Q9C5X4 · ATX1_ARATH
- ProteinHistone H3-lysine(4) N-trimethyltransferase ATX1
- GeneATX1
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids1062 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
Isoform 1
Binds to the promoter and regulates the transcription of target genes, maintaining them in an active state; at promoters, required for TATA binding proteins (TBPs, e.g. TBP1 and TBP2) and RNA polymerase II (Pol II) recruitment, and, in a subsequent event, is recruited by a phosphorylated form of Pol II to the +300-bp region of transcribed sequences to trimethylates nucleosomes (PubMed:21266657, PubMed:23284292).
Histone trimethyltransferase that trimethylates 'Lys-4' of histone H3 (H3K4me3); H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation and is required for efficient elongation of transcription but not for transcription initiation (PubMed:17881378, PubMed:17965588, PubMed:18375658, PubMed:23284292).
Methylates only a limited fraction of nucleosomes of target genes (e.g. FLC, NAP, XTH33 and WRKY70) (PubMed:18375658).
Necessary for WDR5A occupancy at WRKY70 and LTP7 genes (PubMed:23284292).
Required to maintain the active state of class A (AP1 and AP2), class B (PI and AP3) and class C (AG, AGAMOUS) floral homeotic genes at early stages of flower development (PubMed:17881378).
Together with CLF, modulates AG nucleosome methylation statement (PubMed:17881378).
Involved in epigenetic regulation (e.g. H3K4me3) of the floral repressors FLC, FT and SOC1 to prevent the transition from vegetative to reproductive development, independently of the photoperiod; binds the active FLC locus before flowering, but this interaction is released upon the transition to flowering (PubMed:18375656, PubMed:24102415, PubMed:30150325).
Regulates floral organ identity and flowering transition. Functions as a receptor for the lipid messenger phosphatidylinositol 5-phosphate (PI5P), which negatively regulates its transcriptional activation activity. Exhibits histone methylase activity and subsequent transcriptional regulation on WRKY70 gene, and, to a lower extent on secondary defense-response targets salicylic acid (SA)-responsive gene PR1 and jasmonic acid (JA)-responsive gene THI2.1 (PubMed:17965588).
Involved in response to dehydration stress-response in both abscisic acid (ABA)-dependent and ABA-independent pathways; this includes specific genes (e.g. COR15A, ADH1, CBF4, RD29A, RD29B, RD26, ABF3, NCED3 and ABA3) epigenetic regulation (e.g. H3K4me3 and Pol II recruitment) to promote their transcription and influence ABA production (PubMed:19901554, PubMed:21309869).
Implicated in stomatal closure regulation (PubMed:21309869).
Indirect repressor of XTH genes (XTH33) (PubMed:19154201).
Necessary for the phosphorylation of Pol II NRPB1 (e.g. Ser5P and Ser2P) at the promoters of target genes, thus regulating both early and late stages of transcription (PubMed:21266657).
Controls root growth and architecture by regulating the timing of root development, stem cell niche maintenance (e.g. quiescent center (QC)), and cell patterning during primary and lateral root development (PubMed:25205583).
Modulates cell cycle duration, cell production, and the transition from cell proliferation in the root apical meristem (RAM) to cell elongation (PubMed:25205583).
Histone trimethyltransferase that trimethylates 'Lys-4' of histone H3 (H3K4me3); H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation and is required for efficient elongation of transcription but not for transcription initiation (PubMed:17881378, PubMed:17965588, PubMed:18375658, PubMed:23284292).
Methylates only a limited fraction of nucleosomes of target genes (e.g. FLC, NAP, XTH33 and WRKY70) (PubMed:18375658).
Necessary for WDR5A occupancy at WRKY70 and LTP7 genes (PubMed:23284292).
Required to maintain the active state of class A (AP1 and AP2), class B (PI and AP3) and class C (AG, AGAMOUS) floral homeotic genes at early stages of flower development (PubMed:17881378).
Together with CLF, modulates AG nucleosome methylation statement (PubMed:17881378).
Involved in epigenetic regulation (e.g. H3K4me3) of the floral repressors FLC, FT and SOC1 to prevent the transition from vegetative to reproductive development, independently of the photoperiod; binds the active FLC locus before flowering, but this interaction is released upon the transition to flowering (PubMed:18375656, PubMed:24102415, PubMed:30150325).
Regulates floral organ identity and flowering transition. Functions as a receptor for the lipid messenger phosphatidylinositol 5-phosphate (PI5P), which negatively regulates its transcriptional activation activity. Exhibits histone methylase activity and subsequent transcriptional regulation on WRKY70 gene, and, to a lower extent on secondary defense-response targets salicylic acid (SA)-responsive gene PR1 and jasmonic acid (JA)-responsive gene THI2.1 (PubMed:17965588).
Involved in response to dehydration stress-response in both abscisic acid (ABA)-dependent and ABA-independent pathways; this includes specific genes (e.g. COR15A, ADH1, CBF4, RD29A, RD29B, RD26, ABF3, NCED3 and ABA3) epigenetic regulation (e.g. H3K4me3 and Pol II recruitment) to promote their transcription and influence ABA production (PubMed:19901554, PubMed:21309869).
Implicated in stomatal closure regulation (PubMed:21309869).
Indirect repressor of XTH genes (XTH33) (PubMed:19154201).
Necessary for the phosphorylation of Pol II NRPB1 (e.g. Ser5P and Ser2P) at the promoters of target genes, thus regulating both early and late stages of transcription (PubMed:21266657).
Controls root growth and architecture by regulating the timing of root development, stem cell niche maintenance (e.g. quiescent center (QC)), and cell patterning during primary and lateral root development (PubMed:25205583).
Modulates cell cycle duration, cell production, and the transition from cell proliferation in the root apical meristem (RAM) to cell elongation (PubMed:25205583).
Isoform 3
Trimethylates A4/EF1A post-translationally at Lys-396 (PubMed:21245040).
Required for actin cytoskeleton organization (PubMed:21245040).
Required for actin cytoskeleton organization (PubMed:21245040).
Catalytic activity
Isoform 1
L-lysyl4-[histone H3] + 3 S-adenosyl-L-methionine = N6,N6,N6-trimethyl-L-lysyl4-[histone H3] + 3 S-adenosyl-L-homocysteine + 3 H+This reaction proceeds in the forward direction.Isoform 3
L-lysyl-[protein] + 3 S-adenosyl-L-methionine = N6,N6,N6-trimethyl-L-lysyl-[protein] + 3 S-adenosyl-L-homocysteine + 3 H+This reaction proceeds in the forward direction.
Features
Showing features for binding site.
Type | ID | Position(s) | Description | ||
---|---|---|---|---|---|
Binding site | 908 | S-adenosyl-L-methionine (UniProtKB | ChEBI) | |||
Binding site | 954 | S-adenosyl-L-methionine (UniProtKB | ChEBI) | |||
Binding site | 977-978 | S-adenosyl-L-methionine (UniProtKB | ChEBI) | |||
Binding site | 980 | Zn2+ (UniProtKB | ChEBI) | |||
Binding site | 1026 | Zn2+ (UniProtKB | ChEBI) | |||
Binding site | 1028 | Zn2+ (UniProtKB | ChEBI) | |||
Binding site | 1033 | Zn2+ (UniProtKB | ChEBI) | |||
GO annotations
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameHistone H3-lysine(4) N-trimethyltransferase ATX1
- EC number
- Alternative names
Gene names
Organism names
- Strains
- Taxonomic lineageEukaryota > Viridiplantae > Streptophyta > Embryophyta > Tracheophyta > Spermatophyta > Magnoliopsida > eudicotyledons > Gunneridae > Pentapetalae > rosids > malvids > Brassicales > Brassicaceae > Camelineae > Arabidopsis
Accessions
- Primary accessionQ9C5X4
- Secondary accessions
Proteomes
Organism-specific databases
Genome annotation databases
Subcellular Location
UniProt Annotation
GO Annotation
Isoform 1
Note: Shifts from nucleus to cytoplasm as PIP5 levels increase. When in the nucleus, associated with chromatin. When cytoplasmic, mostly localized along the plasma membrane, associated with PIP5.
Isoform 3
Keywords
- Cellular component
Phenotypes & Variants
Disruption phenotype
Isoform 1
Decreased germination rates, larger stomatal apertures, more rapid transpiration and decreased tolerance to dehydration stress in atx1 plants partly due to reduced ABA biosynthesis as a result of decreased NCED3 transcript levels (PubMed:21309869).
Reduced trimethylated 'Lys-4' histone H3 (H3K4me3) but normal dimethylated 'Lys-4' histone H3 (H3K4me2) at NAP, XTH33, NCED3, LTP and WRKY70 nucleosomes leading to decreased transcript levels in atx1 plants (PubMed:18375658, PubMed:21266657).
Lower Pol II phosphorylation (e.g. Ser5P and Ser2P) and TBP (e.g. TBP1 and TBP2) occupancy at the promoters of NCED3, LTP and WRKY70 associated with reduced gene expression (PubMed:21266657).
Strongly reduced occupancy of WDR5A at WRKY70 and LTP7 genes (PubMed:23284292).
Accelerated transition from vegetative to reproductive development, under both long-day and short-day conditions, especially in medium-day conditions (12 hours light / 12 hours dark), due to FLC, FT and SOC1 epigenetic misregulation; specific depletion in H3K4me3 but increased H3K27me2 associated with reduced FLC, FT and SOC1 levels (PubMed:18375656, PubMed:21245040, PubMed:24102415).
Misexpression of AGAMOUS, recognizable phenotypes (e.g. small and slightly serrated leaves, and early flowering time) and loss of H3K4me3 histone H3-tail marks (PubMed:17881378).
Impaired in primary root growth with irregular shape and expanded quiescent center (QC) cells (PubMed:25205583).
Ectopic expression of QC-specific markers (e.g. QC46, WOX5 and SCR) in the primary RAM and in the developing lateral root primordia (PubMed:25205583).
Lack of coordination between cell division and cell growth leading to atypical distribution of T-divisions, the presence of oblique divisions, and abnormal cell patterning in the root apical meristem (RAM) (PubMed:25205583).
Reduced lateral root (LR) density within the branching zone (PubMed:25205583).
Altered transcription levels of target genes, including several endomembrane and cell wall-associated proteins coding genes, XTH genes being up-regulated (PubMed:18375658, PubMed:19154201).
Derepression of XTH33 in roots, stems and seedlings (PubMed:19154201).
Increased sensitivity to osmotic or dehydration stress due to an altered expression of genes involved in response to drought in both abscisic acid (ABA)-dependent and ABA-independent pathways (e.g. COR15A, ADH1, CBF4, RD29A, RD29B, RD26, ABF3, NCED3 and ABA3) (PubMed:19901554, PubMed:21309869).
Double mutant plants atx1 clf exhibits normal leaf-phenotype and flowering time (PubMed:17881378).
Reduced basal levels and induction of WRKY70 and of the salicylic acid (SA)-responsive gene PR1 upon pathogen infection by Pseudomonas syringae DC3000 or after SA treatment, but increased basal levels of the jasmonic acid (JA)-responsive gene THI2.1or after JA treatment (PubMed:17965588).
Reduced trimethylated 'Lys-4' histone H3 (H3K4me3) but normal dimethylated 'Lys-4' histone H3 (H3K4me2) at NAP, XTH33, NCED3, LTP and WRKY70 nucleosomes leading to decreased transcript levels in atx1 plants (PubMed:18375658, PubMed:21266657).
Lower Pol II phosphorylation (e.g. Ser5P and Ser2P) and TBP (e.g. TBP1 and TBP2) occupancy at the promoters of NCED3, LTP and WRKY70 associated with reduced gene expression (PubMed:21266657).
Strongly reduced occupancy of WDR5A at WRKY70 and LTP7 genes (PubMed:23284292).
Accelerated transition from vegetative to reproductive development, under both long-day and short-day conditions, especially in medium-day conditions (12 hours light / 12 hours dark), due to FLC, FT and SOC1 epigenetic misregulation; specific depletion in H3K4me3 but increased H3K27me2 associated with reduced FLC, FT and SOC1 levels (PubMed:18375656, PubMed:21245040, PubMed:24102415).
Misexpression of AGAMOUS, recognizable phenotypes (e.g. small and slightly serrated leaves, and early flowering time) and loss of H3K4me3 histone H3-tail marks (PubMed:17881378).
Impaired in primary root growth with irregular shape and expanded quiescent center (QC) cells (PubMed:25205583).
Ectopic expression of QC-specific markers (e.g. QC46, WOX5 and SCR) in the primary RAM and in the developing lateral root primordia (PubMed:25205583).
Lack of coordination between cell division and cell growth leading to atypical distribution of T-divisions, the presence of oblique divisions, and abnormal cell patterning in the root apical meristem (RAM) (PubMed:25205583).
Reduced lateral root (LR) density within the branching zone (PubMed:25205583).
Altered transcription levels of target genes, including several endomembrane and cell wall-associated proteins coding genes, XTH genes being up-regulated (PubMed:18375658, PubMed:19154201).
Derepression of XTH33 in roots, stems and seedlings (PubMed:19154201).
Increased sensitivity to osmotic or dehydration stress due to an altered expression of genes involved in response to drought in both abscisic acid (ABA)-dependent and ABA-independent pathways (e.g. COR15A, ADH1, CBF4, RD29A, RD29B, RD26, ABF3, NCED3 and ABA3) (PubMed:19901554, PubMed:21309869).
Double mutant plants atx1 clf exhibits normal leaf-phenotype and flowering time (PubMed:17881378).
Reduced basal levels and induction of WRKY70 and of the salicylic acid (SA)-responsive gene PR1 upon pathogen infection by Pseudomonas syringae DC3000 or after SA treatment, but increased basal levels of the jasmonic acid (JA)-responsive gene THI2.1or after JA treatment (PubMed:17965588).
Isoform 3
Precocious flowering, asymmetric rosettes, aberrant flowers and chlorosis (PubMed:21245040).
Dramatically different pattern of reduced actin bundles and absent actin transvacuolar cytoplasmic strands (TVSs) (PubMed:21245040).
Dramatically different pattern of reduced actin bundles and absent actin transvacuolar cytoplasmic strands (TVSs) (PubMed:21245040).
Features
Showing features for mutagenesis.
Type | ID | Position(s) | Description | ||
---|---|---|---|---|---|
Mutagenesis | 927 | Deficient methyltransferase catalytic activity associated with early-flowering phenotype and reduced WRKY 70 and LTP7 transcripts levels but normal recruitment of WDR5A at target genes but without histone modification; when associated with A-945, A-954, A-1013 and A-1015. | |||
Mutagenesis | 945 | Deficient methyltransferase catalytic activity associated with early-flowering phenotype and reduced WRKY 70 and LTP7 transcripts levels but normal recruitment of WDR5A at target genes but without histone modification; when associated with A-927, A-954, A-1013 and A-1015. | |||
Mutagenesis | 947 | Repressed FLC transcription activation associated with reduced activation by SEC-mediated O-GlcNAcylation and lower methyltransferase catalytic activity. | |||
Mutagenesis | 954 | Deficient methyltransferase catalytic activity associated with early-flowering phenotype and reduced WRKY 70 and LTP7 transcripts levels but normal recruitment of WDR5A at target genes but without histone modification; when associated with A-927, A-945, A-1013 and A-1015. | |||
Mutagenesis | 1013 | Deficient methyltransferase catalytic activity associated with early-flowering phenotype and reduced WRKY 70 and LTP7 transcripts levels but normal recruitment of WDR5A at target genes but without histone modification; when associated with A-927, A-945, A-954 and A-1015. | |||
Mutagenesis | 1015 | Deficient methyltransferase catalytic activity associated with early-flowering phenotype and reduced WRKY 70 and LTP7 transcripts levels but normal recruitment of WDR5A at target genes but without histone modification; when associated with A-927, A-945, A-954 and A-1013. | |||
Variants
We now provide the "Disease & Variants" viewer in its own tab.
The viewer provides 73 variants from UniProt as well as other sources including ClinVar and dbSNP.
PTM/Processing
Features
Showing features for chain, glycosylation.
Type | ID | Position(s) | Description | ||
---|---|---|---|---|---|
Chain | PRO_0000233354 | 1-1062 | Histone H3-lysine4 N-trimethyltransferase ATX1 | ||
Glycosylation | 947 | O-linked (GlcNAc) serine | |||
Post-translational modification
Activated via O-glycosylation by SEC; this modification triggers FLC locus H3K4me3 histone modification, thus preventing premature flowering.
Keywords
- PTM
Proteomic databases
PTM databases
Expression
Tissue specificity
Isoform 1
Strongly expressed in cotyledons, but weak levels in the first true leaves, except at the hydothodes (PubMed:21245040).
Ubiquitous with higher levels in dividing tissues, including inflorescence meristem and flower primordia (PubMed:11418242, PubMed:12699618, PubMed:18375658).
Expressed also in leaves (especially at hydathodes), in growing inflorescence stems and in the mature flowers (PubMed:18375658).
Ubiquitous with higher levels in dividing tissues, including inflorescence meristem and flower primordia (PubMed:11418242, PubMed:12699618, PubMed:18375658).
Expressed also in leaves (especially at hydathodes), in growing inflorescence stems and in the mature flowers (PubMed:18375658).
Isoform 3
Strongly expressed in young seedlings.
Developmental stage
Isoform 1
Expression is associated with the initiation of flower organs and ovules (PubMed:12699618, PubMed:18375658).
Accumulates in the tissues of young seedlings but also in adult plants (PubMed:18375658, PubMed:21245040).
In flowers, present in sepals, in the vasculature of petals, and in the filaments of the stamens and, at low levels, at the tips of the stigma (PubMed:18375658).
In seedlings, observed in the vasculature of the cotyledons, hypocotyls, stems, and the first pair of leaves (PubMed:18375656, PubMed:21245040).
Just prior to flowering, a strong reduction in expression levels occurs in the vasculature (PubMed:18375656).
Accumulates in the tissues of young seedlings but also in adult plants (PubMed:18375658, PubMed:21245040).
In flowers, present in sepals, in the vasculature of petals, and in the filaments of the stamens and, at low levels, at the tips of the stigma (PubMed:18375658).
In seedlings, observed in the vasculature of the cotyledons, hypocotyls, stems, and the first pair of leaves (PubMed:18375656, PubMed:21245040).
Just prior to flowering, a strong reduction in expression levels occurs in the vasculature (PubMed:18375656).
Isoform 3
Expressed in young seedlings (PubMed:21245040).
Later in development, confined to cells at attachment sites of organ to stems (PubMed:21245040).
Later in development, confined to cells at attachment sites of organ to stems (PubMed:21245040).
Gene expression databases
Interaction
Subunit
Isoform 1
Interacts with PIP5 (PubMed:16585509).
Interacts with WDR5A (PubMed:19567704, PubMed:23284292).
Binds to CLF in the nucleus (PubMed:17881378).
Interacts with NRPB1 CTD domain, especially when NRPB1 is phosphorylated on 'Ser-5' of the heptapeptide repeat (PubMed:21266657).
Component of a nuclear protein complex containing at least TATA binding proteins (TBPs, e.g. TBP1 and TBP2) and ATX1 (PubMed:21266657).
Associates with ULT1 for trimethylating 'Lys-4' on histone H3 (H3K4me3) at flower MADS box gene loci (PubMed:23632855).
Interacts with SEC (PubMed:30150325).
Interacts with WDR5A (PubMed:19567704, PubMed:23284292).
Binds to CLF in the nucleus (PubMed:17881378).
Interacts with NRPB1 CTD domain, especially when NRPB1 is phosphorylated on 'Ser-5' of the heptapeptide repeat (PubMed:21266657).
Component of a nuclear protein complex containing at least TATA binding proteins (TBPs, e.g. TBP1 and TBP2) and ATX1 (PubMed:21266657).
Associates with ULT1 for trimethylating 'Lys-4' on histone H3 (H3K4me3) at flower MADS box gene loci (PubMed:23632855).
Interacts with SEC (PubMed:30150325).
Isoform 3
Interacts with A4/EF1A in the cytoplasm on the nuclear periphery.
Protein-protein interaction databases
Structure
Family & Domains
Features
Showing features for region, domain, compositional bias, zinc finger.
Type | ID | Position(s) | Description | ||
---|---|---|---|---|---|
Region | 159-184 | Disordered | |||
Domain | 301-365 | PWWP | |||
Region | 401-424 | Disordered | |||
Compositional bias | 404-423 | Polar residues | |||
Domain | 441-500 | FYR N-terminal | |||
Domain | 504-586 | FYR C-terminal | |||
Zinc finger | 591-647 | Phorbol-ester/DAG-type | |||
Region | 599-1062 | Interaction with PIP5 | |||
Zinc finger | 609-660 | PHD-type 1 | |||
Zinc finger | 665-698 | C2HC pre-PHD-type | |||
Zinc finger | 722-785 | PHD-type 2 | |||
Domain | 898-1016 | SET | |||
Domain | 1022-1038 | Post-SET | |||
Sequence similarities
Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. TRX/MLL subfamily.
Keywords
- Domain
Phylogenomic databases
Family and domain databases
Sequence & Isoforms
- Sequence statusComplete
This entry describes 3 isoforms produced by Alternative splicing.
Q9C5X4-1
This isoform has been chosen as the canonical sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
- Name1
- Length1,062
- Mass (Da)119,711
- Last updated2006-05-02 v2
- MD5 ChecksumDE1225D69BF8D139ABF1888EAD75CB8E
Q9C5X4-2
- Name2
- Differences from canonical
- 1-583: Missing
Q9C5X4-3
- Name3
- SynonymsSoloSET
- Differences from canonical
- 1-875: Missing
Sequence caution
Features
Showing features for alternative sequence, sequence conflict, compositional bias.
Type | ID | Position(s) | Description | ||
---|---|---|---|---|---|
Alternative sequence | VSP_018132 | 1-583 | in isoform 2 | ||
Alternative sequence | VSP_060526 | 1-875 | in isoform 3 | ||
Sequence conflict | 4 | in Ref. 1; AAK01237 | |||
Sequence conflict | 23 | in Ref. 1; AAK01237 | |||
Sequence conflict | 194 | in Ref. 1; AAK01237 | |||
Sequence conflict | 313 | in Ref. 1; AAK01237 | |||
Compositional bias | 404-423 | Polar residues | |||
Sequence conflict | 667 | in Ref. 1; AAK01237 | |||
Keywords
- Coding sequence diversity
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
AF329273 EMBL· GenBank· DDBJ | AAK01237.1 EMBL· GenBank· DDBJ | mRNA | ||
AC007071 EMBL· GenBank· DDBJ | AAD24842.1 EMBL· GenBank· DDBJ | Genomic DNA | Sequence problems. | |
CP002685 EMBL· GenBank· DDBJ | AEC08569.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
BT002941 EMBL· GenBank· DDBJ | AAO22754.1 EMBL· GenBank· DDBJ | mRNA |