DCL4_ORYSJ
ID DCL4_ORYSJ Reviewed; 1657 AA.
AC A7LFZ6; A0A0P0WCA9; A7VMN4; B7ECE3; Q0JBU5; Q7XQ14;
DT 07-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 11-SEP-2007, sequence version 1.
DT 03-AUG-2022, entry version 94.
DE RecName: Full=Endoribonuclease Dicer homolog 4;
DE EC=3.1.26.-;
DE AltName: Full=Dicer-like protein 4;
DE Short=OsDCL4;
DE AltName: Full=Protein SHOOT ORGANIZATION 1;
GN Name=DCL4; Synonyms=SHO1; OrderedLocusNames=Os04g0509300, LOC_Os04g43050;
GN ORFNames=OSJNBb0065L13.5;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=17905898; DOI=10.1105/tpc.107.052209;
RA Liu B., Chen Z., Song X., Liu C., Cui X., Zhao X., Fang J., Xu W.,
RA Zhang H., Wang X., Chu C., Deng X., Xue Y., Cao X.;
RT "Oryza sativa dicer-like4 reveals a key role for small interfering RNA
RT silencing in plant development.";
RL Plant Cell 19:2705-2718(2007).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), FUNCTION, TISSUE SPECIFICITY, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=cv. Nipponbare;
RX PubMed=17804793; DOI=10.1073/pnas.0704339104;
RA Nagasaki H., Itoh J., Hayashi K., Hibara K., Satoh-Nagasawa N., Nosaka M.,
RA Mukouhata M., Ashikari M., Kitano H., Matsuoka M., Nagato Y., Sato Y.;
RT "The small interfering RNA production pathway is required for shoot
RT meristem initiation in rice.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:14867-14871(2007).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12447439; DOI=10.1038/nature01183;
RA Feng Q., Zhang Y., Hao P., Wang S., Fu G., Huang Y., Li Y., Zhu J., Liu Y.,
RA Hu X., Jia P., Zhang Y., Zhao Q., Ying K., Yu S., Tang Y., Weng Q.,
RA Zhang L., Lu Y., Mu J., Lu Y., Zhang L.S., Yu Z., Fan D., Liu X., Lu T.,
RA Li C., Wu Y., Sun T., Lei H., Li T., Hu H., Guan J., Wu M., Zhang R.,
RA Zhou B., Chen Z., Chen L., Jin Z., Wang R., Yin H., Cai Z., Ren S., Lv G.,
RA Gu W., Zhu G., Tu Y., Jia J., Zhang Y., Chen J., Kang H., Chen X., Shao C.,
RA Sun Y., Hu Q., Zhang X., Zhang W., Wang L., Ding C., Sheng H., Gu J.,
RA Chen S., Ni L., Zhu F., Chen W., Lan L., Lai Y., Cheng Z., Gu M., Jiang J.,
RA Li J., Hong G., Xue Y., Han B.;
RT "Sequence and analysis of rice chromosome 4.";
RL Nature 420:316-320(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [6]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 568-1657.
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [8]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=18826656; DOI=10.1186/1471-2164-9-451;
RA Kapoor M., Arora R., Lama T., Nijhawan A., Khurana J.P., Tyagi A.K.,
RA Kapoor S.;
RT "Genome-wide identification, organization and phylogenetic analysis of
RT dicer-like, argonaute and RNA-dependent RNA polymerase gene families and
RT their expression analysis during reproductive development and stress in
RT rice.";
RL BMC Genomics 9:451-451(2008).
CC -!- FUNCTION: Involved in the RNA silencing pathway. Cleaves double-
CC stranded RNA to produce small interfering RNAs (siRNAs) which target
CC the selective destruction of complementary RNAs. Required for the
CC production of 21 nucleotide siRNAs. Regulates shoot apical meristem
CC (SAM) initiation and maintenance, leaf polarization and lemma polarity
CC through the trans-acting siRNAS (ta-siRNAs) pathway, which probably
CC modulate the expression of the ARF2, ARF3, ARF4, ARF14 and ARF15 genes.
CC Can process endogenous 21 nucleotide siRNAs derived from an imperfect
CC inverted repeat. May not be involved in microRNAs (miRNAs) production.
CC {ECO:0000269|PubMed:17804793, ECO:0000269|PubMed:17905898}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC -!- SUBUNIT: May interact with ARGONAUTE1 or PINHEAD through their common
CC PAZ domains. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=A7LFZ6-1; Sequence=Displayed;
CC Name=2;
CC IsoId=A7LFZ6-2; Sequence=VSP_037580;
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaf blades, leaf sheaths,
CC shoot apices and spikelets. {ECO:0000269|PubMed:17804793}.
CC -!- DISRUPTION PHENOTYPE: Formation of an incomplete shoot apical meristem
CC (SAM), abnormal vegetative development with alteration of
CC adaxial/abaxial polarity in both coleoptiles and the first leaves.
CC Abnormal spikelet morphology with disruption of organ identity and
CC lemma polarity. {ECO:0000269|PubMed:17804793,
CC ECO:0000269|PubMed:17905898}.
CC -!- SIMILARITY: Belongs to the helicase family. Dicer subfamily.
CC {ECO:0000255|PROSITE-ProRule:PRU00657}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAF15192.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAG90040.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=CAE03362.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; EU009924; ABS32306.1; -; mRNA.
DR EMBL; AB353922; BAF80150.1; -; mRNA.
DR EMBL; AL606607; CAE03362.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008210; BAF15192.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014960; BAS90022.1; -; Genomic_DNA.
DR EMBL; AP014960; BAS90023.1; -; Genomic_DNA.
DR EMBL; AK066586; BAG90040.1; ALT_INIT; mRNA.
DR RefSeq; XP_015636293.1; XM_015780807.1. [A7LFZ6-2]
DR AlphaFoldDB; A7LFZ6; -.
DR SMR; A7LFZ6; -.
DR STRING; 4530.OS04T0509300-01; -.
DR PRIDE; A7LFZ6; -.
DR EnsemblPlants; Os04t0509300-01; Os04t0509300-01; Os04g0509300. [A7LFZ6-2]
DR EnsemblPlants; Os04t0509300-02; Os04t0509300-02; Os04g0509300. [A7LFZ6-1]
DR GeneID; 4336362; -.
DR Gramene; Os04t0509300-01; Os04t0509300-01; Os04g0509300. [A7LFZ6-2]
DR Gramene; Os04t0509300-02; Os04t0509300-02; Os04g0509300. [A7LFZ6-1]
DR KEGG; osa:4336362; -.
DR eggNOG; KOG0701; Eukaryota.
DR HOGENOM; CLU_000907_4_5_1; -.
DR InParanoid; A7LFZ6; -.
DR OrthoDB; 1337630at2759; -.
DR Proteomes; UP000000763; Chromosome 4.
DR Proteomes; UP000059680; Chromosome 4.
DR Genevisible; A7LFZ6; OS.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004525; F:ribonuclease III activity; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0006353; P:DNA-templated transcription, termination; IEA:EnsemblPlants.
DR GO; GO:0010599; P:lsiRNA processing; IEA:EnsemblPlants.
DR GO; GO:0010216; P:maintenance of DNA methylation; IEA:EnsemblPlants.
DR GO; GO:0010492; P:maintenance of shoot apical meristem identity; IMP:UniProtKB.
DR GO; GO:0009944; P:polarity specification of adaxial/abaxial axis; IMP:UniProtKB.
DR GO; GO:0048608; P:reproductive structure development; IMP:UniProtKB.
DR GO; GO:0051214; P:RNAi-mediated antiviral immunity against RNA virus; IEA:EnsemblPlants.
DR GO; GO:0030422; P:siRNA processing; IBA:GO_Central.
DR GO; GO:0010267; P:ta-siRNA processing; IDA:UniProtKB.
DR GO; GO:0010050; P:vegetative phase change; IEA:EnsemblPlants.
DR CDD; cd00593; RIBOc; 2.
DR Gene3D; 1.10.1520.10; -; 2.
DR Gene3D; 3.30.160.380; -; 1.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR038248; Dicer_dimer_sf.
DR InterPro; IPR005034; Dicer_dimerisation_dom.
DR InterPro; IPR014720; dsRBD_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR003100; PAZ_dom.
DR InterPro; IPR036085; PAZ_dom_sf.
DR InterPro; IPR000999; RNase_III_dom.
DR InterPro; IPR036389; RNase_III_sf.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF02170; PAZ; 1.
DR Pfam; PF00636; Ribonuclease_3; 2.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00358; DSRM; 2.
DR SMART; SM00490; HELICc; 1.
DR SMART; SM00949; PAZ; 1.
DR SMART; SM00535; RIBOc; 2.
DR SUPFAM; SSF101690; SSF101690; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR SUPFAM; SSF69065; SSF69065; 2.
DR PROSITE; PS51327; DICER_DSRBF; 1.
DR PROSITE; PS50137; DS_RBD; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS50821; PAZ; 1.
DR PROSITE; PS00517; RNASE_3_1; 1.
DR PROSITE; PS50142; RNASE_3_2; 2.
PE 2: Evidence at transcript level;
KW Alternative splicing; ATP-binding; Endonuclease; Helicase; Hydrolase;
KW Magnesium; Manganese; Metal-binding; Nuclease; Nucleotide-binding; Nucleus;
KW Reference proteome; Repeat; RNA-binding; RNA-mediated gene silencing.
FT CHAIN 1..1657
FT /note="Endoribonuclease Dicer homolog 4"
FT /id="PRO_0000378421"
FT DOMAIN 37..214
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 400..567
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT DOMAIN 585..675
FT /note="Dicer dsRNA-binding fold"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00657"
FT DOMAIN 845..978
FT /note="PAZ"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00142"
FT DOMAIN 1010..1173
FT /note="RNase III 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT DOMAIN 1214..1358
FT /note="RNase III 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT DOMAIN 1384..1451
FT /note="DRBM 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00266"
FT DOMAIN 1569..1645
FT /note="DRBM 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00266"
FT REGION 1..26
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1525..1556
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 157..160
FT /note="DECH box"
FT /evidence="ECO:0000250"
FT COMPBIAS 1525..1551
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 50..57
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 1252
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 1344
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 1347
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT SITE 1340
FT /note="Important for activity"
FT /evidence="ECO:0000250"
FT VAR_SEQ 202..227
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:17804793"
FT /id="VSP_037580"
SQ SEQUENCE 1657 AA; 186989 MW; 59E754B94692266D CRC64;
MGDAAAAAPA AAAAGPSSTR GEPKDPRTIA RKYQLDLCKR AVEENIIVYL GTGCGKTHIA
VLLIYELGHL IRKPSREVCI FLAPTIPLVR QQAVVIASST DFKVQCYYGN GKNSRDHQEW
ENDMREFEVL VMTPQILLQS LRHCFIKMNS IALLILDECH HAQPQKRHPY AQIMKEFYNS
NSVEKFPRVF GMTASPIIGK GVMPSHSFTE KGGRSPCQPL IFFLPKGGSN KLNYTKCINS
LEELLHAKVC SVDNEELESV VASPDMEVYF YGPVNHSNLT TICIKELDSL KLQSERMLRA
SLCDFKDSQK KLKSLWRLHE NIIFCLQELG SFGALQAART FLSFDGDKLD RREVDLNGST
SSFAHHYLNG ATSILSRNKT DGSHAGSFDL EKLEEPFFSN KFSVLINVLS RYGLQENMKC
IVFVKRITVA RAISNILQNL KCLEFWKCEF LVGCHSGSKN MSRNKMDAIV QRFSSGEVNL
LVATSVGEEG LDIQTCCLVV RFDLPETVAS FIQSRGRARM TKSKYVVLLE RENQSHEKLL
NGYIAGESIM NEEIDSRTSN DMFDCLEENI YQVDNTGASI STACSVSLLH CYCDNLPRDM
FFTPSPVFFY IDGIEGIICR LILPPNAAFR QADGQPCLSK DEAKRDACLK ACVKLHKLGA
LTDFLLPGPG SRKNKVSVTN NSSNNKVEDD SLREELHEML IPAVLKPSGL KLDSLSNLHF
YYVKFIPIPE DRRYQMFGLF VINPLPVEAE TLQVDLHLAR GRIVKAGIKH LGKIAFEKEK
MMLAHKFQEM CLKILLDRSE FTSPHVKLGN DVTLEINSTF YLLLPIKQKC YGDRFMIDWP
AVERCLSSPI FKDPIDVSVH ASYSSNESLR LLDGIFSKTD VVGSVVFSPH NNIFFFVDGI
LDEINAWSEH SGATYAEHFK ERFRIELSHP EQPLLKAKQI FNLRNLLHNR LPETTESEGR
ELLEHFVELP PELCSLKVIG FSKDMGSSLS LLPSLMYRLE NLLVAIELKD VMLSSFPEAS
QISASGILEA LTTEKCLERI SLERFEVLGD AFLKYVVGRH KFITYEGLDE GQLTRRRSDV
VNNSHLYELS IRKKLQVYIR DQQFEPTQFF APGRPCKVVC NTDVEVRLHQ MDIHPDNREN
CNLRCTRSHH WLHRKVIADV VESLIGAFLV EGGFKAAFAF LHWIGIDVDF NNPALYRVLD
SSSINLSLMD YTDIAGLEEL IGYKFKHKGL LLQAFVHPSF SQHSGGCYQR LEFLGDAVLE
YVITSYLYST YPDIKPGQIT DLRSLAVGND SLAYAAVEKS IHKHLIKDSN HLTSAISKFE
MYVKLSNSEK DLLEEPACPK ALGDIVESCI GAVLLDSGFN LNYVWKVMLM LLKPVLTFAN
MHTNPMRELR ELCQCHGFEL GLPKPMKADG EYHVKVEVNI KSKIIICTAA NRNSKAARKF
AAQETLSKLK NYGYKHRNKS LEEILIVARK RESELIGYNE DPIDVEADIS VKMKSPHIHE
ENIPFQNTET SFTRSSKFHN QIIAGSGKHD VNNGRNNQPK LATQSGRLPS EATEKSNKKV
YHGDMVHKTA RSFLFELCAA NYWKPPEFKL CKEEGPSHLR KFTYKVVVEI KGASATLLEC
HSDGKLQKKA AQEHAAQGAL WCLKQLGHLP KEEDVRV
