EXOS3_DROME
ID EXOS3_DROME Reviewed; 232 AA.
AC Q8IPX7;
DT 02-DEC-2020, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 164.
DE RecName: Full=Exosome complex component RRP40 {ECO:0000303|PubMed:12490954};
DE AltName: Full=Ribosomal RNA-processing protein 40 {ECO:0000312|FlyBase:FBgn0260648};
GN Name=Rrp40 {ECO:0000312|FlyBase:FBgn0260648};
GN ORFNames=CG31938 {ECO:0000312|FlyBase:FBgn0260648};
OS Drosophila melanogaster (Fruit fly).
OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea;
OC Drosophilidae; Drosophila; Sophophora.
OX NCBI_TaxID=7227 {ECO:0000312|Proteomes:UP000000803};
RN [1] {ECO:0000312|Proteomes:UP000000803}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Berkeley;
RX PubMed=10731132; DOI=10.1126/science.287.5461.2185;
RA Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
RA Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
RA George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
RA Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C.,
RA Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C.,
RA Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A.,
RA An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A.,
RA Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V.,
RA Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J.,
RA Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E.,
RA Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B.,
RA Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I.,
RA Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C.,
RA Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S.,
RA Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M.,
RA Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
RA Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D.,
RA Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F.,
RA Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D.,
RA Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A.,
RA Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C.,
RA McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C.,
RA Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L.,
RA Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R.,
RA Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V.,
RA Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F.,
RA Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
RA Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R.,
RA Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y.,
RA Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T.,
RA Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S.,
RA Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W.,
RA Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M.,
RA Venter J.C.;
RT "The genome sequence of Drosophila melanogaster.";
RL Science 287:2185-2195(2000).
RN [2] {ECO:0000312|Proteomes:UP000000803}
RP GENOME REANNOTATION.
RC STRAIN=Berkeley;
RX PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
RA Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
RA Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
RA Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
RA Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
RA Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M.,
RA Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E.;
RT "Annotation of the Drosophila melanogaster euchromatic genome: a systematic
RT review.";
RL Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
RN [3] {ECO:0000312|EMBL:AAZ66314.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=Berkeley {ECO:0000312|EMBL:AAZ66314.1};
RA Stapleton M., Carlson J., Chavez C., Frise E., George R., Pacleb J.,
RA Park S., Wan K., Yu C., Celniker S.;
RL Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases.
RN [4] {ECO:0000305}
RP IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE RNA EXOSOME
RP COMPLEX, AND SUBCELLULAR LOCATION.
RX PubMed=12490954; DOI=10.1038/nature01181;
RA Andrulis E.D., Werner J., Nazarian A., Erdjument-Bromage H., Tempst P.,
RA Lis J.T.;
RT "The RNA processing exosome is linked to elongating RNA polymerase II in
RT Drosophila.";
RL Nature 420:837-841(2002).
RN [5] {ECO:0000305}
RP DISRUPTION PHENOTYPE.
RX PubMed=25892215; DOI=10.1080/15476286.2015.1040978;
RA Towler B.P., Jones C.I., Viegas S.C., Apura P., Waldron J.A., Smalley S.K.,
RA Arraiano C.M., Newbury S.F.;
RT "The 3'-5' exoribonuclease Dis3 regulates the expression of specific
RT microRNAs in Drosophila wing imaginal discs.";
RL RNA Biol. 12:728-741(2015).
RN [6] {ECO:0000305}
RP FUNCTION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF GLY-11 AND ASP-87.
RX PubMed=32645003; DOI=10.1371/journal.pgen.1008901;
RA Morton D.J., Jalloh B., Kim L., Kremsky I., Nair R.J., Nguyen K.B.,
RA Rounds J.C., Sterrett M.C., Brown B., Le T., Karkare M.C., McGaughey K.D.,
RA Sheng S., Leung S.W., Fasken M.B., Moberg K.H., Corbett A.H.;
RT "A Drosophila model of Pontocerebellar Hypoplasia reveals a critical role
RT for the RNA exosome in neurons.";
RL PLoS Genet. 16:e1008901-e1008901(2020).
CC -!- FUNCTION: Non-catalytic component of the RNA exosome complex which has
CC 3'->5' exoribonuclease activity and participates in a multitude of
CC cellular RNA processing and degradation events (By similarity). In the
CC nucleus, the RNA exosome complex is involved in proper maturation of
CC stable RNA species such as rRNA, snRNA and snoRNA, in the elimination
CC of RNA processing by-products and non-coding 'pervasive' transcripts
CC such as antisense RNA species, and of mRNAs with processing defects,
CC thereby limiting or excluding their export to the cytoplasm (By
CC similarity). In the cytoplasm, the RNA exosome complex is involved in
CC general mRNA turnover and specifically degrades inherently unstable
CC mRNAs containing AU-rich elements (AREs) within their 3' untranslated
CC regions, and in RNA surveillance pathways, preventing translation of
CC aberrant mRNAs (By similarity). The catalytic inactive RNA exosome core
CC complex of 9 subunits is proposed to play a pivotal role in the binding
CC and presentation of RNA for ribonucleolysis, and to serve as a scaffold
CC for the association with catalytic subunits and accessory proteins or
CC complexes (By similarity). Required generally for normal embryonic and
CC neuronal development (PubMed:32645003). Also plays a critical role in
CC the maintenance of neuronal function in mature flies by controlling the
CC levels of specific mRNAs such as the synaptic regulator Arc1
CC (PubMed:32645003). {ECO:0000250|UniProtKB:Q9NQT5,
CC ECO:0000269|PubMed:32645003}.
CC -!- SUBUNIT: Component of the RNA exosome complex (PubMed:12490954).
CC Specifically part of the catalytically inactive RNA exosome core
CC complex (By similarity). {ECO:0000250|UniProtKB:Q9NQT5,
CC ECO:0000269|PubMed:12490954}.
CC -!- INTERACTION:
CC Q8IPX7; Q9VGZ2: Rrp46; NbExp=4; IntAct=EBI-106288, EBI-166198;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q9NQT5}.
CC Nucleus, nucleolus {ECO:0000250|UniProtKB:Q9NQT5}. Nucleus
CC {ECO:0000269|PubMed:12490954}.
CC -!- DISRUPTION PHENOTYPE: RNAi-mediated knockdown in the whole body,
CC neurons, glia or muscles is lethal (PubMed:32645003). RNAi-mediated
CC knockdown in mushroom bodies affects the morphology of the alpha- and
CC beta-lobes as well as ellipsoid bodies (PubMed:32645003). RNAi-mediated
CC knockdown in the wing pouch results in severe wing development
CC phenotypes and increase of miR-252-5p expression (PubMed:25892215).
CC {ECO:0000269|PubMed:25892215, ECO:0000269|PubMed:32645003}.
CC -!- SIMILARITY: Belongs to the RRP40 family. {ECO:0000305}.
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DR EMBL; AE014134; AAN10459.1; -; Genomic_DNA.
DR EMBL; AE014134; AHN54080.1; -; Genomic_DNA.
DR EMBL; BT023807; AAZ66314.1; -; mRNA.
DR RefSeq; NP_001285565.1; NM_001298636.1.
DR RefSeq; NP_722725.1; NM_164435.3.
DR AlphaFoldDB; Q8IPX7; -.
DR SMR; Q8IPX7; -.
DR IntAct; Q8IPX7; 16.
DR STRING; 7227.FBpp0077551; -.
DR PaxDb; Q8IPX7; -.
DR PRIDE; Q8IPX7; -.
DR DNASU; 319033; -.
DR EnsemblMetazoa; FBtr0077883; FBpp0077551; FBgn0260648.
DR EnsemblMetazoa; FBtr0345430; FBpp0311555; FBgn0260648.
DR GeneID; 319033; -.
DR KEGG; dme:Dmel_CG31938; -.
DR UCSC; CG31938-RA; d. melanogaster.
DR CTD; 319033; -.
DR FlyBase; FBgn0260648; Rrp40.
DR VEuPathDB; VectorBase:FBgn0260648; -.
DR eggNOG; KOG1004; Eukaryota.
DR GeneTree; ENSGT00940000153596; -.
DR HOGENOM; CLU_069847_5_1_1; -.
DR InParanoid; Q8IPX7; -.
DR OMA; SYMAFPN; -.
DR OrthoDB; 1284731at2759; -.
DR PhylomeDB; Q8IPX7; -.
DR Reactome; R-DME-429958; mRNA decay by 3' to 5' exoribonuclease.
DR Reactome; R-DME-450385; Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA.
DR Reactome; R-DME-450513; Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA.
DR Reactome; R-DME-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR SignaLink; Q8IPX7; -.
DR BioGRID-ORCS; 319033; 0 hits in 1 CRISPR screen.
DR GenomeRNAi; 319033; -.
DR Proteomes; UP000000803; Chromosome 2L.
DR Bgee; FBgn0260648; Expressed in eye disc (Drosophila) and 21 other tissues.
DR GO; GO:0005737; C:cytoplasm; IDA:FlyBase.
DR GO; GO:0000177; C:cytoplasmic exosome (RNase complex); IBA:GO_Central.
DR GO; GO:0000178; C:exosome (RNase complex); IDA:FlyBase.
DR GO; GO:0000176; C:nuclear exosome (RNase complex); IDA:FlyBase.
DR GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0007420; P:brain development; IMP:UniProtKB.
DR GO; GO:0071034; P:CUT catabolic process; IBA:GO_Central.
DR GO; GO:0043928; P:exonucleolytic catabolism of deadenylated mRNA; IBA:GO_Central.
DR GO; GO:0000467; P:exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IBA:GO_Central.
DR GO; GO:0035167; P:larval lymph gland hemopoiesis; IMP:FlyBase.
DR GO; GO:0016319; P:mushroom body development; IMP:UniProtKB.
DR GO; GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IBA:GO_Central.
DR GO; GO:0071038; P:nuclear polyadenylation-dependent tRNA catabolic process; IBA:GO_Central.
DR GO; GO:0034427; P:nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'; IBA:GO_Central.
DR GO; GO:0071051; P:polyadenylation-dependent snoRNA 3'-end processing; IBA:GO_Central.
DR GO; GO:0045995; P:regulation of embryonic development; IMP:UniProtKB.
DR GO; GO:0010468; P:regulation of gene expression; IMP:FlyBase.
DR GO; GO:0034475; P:U4 snRNA 3'-end processing; IBA:GO_Central.
DR CDD; cd05790; S1_Rrp40; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.30.1370.10; -; 1.
DR InterPro; IPR026699; Exosome_RNA_bind1/RRP40/RRP4.
DR InterPro; IPR004088; KH_dom_type_1.
DR InterPro; IPR036612; KH_dom_type_1_sf.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR037319; Rrp40_S1.
DR PANTHER; PTHR21321; PTHR21321; 1.
DR Pfam; PF15985; KH_6; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF54791; SSF54791; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Exosome; Nucleus; Reference proteome; RNA-binding;
KW rRNA processing.
FT CHAIN 1..232
FT /note="Exosome complex component RRP40"
FT /id="PRO_0000451458"
FT MUTAGEN 11
FT /note="G->A: Results in reduced viability, shortened
FT lifespan, age-dependent wing posture and locomotor defects.
FT Shows a mushroom body beta-lobe midline-crossing defect.
FT Results in increased steady-state levels of specific
FT neuronal mRNAs such as Arc1 and wfs1."
FT /evidence="ECO:0000269|PubMed:32645003"
FT MUTAGEN 87
FT /note="D->A: Results in reduced viability, shortened
FT lifespan, age-dependent wing posture and locomotor defects.
FT Results in increased steady-state levels of specific
FT neuronal mRNAs such as Arc1 and wfs1."
FT /evidence="ECO:0000269|PubMed:32645003"
SQ SEQUENCE 232 AA; 25026 MW; 5CCAB9DEECD84C7F CRC64;
MSATSTIVMP GERIAAIEEL AKSKRVILGP GLRRLDDTVV ASKAGPLRHK EPGTFWVDNY
QRRYIPARGD LILGIVRAKA GDLYRVDIGA TDTASISYLA FEAASKKNRP DLIPGDLIYA
RVLNASADIE PELVCVNSVG KSGKLGVLTD GFFFKCSLNL GRMLLRENCP VLAALTRELP
YEIAVGVNGR IWLKAHSLKE TVALANAISA LEQSGCAEID KICGNLGDFL QA
