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ATML1 Homeobox-leucine zipper family protein / lipid-binding START domain-containing protein [ Arabidopsis thaliana (thale cress) ]

Gene ID: 828263, updated on 18-Sep-2024

Summary

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Official Symbol
ATML1
Official Full Name
Homeobox-leucine zipper family protein / lipid-binding START domain-containing protein
Primary source
TAIR:AT4G21750
Locus tag
AT4G21750
See related
Araport:AT4G21750
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Arabidopsis thaliana (ecotype: Columbia)
Lineage
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Also known as
F17L22.210; F17L22_210; MERISTEM LAYER 1
Summary
Encodes a homeobox protein similar to GL2. It is expressed in both the apical and basal daughter cells of the zygote as well as their progeny. Expression is detected starting the two-celled stage of embryo development and is later restricted to the outermost, epidermal cell layer from its inception. Its promoter is highly modular with each region contributing to specific aspects of the gene's spatial and temporal expression. Double mutant analysis with PDF2, another L1-specific gene, suggests that their functions are partially redundant and the absence of both of the genes result in abnormal shoot development.
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Genomic context

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See ATML1 in Genome Data Viewer
Location:
chromosome: 4
Exon count:
12
Sequence:
Chromosome: 4; NC_003075.7 (11555039..11560771)

Chromosome 4 - NC_003075.7Genomic Context describing neighboring genes Neighboring gene uncharacterized protein Neighboring gene PAK-box/P21-Rho-binding family protein Neighboring gene beta-glucosidase 47 Neighboring gene Pseudouridine synthase family protein Neighboring gene uncharacterized protein

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_003075.7

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Epidermal injury-induced derepression of key regulator ATML1 in newly exposed cells elicits epidermis regeneration. Iida H, et al. Nat Commun, 2023 Feb 23. PMID 36823419, Free PMC Article
  2. ATML1 activity is restricted to the outermost cells of the embryo through post-transcriptional repressions. Iida H, et al. Development, 2019 Feb 22. PMID 30760483
  3. Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal. Meyer HM, et al. Elife, 2017 Feb 1. PMID 28145865, Free PMC Article
  4. The coordination of ploidy and cell size differs between cell layers in leaves. Katagiri Y, et al. Development, 2016 Apr 1. PMID 26903507, Free PMC Article
  5. Post-embryonic induction of ATML1-SRDX alters the morphology of seedlings. Takada S. PLoS One, 2013. PMID 24205380, Free PMC Article

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Epidermal injury-induced derepression of key regulator ATML1 in newly exposed cells elicits epidermis regeneration.
    Title: Epidermal injury-induced derepression of key regulator ATML1 in newly exposed cells elicits epidermis regeneration.
  2. post-transcriptional repressions of ATML1 contribute to the restriction of master transcriptional regulator activity in specific cells to enable position-dependent cell differentiation
    Title: ATML1 activity is restricted to the outermost cells of the embryo through post-transcriptional repressions.
  3. The authors find that ATML1 is expressed in all epidermal cells. However, its level fluctuates in each of these cells. If ATML1 levels surpass a threshold during the G2 phase of the cell cycle, the cell will likely enter a state of endoreduplication and become giant.
    Title: Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal.
  4. Induction of epidermis cell identity based on the expression of the homeobox gene ATML1 in mesophyll cells enhanced the level of correlation between ploidy and cell volume to near that of wild-type epidermal cells.
    Title: The coordination of ploidy and cell size differs between cell layers in leaves.
  5. These results indicate that ATML1 and PDF2 act redundantly as a positive regulator of shoot epidermal cell differentiation and at least one copy of these genes is essential for embryo development.
    Title: ATML1 and PDF2 Play a Redundant and Essential Role in Arabidopsis Embryo Development.
  6. Upon seed imbibition, increased Gibberellin (GA)levels reduce DELLA protein abundance and release ATML1/PDF2 to activate L1 box gene expression, thus enhancing germination potential.
    Title: Arabidopsis DELLA and two HD-ZIP transcription factors regulate GA signaling in the epidermis through the L1 box cis-element.
  7. ATML1 and its target genes are associated with the initial specification of epidermal cell fate and the maintenance of epidermal cells in later stages.
    Title: Post-embryonic induction of ATML1-SRDX alters the morphology of seedlings.
  8. ACR4 positively affects the expression of ATML1 and PDF2 in seedlings. In contrast, ATML1- and PDF2-containing complexes directly and negatively affect both their own expression and that of ACR4.
    Title: Epidermal identity is maintained by cell-cell communication via a universally active feedback loop in Arabidopsis thaliana.
  9. ATML1 is a master regulator for shoot epidermis identity.
    Title: ATML1 promotes epidermal cell differentiation in Arabidopsis shoots.
  10. A 101 bp fragment that conferred all aspects of ATML1 expression contained known binding sites for homeodomain transcription factors and other regulatory sequences.
    Title: Transcriptional regulation of epidermal cell fate in the Arabidopsis embryo.
Submit: New GeneRIF Correction

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

NM_001036615.3
NM_001341510.1
NM_001341511.1
NM_118295.7

Gene Ontology Provided by TAIR

Function Evidence Code Pubs
enables DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables DNA-binding transcription factor activity ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
  
enables lipid binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_positive_effect cell differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within cotyledon development IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within plant epidermal cell differentiation IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within plant epidermal cell differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in regulation of seed dormancy process IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in regulation of seed germination IEP
Inferred from Expression Pattern
more info
 PubMed 
acts_upstream_of_or_within seed germination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus ISM
Inferred from Sequence Model
more info
  

General protein information

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Preferred Names
Homeobox-leucine zipper family protein / lipid-binding START domain-containing protein
NP_001031692.1
  • MERISTEM LAYER 1 (ATML1); FUNCTIONS IN: sequence-specific DNA binding, DNA binding, sequence-specific DNA binding transcription factor activity; INVOLVED IN: epidermal cell differentiation, regulation of transcription, DNA-dependent, cotyledon development; LOCATED IN: nucleus; EXPRESSED IN: 29 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: Homeobox, conserved site (InterPro:IPR017970), Homeobox (InterPro:IPR001356), Homeodomain-like (InterPro:IPR009057), Lipid-binding START (InterPro:IPR002913), Homeodomain-related (InterPro:IPR012287); BEST Arabidopsis thaliana protein match is: protodermal factor 2 (TAIR:AT4G04890.1); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (source: NCBI BLink).
NP_193906.2
  • MERISTEM LAYER 1 (ATML1); FUNCTIONS IN: sequence-specific DNA binding, DNA binding, sequence-specific DNA binding transcription factor activity; INVOLVED IN: epidermal cell differentiation, regulation of transcription, DNA-dependent, cotyledon development; LOCATED IN: nucleus; EXPRESSED IN: 29 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: Homeobox, conserved site (InterPro:IPR017970), Homeobox (InterPro:IPR001356), Homeodomain-like (InterPro:IPR009057), Lipid-binding START (InterPro:IPR002913), Homeodomain-related (InterPro:IPR012287); BEST Arabidopsis thaliana protein match is: protodermal factor 2 (TAIR:AT4G04890.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink).

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

  1. NC_003075.7 Reference assembly

    Range
    11555039..11560771
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001036615.3 → NP_001031692.1  Homeobox-leucine zipper family protein / lipid-binding START domain-containing protein [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_001031692.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q38887, Q8RWU4, Q9SVS2
    UniProtKB/TrEMBL
    A0A178UZ61, A0A5S9XUY9, A0A654FRI1
    Conserved Domains (3) summary
    cd08875
    Location:257 → 480
    START_ArGLABRA2_like; C-terminal lipid-binding START domain of the Arabidopsis homeobox protein GLABRA 2 and related proteins
    COG5576
    Location:45 → 155
    COG5576; Homeodomain-containing transcription factor [Transcription]
    pfam00046
    Location:65 → 118
    Homeobox; Homeobox domain

  2. NM_001341510.1 → NP_001329394.1  Homeobox-leucine zipper family protein / lipid-binding START domain-containing protein [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q38887, Q8RWU4, Q9SVS2
    UniProtKB/TrEMBL
    A0A178UZ61, A0A5S9XUY9, A0A654FRI1
    Conserved Domains (3) summary
    cd08875
    Location:257 → 480
    START_ArGLABRA2_like; C-terminal lipid-binding START domain of the Arabidopsis homeobox protein GLABRA 2 and related proteins
    COG5576
    Location:45 → 155
    COG5576; Homeodomain-containing transcription factor [Transcription]
    pfam00046
    Location:65 → 118
    Homeobox; Homeobox domain

  3. NM_001341511.1 → NP_001329395.1  Homeobox-leucine zipper family protein / lipid-binding START domain-containing protein [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q38887, Q8RWU4, Q9SVS2
    UniProtKB/TrEMBL
    A0A178UZ61, A0A5S9XUY9, A0A654FRI1
    Conserved Domains (3) summary
    cd08875
    Location:257 → 480
    START_ArGLABRA2_like; C-terminal lipid-binding START domain of the Arabidopsis homeobox protein GLABRA 2 and related proteins
    COG5576
    Location:45 → 155
    COG5576; Homeodomain-containing transcription factor [Transcription]
    pfam00046
    Location:65 → 118
    Homeobox; Homeobox domain

  4. NM_118295.7 → NP_193906.2  Homeobox-leucine zipper family protein / lipid-binding START domain-containing protein [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_193906.2

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q38887, Q8RWU4, Q9SVS2
    UniProtKB/TrEMBL
    A0A178UZ61, A0A5S9XUY9, A0A654FRI1
    Conserved Domains (3) summary
    cd08875
    Location:257 → 480
    START_ArGLABRA2_like; C-terminal lipid-binding START domain of the Arabidopsis homeobox protein GLABRA 2 and related proteins
    COG5576
    Location:45 → 155
    COG5576; Homeodomain-containing transcription factor [Transcription]
    pfam00046
    Location:65 → 118
    Homeobox; Homeobox domain
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8RWU4.1

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