ROS1A_ORYSJ
ID ROS1A_ORYSJ Reviewed; 1952 AA.
AC C7IW64;
DT 05-DEC-2018, integrated into UniProtKB/Swiss-Prot.
DT 05-DEC-2018, sequence version 2.
DT 03-AUG-2022, entry version 59.
DE RecName: Full=Protein ROS1A {ECO:0000303|PubMed:22448681};
DE EC=3.2.2.- {ECO:0000305};
DE AltName: Full=Protein REPRESSOR OF SILENCING 1 homolog a {ECO:0000305};
DE AltName: Full=Protein ROS1 homolog {ECO:0000303|PubMed:30275307};
DE Short=OsROS1 {ECO:0000303|PubMed:30275307};
DE AltName: Full=Protein THICK ALEURONE 2 {ECO:0000303|PubMed:30275307};
GN Name=ROS1A {ECO:0000303|PubMed:22448681};
GN Synonyms=ROS1 {ECO:0000303|PubMed:30275307},
GN TA2 {ECO:0000303|PubMed:30275307};
GN OrderedLocusNames=Os01g0218032 {ECO:0000312|EMBL:BAS71045.1},
GN LOC_Os01g11900 {ECO:0000305};
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12447438; DOI=10.1038/nature01184;
RA Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT "The genome sequence and structure of rice chromosome 1.";
RL Nature 420:312-316(2002).
RN [2]
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 [3]
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 [4]
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 [5]
RP FUNCTION, TISSUE SPECIFICITY, AND DISRUPTION PHENOTYPE.
RX PubMed=22448681; DOI=10.1111/j.1365-313x.2012.05009.x;
RA Ono A., Yamaguchi K., Fukada-Tanaka S., Terada R., Mitsui T., Iida S.;
RT "A null mutation of ROS1a for DNA demethylation in rice is not
RT transmittable to progeny.";
RL Plant J. 71:564-574(2012).
RN [6]
RP FUNCTION, TISSUE SPECIFICITY, BIOTECHNOLOGY, AND MUTAGENESIS OF ALA-441;
RP ARG-482; SER-1357; SER-1413; ASP-1425 AND GLU-1856.
RX PubMed=30275307; DOI=10.1073/pnas.1806304115;
RA Liu J., Wu X., Yao X., Yu R., Larkin P.J., Liu C.M.;
RT "Mutations in the DNA demethylase OsROS1 result in a thickened aleurone and
RT improved nutritional value in rice grains.";
RL Proc. Natl. Acad. Sci. U.S.A. 115:11327-11332(2018).
CC -!- FUNCTION: Bifunctional DNA glycosylase/lyase, which excises 5-
CC methylcytosine (5-meC) and 5-hydroxymethylcytosine (5-hmeC), leaving an
CC apyrimidinic (AP) site that is subsequently incised by the lyase
CC activity (Probable). DNA demethylase that is indispensable in both male
CC and female gametophyte development (PubMed:22448681). Involved in the
CC regulation of DNA methylation in the promoters of RISBZ1/BZIP58 and
CC DOF3/RPBF, two transcription factors that functions synergistically to
CC positively regulate genes that are key players in the development of
CC aleurone layers (PubMed:30275307). Active DNA demethylation carried out
CC by ROS1A in rice endosperms may restrict the number of aleurone cell
CC layers (PubMed:30275307). {ECO:0000269|PubMed:22448681,
CC ECO:0000269|PubMed:30275307, ECO:0000305|PubMed:22448681}.
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000250|UniProtKB:P0AB83};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster does not appear to play a
CC role in catalysis, but is probably involved in the proper positioning
CC of the enzyme along the DNA strand. {ECO:0000250|UniProtKB:P0AB83};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:B8YIE8}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaf blades, leaf sheaths,
CC apical and lateral shoot meristems, inflorescence meristems, lodicules,
CC pollen grains, ovules and seeds (PubMed:22448681). Expressed in
CC vascular tissues of roots and leaves, pollen grains, pericarp,
CC aleurone, and starchy endosperm (PubMed:30275307).
CC {ECO:0000269|PubMed:22448681, ECO:0000269|PubMed:30275307}.
CC -!- DISRUPTION PHENOTYPE: Sterility and inability to set normal seeds due
CC to severe defects in both male and female gametogenesis.
CC {ECO:0000269|PubMed:22448681}.
CC -!- BIOTECHNOLOGY: Reducing ROS1A activity may be a potential tool to
CC increase aleurone content, and improve the nutritional value of rice
CC grains (PubMed:30275307). Aleurone cells are rich in an array of
CC proteins, vitamins and minerals (PubMed:30275307).
CC {ECO:0000269|PubMed:30275307}.
CC -!- SIMILARITY: Belongs to the DNA glycosylase family. DEMETER subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAH90964.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAS71045.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AP008207; BAH90964.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014957; BAS71045.1; ALT_SEQ; Genomic_DNA.
DR RefSeq; XP_015650531.1; XM_015795045.1.
DR RefSeq; XP_015650539.1; XM_015795053.1.
DR AlphaFoldDB; C7IW64; -.
DR SMR; C7IW64; -.
DR STRING; 39947.C7IW64; -.
DR PRIDE; C7IW64; -.
DR EnsemblPlants; Os01t0218032-01; Os01t0218032-01; Os01g0218032.
DR GeneID; 9271145; -.
DR Gramene; Os01t0218032-01; Os01t0218032-01; Os01g0218032.
DR KEGG; osa:9271145; -.
DR eggNOG; ENOG502QQKH; Eukaryota.
DR HOGENOM; CLU_2765416_0_0_1; -.
DR InParanoid; C7IW64; -.
DR OrthoDB; 164157at2759; -.
DR Proteomes; UP000000763; Chromosome 1.
DR Proteomes; UP000059680; Chromosome 1.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0035514; F:DNA demethylase activity; IDA:UniProtKB.
DR GO; GO:0019104; F:DNA N-glycosylase activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006284; P:base-excision repair; IEA:InterPro.
DR GO; GO:0080111; P:DNA demethylation; IDA:UniProtKB.
DR GO; GO:0048229; P:gametophyte development; IMP:UniProtKB.
DR CDD; cd00056; ENDO3c; 1.
DR Gene3D; 1.10.1670.10; -; 1.
DR InterPro; IPR044811; DME/ROS1.
DR InterPro; IPR011257; DNA_glycosylase.
DR InterPro; IPR003651; Endonuclease3_FeS-loop_motif.
DR InterPro; IPR003265; HhH-GPD_domain.
DR InterPro; IPR023170; HhH_base_excis_C.
DR InterPro; IPR028924; Perm-CXXC.
DR InterPro; IPR028925; RRM_DME.
DR PANTHER; PTHR46213; PTHR46213; 1.
DR Pfam; PF15629; Perm-CXXC; 1.
DR Pfam; PF15628; RRM_DME; 1.
DR SMART; SM00478; ENDO3c; 1.
DR SMART; SM00525; FES; 1.
DR SUPFAM; SSF48150; SSF48150; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; DNA-binding; Hydrolase; Iron; Iron-sulfur; Metal-binding; Nucleus;
KW Reference proteome.
FT CHAIN 1..1952
FT /note="Protein ROS1A"
FT /id="PRO_0000445979"
FT REGION 72..157
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 693..778
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1302..1334
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1367..1398
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 713..746
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1368..1398
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 1582
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P0AB83"
FT BINDING 1589
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P0AB83"
FT BINDING 1592
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P0AB83"
FT BINDING 1598
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P0AB83"
FT MUTAGEN 441
FT /note="A->V: In ta2-6; increased number of aleurone cell
FT layers in the grain."
FT /evidence="ECO:0000269|PubMed:30275307"
FT MUTAGEN 482
FT /note="R->K: In ta2-5; increased number of aleurone cell
FT layers in the grain."
FT /evidence="ECO:0000269|PubMed:30275307"
FT MUTAGEN 1357
FT /note="S->F: In ta2-4; increased number of aleurone cell
FT layers in the grain."
FT /evidence="ECO:0000269|PubMed:30275307"
FT MUTAGEN 1413
FT /note="S->N: In ta2-3; increased number of aleurone cell
FT layers in the grain."
FT /evidence="ECO:0000269|PubMed:30275307"
FT MUTAGEN 1425
FT /note="D->N: In ta2-2; increased number of aleurone cell
FT layers in the grain."
FT /evidence="ECO:0000269|PubMed:30275307"
FT MUTAGEN 1856
FT /note="E->ECSNVMRQ: In ta2-1; increased number of aleurone
FT cell layers in the grain."
FT /evidence="ECO:0000269|PubMed:30275307"
SQ SEQUENCE 1952 AA; 215862 MW; 1E8CDC3EA36D04CC CRC64;
MQDFGQWLPQ SQTTADLYFS SIPIPSQFDT SIETQTRTSA VVSSEKESAN SFVPHNGTGL
VERISNDAGL TEVVGSSAGP TECIDLNKTP ARKPKKKKHR PKVLKDDKPS KTPKSATPIP
STEKVEKPSG KRKYVRKKTS PGQPPAEQAA SSHCRSELKS VKRSLDFGGE VLQESTQSGS
QVPVAEICTG PKRQSIPSTI QRDSQSQLAC HVVSSTSSIH TSASQMVNAH LFPPDNMPNG
VLLDLNNSTS QLQNEHAKFV DSPARLFGSR IRQTSGKNSL LEIYAGMSDR NVPDLNSSIS
QTHSMSTDFA QYLLSSSQAS VRETQMANQM LNGHRMPENP ITPSHCIERA ALKEHLNHVP
HAKAAVMNGQ MPHSYRLAQN PILPPNHIEG YQVMENLSEL VTTNDYLTAS PFSQTGAANR
QHNIGDSMHI HALDPRRESN ASSGSWISLG VNFNQQNNGW ASAGAADAAS SHAPYFSEPH
KRMRTAYLNN YPNGVVGHFS TSSTDLSNNE NENVASAINS NVFTLADAQR LIAREKSRAS
QRMISFRSSK NDMVNRSEMV HQHGRPAPHG SACRESIEVP DKQFGLMTEE LTQLPSMPNN
PQREKYIPQT GSCQLQSLEH DMVKGHNLAG ELHKQVTSPQ VVIQSNFCVT PPDVLGRRTS
GEHLRTLIAP THASTCKDTL KALSCQLESS RDIIRPPVNP IGPSSADVPR TDNHQVKVSE
ETVTAKLPEK RKVGRPRKEL KPGEKPKPRG RPRKGKVVGG ELASKDSHTN PLQNESTSCS
YGPYAGEASV GRAVKANRVG ENISGAMVSL LDSLDIVIQK IKVLDINKSE DPVTAEPHGA
LVPYNGEFGP IVPFEGKVKR KRSRAKVDLD PVTALMWKLL MGPDMSDCAE GMDKDKEKWL
NEERKIFQGR VDSFIARMHL VQGDRRFSPW KGSVVDSVVG VFLTQNVSDH LSSSAFMALA
AKFPVKPEAS EKPANVMFHT ISENGDCSGL FGNSVKLQGE ILVQEASNTA ASFITTEDKE
GSNSVELLGS SFGDGVDGAA GVYSNIYENL PARLHATRRP VVQTGNAVEA EDGSLEGVVS
SENSTISSQN SSDYLFHMSD HMFSSMLLNF TAEDIGSRNM PKATRTTYTE LLRMQELKNK
SNETIESSEY HGVPVSCSNN IQVLNGIQNI GSKHQPLHSS ISYHQTGQVH LPDIVHASDL
EQSVYTGLNR VLDSNVTQTS YYPSPHPGIA CNNETQKADS LSNMLYGIDR SDKTTSLSEP
TPRIDNCFQP LSSEKMSFAR EQSSSENYLS RNEAEAAFVK QHGTSNVQGD NTVRTEQNGG
ENSQSGYSQQ DDNVGFQTAT TSNLYSSNLC QNQKANSEVL HGVSSNLIEN SKDDKKTSPK
VPVDGSKAKR PRVGAGKKKT YDWDMLRKEV LYSHGNKERS QNAKDSIDWE TIRQAEVKEI
SDTIRERGMN NMLAERIKDF LNRLVRDHGS IDLEWLRYVD SDKAKDYLLS IRGLGLKSVE
CVRLLTLHHM AFPVDTNVGR ICVRLGWVPL QPLPESLQLH LLEMYPMLEN IQKYLWPRLC
KLDQRTLYEL HYQMITFGKV FCTKSKPNCN ACPMRAECKH FASAFASARL ALPGPEEKSL
VTSGTPIAAE TFHQTYISSR PVVSQLEWNS NTCHHGMNNR QPIIEEPASP EPEHETEEMK
ECAIEDSFVD DPEEIPTIKL NFEEFTQNLK SYMQANNIEI EDADMSKALV AITPEVASIP
TPKLKNVSRL RTEHQVYELP DSHPLLEGFN QREPDDPCPY LLSIWTPGET AQSTDAPKSV
CNSQENGELC ASNTCFSCNS IREAQAQKVR GTLLIPCRTA MRGSFPLNGT YFQVNEVFAD
HDSSRNPIDV PRSWIWNLPR RTVYFGTSIP TIFKGLTTEE IQHCFWRGFV CVRGFDRTSR
APRPLYARLH FPASKITRNK KSAGSAPGRD DE
