SRRT_ARATH
ID SRRT_ARATH Reviewed; 720 AA.
AC Q9ZVD0; Q93W84;
DT 22-SEP-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 2.
DT 03-AUG-2022, entry version 160.
DE RecName: Full=Serrate RNA effector molecule;
GN Name=SE; OrderedLocusNames=At2g27100; ORFNames=T20P8.15;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=11402159; DOI=10.2307/3871294;
RA Prigge M.J., Wagner D.R.;
RT "The arabidopsis serrate gene encodes a zinc-finger protein required for
RT normal shoot development.";
RL Plant Cell 13:1263-1279(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP FUNCTION.
RX PubMed=16222298; DOI=10.1038/nature04052;
RA Grigg S.P., Canales C., Hay A., Tsiantis M.;
RT "SERRATE coordinates shoot meristem function and leaf axial patterning in
RT Arabidopsis.";
RL Nature 437:1022-1026(2005).
RN [6]
RP FUNCTION, INTERACTION WITH HYL1, AND DISRUPTION PHENOTYPE.
RX PubMed=16977334; DOI=10.1038/sj.embor.7400806;
RA Lobbes D., Rallapalli G., Schmidt D.D., Martin C., Clarke J.;
RT "SERRATE: a new player on the plant microRNA scene.";
RL EMBO Rep. 7:1052-1058(2006).
RN [7]
RP FUNCTION, SUBCELLULAR LOCATION, AND INTERACTION WITH HYL1.
RX PubMed=16889646; DOI=10.1111/j.1365-313x.2006.02835.x;
RA Yang L., Liu Z., Lu F., Dong A., Huang H.;
RT "SERRATE is a novel nuclear regulator in primary microRNA processing in
RT Arabidopsis.";
RL Plant J. 47:841-850(2006).
RN [8]
RP SUBCELLULAR LOCATION.
RX PubMed=17442570; DOI=10.1016/j.cub.2007.04.005;
RA Fang Y., Spector D.L.;
RT "Identification of nuclear dicing bodies containing proteins for microRNA
RT biogenesis in living Arabidopsis plants.";
RL Curr. Biol. 17:818-823(2007).
RN [9]
RP SUBCELLULAR LOCATION.
RX PubMed=17675322; DOI=10.1093/pcp/pcm099;
RA Fujioka Y., Utsumi M., Ohba Y., Watanabe Y.;
RT "Location of a possible miRNA processing site in SmD3/SmB nuclear bodies in
RT Arabidopsis.";
RL Plant Cell Physiol. 48:1243-1253(2007).
RN [10]
RP FUNCTION.
RX PubMed=18632569; DOI=10.1073/pnas.0803356105;
RA Dong Z., Han M.-H., Fedoroff N.;
RT "The RNA-binding proteins HYL1 and SE promote accurate in vitro processing
RT of pri-miRNA by DCL1.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:9970-9975(2008).
RN [11]
RP FUNCTION.
RX PubMed=18550839; DOI=10.1073/pnas.0802493105;
RA Laubinger S., Sachsenberg T., Zeller G., Busch W., Lohmann J.U.,
RA Raetsch G., Weigel D.;
RT "Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA
RT splicing and microRNA processing in Arabidopsis thaliana.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:8795-8800(2008).
RN [12]
RP SUBCELLULAR LOCATION, PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-689,
RP AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Columbia;
RX PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
RA Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E.,
RA Rathjen J.P., Peck S.C.;
RT "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis
RT thaliana.";
RL J. Proteomics 72:439-451(2009).
RN [13]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-76; SER-90 AND SER-92, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [14]
RP INTERACTION WITH RCF3; RS40 AND RS41, AND SUBCELLULAR LOCATION.
RX PubMed=26227967; DOI=10.1093/nar/gkv751;
RA Chen T., Cui P., Xiong L.;
RT "The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and
RT RS41 participate in miRNA biogenesis in Arabidopsis.";
RL Nucleic Acids Res. 43:8283-8298(2015).
RN [15]
RP X-RAY CRYSTALLOGRAPHY (2.74 ANGSTROMS) OF 194-543.
RX PubMed=21685453; DOI=10.1093/nar/gkr428;
RA Machida S., Chen H.Y., Adam Yuan Y.;
RT "Molecular insights into miRNA processing by Arabidopsis thaliana
RT SERRATE.";
RL Nucleic Acids Res. 39:7828-7836(2011).
CC -!- FUNCTION: Acts as a mediator between the cap-binding complex (CBC) and
CC both the pre-mRNA splicing and primary microRNAs (miRNAs) processing
CC machinery. Required for proper processing of primary miRNAs to miRNAs,
CC thereby playing a role in RNA-mediated gene silencing (RNAi) by miRNAs.
CC Does not participate in sense post-transcriptional gene silencing. Acts
CC as a regulator of meristem activity and adaxial leaf fate via the miRNA
CC gene-silencing pathway by regulating the expression of PHB and by
CC limiting the competence of shoot tissue to respond to KNOX expression.
CC Its function is however not limited to miRNA-mediated repression of
CC leaf polarity genes, but rather acts as a general regulator of primary
CC microRNAs processing. Also critical for the accumulation of the trans-
CC acting small interfering RNA (ta-siRNA). Required for pre-mRNA
CC splicing. {ECO:0000269|PubMed:16222298, ECO:0000269|PubMed:16889646,
CC ECO:0000269|PubMed:16977334, ECO:0000269|PubMed:18550839,
CC ECO:0000269|PubMed:18632569}.
CC -!- SUBUNIT: Interacts with HYL1 (PubMed:16889646, PubMed:16977334).
CC Interacts with RCF3, RS40 and RS41 (PubMed:26227967).
CC {ECO:0000269|PubMed:16889646, ECO:0000269|PubMed:16977334,
CC ECO:0000269|PubMed:26227967}.
CC -!- INTERACTION:
CC Q9ZVD0; Q6EVK6: BRM; NbExp=6; IntAct=EBI-6553299, EBI-2025535;
CC Q9ZVD0; Q5YDB6: CPL1; NbExp=7; IntAct=EBI-6553299, EBI-1786459;
CC Q9ZVD0; O04492: DRB1; NbExp=7; IntAct=EBI-6553299, EBI-632620;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:16889646,
CC ECO:0000269|PubMed:17442570, ECO:0000269|PubMed:17675322,
CC ECO:0000269|PubMed:19245862}. Nucleus speckle
CC {ECO:0000269|PubMed:26227967}. Note=Localizes to nuclear dicing body
CC (also named D body), a nuclear body distributed throughout the
CC nucleoplasm involved in miRNA processing.
CC -!- TISSUE SPECIFICITY: Expressed in shoot meristems and in emerging organ
CC primordia throughout development. {ECO:0000269|PubMed:11402159}.
CC -!- DISRUPTION PHENOTYPE: Death during embryogenesis. Weaker mutants (se-1,
CC se-2 and se-3) also exist. Mutant se-1 displays defects in shoot and
CC leaf development. Mutants se-2 and se-3 show adaxial leaf curling, loss
CC of asymmetric differentiation of abaxial and adaxial cell types and
CC development of trumpet-shaped or radial leaves. Vascular polarity of
CC se-3 leaves is also perturbed, with xylem elements forming both
CC adaxially and abaxially in the vascular bundle.
CC {ECO:0000269|PubMed:11402159, ECO:0000269|PubMed:16977334}.
CC -!- SIMILARITY: Belongs to the ARS2 family. {ECO:0000305}.
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DR EMBL; AF311221; AAK63206.1; -; mRNA.
DR EMBL; AC005623; AAC77868.2; -; Genomic_DNA.
DR EMBL; CP002685; AEC07936.1; -; Genomic_DNA.
DR EMBL; AF428305; AAL16137.1; -; mRNA.
DR EMBL; AY039915; AAK64019.1; -; mRNA.
DR EMBL; AY142569; AAN13138.1; -; mRNA.
DR EMBL; AY143937; AAN28876.1; -; mRNA.
DR PIR; G84668; G84668.
DR RefSeq; NP_565635.1; NM_128268.3.
DR PDB; 3AX1; X-ray; 2.74 A; A=194-543.
DR PDBsum; 3AX1; -.
DR AlphaFoldDB; Q9ZVD0; -.
DR SMR; Q9ZVD0; -.
DR BioGRID; 2604; 13.
DR DIP; DIP-58979N; -.
DR IntAct; Q9ZVD0; 5.
DR STRING; 3702.AT2G27100.1; -.
DR iPTMnet; Q9ZVD0; -.
DR PaxDb; Q9ZVD0; -.
DR PRIDE; Q9ZVD0; -.
DR ProteomicsDB; 226823; -.
DR EnsemblPlants; AT2G27100.1; AT2G27100.1; AT2G27100.
DR GeneID; 817252; -.
DR Gramene; AT2G27100.1; AT2G27100.1; AT2G27100.
DR KEGG; ath:AT2G27100; -.
DR Araport; AT2G27100; -.
DR TAIR; locus:2059294; AT2G27100.
DR eggNOG; KOG2295; Eukaryota.
DR HOGENOM; CLU_021946_1_0_1; -.
DR InParanoid; Q9ZVD0; -.
DR OMA; LHKREEW; -.
DR OrthoDB; 525905at2759; -.
DR PhylomeDB; Q9ZVD0; -.
DR EvolutionaryTrace; Q9ZVD0; -.
DR PRO; PR:Q9ZVD0; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q9ZVD0; baseline and differential.
DR Genevisible; Q9ZVD0; AT.
DR GO; GO:0016604; C:nuclear body; IBA:GO_Central.
DR GO; GO:0005846; C:nuclear cap binding complex; IPI:TAIR.
DR GO; GO:0010445; C:nuclear dicing body; IDA:UniProtKB.
DR GO; GO:0016607; C:nuclear speck; IDA:TAIR.
DR GO; GO:0005730; C:nucleolus; HDA:TAIR.
DR GO; GO:0005634; C:nucleus; ISS:TAIR.
DR GO; GO:0003677; F:DNA binding; ISS:TAIR.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; ISS:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0031053; P:primary miRNA processing; IMP:UniProtKB.
DR GO; GO:2000011; P:regulation of adaxial/abaxial pattern formation; IMP:TAIR.
DR GO; GO:0000381; P:regulation of alternative mRNA splicing, via spliceosome; IMP:TAIR.
DR GO; GO:0048509; P:regulation of meristem development; IMP:TAIR.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; TAS:TAIR.
DR GO; GO:0008380; P:RNA splicing; IMP:UniProtKB.
DR GO; GO:0048367; P:shoot system development; IMP:TAIR.
DR GO; GO:0010267; P:ta-siRNA processing; IMP:TAIR.
DR DisProt; DP02392; -.
DR InterPro; IPR039727; SE/Ars2.
DR InterPro; IPR007042; SERRATE/Ars2_C.
DR InterPro; IPR021933; SERRATE/Ars2_N.
DR InterPro; IPR013087; Znf_C2H2_type.
DR PANTHER; PTHR13165; PTHR13165; 1.
DR Pfam; PF04959; ARS2; 1.
DR Pfam; PF12066; SERRATE_Ars2_N; 1.
DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Metal-binding; mRNA processing; mRNA splicing; Nucleus;
KW Phosphoprotein; Reference proteome; RNA-mediated gene silencing; Zinc;
KW Zinc-finger.
FT CHAIN 1..720
FT /note="Serrate RNA effector molecule"
FT /id="PRO_0000385228"
FT ZN_FING 498..523
FT /note="C2H2-type"
FT REGION 1..192
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 288..335
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 361..380
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 543..622
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 666..687
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 44..125
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 142..171
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 302..317
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 361..377
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 546..560
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 562..607
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 76
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19376835"
FT MOD_RES 90
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19376835"
FT MOD_RES 92
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19376835"
FT MOD_RES 689
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19245862"
FT HELIX 198..201
FT /evidence="ECO:0007829|PDB:3AX1"
FT HELIX 202..204
FT /evidence="ECO:0007829|PDB:3AX1"
FT TURN 205..207
FT /evidence="ECO:0007829|PDB:3AX1"
FT HELIX 211..237
FT /evidence="ECO:0007829|PDB:3AX1"
FT HELIX 241..247
FT /evidence="ECO:0007829|PDB:3AX1"
FT HELIX 249..275
FT /evidence="ECO:0007829|PDB:3AX1"
FT STRAND 283..286
FT /evidence="ECO:0007829|PDB:3AX1"
FT HELIX 331..333
FT /evidence="ECO:0007829|PDB:3AX1"
FT HELIX 336..357
FT /evidence="ECO:0007829|PDB:3AX1"
FT STRAND 386..388
FT /evidence="ECO:0007829|PDB:3AX1"
FT STRAND 395..397
FT /evidence="ECO:0007829|PDB:3AX1"
FT HELIX 400..414
FT /evidence="ECO:0007829|PDB:3AX1"
FT HELIX 418..420
FT /evidence="ECO:0007829|PDB:3AX1"
FT HELIX 446..460
FT /evidence="ECO:0007829|PDB:3AX1"
FT HELIX 464..469
FT /evidence="ECO:0007829|PDB:3AX1"
FT HELIX 471..482
FT /evidence="ECO:0007829|PDB:3AX1"
FT HELIX 483..485
FT /evidence="ECO:0007829|PDB:3AX1"
FT STRAND 486..490
FT /evidence="ECO:0007829|PDB:3AX1"
FT STRAND 492..500
FT /evidence="ECO:0007829|PDB:3AX1"
FT STRAND 502..504
FT /evidence="ECO:0007829|PDB:3AX1"
FT STRAND 508..511
FT /evidence="ECO:0007829|PDB:3AX1"
FT HELIX 512..522
FT /evidence="ECO:0007829|PDB:3AX1"
FT HELIX 524..543
FT /evidence="ECO:0007829|PDB:3AX1"
SQ SEQUENCE 720 AA; 81098 MW; 44D7041FAEA4A857 CRC64;
MADVNLPPSD SVDNRLPEKS TSSSPPPPPP SSSLPQQEQE QDQQQLPLRR ERDSRERRDE
RDIERPPPNR RERDRSPLPP PRRDYKRRPS LSPPPPYRDR RHSPPQRRSP PQKRYRRDDN
GYDGRRGSPR GGYGPPDRRF GYDHGGGYDR EMGGRPGYGD ERPHGRFMGR YQDWEGGRGG
YGDASNSGNP QRDGLMSYKQ FIQELEDDIL PSEAERRYQE YKSEYITTQK RAFFNTHKEE
DWLKNKYHPT NLLSVIERRN DLAQKVAKDF LLDLQSGTLD LGPAVTALNK SGRTSEPNSE
DEAAGVGKRK RHGMGGAKEN ELLSAAPKAP SFTSDPKRIL TDVEQTQALV RKLDSEKKIE
ENVLQGSETE KSGREKLHSG STGPVVIIRG LTSVKGLEGV ELLDTLVTYL WRVHGLDYYG
KVETNEAKGL RHVRAEGKVS DAKGDENESK FDSHWQERLK GQDPLEVMAA KEKIDAAATE
ALDPHVRKIR DEKYGWKYGC GAKGCTKLFH AAEFVYKHLK LKHTELVTEL TTKVREELYF
QNYMNDPNAP GGQPATQQSG PRDRPIRRKP SMENRLRDDR GGRRERDGRA NGNDRNDRSE
DQQRGDNDGG NPGEVGYDAF GGQGGVHVPP FLSDINPPPM LMPVPGAGPL GPFVPAPPEV
AMQMFRDPSG PNPPFEGSGR GGPAPFLLSP AFRQDPRRLR SYQDLDAPEE EVTVIDYRSL
