ATX1_ARATH
ID ATX1_ARATH Reviewed; 1062 AA.
AC Q9C5X4; Q84WP4; Q9SIP3;
DT 02-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 02-MAY-2006, sequence version 2.
DT 03-AUG-2022, entry version 149.
DE RecName: Full=Histone H3-lysine(4) N-trimethyltransferase ATX1 {ECO:0000303|PubMed:12699618};
DE EC=2.1.1.354 {ECO:0000269|PubMed:12699618, ECO:0000269|PubMed:17965588, ECO:0000269|PubMed:18375658};
DE AltName: Full=Protein SET DOMAIN GROUP 27 {ECO:0000303|PubMed:11691919};
DE AltName: Full=Protein-lysine N-trimethyltransferase ATX1-SoloSET {ECO:0000303|PubMed:21245040};
DE EC=2.1.1.- {ECO:0000269|PubMed:21245040};
DE AltName: Full=Trithorax-homolog protein 1 {ECO:0000303|PubMed:11418242};
DE Short=TRX-homolog protein 1 {ECO:0000303|PubMed:11418242};
GN Name=ATX1 {ECO:0000303|PubMed:12699618};
GN Synonyms=SDG27 {ECO:0000303|PubMed:11691919},
GN SET27 {ECO:0000303|PubMed:11691919}, TRX1 {ECO:0000303|PubMed:11418242};
GN OrderedLocusNames=At2g31650 {ECO:0000312|Araport:AT2G31650};
GN ORFNames=T9H9.17 {ECO:0000312|EMBL:AAD24842.1};
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 [MRNA] (ISOFORM 1), AND TISSUE SPECIFICITY.
RC STRAIN=cv. Wassilewskija;
RX PubMed=11418242; DOI=10.1016/s0378-1119(01)00524-8;
RA Alvarez-Venegas R., Avramova Z.;
RT "Two Arabidopsis homologs of the animal trithorax genes: a new structural
RT domain is a signature feature of the trithorax gene family.";
RL Gene 271:215-221(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] (ISOFORM 2).
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 NOMENCLATURE.
RX PubMed=11691919; DOI=10.1093/nar/29.21.4319;
RA Baumbusch L.O., Thorstensen T., Krauss V., Fischer A., Naumann K.,
RA Assalkhou R., Schulz I., Reuter G., Aalen R.B.;
RT "The Arabidopsis thaliana genome contains at least 29 active genes encoding
RT SET domain proteins that can be assigned to four evolutionarily conserved
RT classes.";
RL Nucleic Acids Res. 29:4319-4333(2001).
RN [6]
RP FUNCTION, TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RX PubMed=12699618; DOI=10.1016/s0960-9822(03)00243-4;
RA Alvarez-Venegas R., Pien S., Sadder M., Witmer X., Grossniklaus U.,
RA Avramova Z.;
RT "ATX-1, an Arabidopsis homolog of trithorax, activates flower homeotic
RT genes.";
RL Curr. Biol. 13:627-637(2003).
RN [7]
RP FUNCTION, SUBCELLULAR LOCATION, AND INTERACTION WITH PIP5.
RX PubMed=16585509; DOI=10.1073/pnas.0600944103;
RA Alvarez-Vnegas R., Sadder M., Hlavacka A., Baluska F., Xia Y., Lu G.,
RA Firsov A., Sarath G., Moriyama H., Dubrovsky J.G., Avramova Z.;
RT "The Arabidopsis homolog of trithorax, ATX1, binds phosphatidylinositol 5-
RT phosphate, and the two regulate a common set of target genes.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:6049-6054(2006).
RN [8]
RP FUNCTION, DISRUPTION PHENOTYPE, AND CATALYTIC ACTIVITY.
RC STRAIN=cv. Columbia;
RX PubMed=17965588; DOI=10.4161/epi.2.2.4404;
RA Alvarez-Venegas R., Abdallat A.A., Guo M., Alfano J.R., Avramova Z.;
RT "Epigenetic control of a transcription factor at the cross section of two
RT antagonistic pathways.";
RL Epigenetics 2:106-113(2007).
RN [9]
RP FUNCTION, DISRUPTION PHENOTYPE, INTERACTION WITH CLF, AND SUBCELLULAR
RP LOCATION.
RC STRAIN=cv. Wassilewskija;
RX PubMed=17881378; DOI=10.1093/nar/gkm464;
RA Saleh A., Al-Abdallat A., Ndamukong I., Alvarez-Venegas R., Avramova Z.;
RT "The Arabidopsis homologs of trithorax (ATX1) and enhancer of zeste (CLF)
RT establish 'bivalent chromatin marks' at the silent AGAMOUS locus.";
RL Nucleic Acids Res. 35:6290-6296(2007).
RN [10]
RP FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE,
RP AND CATALYTIC ACTIVITY.
RC STRAIN=cv. Columbia;
RX PubMed=18375658; DOI=10.1105/tpc.107.056614;
RA Saleh A., Alvarez-Venegas R., Yilmaz M., Le O., Hou G., Sadder M.,
RA Al-Abdallat A., Xia Y., Lu G., Ladunga I., Avramova Z.;
RT "The highly similar Arabidopsis homologs of trithorax ATX1 and ATX2 encode
RT proteins with divergent biochemical functions.";
RL Plant Cell 20:568-579(2008).
RN [11]
RP FUNCTION, DISRUPTION PHENOTYPE, AND DEVELOPMENTAL STAGE.
RC STRAIN=cv. Columbia, and cv. Wassilewskija;
RX PubMed=18375656; DOI=10.1105/tpc.108.058172;
RA Pien S., Fleury D., Mylne J.S., Crevillen P., Inze D., Avramova Z.,
RA Dean C., Grossniklaus U.;
RT "ARABIDOPSIS TRITHORAX1 dynamically regulates FLOWERING LOCUS C activation
RT via histone 3 lysine 4 trimethylation.";
RL Plant Cell 20:580-588(2008).
RN [12]
RP REVIEW.
RX PubMed=19412892; DOI=10.1387/ijdb.082664za;
RA Avramova Z.;
RT "Evolution and pleiotropy of TRITHORAX function in Arabidopsis.";
RL Int. J. Dev. Biol. 53:371-381(2009).
RN [13]
RP INTERACTION WITH WDR5A.
RX PubMed=19567704; DOI=10.1105/tpc.109.067967;
RA Jiang D., Gu X., He Y.;
RT "Establishment of the winter-annual growth habit via FRIGIDA-mediated
RT histone methylation at FLOWERING LOCUS C in Arabidopsis.";
RL Plant Cell 21:1733-1746(2009).
RN [14]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=19154201; DOI=10.1111/j.1365-313x.2009.03798.x;
RA Ndamukong I., Chetram A., Saleh A., Avramova Z.;
RT "Wall-modifying genes regulated by the Arabidopsis homolog of trithorax,
RT ATX1: repression of the XTH33 gene as a test case.";
RL Plant J. 58:541-553(2009).
RN [15]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=19901554; DOI=10.4161/psb.4.11.10103;
RA Ding Y., Lapko H., Ndamukong I., Xia Y., Al-Abdallat A., Lalithambika S.,
RA Sadder M., Saleh A., Fromm M., Riethoven J.-J., Lu G., Avramova Z.;
RT "The Arabidopsis chromatin modifier ATX1, the myotubularin-like AtMTM and
RT the response to drought.";
RL Plant Signal. Behav. 4:1049-1058(2009).
RN [16]
RP PROTEIN SEQUENCE OF 876-883, IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION,
RP DISRUPTION PHENOTYPE, CATALYTIC ACTIVITY, ISOFORMS 1 AND 3, SUBCELLULAR
RP LOCATION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, AND INTERACTION WITH
RP A4/EF1A.
RC STRAIN=cv. Wassilewskija-2;
RX PubMed=21245040; DOI=10.1093/nar/gkq1300;
RA Ndamukong I., Lapko H., Cerny R.L., Avramova Z.;
RT "A cytoplasm-specific activity encoded by the Trithorax-like ATX1 gene.";
RL Nucleic Acids Res. 39:4709-4718(2011).
RN [17]
RP FUNCTION, DISRUPTION PHENOTYPE, INTERACTION WITH NRPB1, AND SUBUNIT.
RC STRAIN=cv. Wassilewskija;
RX PubMed=21266657; DOI=10.1105/tpc.110.080150;
RA Ding Y., Avramova Z., Fromm M.;
RT "Two distinct roles of ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1) at
RT promoters and within transcribed regions of ATX1-regulated genes.";
RL Plant Cell 23:350-363(2011).
RN [18]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Wassilewskija;
RX PubMed=21309869; DOI=10.1111/j.1365-313x.2011.04534.x;
RA Ding Y., Avramova Z., Fromm M.;
RT "The Arabidopsis trithorax-like factor ATX1 functions in dehydration stress
RT responses via ABA-dependent and ABA-independent pathways.";
RL Plant J. 66:735-744(2011).
RN [19]
RP FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF TYR-927; TYR-945; TYR-954;
RP TYR-1013 AND TYR-1015, AND INTERACTION WITH WDR5A.
RC STRAIN=cv. Wassilewskija;
RX PubMed=23284292; DOI=10.1371/journal.pgen.1003111;
RA Ding Y., Ndamukong I., Xu Z., Lapko H., Fromm M., Avramova Z.;
RT "ATX1-generated H3K4me3 is required for efficient elongation of
RT transcription, not initiation, at ATX1-regulated genes.";
RL PLoS Genet. 8:E1003111-E1003111(2012).
RN [20]
RP INTERACTION WITH ULT1.
RC STRAIN=cv. Columbia;
RX PubMed=23632855; DOI=10.1104/pp.112.213223;
RA Pu L., Liu M.-S., Kim S.Y., Chen L.-F.O., Fletcher J.C., Sung Z.R.;
RT "EMBRYONIC FLOWER1 and ULTRAPETALA1 Act Antagonistically on Arabidopsis
RT Development and Stress Response.";
RL Plant Physiol. 162:812-830(2013).
RN [21]
RP REVIEW.
RX PubMed=25047977; DOI=10.1016/j.pbi.2014.07.004;
RA Fromm M., Avramova Z.;
RT "ATX1/AtCOMPASS and the H3K4me3 marks: how do they activate Arabidopsis
RT genes?";
RL Curr. Opin. Plant Biol. 21:75-82(2014).
RN [22]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Wassilewskija;
RX PubMed=25205583; DOI=10.1093/jxb/eru355;
RA Napsucialy-Mendivil S., Alvarez-Venegas R., Shishkova S., Dubrovsky J.G.;
RT "Arabidopsis homolog of trithorax1 (ATX1) is required for cell production,
RT patterning, and morphogenesis in root development.";
RL J. Exp. Bot. 65:6373-6384(2014).
RN [23]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=24102415; DOI=10.1111/nph.12493;
RA Shafiq S., Berr A., Shen W.-H.;
RT "Combinatorial functions of diverse histone methylations in Arabidopsis
RT thaliana flowering time regulation.";
RL New Phytol. 201:312-322(2014).
RN [24]
RP FUNCTION, GLYCOSYLATION AT SER-947, INTERACTION WITH SEC, AND MUTAGENESIS
RP OF SER-947.
RC STRAIN=cv. Columbia;
RX PubMed=30150325; DOI=10.15252/embj.201798115;
RA Xing L., Liu Y., Xu S., Xiao J., Wang B., Deng H., Lu Z., Xu Y., Chong K.;
RT "Arabidopsis O-GlcNAc transferase SEC activates histone methyltransferase
RT ATX1 to regulate flowering.";
RL EMBO J. 37:E98115-E98115(2018).
CC -!- FUNCTION: [Isoform 1]: Binds to the promoter and regulates the
CC transcription of target genes, maintaining them in an active state; at
CC promoters, required for TATA binding proteins (TBPs, e.g. TBP1 and
CC TBP2) and RNA polymerase II (Pol II) recruitment, and, in a subsequent
CC event, is recruited by a phosphorylated form of Pol II to the +300-bp
CC region of transcribed sequences to trimethylates nucleosomes
CC (PubMed:21266657, PubMed:23284292). Histone trimethyltransferase that
CC trimethylates 'Lys-4' of histone H3 (H3K4me3); H3 'Lys-4' methylation
CC represents a specific tag for epigenetic transcriptional activation and
CC is required for efficient elongation of transcription but not for
CC transcription initiation (PubMed:17965588, PubMed:17881378,
CC PubMed:18375658, PubMed:23284292). Methylates only a limited fraction
CC of nucleosomes of target genes (e.g. FLC, NAP, XTH33 and WRKY70)
CC (PubMed:18375658). Necessary for WDR5A occupancy at WRKY70 and LTP7
CC genes (PubMed:23284292). Required to maintain the active state of class
CC A (AP1 and AP2), class B (PI and AP3) and class C (AG, AGAMOUS) floral
CC homeotic genes at early stages of flower development (PubMed:17881378).
CC Together with CLF, modulates AG nucleosome methylation statement
CC (PubMed:17881378). Involved in epigenetic regulation (e.g. H3K4me3) of
CC the floral repressors FLC, FT and SOC1 to prevent the transition from
CC vegetative to reproductive development, independently of the
CC photoperiod; binds the active FLC locus before flowering, but this
CC interaction is released upon the transition to flowering
CC (PubMed:18375656, PubMed:24102415, PubMed:30150325). Regulates floral
CC organ identity and flowering transition. Functions as a receptor for
CC the lipid messenger phosphatidylinositol 5-phosphate (PI5P), which
CC regulates negatively its transcriptional activation activity. Exhibits
CC histone methylase activity and subsequent transcriptional regulation on
CC WRKY70 gene, and, to a lower extent on secondary defense-response
CC targets salicylic acid (SA)-responsive gene PR1 and jasmonic acid (JA)-
CC responsive gene THI2.1 (PubMed:17965588). Involved in response to
CC dehydration stress-response in both abscisic acid (ABA)-dependent and
CC ABA-independent pathways; this includes specific genes (e.g. COR15A,
CC ADH1, CBF4, RD29A, RD29B, RD26, ABF3, NCED3 and ABA3) epigenetic
CC regulation (e.g. H3K4me3 and Pol II recruitment) to promotes their
CC transcription and influence ABA production (PubMed:19901554,
CC PubMed:21309869). Implicated in stomatal closure regulation
CC (PubMed:21309869). Indirect repressor of XTH genes (XTH33)
CC (PubMed:19154201). Necessary for the phosphorylation of Pol II NRPB1
CC (e.g. Ser5P and Ser2P) at the promoters of target genes, thus
CC regulating both early and late stages of transcription
CC (PubMed:21266657). Controls root growth and architecture by regulating
CC the timing of root development, stem cell niche maintenance (e.g.
CC quiescent center (QC)), and cell patterning during primary and lateral
CC root development (PubMed:25205583). Modulates cell cycle duration, cell
CC production, and the transition from cell proliferation in the root
CC apical meristem (RAM) to cell elongation (PubMed:25205583).
CC {ECO:0000269|PubMed:12699618, ECO:0000269|PubMed:16585509,
CC ECO:0000269|PubMed:17881378, ECO:0000269|PubMed:17965588,
CC ECO:0000269|PubMed:18375656, ECO:0000269|PubMed:18375658,
CC ECO:0000269|PubMed:19154201, ECO:0000269|PubMed:19901554,
CC ECO:0000269|PubMed:21266657, ECO:0000269|PubMed:21309869,
CC ECO:0000269|PubMed:23284292, ECO:0000269|PubMed:24102415,
CC ECO:0000269|PubMed:25205583, ECO:0000269|PubMed:30150325}.
CC -!- FUNCTION: [Isoform 3]: Trimethylates A4/EF1A post-translationally at
CC Lys-396 (PubMed:21245040). Required for actin cytoskeleton organization
CC (PubMed:21245040). {ECO:0000269|PubMed:21245040}.
CC -!- CATALYTIC ACTIVITY: [Isoform 1]:
CC Reaction=L-lysyl(4)-[histone H3] + 3 S-adenosyl-L-methionine = 3 H(+) +
CC N(6),N(6),N(6)-trimethyl-L-lysyl(4)-[histone H3] + 3 S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:60260, Rhea:RHEA-COMP:15537, Rhea:RHEA-
CC COMP:15547, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
CC ChEBI:CHEBI:59789, ChEBI:CHEBI:61961; EC=2.1.1.354;
CC Evidence={ECO:0000269|PubMed:12699618, ECO:0000269|PubMed:17965588,
CC ECO:0000269|PubMed:18375658};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60261;
CC Evidence={ECO:0000269|PubMed:12699618, ECO:0000269|PubMed:17965588,
CC ECO:0000269|PubMed:18375658};
CC -!- CATALYTIC ACTIVITY: [Isoform 3]:
CC Reaction=L-lysyl-[protein] + 3 S-adenosyl-L-methionine = 3 H(+) +
CC N(6),N(6),N(6)-trimethyl-L-lysyl-[protein] + 3 S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:54192, Rhea:RHEA-COMP:9752, Rhea:RHEA-
CC COMP:13826, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
CC ChEBI:CHEBI:59789, ChEBI:CHEBI:61961;
CC Evidence={ECO:0000269|PubMed:21245040};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:54193;
CC Evidence={ECO:0000269|PubMed:21245040};
CC -!- SUBUNIT: [Isoform 1]: Interacts with PIP5 (PubMed:16585509). Interacts
CC with WDR5A (PubMed:19567704, PubMed:23284292). Binds to CLF in the
CC nucleus (PubMed:17881378). Interacts with NRPB1 CTD domain, especially
CC when NRPB1 is phosphorylated on 'Ser-5' of the heptapeptide repeat
CC (PubMed:21266657). Component of a nuclear protein complex containing at
CC least TATA binding proteins (TBPs, e.g. TBP1 and TBP2) and ATX1
CC (PubMed:21266657). Associates with ULT1 for trimethylating 'Lys-4' on
CC histone H3 (H3K4me3) at flower MADS box gene loci (PubMed:23632855).
CC Interacts with SEC (PubMed:30150325). {ECO:0000269|PubMed:16585509,
CC ECO:0000269|PubMed:17881378, ECO:0000269|PubMed:19567704,
CC ECO:0000269|PubMed:21266657, ECO:0000269|PubMed:23284292,
CC ECO:0000269|PubMed:23632855, ECO:0000269|PubMed:30150325}.
CC -!- SUBUNIT: [Isoform 3]: Interacts with A4/EF1A in the cytoplasm on the
CC nuclear periphery. {ECO:0000269|PubMed:21245040}.
CC -!- SUBCELLULAR LOCATION: [Isoform 1]: Nucleus
CC {ECO:0000269|PubMed:16585509, ECO:0000269|PubMed:17881378}. Cytoplasm
CC {ECO:0000269|PubMed:16585509}. Note=Shifts from nucleus to cytoplasm as
CC PIP5 levels increase. When in the nucleus, associated with chromatin.
CC When cytoplasmic, mostly localized along the plasma membrane,
CC associated with PIP5. {ECO:0000269|PubMed:16585509}.
CC -!- SUBCELLULAR LOCATION: [Isoform 3]: Cytoplasm
CC {ECO:0000269|PubMed:21245040}. Cytoplasm, perinuclear region
CC {ECO:0000269|PubMed:21245040}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q9C5X4-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9C5X4-2; Sequence=VSP_018132;
CC Name=3; Synonyms=SoloSET {ECO:0000303|PubMed:21245040};
CC IsoId=Q9C5X4-3; Sequence=VSP_060526;
CC -!- TISSUE SPECIFICITY: [Isoform 1]: Strongly expressed in cotyledons, but
CC weak levels in the first true leaves, except at the hydothodes
CC (PubMed:21245040). Ubiquitous with higher levels in dividing tissues,
CC including inflorescence meristem and flower primordia (PubMed:11418242,
CC PubMed:12699618, PubMed:18375658). Expressed also in leaves (especially
CC at hydathodes), in growing inflorescence stems and in the mature
CC flowers (PubMed:18375658). {ECO:0000269|PubMed:11418242,
CC ECO:0000269|PubMed:12699618, ECO:0000269|PubMed:18375658,
CC ECO:0000269|PubMed:21245040}.
CC -!- TISSUE SPECIFICITY: [Isoform 3]: Strongly expressed in young seedlings.
CC {ECO:0000269|PubMed:21245040}.
CC -!- DEVELOPMENTAL STAGE: [Isoform 1]: Expression is associated with the
CC initiation of flower organs and ovules (PubMed:12699618,
CC PubMed:18375658). Accumulates in the tissues of young seedlings but
CC also in adult plants (PubMed:18375658, PubMed:21245040). In flowers,
CC present in sepals, in the vasculature of petals, and in the filaments
CC of the stamens and, at low levels, at the tips of the stigma
CC (PubMed:18375658). In seedlings, observed in the vasculature of the
CC cotyledons, hypocotyls, stems, and the first pair of leaves
CC (PubMed:18375656, PubMed:21245040). Just prior to flowering, a strong
CC reduction in expression levels occurs in the vasculature
CC (PubMed:18375656). {ECO:0000269|PubMed:12699618,
CC ECO:0000269|PubMed:18375656, ECO:0000269|PubMed:18375658,
CC ECO:0000269|PubMed:21245040}.
CC -!- DEVELOPMENTAL STAGE: [Isoform 3]: Expressed in young seedlings
CC (PubMed:21245040). Later in development, confined to cells at
CC attachment sites of organ to stems (PubMed:21245040).
CC {ECO:0000269|PubMed:21245040}.
CC -!- PTM: Activated via O-glycosylation by SEC; this modification triggers
CC FLC locus H3K4me3 histone modification, thus preventing premature
CC flowering. {ECO:0000269|PubMed:30150325}.
CC -!- DISRUPTION PHENOTYPE: [Isoform 1]: Decreased germination rates, larger
CC stomatal apertures, more rapid transpiration and decreased tolerance to
CC dehydration stress in atx1 plants partly due to reduced ABA
CC biosynthesis as a result of decreased NCED3 transcript levels
CC (PubMed:21309869). Reduced trimethylated 'Lys-4' histone H3 (H3K4me3)
CC but normal dimethylated 'Lys-4' histone H3 (H3K4me2) at NAP, XTH33,
CC NCED3, LTP and WRKY70 nucleosomes leading to decreased transcript
CC levels in atx1 plants (PubMed:18375658, PubMed:21266657). Lower Pol II
CC phosphorylation (e.g. Ser5P and Ser2P) and TBP (e.g. TBP1 and TBP2)
CC occupancy at the promoters of NCED3, LTP and WRKY70 associated with
CC reduced gene expression (PubMed:21266657). Strongly reduced occupancy
CC of WDR5A at WRKY70 and LTP7 genes (PubMed:23284292). Accelerated
CC transition from vegetative to reproductive development, under both
CC long-day and short-day conditions, especially in medium-day conditions
CC (12 hours light / 12 hours dark), due to FLC, FT and SOC1 epigenetic
CC misregulation; specific depletion in H3K4me3 but increased H3K27me2
CC associated with reduced FLC, FT and SOC1 levels (PubMed:18375656,
CC PubMed:21245040, PubMed:24102415). Misexpression of AGAMOUS,
CC recognizable phenotypes (e.g. small and slightly serrated leaves, and
CC early flowering time) and loss of H3K4me3 histone H3-tail marks
CC (PubMed:17881378). Impaired in primary root growth with irregular shape
CC and expanded quiescent center (QC) cells (PubMed:25205583). Ectopic
CC expression of QC-specific markers (e.g. QC46, WOX5 and SCR) in the
CC primary RAM and in the developing lateral root primordia
CC (PubMed:25205583). Lack of coordination between cell division and cell
CC growth leading to atypical distribution of T-divisions, the presence of
CC oblique divisions, and abnormal cell patterning in the root apical
CC meristem (RAM) (PubMed:25205583). Reduced lateral root (LR) density
CC within the branching zone (PubMed:25205583). Altered transcription
CC levels of target genes, including several endomembrane and cell wall-
CC associated proteins coding genes, XTH genes being up-regulated
CC (PubMed:18375658, PubMed:19154201). Derepression of XTH33 in roots,
CC stems and seedlings (PubMed:19154201). Increased sensitivity to osmotic
CC or dehydration stress due to an altered expression of genes involved in
CC response to drought in both abscisic acid (ABA)-dependent and ABA-
CC independent pathways (e.g. COR15A, ADH1, CBF4, RD29A, RD29B, RD26,
CC ABF3, NCED3 and ABA3) (PubMed:19901554, PubMed:21309869). Double mutant
CC plants atx1 clf exhibits normal leaf-phenotype and flowering time
CC (PubMed:17881378). Reduced basal levels and induction of WRKY70 and of
CC the salicylic acid (SA)-responsive gene PR1 upon pathogen infection by
CC Pseudomonas syringae DC3000 or after SA treatment, but increased basal
CC levels of the jasmonic acid (JA)-responsive gene THI2.1or after JA
CC treatment (PubMed:17965588). {ECO:0000269|PubMed:17881378,
CC ECO:0000269|PubMed:17965588, ECO:0000269|PubMed:18375656,
CC ECO:0000269|PubMed:18375658, ECO:0000269|PubMed:19154201,
CC ECO:0000269|PubMed:19901554, ECO:0000269|PubMed:21245040,
CC ECO:0000269|PubMed:21266657, ECO:0000269|PubMed:21309869,
CC ECO:0000269|PubMed:23284292, ECO:0000269|PubMed:24102415,
CC ECO:0000269|PubMed:25205583}.
CC -!- DISRUPTION PHENOTYPE: [Isoform 3]: Precocious flowering, asymmetric
CC rosettes, aberrant flowers and chlorosis (PubMed:21245040).
CC Dramatically different pattern of reduced actin bundles and absent
CC actin transvacuolar cytoplasmic strands (TVSs) (PubMed:21245040).
CC {ECO:0000269|PubMed:21245040}.
CC -!- SIMILARITY: Belongs to the class V-like SAM-binding methyltransferase
CC superfamily. Histone-lysine methyltransferase family. TRX/MLL
CC subfamily. {ECO:0000255|PROSITE-ProRule:PRU00190}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD24842.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
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DR EMBL; AF329273; AAK01237.1; -; mRNA.
DR EMBL; AC007071; AAD24842.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002685; AEC08569.1; -; Genomic_DNA.
DR EMBL; BT002941; AAO22754.1; -; mRNA.
DR PIR; D84723; D84723.
DR RefSeq; NP_850170.1; NM_179839.3. [Q9C5X4-1]
DR AlphaFoldDB; Q9C5X4; -.
DR SMR; Q9C5X4; -.
DR BioGRID; 3068; 6.
DR STRING; 3702.AT2G31650.1; -.
DR PaxDb; Q9C5X4; -.
DR PRIDE; Q9C5X4; -.
DR ProteomicsDB; 241094; -. [Q9C5X4-1]
DR EnsemblPlants; AT2G31650.1; AT2G31650.1; AT2G31650. [Q9C5X4-1]
DR GeneID; 817721; -.
DR Gramene; AT2G31650.1; AT2G31650.1; AT2G31650. [Q9C5X4-1]
DR KEGG; ath:AT2G31650; -.
DR Araport; AT2G31650; -.
DR TAIR; locus:2065923; AT2G31650.
DR eggNOG; KOG1080; Eukaryota.
DR HOGENOM; CLU_005729_0_0_1; -.
DR InParanoid; Q9C5X4; -.
DR OMA; EHEPVNG; -.
DR OrthoDB; 181572at2759; -.
DR PhylomeDB; Q9C5X4; -.
DR PRO; PR:Q9C5X4; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q9C5X4; baseline and differential.
DR Genevisible; Q9C5X4; AT.
DR GO; GO:0000785; C:chromatin; IDA:TAIR.
DR GO; GO:0005737; C:cytoplasm; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0048471; C:perinuclear region of cytoplasm; IDA:UniProtKB.
DR GO; GO:0005886; C:plasma membrane; IDA:TAIR.
DR GO; GO:0048188; C:Set1C/COMPASS complex; IDA:TAIR.
DR GO; GO:0003682; F:chromatin binding; IDA:UniProtKB.
DR GO; GO:0018024; F:histone-lysine N-methyltransferase activity; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0010314; F:phosphatidylinositol-5-phosphate binding; IDA:TAIR.
DR GO; GO:0008276; F:protein methyltransferase activity; IMP:UniProtKB.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; IDA:TAIR.
DR GO; GO:0009738; P:abscisic acid-activated signaling pathway; IMP:UniProtKB.
DR GO; GO:0030036; P:actin cytoskeleton organization; IMP:UniProtKB.
DR GO; GO:0051568; P:histone H3-K4 methylation; IDA:TAIR.
DR GO; GO:0080182; P:histone H3-K4 trimethylation; IDA:UniProtKB.
DR GO; GO:0009910; P:negative regulation of flower development; IMP:UniProtKB.
DR GO; GO:0018022; P:peptidyl-lysine methylation; IMP:UniProtKB.
DR GO; GO:1904961; P:quiescent center organization; IMP:UniProtKB.
DR GO; GO:0009909; P:regulation of flower development; IMP:UniProtKB.
DR GO; GO:0040029; P:regulation of gene expression, epigenetic; IMP:UniProtKB.
DR GO; GO:2000023; P:regulation of lateral root development; IMP:UniProtKB.
DR GO; GO:2000280; P:regulation of root development; IMP:UniProtKB.
DR GO; GO:2000067; P:regulation of root morphogenesis; IMP:UniProtKB.
DR GO; GO:0090333; P:regulation of stomatal closure; IMP:UniProtKB.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IDA:UniProtKB.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IMP:TAIR.
DR GO; GO:0009414; P:response to water deprivation; IMP:UniProtKB.
DR GO; GO:0010093; P:specification of floral organ identity; IMP:TAIR.
DR GO; GO:0010228; P:vegetative to reproductive phase transition of meristem; IMP:UniProtKB.
DR CDD; cd15662; ePHD_ATX1_2_like; 1.
DR CDD; cd15494; PHD_ATX1_2_like; 1.
DR Gene3D; 2.170.270.10; -; 1.
DR Gene3D; 3.30.40.10; -; 2.
DR InterPro; IPR041956; ATX1/2_ePHD.
DR InterPro; IPR042010; ATX1/2_PHD.
DR InterPro; IPR034732; EPHD.
DR InterPro; IPR003889; FYrich_C.
DR InterPro; IPR003888; FYrich_N.
DR InterPro; IPR019023; Lamin-B_rcpt_of_tudor.
DR InterPro; IPR002219; PE/DAG-bd.
DR InterPro; IPR003616; Post-SET_dom.
DR InterPro; IPR000313; PWWP_dom.
DR InterPro; IPR001214; SET_dom.
DR InterPro; IPR046341; SET_dom_sf.
DR InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR019787; Znf_PHD-finger.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR Pfam; PF05965; FYRC; 1.
DR Pfam; PF05964; FYRN; 1.
DR Pfam; PF09465; LBR_tudor; 1.
DR Pfam; PF00855; PWWP; 1.
DR Pfam; PF00856; SET; 1.
DR SMART; SM00542; FYRC; 1.
DR SMART; SM00541; FYRN; 1.
DR SMART; SM00249; PHD; 2.
DR SMART; SM00293; PWWP; 1.
DR SMART; SM00317; SET; 1.
DR SUPFAM; SSF57903; SSF57903; 1.
DR SUPFAM; SSF82199; SSF82199; 1.
DR PROSITE; PS51805; EPHD; 1.
DR PROSITE; PS51543; FYRC; 1.
DR PROSITE; PS51542; FYRN; 1.
DR PROSITE; PS50868; POST_SET; 1.
DR PROSITE; PS50812; PWWP; 1.
DR PROSITE; PS50280; SET; 1.
DR PROSITE; PS50081; ZF_DAG_PE_2; 1.
DR PROSITE; PS01359; ZF_PHD_1; 1.
DR PROSITE; PS50016; ZF_PHD_2; 1.
PE 1: Evidence at protein level;
KW Abscisic acid signaling pathway; Alternative splicing; Chromatin regulator;
KW Cytoplasm; Direct protein sequencing; Glycoprotein; Metal-binding;
KW Methyltransferase; Nucleus; Reference proteome; Repeat;
KW S-adenosyl-L-methionine; Stress response; Transcription;
KW Transcription regulation; Transferase; Zinc; Zinc-finger.
FT CHAIN 1..1062
FT /note="Histone H3-lysine(4) N-trimethyltransferase ATX1"
FT /id="PRO_0000233354"
FT DOMAIN 301..365
FT /note="PWWP"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00162"
FT DOMAIN 441..500
FT /note="FYR N-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00875"
FT DOMAIN 504..586
FT /note="FYR C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00876"
FT DOMAIN 898..1016
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT DOMAIN 1022..1038
FT /note="Post-SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00155"
FT ZN_FING 591..647
FT /note="Phorbol-ester/DAG-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00226"
FT ZN_FING 609..660
FT /note="PHD-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT ZN_FING 665..698
FT /note="C2HC pre-PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01146"
FT ZN_FING 722..785
FT /note="PHD-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01146"
FT REGION 159..184
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 401..424
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 599..1062
FT /note="Interaction with PIP5"
FT /evidence="ECO:0000269|PubMed:16585509"
FT COMPBIAS 404..423
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 908
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 954
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 977..978
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q03164"
FT BINDING 980
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q03164"
FT BINDING 1026
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q03164"
FT BINDING 1028
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q03164"
FT BINDING 1033
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q03164"
FT CARBOHYD 947
FT /note="O-linked (GlcNAc) serine"
FT /evidence="ECO:0000269|PubMed:30150325"
FT VAR_SEQ 1..875
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:21245040"
FT /id="VSP_060526"
FT VAR_SEQ 1..583
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_018132"
FT MUTAGEN 927
FT /note="Y->A: Deficient methyltransferase catalytic activity
FT associated with early-flowering phenotype and reduced WRKY
FT 70 and LTP7 transcripts levels but normal recruitment of
FT WDR5A at target genes but without histone modification;
FT when associated with A-945, A-954, A-1013 and A-1015."
FT /evidence="ECO:0000269|PubMed:23284292"
FT MUTAGEN 945
FT /note="Y->A: Deficient methyltransferase catalytic activity
FT associated with early-flowering phenotype and reduced WRKY
FT 70 and LTP7 transcripts levels but normal recruitment of
FT WDR5A at target genes but without histone modification;
FT when associated with A-927, A-954, A-1013 and A-1015."
FT /evidence="ECO:0000269|PubMed:23284292"
FT MUTAGEN 947
FT /note="S->A: Repressed FLC transcription activation
FT associated with reduced activation by SEC-mediated O-
FT GlcNAcylation and lower methyltransferase catalytic
FT activity."
FT /evidence="ECO:0000269|PubMed:30150325"
FT MUTAGEN 954
FT /note="Y->A: Deficient methyltransferase catalytic activity
FT associated with early-flowering phenotype and reduced WRKY
FT 70 and LTP7 transcripts levels but normal recruitment of
FT WDR5A at target genes but without histone modification;
FT when associated with A-927, A-945, A-1013 and A-1015."
FT /evidence="ECO:0000269|PubMed:23284292"
FT MUTAGEN 1013
FT /note="Y->A: Deficient methyltransferase catalytic activity
FT associated with early-flowering phenotype and reduced WRKY
FT 70 and LTP7 transcripts levels but normal recruitment of
FT WDR5A at target genes but without histone modification;
FT when associated with A-927, A-945, A-954 and A-1015."
FT /evidence="ECO:0000269|PubMed:23284292"
FT MUTAGEN 1015
FT /note="Y->A: Deficient methyltransferase catalytic activity
FT associated with early-flowering phenotype and reduced WRKY
FT 70 and LTP7 transcripts levels but normal recruitment of
FT WDR5A at target genes but without histone modification;
FT when associated with A-927, A-945, A-954 and A-1013."
FT /evidence="ECO:0000269|PubMed:23284292"
FT CONFLICT 4
FT /note="F -> V (in Ref. 1; AAK01237)"
FT /evidence="ECO:0000305"
FT CONFLICT 23
FT /note="R -> H (in Ref. 1; AAK01237)"
FT /evidence="ECO:0000305"
FT CONFLICT 194
FT /note="V -> I (in Ref. 1; AAK01237)"
FT /evidence="ECO:0000305"
FT CONFLICT 313
FT /note="A -> S (in Ref. 1; AAK01237)"
FT /evidence="ECO:0000305"
FT CONFLICT 667
FT /note="R -> Q (in Ref. 1; AAK01237)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1062 AA; 119711 MW; 8949A2C5F414B726 CRC64;
MACFSNETQI EIDVHDLVEA PIRYDSIESI YSIPSSALCC VNAVGSHSLM SKKVKAQKLP
MIEQFEIEGS GVSASDDCCR SDDYKLRIQR PEIVRVYYRR RKRPLRECLL DQAVAVKTES
VELDEIDCFE EKKRRKIGNC ELVKSGMESI GLRRCKENNA FSGNKQNGSS RRKGSSSKNQ
DKATLASRSA KKWVRLSYDG VDPTSFIGLQ CKVFWPLDAL WYEGSIVGYS AERKRYTVKY
RDGCDEDIVF DREMIKFLVS REEMELLHLK FCTSNVTVDG RDYDEMVVLA ATLDECQDFE
PGDIVWAKLA GHAMWPAVIV DESIIGERKG LNNKVSGGGS LLVQFFGTHD FARIKVKQAI
SFIKGLLSPS HLKCKQPRFE EGMQEAKMYL KAHRLPERMS QLQKGADSVD SDMANSTEEG
NSGGDLLNDG EVWLRPTEHV DFRHIIGDLL IINLGKVVTD SQFFKDENHI WPEGYTAMRK
FTSLTDHSAS ALYKMEVLRD AETKTHPLFI VTADSGEQFK GPTPSACWNK IYNRIKKVQN
SDSPNILGEE LNGSGTDMFG LSNPEVIKLV QDLSKSRPSS HVSMCKNSLG RHQNQPTGYR
PVRVDWKDLD KCNVCHMDEE YENNLFLQCD KCRMMVHAKC YGELEPCDGA LWLCNLCRPG
APDMPPRCCL CPVVGGAMKP TTDGRWAHLA CAIWIPETCL SDVKKMEPID GVNKVSKDRW
KLMCTICGVS YGACIQCSNN SCRVAYHPLC ARAAGLCVEL ENDMSVEGEE ADQCIRMLSF
CKRHRQTSTA CLGSEDRIKS ATHKTSEYLP PPNPSGCART EPYNCFGRRG RKEPEALAAA
SSKRLFVENQ PYVIGGYSRL EFSTYKSIHG SKVSQMNTPS NILSMAEKYR YMRETYRKRL
AFGKSGIHGF GIFAKLPHRA GDMMIEYTGE LVRPSIADKR EQLIYNSMVG AGTYMFRIDD
ERVIDATRTG SIAHLINHSC VPNCYSRVIT VNGDEHIIIF AKRHIPKWEE LTYDYRFFSI
GERLSCSCGF PGCRGVVNDT EAEEQHAKIC VPRCDLIDWT AE
