AIR2/YDL175C Summary Help

Standard Name AIR2 1
Systematic Name YDL175C
Feature Type ORF, Verified
Description RNA-binding subunit of the TRAMP nuclear RNA surveillance complex; involved in nuclear RNA processing and degradation; involved in TRAMP complex assembly as a bridge between Mtr4p and Trf4p; stimulates the poly(A) polymerase activity of Pap2p in vitro; has 5 zinc knuckle motifs; AIR2 has a paralog, AIR1, that arose from the whole genome duplication (1, 2, 3, 4, 5, 6 and see Summary Paragraph)
Name Description Arginine methyltransferase-Interacting RING finger protein 1
Chromosomal Location
ChrIV:145518 to 144484 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Gbrowse
Gene Ontology Annotations All AIR2 GO evidence and references
  View Computational GO annotations for AIR2
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Mutant phenotypes All AIR2 Phenotype evidence and references
Large-scale survey
null
overexpression
Resources
interactions All AIR2 Interaction evidence and references
112 total interaction(s) for 61 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 38
  • Affinity Capture-RNA: 1
  • Affinity Capture-Western: 8
  • Co-crystal Structure: 1
  • Co-purification: 1
  • Two-hybrid: 4
Genetic Interactions
  • Dosage Growth Defect: 2
  • Dosage Lethality: 1
  • Negative Genetic: 18
  • Phenotypic Enhancement: 2
  • Phenotypic Suppression: 3
  • Positive Genetic: 22
  • Synthetic Growth Defect: 9
  • Synthetic Lethality: 2
Resources
Expression Summary
histogram
Resources
Protein Information All AIR2 Protein evidence and references
Localization
Phosphorylation PhosphoGRID | PhosphoPep Database
Structure
Homologs
sequence information
ChrIV:145518 to 144484 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
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..1035 145518..144484 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 SGDIDS000002334
SUMMARY PARAGRAPH for AIR2

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

References cited on this page View Complete Literature Guide for AIR2
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) Holub P, et al.  (2012) Air2p is critical for the assembly and RNA-binding of the TRAMP complex and the KOW domain of Mtr4p is crucial for exosome activation. Nucleic Acids Res 40(12):5679-93
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