RNJ_ARATH
ID RNJ_ARATH Reviewed; 911 AA.
AC Q84W56; Q67YC1; Q9FMV9; Q9FMW0;
DT 20-JUN-2018, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 150.
DE RecName: Full=Ribonuclease J {ECO:0000303|PubMed:22033332};
DE Short=RNase J {ECO:0000303|PubMed:22033332};
DE EC=3.1.-.- {ECO:0000305};
DE AltName: Full=Protein EMBRYO DEFECTIVE 2746 {ECO:0000303|PubMed:15266054};
DE Flags: Precursor;
GN Name=RNJ {ECO:0000303|PubMed:22033332};
GN Synonyms=EMB2746 {ECO:0000303|PubMed:15266054};
GN OrderedLocusNames=At5g63420 {ECO:0000312|Araport:AT5G63420};
GN ORFNames=MLE2.5 {ECO:0000312|EMBL:BAB08807.1},
GN MLE2.6 {ECO:0000312|EMBL:BAB08808.1};
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=9501997; DOI=10.1093/dnares/4.6.401;
RA Nakamura Y., Sato S., Kaneko T., Kotani H., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence
RT features of the regions of 1,191,918 bp covered by seventeen physically
RT assigned P1 clones.";
RL DNA Res. 4:401-414(1997).
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION [LARGE SCALE ANALYSIS], AND DISRUPTION PHENOTYPE [LARGE SCALE
RP ANALYSIS].
RC STRAIN=cv. Columbia;
RX PubMed=15266054; DOI=10.1104/pp.104.045179;
RA Tzafrir I., Pena-Muralla R., Dickerman A., Berg M., Rogers R., Hutchens S.,
RA Sweeney T.C., McElver J., Aux G., Patton D., Meinke D.;
RT "Identification of genes required for embryo development in Arabidopsis.";
RL Plant Physiol. 135:1206-1220(2004).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
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 [7]
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 [8]
RP FUNCTION, DISRUPTION PHENOTYPE, AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=22033332; DOI=10.1261/rna.028043.111;
RA Sharwood R.E., Halpert M., Luro S., Schuster G., Stern D.B.;
RT "Chloroplast RNase J compensates for inefficient transcription termination
RT by removal of antisense RNA.";
RL RNA 17:2165-2176(2011).
RN [9]
RP FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE,
RP AND INDUCTION BY LIGHT.
RC STRAIN=cv. Col-3, and cv. Columbia;
RX PubMed=25871650; DOI=10.1093/jxb/erv010;
RA Chen H., Zou W., Zhao J.;
RT "Ribonuclease J is required for chloroplast and embryo development in
RT Arabidopsis.";
RL J. Exp. Bot. 66:2079-2091(2015).
CC -!- FUNCTION: Essential protein required during embryogenesis, especially
CC in initiating and maintaining the organization of shoot apical
CC meristems (SAMs), cotyledons, and hypocotyls (PubMed:15266054,
CC PubMed:25871650). Involved in auxin-mediated pathways during
CC embryogenesis (PubMed:25871650). RNase that has both endonuclease and
CC 5'-3' exonuclease activities. Involved in RNA surveillance to prevent
CC overaccumulation of antisense RNA (PubMed:22033332). Probably involved
CC in maturation of rRNA and in some organisms also mRNA maturation and/or
CC decay (By similarity). {ECO:0000250|UniProtKB:Q72JJ7,
CC ECO:0000269|PubMed:15266054, ECO:0000269|PubMed:22033332,
CC ECO:0000269|PubMed:25871650}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250|UniProtKB:Q72JJ7};
CC Note=Binds up to 2 Zn(2+) ions per subunit.
CC {ECO:0000250|UniProtKB:Q72JJ7};
CC -!- SUBUNIT: Homodimer. May be a subunit of the RNA degradosome.
CC {ECO:0000250|UniProtKB:Q72JJ7}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:22033332}.
CC -!- TISSUE SPECIFICITY: Moslty expressed in inflorescences, seedlings,
CC leaves, flowers and flower buds, and, to a lower extent, in stems,
CC siliques and roots. {ECO:0000269|PubMed:25871650}.
CC -!- DEVELOPMENTAL STAGE: During the early stages of embryo development,
CC first observed at the transition stage. In the heart and torpedo
CC stages, predominantly present in the upper part of embryos. In
CC seedlings, strongly expressed in shoot meristems, hypocotyls, in the
CC vascular bundles of cotyledons, and in the veins of mature leaves. In
CC reproductive organs, detected in inflorescences, especially in sepals,
CC filaments, and stigmas, as well as in mature siliques and seeds.
CC {ECO:0000269|PubMed:25871650}.
CC -!- INDUCTION: By light. {ECO:0000269|PubMed:25871650}.
CC -!- DISRUPTION PHENOTYPE: Defective embryo arrested at globular stage
CC (PubMed:15266054, PubMed:25871650). Impaired chloroplast development
CC due to a disturbed formation of internal thylakoid membranes during
CC embryogenesis. Aberrant embryo patterning along the apical-basal axis.
CC Disrupted transport and response of auxin in embryos (PubMed:25871650).
CC Silenced plants exhibit chlorosis and slight disruptions in the
CC cleavage of polycistronic rRNA and mRNA precursors (PubMed:22033332).
CC {ECO:0000269|PubMed:15266054, ECO:0000269|PubMed:22033332,
CC ECO:0000269|PubMed:25871650}.
CC -!- SIMILARITY: Belongs to the metallo-beta-lactamase superfamily. RNA-
CC metabolizing metallo-beta-lactamase-like family. Bacterial RNase J
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB08807.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAB08808.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC -!- WEB RESOURCE: Name=Seed defective Arabidopsis mutants;
CC URL="http://seedgenes.org/MutantList";
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DR EMBL; AB007649; BAB08807.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AB007649; BAB08808.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED97746.1; -; Genomic_DNA.
DR EMBL; BT004210; AAO42228.1; -; mRNA.
DR EMBL; AK176547; BAD44310.1; -; mRNA.
DR EMBL; AK221272; BAD93952.1; -; mRNA.
DR RefSeq; NP_201147.2; NM_125737.4.
DR AlphaFoldDB; Q84W56; -.
DR SMR; Q84W56; -.
DR IntAct; Q84W56; 1.
DR MINT; Q84W56; -.
DR STRING; 3702.AT5G63420.1; -.
DR iPTMnet; Q84W56; -.
DR PaxDb; Q84W56; -.
DR PRIDE; Q84W56; -.
DR ProteomicsDB; 228013; -.
DR EnsemblPlants; AT5G63420.1; AT5G63420.1; AT5G63420.
DR GeneID; 836461; -.
DR Gramene; AT5G63420.1; AT5G63420.1; AT5G63420.
DR KEGG; ath:AT5G63420; -.
DR Araport; AT5G63420; -.
DR TAIR; locus:2167336; AT5G63420.
DR eggNOG; KOG1137; Eukaryota.
DR eggNOG; KOG4282; Eukaryota.
DR HOGENOM; CLU_008727_0_2_1; -.
DR InParanoid; Q84W56; -.
DR OMA; WRDGKAP; -.
DR OrthoDB; 663953at2759; -.
DR PhylomeDB; Q84W56; -.
DR PRO; PR:Q84W56; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q84W56; baseline and differential.
DR GO; GO:0009507; C:chloroplast; IDA:UniProtKB.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0008409; F:5'-3' exonuclease activity; IDA:UniProtKB.
DR GO; GO:0004519; F:endonuclease activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003729; F:mRNA binding; IDA:TAIR.
DR GO; GO:0060918; P:auxin transport; IEP:TAIR.
DR GO; GO:0009734; P:auxin-activated signaling pathway; IEA:UniProtKB-KW.
DR GO; GO:0009658; P:chloroplast organization; IMP:TAIR.
DR GO; GO:0009793; P:embryo development ending in seed dormancy; IMP:TAIR.
DR GO; GO:0009942; P:longitudinal axis specification; IMP:TAIR.
DR GO; GO:0009416; P:response to light stimulus; IEP:UniProtKB.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.10710; -; 1.
DR Gene3D; 3.60.15.10; -; 1.
DR InterPro; IPR001279; Metallo-B-lactamas.
DR InterPro; IPR044822; Myb_DNA-bind_4.
DR InterPro; IPR036866; RibonucZ/Hydroxyglut_hydro.
DR InterPro; IPR011108; RMMBL.
DR InterPro; IPR042173; RNase_J_2.
DR InterPro; IPR001005; SANT/Myb.
DR Pfam; PF12706; Lactamase_B_2; 1.
DR Pfam; PF13837; Myb_DNA-bind_4; 1.
DR Pfam; PF07521; RMMBL; 1.
DR SMART; SM00849; Lactamase_B; 1.
DR SUPFAM; SSF56281; SSF56281; 1.
DR PROSITE; PS50090; MYB_LIKE; 1.
PE 1: Evidence at protein level;
KW Auxin signaling pathway; Chloroplast; Developmental protein; Endonuclease;
KW Exonuclease; Hydrolase; Metal-binding; Nuclease; Plastid;
KW Reference proteome; RNA-binding; rRNA processing; Transit peptide; Zinc.
FT TRANSIT 1..70
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 71..911
FT /note="Ribonuclease J"
FT /id="PRO_0000444599"
FT DOMAIN 813..877
FT /note="Myb-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00133"
FT REGION 58..90
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 695..723
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 735..824
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 58..76
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 742..780
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 781..824
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 175
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q72JJ7"
FT BINDING 177
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q72JJ7"
FT BINDING 179
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q72JJ7"
FT BINDING 180
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q72JJ7"
FT BINDING 245
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q72JJ7"
FT BINDING 267
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q72JJ7"
FT BINDING 267
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q72JJ7"
FT BINDING 336..338
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q72JJ7"
FT BINDING 468..472
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q72JJ7"
FT BINDING 494
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q72JJ7"
FT CONFLICT 328
FT /note="G -> E (in Ref. 4; BAD44310)"
FT /evidence="ECO:0000305"
FT CONFLICT 665
FT /note="N -> D (in Ref. 4; BAD44310)"
FT /evidence="ECO:0000305"
FT CONFLICT 804
FT /note="A -> T (in Ref. 4; BAD44310)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 911 AA; 100554 MW; 920D67FDBCDD1E2C CRC64;
MMKPASLQGF SSHASSSIYS DVRRPATTPS KMAAFSALSL CPYTFTFRQS SRIKSTVSCS
VTSAPASGTS SSSKTPRRRS GRLEGVGKSM EDSVKRKMEQ FYEGTDGPPL RILPIGGLGE
IGMNCMLVGN YDRYILIDAG IMFPDYDEPG IQKIMPDTGF IRRWKHKIEA VVITHGHEDH
IGALPWVIPA LDPNTPIFAS SFTMELIKKR LKEHGIFVQS RLKTFSTRRR FMAGPFEIEP
ITVTHSIPDC SGLFLRCADG NILHTGDWKI DEAPLDGKVF DREALEELSK EGVTLMMSDS
TNVLSPGRTI SEKVVADALV RNVMAAKGRV ITTQFASNIH RLGSIKAAAD ITGRKLVFVG
MSLRTYLEAA WRDGKAPIDP SSLIKVEDIE AYAPKDLLIV TTGSQAEPRA ALNLASYGSS
HAFKLTKEDI ILYSAKVIPG NESRVMKMMN RIADIGPNII MGKNEMLHTS GHAYRGELEE
VLKIVKPQHF LPIHGELLFL KEHELLGKST GIRHTTVIKN GEMLGVSHLR NRRVLSNGFS
SLGRENLQLM YSDGDKAFGT SSELCIDERL RISSDGIIVL SMEIMRPGVS ENTLKGKIRI
TTRCMWLDKG RLLDALHKAA HAALSSCPVT CPLSHMERTV SEVLRKIVRK YSGKRPEVIA
IATENPMAVR ADEVSARLSG DPSVGSGVAA LRKVVEGNDK RSRAKKAPSQ EASPKEVDRT
LEDDIIDSAR LLAEEETAAS TYTEEVDTPV GSSSEESDDF WKSFINPSSS PSPSETENMN
KVADTEPKAE GKENSRDDDE LADASDSETK SSPKRVRKNK WKPEEIKKVI RMRGELHSRF
QVVKGRMALW EEISSNLSAE GINRSPGQCK SLWASLIQKY EESKADERSK TSWPHFEDMN
NILSELGTPA S
