AIR1/YIL079C Summary Help

Standard Name AIR1 1
Systematic Name YIL079C
Feature Type ORF, Verified
Description Zinc knuckle protein; involved in nuclear RNA processing and degradation as a component of the TRAMP complex; stimulates the poly(A) polymerase activity of Pap2p in vitro; AIR1 has a paralog, AIR2, that arose from the whole genome duplication; although Air1p and Air2p are homologous TRAMP subunits, they have nonredundant roles in regulation of substrate specificity of the exosome (1, 2, 3, 4, 5, 6 and see Summary Paragraph)
Name Description Arginine methyltransferase-Interacting RING finger protein 1
Chromosomal Location
ChrIX:212005 to 210923 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Gbrowse
Gene Ontology Annotations All AIR1 GO evidence and references
  View Computational GO annotations for AIR1
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 2 genes
Resources
Large-scale survey
null
Resources
111 total interaction(s) for 76 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 14
  • Affinity Capture-Western: 7
  • Reconstituted Complex: 2
  • Two-hybrid: 6

Genetic Interactions
  • Negative Genetic: 34
  • Phenotypic Enhancement: 3
  • Phenotypic Suppression: 1
  • Positive Genetic: 15
  • Synthetic Growth Defect: 9
  • Synthetic Lethality: 19
  • Synthetic Rescue: 1

Resources
Expression Summary
histogram
Resources
Length (a.a.) 360
Molecular Weight (Da) 41,631
Isoelectric Point (pI) 9.33
Localization
Phosphorylation PhosphoGRID | PhosphoPep Database
Structure
Homologs
sequence information
ChrIX:212005 to 210923 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
SGD ORF map
Last Update Coordinates: 2011-02-03 | Sequence: 1994-12-10
Subfeature details
Relative
Coordinates
Chromosomal
Coordinates
Most Recent Updates
Coordinates Sequence
CDS 1..1083 212005..210923 2011-02-03 1994-12-10
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 SGDIDS000001341
SUMMARY PARAGRAPH for AIR1

The TRAMP complex is a nuclear complex that functions in RNA processing, degradation and surveillance. The TRAMP (TRf4/5p, Air1/2p, Mtr4p Polyadenylation) complex polyadenylates a variety of nuclear RNAs, thereby targeting these RNAs for processing or degradation by the exosome. Characterized substrates of the TRAMP complex include aberrant and hypomodified tRNAs; aberrant and precursor snoRNAs, snRNAs and rRNAs; and cryptic unstable transcripts (CUTs) (2, 3, 4, and reviewed in 7, 8, and 9). In addition, mutant analysis indicates that TRAMP and the exosome also contribute to the regulation of some mRNAs, such as those encoding histones (10).

The TRAMP complex contains three proteins: a non-canonical poly(A) polymerase (either Pap2p (aka Trf4p) or Trf5p), a DExD/H family RNA helicase (Mtr4p) and a zinc knuckle domain protein (either Air1p or Air2p). Analysis of PAP2 and TRF5 mutants show that these genes have overlapping but not redundant functions, and the terms "TRAMP4" and "TRAMP5" are sometimes used to distinguish complexes containing Pap2p from those containing Trf5p (11, 12, 13, 14, 15). AIR1 and AIR2 appear to be functionally redundant, as deletion of either gene does not cause a detectable phenotype, but the air1air2 double deletion is variously described as synthetically lethal (1) or as slow growth (3).

Although the TRAMP complex has not yet been isolated in humans, the human genome does contain sequences homologous to all three yeast TRAMP components. TRF4-1 and TRF4-2 have been identified as Pap2p and Trf5p homologs (16), SKIV2L2 has been identified as the Mtr4p homolog (17, 18, 19) and ZCCHC7 may be the Air1/2p homolog (7).

The TRAMP components Air1p and Air2p are closely related proteins that were originally identified in a screen for factors influencing modification of heterogeneous nuclear ribonucleoproteins (hnRNPs), such as Npl3p (1). Air1/2 proteins have been described as containing "RING-finger" (1) or "zinc knuckle" (2, 3) interaction domains and it is hypothesized that these proteins may serve as the RNA-binding component of the TRAMP complex. Either Air1p or Air2p is required for poly(A) polymerase activity of Pap2p in vitro (3, 4).

Last updated: 2009-09-09 Contact SGD

References cited on this page View Complete Literature Guide for AIR1
1) Inoue K, et al.  (2000) Novel RING finger proteins, Air1p and Air2p, interact with Hmt1p and inhibit the arginine methylation of Npl3p. J Biol Chem 275(42):32793-9
2) Vanacova S, et al.  (2005) A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol 3(6):e189
3) LaCava J, et al.  (2005) RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121(5):713-24
4) Wyers F, et al.  (2005) Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121(5):725-37
5) Byrne KP and Wolfe KH  (2005) The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res 15(10):1456-61
6) Schmidt K, et al.  (2012) Air proteins control differential TRAMP substrate specificity for nuclear RNA surveillance. RNA 18(10):1934-45
7) Houseley J and Tollervey D  (2008) The nuclear RNA surveillance machinery: The link between ncRNAs and genome structure in budding yeast? Biochim Biophys Acta 1779(4):239-46
8) Lebreton A and Seraphin B  (2008) Exosome-mediated quality control: substrate recruitment and molecular activity. Biochim Biophys Acta 1779(9):558-65
9) Reinisch KM and Wolin SL  (2007) Emerging themes in non-coding RNA quality control. Curr Opin Struct Biol 17(2):209-14
10) Reis CC and Campbell JL  (2007) Contribution of Trf4/5 and the nuclear exosome to genome stability through regulation of histone mRNA levels in Saccharomyces cerevisiae. Genetics 175(3):993-1010
11) Houseley J and Tollervey D  (2006) Yeast Trf5p is a nuclear poly(A) polymerase. EMBO Rep 7(2):205-11
12) Egecioglu DE, et al.  (2006) Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome. RNA 12(1):26-32
13) Dez C, et al.  (2007) Roles of the HEAT repeat proteins Utp10 and Utp20 in 40S ribosome maturation. RNA 13(9):1516-27
14) Kadaba S, et al.  (2006) Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-dependent polyadenylation of nascent hypomethylated tRNA and an aberrant form of 5S rRNA. RNA 12(3):508-21
15) San Paolo S, et al.  (2009) Distinct roles of non-canonical poly(A) polymerases in RNA metabolism. PLoS Genet 5(7):e1000555
16) Walowsky C, et al.  (1999) The topoisomerase-related function gene TRF4 affects cellular sensitivity to the antitumor agent camptothecin. J Biol Chem 274(11):7302-8
17) Schilders G, et al.  (2007) C1D and hMtr4p associate with the human exosome subunit PM/Scl-100 and are involved in pre-rRNA processing. Nucleic Acids Res 35(8):2564-72
18) Chen CY, et al.  (2001) AU binding proteins recruit the exosome to degrade ARE-containing mRNAs. Cell 107(4):451-64
19) Nagahama M, et al.  (2006) The AAA-ATPase NVL2 is a component of pre-ribosomal particles that interacts with the DExD/H-box RNA helicase DOB1. Biochem Biophys Res Commun 346(3):1075-82