RID2_ARATH
ID RID2_ARATH Reviewed; 289 AA.
AC Q9LVD0;
DT 25-OCT-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=18S rRNA (guanine-N(7))-methyltransferase RID2 {ECO:0000305};
DE EC=2.1.1.309 {ECO:0000250|UniProtKB:P25627};
DE AltName: Full=Protein ROOT INITIATION DEFECTIVE 2 {ECO:0000303|PubMed:14522871};
GN Name=RID2 {ECO:0000303|PubMed:14522871};
GN OrderedLocusNames=At5g57280 {ECO:0000312|Araport:AT5G57280};
GN ORFNames=MJB24.9 {ECO:0000312|EMBL:BAA96951.1};
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10718197; DOI=10.1093/dnares/7.1.31;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence
RT features of the regions of 3,076,755 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:31-63(2000).
RN [2]
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 [3]
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 [4]
RP FUNCTION, AND MUTAGENESIS OF ARG-110.
RC STRAIN=cv. Landsberg erecta;
RX PubMed=14522871; DOI=10.1242/dev.00794;
RA Konishi M., Sugiyama M.;
RT "Genetic analysis of adventitious root formation with a novel series of
RT temperature-sensitive mutants of Arabidopsis thaliana.";
RL Development 130:5637-5647(2003).
RN [5]
RP FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF ARG-110, SUBCELLULAR
RP LOCATION, TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RC STRAIN=cv. Columbia, and cv. Landsberg erecta;
RX PubMed=21401745; DOI=10.1111/j.1365-313x.2011.04574.x;
RA Ohbayashi I., Konishi M., Ebine K., Sugiyama M.;
RT "Genetic identification of Arabidopsis RID2 as an essential factor involved
RT in pre-rRNA processing.";
RL Plant J. 67:49-60(2011).
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=27334696; DOI=10.1242/bio.019109;
RA Matsumura Y., Ohbayashi I., Takahashi H., Kojima S., Ishibashi N., Keta S.,
RA Nakagawa A., Hayashi R., Saez-Vasquez J., Echeverria M., Sugiyama M.,
RA Nakamura K., Machida C., Machida Y.;
RT "A genetic link between epigenetic repressor AS1-AS2 and a putative small
RT subunit processome in leaf polarity establishment of Arabidopsis.";
RL Biol. Open 5:942-954(2016).
CC -!- FUNCTION: Essential protein (PubMed:21401745). S-adenosyl-L-methionine-
CC dependent methyltransferase that specifically methylates the N(7)
CC position of a guanine in 18S rRNA. Requires the methyltransferase
CC adapter protein TRM112 for full rRNA methyltransferase activity.
CC Important for biogenesis end export of the 40S ribosomal subunit
CC independent on its methyltransferase activity (By similarity). Involved
CC in the pre-rRNA processing steps in the nucleolus leading to small-
CC subunit rRNA production independently of its RNA-modifying catalytic
CC activity. Supports cell proliferation (PubMed:21401745). Required for
CC the initiation of lateral root primordia formation and for the root
CC apical meristem (RAM) organization as well as for leaves development
CC (PubMed:14522871). During callus formation from hypocotyl and root
CC explants, required for the initial stage of reactivation of cell
CC proliferation in the hypocotyl stele (PubMed:21401745). Involved in
CC leaf polarity establishment by functioning cooperatively with AS2 to
CC repress abaxial genes ARF3, ARF4, KAN1, KAN2, YAB1 and YAB5, and the
CC knox homeobox genes KNAT1, KNAT2, KNAT6, and STM to promote adaxial
CC development in leaf primordia at shoot apical meristems at high
CC temperatures (PubMed:27334696). {ECO:0000250|UniProtKB:P25627,
CC ECO:0000269|PubMed:14522871, ECO:0000269|PubMed:21401745,
CC ECO:0000269|PubMed:27334696}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=guanosine(1575) in yeast 18S rRNA + S-adenosyl-L-methionine =
CC N(7)-methylguanosine(1575) in yeast 18S rRNA + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:43172, Rhea:RHEA-COMP:10387, Rhea:RHEA-
CC COMP:10388, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:74269,
CC ChEBI:CHEBI:74480; EC=2.1.1.309;
CC Evidence={ECO:0000250|UniProtKB:P25627};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00768,
CC ECO:0000269|PubMed:21401745}. Nucleus, nucleoplasm
CC {ECO:0000250|UniProtKB:O43709}. Cytoplasm, perinuclear region
CC {ECO:0000250|UniProtKB:O43709}. Cytoplasm
CC {ECO:0000250|UniProtKB:P25627}. Nucleus, nucleolus
CC {ECO:0000269|PubMed:21401745}.
CC -!- TISSUE SPECIFICITY: Expressed in seedlings, roots and flowers.
CC {ECO:0000269|PubMed:21401745}.
CC -!- DEVELOPMENTAL STAGE: In seedlings, expressed in the subapical region of
CC the primary roots, in lateral root primordia, in developing trichomes
CC and in stipules. In flowers, observed in pollens, embryo sacs and
CC embryos. In roots, present at low levels in the stele. When grown on
CC callus-inducing medium (CIM), accumulates strongly in the root stele
CC where callus formation starts. {ECO:0000269|PubMed:21401745}.
CC -!- DISRUPTION PHENOTYPE: Plants homozygous for the rid2-2 or rid2-3
CC mutation are lethal (PubMed:21401745). Exhibits pointed leaves. Plants
CC with double mutations in this protein and in AS2 have short filamentous
CC leaves at high temperatures (PubMed:27334696).
CC {ECO:0000269|PubMed:21401745, ECO:0000269|PubMed:27334696}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. BUD23/WBSCR22 family. {ECO:0000305}.
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DR EMBL; AB019233; BAA96951.1; -; Genomic_DNA.
DR EMBL; CP002688; AED96876.1; -; Genomic_DNA.
DR EMBL; AY065258; AAL38734.1; -; mRNA.
DR EMBL; AY096365; AAM20006.1; -; mRNA.
DR RefSeq; NP_200538.1; NM_125110.6.
DR AlphaFoldDB; Q9LVD0; -.
DR SMR; Q9LVD0; -.
DR STRING; 3702.AT5G57280.1; -.
DR PaxDb; Q9LVD0; -.
DR PRIDE; Q9LVD0; -.
DR ProteomicsDB; 236977; -.
DR EnsemblPlants; AT5G57280.1; AT5G57280.1; AT5G57280.
DR GeneID; 835833; -.
DR Gramene; AT5G57280.1; AT5G57280.1; AT5G57280.
DR KEGG; ath:AT5G57280; -.
DR Araport; AT5G57280; -.
DR TAIR; locus:2165610; AT5G57280.
DR eggNOG; KOG1541; Eukaryota.
DR HOGENOM; CLU_055194_0_2_1; -.
DR InParanoid; Q9LVD0; -.
DR OMA; PHVWVGM; -.
DR OrthoDB; 1138059at2759; -.
DR PhylomeDB; Q9LVD0; -.
DR PRO; PR:Q9LVD0; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9LVD0; baseline and differential.
DR GO; GO:0005730; C:nucleolus; IDA:TAIR.
DR GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0048471; C:perinuclear region of cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0016435; F:rRNA (guanine) methyltransferase activity; IBA:GO_Central.
DR GO; GO:1990110; P:callus formation; IMP:UniProtKB.
DR GO; GO:0048527; P:lateral root development; IMP:UniProtKB.
DR GO; GO:0010078; P:maintenance of root meristem identity; IMP:UniProtKB.
DR GO; GO:0048364; P:root development; IMP:UniProtKB.
DR GO; GO:0070476; P:rRNA (guanine-N7)-methylation; IBA:GO_Central.
DR GO; GO:0006364; P:rRNA processing; IMP:TAIR.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR039769; Bud23-like.
DR InterPro; IPR022238; Bud23_C.
DR InterPro; IPR013216; Methyltransf_11.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR PANTHER; PTHR12734; PTHR12734; 1.
DR Pfam; PF08241; Methyltransf_11; 1.
DR Pfam; PF12589; WBS_methylT; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Methyltransferase; Nucleus; Reference proteome; Repressor;
KW rRNA processing; S-adenosyl-L-methionine; Stress response; Transferase.
FT CHAIN 1..289
FT /note="18S rRNA (guanine-N(7))-methyltransferase RID2"
FT /id="PRO_0000442038"
FT REGION 215..289
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 268..275
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT COMPBIAS 253..282
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 110
FT /note="R->C: In rid2-1; temperature-sensitive mutant with
FT altered reactivation of cell proliferation in the hypocotyl
FT stele during callus formation from hypocotyl and root
FT explants above 28 degrees Celsius. Impaired initiation of
FT lateral root primordia formation. Exhibits abnormalities in
FT the formation of the root apical meristem (RAM). Various
FT (acute and non-acute) temperature sensitive inhibitory
FT effects on different aspects of cell proliferation leading
FT to reduced roots and leaves development during seedling
FT growth. Nucleolar vacuolation and excessive accumulation of
FT various intermediates of pre-rRNA processing. Abnormally
FT swollen cells during culture on callus-inducing medium
FT (CIM) with extraordinarily large nucleoli."
FT /evidence="ECO:0000269|PubMed:14522871,
FT ECO:0000269|PubMed:21401745"
SQ SEQUENCE 289 AA; 32387 MW; 0C90EB7B143BB610 CRC64;
MSNRPELLAP PEIFYDDTEA RKYTSSSRIV EIQAKLSERA LELLALPEDG VPRFLLDIGC
GSGLSGETLS EDGHHWIGLD ISASMLHVAV EREVEGDLLL GDMGQGLGLR SGVIDGAISI
SAVQWLCNAD KSSHEPRLRL KAFFGSLYRC LSRGARAVFQ VYPENIAQRE LILRQALQAG
FGGGLVVDYP HSTKKRKEFL VLTCGTVQTS IQTSKNEYDE SCSEDDNSDD EESEEVGVSD
RNRPRKRQRT NTKVKGREWV LRKKEQSRRK GKNVPADSKF TSRKRRTRF
