
reduction of function
Resources
108 total interaction(s) for 32 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 78
  • Affinity Capture-RNA: 3
  • Affinity Capture-Western: 11
  • Co-fractionation: 2
  • Co-purification: 1
  • Reconstituted Complex: 3
  • Two-hybrid: 8

Genetic Interactions
  • Synthetic Growth Defect: 1
  • Synthetic Lethality: 1

Resources
Expression Summary
histogram
Resources
Length (a.a.) 394
Molecular Weight (Da) 44,011
Isoelectric Point (pI) 4.71
Localization
Phosphorylation PhosphoGRID | PhosphoPep Database
Structure
Homologs
sequence information
ChrIII:193018 to 191834 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
SGD ORF map
Last Update Coordinates: 2011-02-03 | Sequence: 2000-09-13
Subfeature details
Relative
Coordinates
Chromosomal
Coordinates
Most Recent Updates
Coordinates Sequence
CDS 1..1185 193018..191834 2011-02-03 2000-09-13
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 SGDIDS000000631
SUMMARY PARAGRAPH for RRP43

The exosome complex possesses 3'-5' exonuclease and endoribonucleolytic activities that are essential for diverse ribonucleolytic processes in both the nucleus and the cytoplasm (1, 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 (1), 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).

RRP43 encodes a core subunit of the exosome and has similarity to the RNase PH class of RNases (2, 1, 3, and references therein). Like most exosome components, Rrp43p is highly conserved among eukaryotes, including humans (hRrp43p (OIP2, EXOSC8)) (4 and references therein). RRP43 is an essential gene, but cells depleted for Rrp43p accumulate aberrant forms of rRNA (1, 15, 12) and temperature sensitive mutants have defects in rRNA processing and mRNA decay at the restrictive temperature 16.

Last updated: 2009-09-09 Contact SGD

References cited on this page View Complete Literature Guide for RRP43
1) Mitchell P, et al.  (1997) The exosome: a conserved eukaryotic RNA processing complex containing multiple 3'-->5' exoribonucleases. Cell 91(4):457-66
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) 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) Tkach JM, et al.  (2012) Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat Cell Biol 14(9):966-76
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) Zanchin NI and Goldfarb DS  (1999) The exosome subunit Rrp43p is required for the efficient maturation of 5.8S, 18S and 25S rRNA. Nucleic Acids Res 27(5):1283-8
16) Oliveira CC, et al.  (2002) Temperature-sensitive mutants of the exosome subunit Rrp43p show a deficiency in mRNA degradation and no longer interact with the exosome. Nucleic Acids Res 30(19):4186-98