DEK1 [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: DEK1
Primary source: Araport:AT1G55350
Locus tag: AT1G55350
See related: TAIR: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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Location:: chromosome: 1

Exon count:: 32

Sequence:: Chromosome: 1; NC_003070.9 (20653740..20665110, complement)

Chromosome 1 - NC_003070.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003070.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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).
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.
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.
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.
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.
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.
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.
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.
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.
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.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

NM_001198309.1

Supported by ESTs:

NM_001333706.1

Supported by ESTs:

NM_104411.4

Supported by ESTs:

NM_180635.1

Supported by ESTs:

NM_180636.1

Supported by ESTs:

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 more info	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

NC_003070.9 Reference assembly

Range

20653740..20665110 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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 ...