YBOX1_DANRE
ID YBOX1_DANRE Reviewed; 310 AA.
AC B5DE31; A0A0R4IK84; A1A605; F1RB19; O93584; Q6NSP3; Q7ZU03;
DT 16-OCT-2019, integrated into UniProtKB/Swiss-Prot.
DT 14-OCT-2008, sequence version 1.
DT 03-AUG-2022, entry version 85.
DE RecName: Full=Y-box-binding protein 1 {ECO:0000303|PubMed:31399345};
DE Short=YB-1 {ECO:0000303|PubMed:10446383};
DE Short=ZfY1 {ECO:0000303|PubMed:10446383};
DE AltName: Full=Y-box transcription factor {ECO:0000305};
GN Name=ybx1 {ECO:0000303|PubMed:31399345,
GN ECO:0000312|ZFIN:ZDB-GENE-000629-3};
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RX PubMed=10446383; DOI=10.1016/s0167-4838(99)00142-9;
RA Chang B.E., Lin C.Y., Kuo C.M.;
RT "Molecular cloning of a cold-shock domain protein, zfY1, in zebrafish
RT embryo.";
RL Biochim. Biophys. Acta 1433:343-349(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC TISSUE=Embryo;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (AUG-2008) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=30135188; DOI=10.1242/dev.166587;
RA Sun J., Yan L., Shen W., Meng A.;
RT "Maternal Ybx1 safeguards zebrafish oocyte maturation and maternal-to-
RT zygotic transition by repressing global translation.";
RL Development 145:0-0(2018).
RN [5] {ECO:0007744|PDB:6A6J}
RP X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) OF 30-122 IN COMPLEX WITH METHYLATED
RP RNA, FUNCTION, INTERACTION WITH PABPC1A, DOMAIN, DISRUPTION PHENOTYPE,
RP DEVELOPMENTAL STAGE, AND MUTAGENESIS OF TRP-45.
RX PubMed=31399345; DOI=10.1016/j.molcel.2019.06.033;
RA Yang Y., Wang L., Han X., Yang W.L., Zhang M., Ma H.L., Sun B.F., Li A.,
RA Xia J., Chen J., Heng J., Wu B., Chen Y.S., Xu J.W., Yang X., Yao H.,
RA Sun J., Lyu C., Wang H.L., Huang Y., Sun Y.P., Zhao Y.L., Meng A., Ma J.,
RA Liu F., Yang Y.G.;
RT "RNA 5-methylcytosine facilitates the maternal-to-zygotic transition by
RT preventing maternal mRNA decay.";
RL Mol. Cell 0:0-0(2019).
CC -!- FUNCTION: DNA- and RNA-binding protein involved in various processes,
CC such as translational repression, RNA stabilization, mRNA splicing and
CC transcription regulation (PubMed:30135188, PubMed:31399345). Binds
CC preferentially to the 5'-[CU]CUGCG-3' RNA motif and specifically
CC recognizes mRNA transcripts modified by C5-methylcytosine (m5C)
CC (PubMed:31399345). Promotes mRNA stabilization: acts by binding to m5C-
CC containing mRNAs and recruiting pabpc1a, thereby preventing mRNA decay
CC (PubMed:31399345). Plays a role in the maternal-to-zygotic transition
CC in early embryo by binding to m5C-containing maternal mRNAs and
CC preventing their degradation (PubMed:31399345). Also promotes maternal-
CC to-zygotic transition in oocytes and embryos by promoting translation
CC repression; molecular mechanisms governing translation repression are
CC unknown (PubMed:30135188). Plays a key role in RNA composition of
CC extracellular exosomes by defining the sorting of small non-coding
CC RNAs, such as tRNAs, Y RNAs, Vault RNAs and miRNAs. Probably sorts RNAs
CC in exosomes by recognizing and binding C5-methylcytosine (m5C)-
CC containing RNAs (By similarity). Acts as a key effector of epidermal
CC progenitors by preventing epidermal progenitor senescence: acts by
CC regulating the translation of a senescence-associated subset of
CC cytokine mRNAs, possibly by binding to m5C-containing mRNAs (By
CC similarity). Also involved in pre-mRNA alternative splicing regulation:
CC binds to splice sites in pre-mRNA and regulates splice site selection
CC (By similarity). Also able to bind DNA and regulate transcription.
CC Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'). Promotes
CC separation of DNA strands that contain mismatches or are modified by
CC cisplatin. Has endonucleolytic activity and can introduce nicks or
CC breaks into double-stranded DNA, suggesting a role in DNA repair. The
CC secreted form acts as an extracellular mitogen and stimulates cell
CC migration and proliferation (By similarity).
CC {ECO:0000250|UniProtKB:P67809, ECO:0000269|PubMed:30135188,
CC ECO:0000269|PubMed:31399345}.
CC -!- SUBUNIT: Interacts with pabpc1a; leading to pabpc1a recruitment on C5-
CC methylcytosine (m5C)-containing mRNAs. {ECO:0000269|PubMed:31399345}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:P67809}. Nucleus
CC {ECO:0000250|UniProtKB:P67809}. Cytoplasmic granule
CC {ECO:0000250|UniProtKB:P67809}. Secreted
CC {ECO:0000250|UniProtKB:P67809}. Secreted, extracellular exosome
CC {ECO:0000250|UniProtKB:P67809}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=B5DE31-1; Sequence=Displayed;
CC Name=2;
CC IsoId=B5DE31-2; Sequence=VSP_060390;
CC -!- DEVELOPMENTAL STAGE: Expressed both maternally and zygotically.
CC {ECO:0000269|PubMed:31399345}.
CC -!- DOMAIN: In the CSD domain, Trp-45 specifically recognizes C5-
CC methylcytosine (m5C) modification through its indole ring.
CC {ECO:0000269|PubMed:31399345}.
CC -!- DISRUPTION PHENOTYPE: Embryonic lethality caused by early gastrulation
CC arrest: maternal mutant embryos fail to undergo normal cleavage and the
CC maternal-to-zygotic transition (PubMed:30135188, PubMed:31399345).
CC Early embryos show severe developmental arrest at the shield stage in
CC maternal ybx1 knockout embryos, leading to lethality at 8 hours post-
CC fertilization (hpf) (PubMed:31399345). {ECO:0000269|PubMed:30135188,
CC ECO:0000269|PubMed:31399345}.
CC -!- SIMILARITY: Belongs to the YBX1 family. {ECO:0000305}.
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DR EMBL; AF093129; AAC62774.1; -; mRNA.
DR EMBL; CR792439; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC050156; AAH50156.1; -; mRNA.
DR EMBL; BC070000; AAH70000.1; -; mRNA.
DR EMBL; BC128885; AAI28886.1; -; mRNA.
DR EMBL; BC160650; AAI60650.1; -; mRNA.
DR EMBL; BC168507; AAI68507.1; -; mRNA.
DR RefSeq; NP_001119929.1; NM_001126457.1. [B5DE31-2]
DR RefSeq; NP_571695.1; NM_131620.1.
DR PDB; 6A6J; X-ray; 2.25 A; A/C=30-122.
DR PDBsum; 6A6J; -.
DR AlphaFoldDB; B5DE31; -.
DR SMR; B5DE31; -.
DR STRING; 7955.ENSDARP00000010482; -.
DR Ensembl; ENSDART00000024320; ENSDARP00000010482; ENSDARG00000004757. [B5DE31-2]
DR Ensembl; ENSDART00000110512; ENSDARP00000101517; ENSDARG00000004757. [B5DE31-1]
DR Ensembl; ENSDART00000163922; ENSDARP00000135135; ENSDARG00000004757. [B5DE31-1]
DR GeneID; 795398; -.
DR KEGG; dre:795398; -.
DR CTD; 4904; -.
DR ZFIN; ZDB-GENE-000629-3; ybx1.
DR eggNOG; KOG3070; Eukaryota.
DR GeneTree; ENSGT00940000153341; -.
DR HOGENOM; CLU_063071_1_0_1; -.
DR OMA; GDKKVIX; -.
DR OrthoDB; 1431946at2759; -.
DR TreeFam; TF317306; -.
DR Reactome; R-DRE-72163; mRNA Splicing - Major Pathway.
DR Reactome; R-DRE-72165; mRNA Splicing - Minor Pathway.
DR PRO; PR:B5DE31; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 8.
DR Bgee; ENSDARG00000004757; Expressed in bone element and 32 other tissues.
DR ExpressionAtlas; B5DE31; baseline and differential.
DR GO; GO:0070062; C:extracellular exosome; ISS:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:ZFIN.
DR GO; GO:0000932; C:P-body; IDA:ZFIN.
DR GO; GO:0062153; F:C5-methylcytidine-containing RNA binding; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0008190; F:eukaryotic initiation factor 4E binding; IDA:ZFIN.
DR GO; GO:0035198; F:miRNA binding; ISS:UniProtKB.
DR GO; GO:0003676; F:nucleic acid binding; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IPI:ZFIN.
DR GO; GO:0007343; P:egg activation; IMP:ZFIN.
DR GO; GO:0048598; P:embryonic morphogenesis; IMP:UniProtKB.
DR GO; GO:0008544; P:epidermis development; ISS:UniProtKB.
DR GO; GO:0051236; P:establishment of RNA localization; IMP:ZFIN.
DR GO; GO:1990428; P:miRNA transport; ISS:UniProtKB.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0048255; P:mRNA stabilization; IMP:UniProtKB.
DR GO; GO:2000773; P:negative regulation of cellular senescence; ISS:UniProtKB.
DR GO; GO:1900364; P:negative regulation of mRNA polyadenylation; IMP:ZFIN.
DR GO; GO:0050686; P:negative regulation of mRNA processing; IMP:ZFIN.
DR GO; GO:0048025; P:negative regulation of mRNA splicing, via spliceosome; IMP:ZFIN.
DR GO; GO:0017148; P:negative regulation of translation; IMP:UniProtKB.
DR GO; GO:0045947; P:negative regulation of translational initiation; IMP:ZFIN.
DR GO; GO:0001556; P:oocyte maturation; IMP:ZFIN.
DR GO; GO:0010468; P:regulation of gene expression; IBA:GO_Central.
DR GO; GO:0008380; P:RNA splicing; IEA:UniProtKB-KW.
DR GO; GO:0050658; P:RNA transport; ISS:UniProtKB.
DR GO; GO:0051031; P:tRNA transport; ISS:UniProtKB.
DR CDD; cd04458; CSP_CDS; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR InterPro; IPR011129; CSD.
DR InterPro; IPR019844; CSD_1.
DR InterPro; IPR002059; CSP_DNA-bd.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR Pfam; PF00313; CSD; 1.
DR PRINTS; PR00050; COLDSHOCK.
DR SMART; SM00357; CSP; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR PROSITE; PS00352; CSD_1; 1.
DR PROSITE; PS51857; CSD_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Cytoplasm; DNA-binding;
KW mRNA processing; mRNA splicing; Nucleus; Reference proteome; RNA-binding;
KW Secreted; Transcription; Transcription regulation.
FT CHAIN 1..310
FT /note="Y-box-binding protein 1"
FT /id="PRO_0000448383"
FT DOMAIN 38..107
FT /note="CSD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01204"
FT REGION 1..31
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 45..50
FT /note="C5-methylcytosine binding"
FT /evidence="ECO:0000269|PubMed:31399345,
FT ECO:0007744|PDB:6A6J"
FT REGION 102..310
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..15
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 132..160
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 238..267
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 278..294
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 45
FT /note="Important for C5-methylcytosine-recognition"
FT /evidence="ECO:0000269|PubMed:31399345"
FT VAR_SEQ 234
FT /note="Missing (in isoform 2)"
FT /id="VSP_060390"
FT MUTAGEN 45
FT /note="W->A: Abolished binding to C5-methylcytosine (m5C)-
FT containing mRNAs."
FT /evidence="ECO:0000269|PubMed:31399345"
FT MUTAGEN 45
FT /note="W->F: Decreased binding to C5-methylcytosine (m5C)-
FT containing mRNAs. Decreased ability to discriminate between
FT m5C-containing and unmethylated mRNAs."
FT /evidence="ECO:0000269|PubMed:31399345"
FT CONFLICT 92
FT /note="D -> A (in Ref. 3; AAH70000)"
FT /evidence="ECO:0000305"
FT CONFLICT 238
FT /note="S -> P (in Ref. 1; AAC62774)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 310 AA; 35012 MW; 678FC23A1199D0DE CRC64;
MSSEAETQQP PQPAADAESP SSPAAAATAG DKKVIATKVL GTVKWFNVRN GYGFINRNDT
KEDVFVHQTA IKKNNPRKYL RSVGDGETVE FDVVEGEKGA EAANVTGPGG VPVQGSKYAA
DRNRYRRYPR RRAPPRDYQE NYQSDPEAEP REKREGAESA PEGEMQQQQR RPTYPGRRRY
PPYFVRRRYG RRPPYTNSQR GEMTEGGEGE ENQGGPDQGN KPMRQNYYRG FRPSRGPSRP
RPVRDGEEDK ENQSESGQNQ EPRQRRYRRN FNYRRRRPQT TKPQDGKDSK AADASADKSA
APEAEQGGAD
