PDF2 protodermal factor 2 [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: PDF2
Official Full Name: protodermal factor 2
Primary source: TAIR:AT4G04890
Locus tag: AT4G04890
See related: Araport:AT4G04890
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: protodermal factor 2; T1J1.3; T1J1_3
Summary: Encodes a homeodomain protein that is expressed in the LI layer of the vegetative, floral and inflorescence meristems. Binds to the L1 box promoter element which is required in some proteins for L1 specific expression.
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Genomic context

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See PDF2 in Genome Data Viewer

Location:: chromosome: 4

Exon count:: 13

Sequence:: Chromosome: 4; NC_003075.7 (2476390..2482447, complement)

Chromosome 4 - NC_003075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003075.7

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Arabidopsis PROTODERMAL FACTOR2 binds lysophosphatidylcholines and transcriptionally regulates phospholipid metabolism.
Title: Arabidopsis PROTODERMAL FACTOR2 binds lysophosphatidylcholines and transcriptionally regulates phospholipid metabolism.
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.
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.
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.
The allele-specific effect caused by pdf2-1, which carries a T-DNA in a steroidogenic acute regulatory protein-related lipid transfer (START) domain-encoding region, suggests the importance of the START domain in proper function of HD-ZIP IV proteins.
Title: Allele-specific effects of PDF2 on floral morphology in Arabidopsis thaliana.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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NM_001340517.1

Supported by ESTs:

NM_116727.4

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	IPI Inferred from Physical Interaction 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 transcription cis-regulatory region binding	IPI Inferred from Physical Interaction 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 maintenance of floral organ identity	IGI Inferred from Genetic Interaction more info	PubMed
involved_in maintenance of floral organ identity	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within plant epidermal cell differentiation	IMP Inferred from Mutant Phenotype 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: protodermal factor 2

NP_567274.1

protodermal factor 2 (PDF2); FUNCTIONS IN: 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: 26 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: Homeobox-leucine zipper family protein / lipid-binding START domain-containing protein (TAIR:AT4G21750.2); 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

NC_003075.7 Reference assembly

Range

2476390..2482447 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_116727.4 → NP_567274.1 protodermal factor 2 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_567274.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q93V99, Q9M0Z0, Q9ZPH7

UniProtKB/TrEMBL

A0A178V5B8, A0A5S9XPU3

Conserved Domains (3) summary

cd08875
Location:248 → 472

START_ArGLABRA2_like; C-terminal lipid-binding START domain of the Arabidopsis homeobox protein GLABRA 2 and related proteins

COG5576
Location:47 → 155

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam00046
Location:65 → 118

Homeobox; Homeobox domain
NM_001340517.1 → NP_001329475.1 protodermal factor 2 [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/Swiss-Prot

Q93V99, Q9M0Z0, Q9ZPH7

UniProtKB/TrEMBL

A0A178V5B8, A0A5S9XPU3