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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. 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
    2. Identification of a meristem L1 layer-specific gene in Arabidopsis that is expressed during embryonic pattern formation and defines a new class of homeobox genes. Lu P, et al. Plant Cell, 1996 Dec. PMID 8989876, Free PMC Article
    3. Identification of a cis-regulatory element for L1 layer-specific gene expression, which is targeted by an L1-specific homeodomain protein. Abe M, et al. Plant J, 2001 Jun. PMID 11439135
    4. Transcriptional regulation of epidermal cell fate in the Arabidopsis embryo. Takada S, et al. Development, 2007 Mar. PMID 17301085
    5. ATML1 promotes epidermal cell differentiation in Arabidopsis shoots. Takada S, et al. Development, 2013 May. PMID 23515472

    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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    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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