PUF60_CAEEL
ID PUF60_CAEEL Reviewed; 749 AA.
AC Q9N3S4; Q8MXS9; Q9N3S3;
DT 10-FEB-2021, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 159.
DE RecName: Full=Poly(U)-binding-splicing factor rnp-6 {ECO:0000250|UniProtKB:Q9UHX1};
DE AltName: Full=60 kDa poly(U)-binding-splicing factor rnp-6 {ECO:0000250|UniProtKB:Q9UHX1};
GN Name=rnp-6 {ECO:0000312|WormBase:Y47G6A.20b};
GN ORFNames=Y47G6A.20 {ECO:0000312|WormBase:Y47G6A.20b};
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6239 {ECO:0000312|Proteomes:UP000001940};
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Bristol N2 {ECO:0000312|Proteomes:UP000001940};
RX PubMed=9851916; DOI=10.1126/science.282.5396.2012;
RG The C. elegans sequencing consortium;
RT "Genome sequence of the nematode C. elegans: a platform for investigating
RT biology.";
RL Science 282:2012-2018(1998).
RN [2]
RP FUNCTION, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF
RP GLY-281.
RX PubMed=32538777; DOI=10.7554/elife.57591;
RA Kew C., Huang W., Fischer J., Ganesan R., Robinson N., Antebi A.;
RT "Evolutionarily conserved regulation of immunity by the splicing factor
RT RNP-6/PUF60.";
RL Elife 9:0-0(2020).
CC -!- FUNCTION: DNA- and RNA-binding protein, involved in several nuclear
CC processes such as pre-mRNA splicing, apoptosis and transcription
CC regulation (Probable). Ensures the correct splicing of genes involved
CC in immunity to promote longevity in response to infection by pathogenic
CC bacteria such as S.aureus (PubMed:32538777).
CC {ECO:0000269|PubMed:32538777, ECO:0000305|PubMed:32538777}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305|PubMed:32538777}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=b {ECO:0000312|WormBase:Y47G6A.20b};
CC IsoId=Q9N3S4-1; Sequence=Displayed;
CC Name=a {ECO:0000312|WormBase:Y47G6A.20a};
CC IsoId=Q9N3S4-2; Sequence=VSP_060862, VSP_060863;
CC Name=c {ECO:0000312|WormBase:Y47G6A.20c};
CC IsoId=Q9N3S4-3; Sequence=VSP_060861, VSP_060864;
CC -!- DOMAIN: The third RNA recognition motif, called PUMP domain, is
CC atypical and may rather mediate homodimerization and/or protein-protein
CC interactions. {ECO:0000250|UniProtKB:Q8T6B9}.
CC -!- DISRUPTION PHENOTYPE: RNAi-mediated knockdown increases survival
CC following infection by pathogenic bacteria S.aureus (PubMed:32538777).
CC RNAi-mediated knockdown impairs the splicing of genes such as prg-2 and
CC tos-1 following infection by S.aureus (PubMed:32538777). RNAi-mediated
CC knockdown induces the expression of nlp-34, lys-3, irg-2, irg-1,
CC M01G12.9, fmo-2 and cyp-37B1 under non-infected conditions
CC (PubMed:32538777). RNAi-mediated knockdown increases the
CC phosphorylation of pmk-1 (PubMed:32538777).
CC {ECO:0000269|PubMed:32538777}.
CC -!- SIMILARITY: Belongs to the RRM half pint family. {ECO:0000305}.
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DR EMBL; BX284601; CCD72564.1; -; Genomic_DNA.
DR EMBL; BX284601; CCD72565.1; -; Genomic_DNA.
DR EMBL; BX284601; CCD72566.1; -; Genomic_DNA.
DR RefSeq; NP_491176.1; NM_058775.5. [Q9N3S4-1]
DR RefSeq; NP_491177.1; NM_058776.4.
DR RefSeq; NP_740829.1; NM_170843.3. [Q9N3S4-3]
DR AlphaFoldDB; Q9N3S4; -.
DR SMR; Q9N3S4; -.
DR STRING; 6239.Y47G6A.20b; -.
DR EPD; Q9N3S4; -.
DR PaxDb; Q9N3S4; -.
DR PeptideAtlas; Q9N3S4; -.
DR EnsemblMetazoa; Y47G6A.20a.1; Y47G6A.20a.1; WBGene00004389. [Q9N3S4-2]
DR EnsemblMetazoa; Y47G6A.20b.1; Y47G6A.20b.1; WBGene00004389. [Q9N3S4-1]
DR EnsemblMetazoa; Y47G6A.20c.1; Y47G6A.20c.1; WBGene00004389. [Q9N3S4-3]
DR GeneID; 171922; -.
DR KEGG; cel:CELE_Y47G6A.20; -.
DR UCSC; Y47G6A.20b; c. elegans.
DR CTD; 171922; -.
DR WormBase; Y47G6A.20a; CE24365; WBGene00004389; rnp-6. [Q9N3S4-2]
DR WormBase; Y47G6A.20b; CE24366; WBGene00004389; rnp-6. [Q9N3S4-1]
DR WormBase; Y47G6A.20c; CE31375; WBGene00004389; rnp-6. [Q9N3S4-3]
DR eggNOG; KOG0124; Eukaryota.
DR GeneTree; ENSGT00940000155594; -.
DR HOGENOM; CLU_802228_0_0_1; -.
DR InParanoid; Q9N3S4; -.
DR OMA; VHTHKGY; -.
DR OrthoDB; 861359at2759; -.
DR PhylomeDB; Q9N3S4; -.
DR Reactome; R-CEL-72163; mRNA Splicing - Major Pathway.
DR Proteomes; UP000001940; Chromosome I.
DR Bgee; WBGene00004389; Expressed in embryo and 4 other tissues.
DR ExpressionAtlas; Q9N3S4; baseline and differential.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0000380; P:alternative mRNA splicing, via spliceosome; IBA:GO_Central.
DR GO; GO:0006376; P:mRNA splice site selection; IBA:GO_Central.
DR GO; GO:0000381; P:regulation of alternative mRNA splicing, via spliceosome; IBA:GO_Central.
DR CDD; cd12370; RRM1_PUF60; 1.
DR CDD; cd12371; RRM2_PUF60; 1.
DR Gene3D; 3.30.70.330; -; 3.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR006532; PUF60-like.
DR InterPro; IPR034209; PUF60_RRM1.
DR InterPro; IPR034211; PUF60_RRM2.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR000504; RRM_dom.
DR InterPro; IPR003954; RRM_dom_euk.
DR Pfam; PF00076; RRM_1; 3.
DR SMART; SM00360; RRM; 3.
DR SMART; SM00361; RRM_1; 2.
DR SUPFAM; SSF54928; SSF54928; 3.
DR TIGRFAMs; TIGR01645; half-pint; 1.
DR PROSITE; PS50102; RRM; 2.
PE 1: Evidence at protein level;
KW Alternative splicing; DNA-binding; mRNA processing; mRNA splicing; Nucleus;
KW Reference proteome; Repressor; Ribonucleoprotein; RNA-binding;
KW Transcription; Transcription regulation.
FT CHAIN 1..749
FT /note="Poly(U)-binding-splicing factor rnp-6"
FT /id="PRO_0000451762"
FT DOMAIN 102..176
FT /note="RRM 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT DOMAIN 207..285
FT /note="RRM 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT DOMAIN 658..739
FT /note="RRM 3; atypical"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT REGION 323..388
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 457..480
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 343..361
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 280..346
FT /note="VGKCVTPPDALTYLQPASVSAIPASVSVACAAITAKVMAAEAAAGSSPKTPS
FT ESGGSRAASPAPRAQ -> NFTTFGLYHHQRRQMCNSTGCSYLSSTGIRQCNSSKCISC
FT VCSNYRKSDGCRSSSRFLTGRCNKPVL (in isoform c)"
FT /evidence="ECO:0000305"
FT /id="VSP_060861"
FT VAR_SEQ 328..339
FT /note="KTPSESGGSRAA -> VGATNLFSNSPR (in isoform a)"
FT /evidence="ECO:0000305"
FT /id="VSP_060862"
FT VAR_SEQ 340..749
FT /note="Missing (in isoform a)"
FT /evidence="ECO:0000305"
FT /id="VSP_060863"
FT VAR_SEQ 347..749
FT /note="Missing (in isoform c)"
FT /evidence="ECO:0000305"
FT /id="VSP_060864"
FT MUTAGEN 281
FT /note="G->D: In dh1127; reduces brood size, there is a
FT developmental delay in reaching adulthood and results in a
FT shorter body size. Does not affect pharyngeal pumping rate.
FT Resistant to heat and oxidative stress. Increased
FT sensitivity to pathogenic bacteria such as S.aureus,
FT E.faecalis and P.aeruginosa at both 20 and 25 degrees
FT Celsius. Splicing defects of genes such as prg-2, gyg-1 and
FT tos-1 upon infection by S.aureus. Reduces expression of
FT nlp-34, M01G12.9 and cyp-37B1 following S.aureus infection.
FT Increases expression of lys-3, irg-2, irg-1 and fmo-2 under
FT non-infected conditions."
FT /evidence="ECO:0000269|PubMed:32538777"
SQ SEQUENCE 749 AA; 81616 MW; 835451FA96ED65A4 CRC64;
MEENSADIEN RPVAAFRPAV SVPMPVLPQD GEVFVGPGGK KDAQKIGLGL SKLSSKRKDD
IQMAKKYAMD ISIKQILLRQ QKQQQENQQR QQMYSQALSI MSRIYVGSIS FEIREDMLRR
AFDPFGPIKS INMSWDPATG HHKTFAFVEY EVPEAALLAQ ESMNGQMLGG RNLKVNSMMF
QEMRLPQNMP QAQPIIDMVQ KDAKKYFRVY VSSVHPDLSE TDLKSVFEAF GEIVKCQLAR
APTGRGHRGF GYLEFNNLTS QSEAIAGMNM FDLGGQYLRV GKCVTPPDAL TYLQPASVSA
IPASVSVACA AITAKVMAAE AAAGSSPKTP SESGGSRAAS PAPRAQSPAT PSSSLPTDIE
NKAVISSPKK EPEEIEVPPL PPSAPDVVKD EPMEIEEEEE YTIPEEKPKP VAIVPPPGLA
IPSLVAPPGL IAPTEIGIVV PNPSFLAQQQ QKIEEKIEEE EEARTERVKL STSQRKKMKR
EKLNQMTFEE KMAQVLGQQK AVQNQRMADP VTFGALDDTV AWKDPSNEDQ TSEDGKMLAI
MGPGRGGDNV ASMALALMDG GSSLMLANNA KAKEAAAALA LEPKKKKKVK EGKKIQPKLN
TAQALAAAAK AGEMSDALKN EVMNSEDASL ASQEGLEIRG NDARHLLMTK LMRTNRSNVI
VLRNMVTPQD IDEFLEGEIR EECGKYGNVI DVVIANFASS GLVKIFVKYS DSMQVDRAKA
ALDGRFFGGN TVKAEAYDQI LFDHADYTG
