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    DEK1 calpain-type cysteine protease family [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 841981, updated on 18-Sep-2024

    Summary

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    Official Symbol
    DEK1
    Official Full Name
    calpain-type cysteine protease family
    Primary source
    TAIR:AT1G55350
    Locus tag
    AT1G55350
    See related
    Araport:AT1G55350
    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
    ATDEK1; DEFECTIVE KERNEL 1; EMB1275; EMB80; embryo defective 1275; EMBRYO DEFECTIVE 80; F7A10.23; F7A10_23
    Summary
    Similar to maize DEK1, a gene encoding a membrane protein of the calpain gene superfamily required for aleurone cell development in the endosperm of maize grains. A key component of the embryonic L1 cell-layer specification pathway. It localizes to membranes and undergoes intramolecular autolytic cleavage events that release the calpain domain into the cytoplasm.
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    Genomic context

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    See DEK1 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    32
    Sequence:
    Chromosome: 1; NC_003070.9 (20653740..20665110, complement)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene RNA polymerase II transcription mediator Neighboring gene uncharacterized protein Neighboring gene arabinogalactan protein 21 Neighboring gene hypothetical protein (DUF1639) Neighboring gene tRNA-splicing ligase (DUF239) Neighboring gene uncharacterized protein Neighboring gene NDH-dependent cyclic electron flow 5

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003070.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. A mechanosensitive Ca(2+) channel activity is dependent on the developmental regulator DEK1. Tran D, et al. Nat Commun, 2017 Oct 18. PMID 29044106, Free PMC Article
    2. Regulation of cell wall genes in response to DEFECTIVE KERNEL1 (DEK1)-induced cell wall changes. Amanda D, et al. Plant Signal Behav, 2017 Aug 3. PMID 28692330, Free PMC Article
    3. DEFECTIVE KERNEL1 (DEK1) Regulates Cell Walls in the Leaf Epidermis. Amanda D, et al. Plant Physiol, 2016 Dec. PMID 27756823, Free PMC Article
    4. Calpain-Mediated Positional Information Directs Cell Wall Orientation to Sustain Plant Stem Cell Activity, Growth and Development. Liang Z, et al. Plant Cell Physiol, 2015 Sep. PMID 26220906
    5. DEFECTIVE KERNEL 1 promotes and maintains plant epidermal differentiation. Galletti R, et al. Development, 2015 Jun 1. PMID 25953348

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Here we describe a protocol for monitoring the DEK1 promoter activity in different tissues in Arabidopsis by GUS staining
      Title: Use of the β-Glucuronidase (GUS) Reporter System to Localize Promoter Activities of the Endogenous Plant Calpain DEFECTIVE KERNEL1 (DEK1).
    2. Studies provide evidence that MSL10 and DEK1 are associated with two distinct mechanosensitive (MS) channel activities. MSL10 mediates large fluxes of anions while DEK1 mediates small fluxes of calcium. MSL10 and DEK1 encode bifunctional proteins whose cytosolic domain functioning differently from the MS channel. [review]
      Title: Sensing and transducing forces in plants with MSL10 and DEK1 mechanosensors.
    3. Cell wall related genes are regulated by a feedback mechanism in response to DEK1-induced changes in the cell wall, and contribute to the phenotypes seen in plants with altered DEK1 expression.
      Title: Regulation of cell wall genes in response to DEFECTIVE KERNEL1 (DEK1)-induced cell wall changes.
    4. DEK1 which is essential for development beyond early embryogenesis, is associated with a mechanically activated Ca(2+) current.
      Title: A mechanosensitive Ca(2+) channel activity is dependent on the developmental regulator DEK1.
    5. a novel role for DEK1 in the regulation of leaf epidermal cell wall structure, is reported.
      Title: DEFECTIVE KERNEL1 (DEK1) Regulates Cell Walls in the Leaf Epidermis.
    6. A role for DEK1 in regulating microtubule-orchestrated cell wall orientation during cell division can explain its effects on embryonic development, and suggests a more general function for calpains in microtubule organization in eukaryotic cells.
      Title: Calpain-Mediated Positional Information Directs Cell Wall Orientation to Sustain Plant Stem Cell Activity, Growth and Development.
    7. DEK1 influences HD-ZIP IV gene expression, and thus epidermis differentiation, by promoting cell adhesion and communication in the epidermis.
      Title: DEFECTIVE KERNEL 1 promotes and maintains plant epidermal differentiation.
    8. DEK1 has a role in growth regulation.
      Title: The phytocalpain defective kernel 1 is a novel Arabidopsis growth regulator whose activity is regulated by proteolytic processing.
    9. Data suggest a model for aleurone cell fate specification in which DEK1 perceives and/or transmits a positional signal
      Title: Subcellular localization and functional domain studies of DEFECTIVE KERNEL1 in maize and Arabidopsis suggest a model for aleurone cell fate specification involving CRINKLY4 and SUPERNUMERARY ALEURONE LAYER1.
    10. A specific role for AtDEK1 during embryogenesis and the potential key importance of L1 specification at the globular stage for subsequent progression through embryogenesis are reported.
      Title: AtDEK1 is essential for specification of embryonic epidermal cell fate.
    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_001198309.1
    NM_001333706.1
    NM_104411.4
    NM_180635.1
    NM_180636.1

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables calcium-dependent cysteine-type endopeptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cysteine-type endopeptidase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables cysteine-type peptidase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within cell fate specification IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within embryo development ending in seed dormancy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in embryo development ending in seed dormancy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within embryo development ending in seed dormancy NAS
    Non-traceable Author Statement
    more info
    		  
    NOT involved_in endosperm development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in plant epidermal cell fate specification IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of DNA endoreduplication IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of DNA endoreduplication IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of adaxial/abaxial pattern formation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of cell growth IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of endosperm development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of leaf development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of meristem structural organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of multicellular organism growth IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in self proteolysis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_positive_effect sepal giant cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in sepal giant cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane HDA PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    calpain-type cysteine protease family
    NP_001185238.1
    • DEFECTIVE KERNEL 1 (DEK1); FUNCTIONS IN: cysteine-type endopeptidase activity, calcium-dependent cysteine-type endopeptidase activity; INVOLVED IN: cell fate specification, embryo development ending in seed dormancy; LOCATED IN: plasma membrane; EXPRESSED IN: 26 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Peptidase C2, calpain, domain III (InterPro:IPR022683), Peptidase C2, calpain, large subunit, domain III (InterPro:IPR022682), Peptidase, cysteine peptidase active site (InterPro:IPR000169), Concanavalin A-like lectin/glucanase (InterPro:IPR008985), Peptidase C2, calpain, catalytic domain (InterPro:IPR001300), Peptidase C2, calpain family (InterPro:IPR022684).
    NP_001319240.1
    • DEFECTIVE KERNEL 1 (DEK1); FUNCTIONS IN: cysteine-type endopeptidase activity, calcium-dependent cysteine-type endopeptidase activity; INVOLVED IN: cell fate specification, embryo development ending in seed dormancy; LOCATED IN: plasma membrane; EXPRESSED IN: 27 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Peptidase C2, calpain, domain III (InterPro:IPR022683), Peptidase C2, calpain, large subunit, domain III (InterPro:IPR022682), Peptidase, cysteine peptidase active site (InterPro:IPR000169), Concanavalin A-like lectin/glucanase (InterPro:IPR008985), Peptidase C2, calpain, catalytic domain (InterPro:IPR001300), Peptidase C2, calpain family (InterPro:IPR022684); Has 3377 Blast hits to 2425 proteins in 256 species: Archae - 0; Bacteria - 87; Metazoa - 1580; Fungi - 264; Plants - 115; Viruses - 0; Other Eukaryotes - 1331 (source: NCBI BLink).
    NP_175932.2
    • DEFECTIVE KERNEL 1 (DEK1); FUNCTIONS IN: cysteine-type endopeptidase activity, calcium-dependent cysteine-type endopeptidase activity; INVOLVED IN: cell fate specification, embryo development ending in seed dormancy; LOCATED IN: plasma membrane; EXPRESSED IN: 27 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Peptidase C2, calpain, domain III (InterPro:IPR022683), Peptidase C2, calpain, large subunit, domain III (InterPro:IPR022682), Peptidase, cysteine peptidase active site (InterPro:IPR000169), Concanavalin A-like lectin/glucanase (InterPro:IPR008985), Peptidase C2, calpain, catalytic domain (InterPro:IPR001300), Peptidase C2, calpain family (InterPro:IPR022684); Has 3377 Blast hits to 2425 proteins in 256 species: Archae - 0; Bacteria - 87; Metazoa - 1580; Fungi - 264; Plants - 115; Viruses - 0; Other Eukaryotes - 1331 (source: NCBI BLink).
    NP_850966.1
    • DEFECTIVE KERNEL 1 (DEK1); FUNCTIONS IN: cysteine-type endopeptidase activity, calcium-dependent cysteine-type endopeptidase activity; INVOLVED IN: cell fate specification, embryo development ending in seed dormancy; LOCATED IN: plasma membrane; EXPRESSED IN: 27 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Peptidase C2, calpain, domain III (InterPro:IPR022683), Peptidase C2, calpain, large subunit, domain III (InterPro:IPR022682), Peptidase, cysteine peptidase active site (InterPro:IPR000169), Concanavalin A-like lectin/glucanase (InterPro:IPR008985), Peptidase C2, calpain, catalytic domain (InterPro:IPR001300), Peptidase C2, calpain family (InterPro:IPR022684); Has 3377 Blast hits to 2425 proteins in 256 species: Archae - 0; Bacteria - 87; Metazoa - 1580; Fungi - 264; Plants - 115; Viruses - 0; Other Eukaryotes - 1331 (source: NCBI BLink).
    NP_850967.1
    • DEFECTIVE KERNEL 1 (DEK1); FUNCTIONS IN: cysteine-type endopeptidase activity, calcium-dependent cysteine-type endopeptidase activity; INVOLVED IN: cell fate specification, embryo development ending in seed dormancy; LOCATED IN: plasma membrane; EXPRESSED IN: 27 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Peptidase C2, calpain, domain III (InterPro:IPR022683), Peptidase C2, calpain, large subunit, domain III (InterPro:IPR022682), Peptidase, cysteine peptidase active site (InterPro:IPR000169), Concanavalin A-like lectin/glucanase (InterPro:IPR008985), Peptidase C2, calpain, catalytic domain (InterPro:IPR001300), Peptidase C2, calpain family (InterPro:IPR022684); Has 3377 Blast hits to 2425 proteins in 256 species: Archae - 0; Bacteria - 87; Metazoa - 1580; Fungi - 264; Plants - 115; Viruses - 0; Other Eukaryotes - 1331 (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_003070.9 Reference assembly

      Range
      20653740..20665110 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001333707.1 → NP_001321273.1  calpain-type cysteine protease family [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8RVL2, Q8VXW6, Q949X8, Q9C8A6
      UniProtKB/TrEMBL
      A0A178WD40, A0A5S9WQ51, A0A654EJ68
      Conserved Domains (3) summary
      cd00044
      Location:1696 → 1995
      CysPc; Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
      cd00214
      Location:2001 → 2151
      Calpain_III; Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are ...
      pfam13868
      Location:1246 → 1333
      TPH; Trichohyalin-plectin-homology domain

    2. NM_104411.4 → NP_175932.2  calpain-type cysteine protease family [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_175932.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8RVL2, Q8VXW6, Q949X8, Q9C8A6
      UniProtKB/TrEMBL
      A0A178WD40, A0A5S9WQ51, A0A654EJ68
      Conserved Domains (3) summary
      cd00044
      Location:1696 → 1995
      CysPc; Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
      cd00214
      Location:2001 → 2151
      Calpain_III; Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are ...
      pfam13868
      Location:1246 → 1333
      TPH; Trichohyalin-plectin-homology domain

    3. NM_001333706.1 → NP_001319240.1  calpain-type cysteine protease family [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8RVL2, Q8VXW6, Q949X8, Q9C8A6
      UniProtKB/TrEMBL
      A0A178WD40, A0A5S9WQ51, A0A654EJ68
      Conserved Domains (3) summary
      cd00044
      Location:1696 → 1995
      CysPc; Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
      cd00214
      Location:2001 → 2151
      Calpain_III; Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are ...
      pfam13868
      Location:1246 → 1333
      TPH; Trichohyalin-plectin-homology domain

    4. NM_180635.1 → NP_850966.1  calpain-type cysteine protease family [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_850966.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8RVL2, Q8VXW6, Q949X8, Q9C8A6
      UniProtKB/TrEMBL
      A0A178WD40, A0A5S9WQ51, A0A654EJ68
      Conserved Domains (3) summary
      cd00044
      Location:1696 → 1995
      CysPc; Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
      cd00214
      Location:2001 → 2151
      Calpain_III; Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are ...
      pfam13868
      Location:1246 → 1333
      TPH; Trichohyalin-plectin-homology domain

    5. NM_180636.1 → NP_850967.1  calpain-type cysteine protease family [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_850967.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8RVL2, Q8VXW6, Q949X8, Q9C8A6
      UniProtKB/TrEMBL
      A0A178WD40, A0A5S9WQ51, A0A654EJ68
      Conserved Domains (3) summary
      cd00044
      Location:1696 → 1995
      CysPc; Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
      cd00214
      Location:2001 → 2151
      Calpain_III; Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are ...
      pfam13868
      Location:1246 → 1333
      TPH; Trichohyalin-plectin-homology domain

    6. NM_001198309.1 → NP_001185238.1  calpain-type cysteine protease family [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001185238.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178WD40, A0A654EJ68, F4I0A4
      Conserved Domains (4) summary
      cd00214
      Location:2029 → 2179
      Calpain_III; Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are ...
      pfam00648
      Location:1724 → 2023
      Peptidase_C2; Calpain family cysteine protease
      pfam03879
      Location:1269 → 1324
      Cgr1; Cgr1 family
      cl22861
      Location:1453 → 1613
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8RVL2.1

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