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Gene : VAR2 A. thaliana

Gene ID  ? AT2G30950
Brief Description  FtsH extracellular protease family  Source: Araport11 (06/2016).
Is Obsolete?  false
Computational Description  ? VARIEGATED 2 (VAR2); FUNCTIONS IN: metallopeptidase activity, ATP-dependent peptidase activity, ATPase activity, zinc ion binding; INVOLVED IN: photoinhibition, oxygen and reactive oxygen species metabolic process, thylakoid membrane organization, PSII associated light-harvesting complex II catabolic process, protein catabolic process; LOCATED IN: in 6 components; EXPRESSED IN: 26 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Peptidase M41, FtsH (InterPro:IPR005936), ATPase, AAA type, core (InterPro:IPR003593), ATPase, AAA-type, core (InterPro:IPR003959), ATPase, AAA-type, conserved site (InterPro:IPR003960), Peptidase M41 (InterPro:IPR000642), Peptidase M41, FtsH extracellular (InterPro:IPR011546); BEST Arabidopsis thaliana protein match is: FTSH protease 8 (TAIR:AT1G06430.1).  Source: TAIR, Jun 30, 2015.
Curator Summary  ? Metalloprotease that functions in thylakoid membrane biogenesis. Involved in the repair of PSII following damaged incurred during photoinhibition. Forms a complex with VAR1. Mutants show a variegated phenotype, which decreases during development. Transcript and protein levels increase with light intensity. In plsp1-1 mutant plastids, the nonmature form of the protein localizes in the membrane.  Source: TAIR, Jun 30, 2015.
  • synonyms:
  • FTSH2

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16 GeneRIFs (Gene References Into Functions)

Data Source: NCBI

Annotation PubMed Id
Results showed that the conserved Gly-Ala-Asp motif plays an important role in FtsH activity and characterization of the var2 alleles could help to identify the physiologically important domain of FtsH. 15803409
A model has been proposed to explain the mechanism of var2 variegation, which suggests that threshold levels of FtsH complexes are required for green sector formation. 16449381
The white sectors in var2 are made by viable cells that have plastids arrested in thylakoid formation. 17449646
These results indicate that photo-oxidative stress by excess light is involved in the regulation of respiratory gene expression and the modulation of respiratory properties, especially the AOX up-regulation. 18296449
Data show that var2-mediated leaf variegation in Arabidopsis can be suppressed by mutations in SUPPRESSOR OF VARIEGATIONS. 18599582
Chloroplast development promoted by the ectopic expression of GPA1 is dependent on FtsH2. 19228339
The effect of FtsHs in D1 degradation was investigated in Arabidopsis (Arabidopsis thaliana) mutants lacking FtsH2 (yellow variegated2 [var2]) or FtsH5 (var1). 19767385
Findings reinforce the strong genetic link between VAR2 and chloroplast translation, and point to a critical role of SVR3, and possibly some aspects of chloroplast translation, in the response of plants to chilling stress. 21187014
The Tat pathway integrates FtsH2 into thylakoids. 21214651
In Arabidopsis thaliana, ATP-dependent chloroplast proteases belonging to FtsH family (especially FtsH2) are considered to be involved in aspects of chloroplast and whole plant maintenance under non-stressing as well as stressing conditions 21735825
Chloroplastic N-terminal methionine excision(cNME) acts upstream of the FtsH protease complex. Developmental defects and higher sensitivity to photoinhibition associated with the ftsh2 mutation were abolished when cNME was inhibited. 22010036
To gain structural information of the possible complexes, the Arabidopsis FtsH2 (type B) and FtsH5 (type A) were modeled. 22558304
These data demonstrate in vivo cooperative degradation of D1, in which Deg cleavage assists FtsH processive degradation under photoinhibitory conditions. 22698923
A brief update of im and var2 and the functions of PTOX and AtFtsH2, is provided. 23703455
The disruption of specific aspects of chloroplast translation, rather than a general impairment in chloroplast translation, suppress var2 variegation and the existence of complex genetic interactions in chloroplast development. 23721655
The virescent clpR4-3 mutation suppresses leaf variegation of thf1 and var2. 24124904


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12 Flanking Regions

Flank size: from most upstream transcription start site, or most downstream transcription stop site

Region Name Flank Size Direction Length Gene Included? Chromosome Location
AT2G30950 0.5kb upstream 0.5kb upstream 3445   true Chr2: 13173779-13177223
AT2G30950 0.5kb upstream 0.5kb upstream 500   false Chr2: 13173779-13174278
AT2G30950 0.5kb downstream 0.5kb downstream 3445   true Chr2: 13174279-13177723
AT2G30950 0.5kb downstream 0.5kb downstream 500   false Chr2: 13177224-13177723
AT2G30950 1.0kb upstream 1.0kb upstream 3945   true Chr2: 13173279-13177223
AT2G30950 1.0kb upstream 1.0kb upstream 1000   false Chr2: 13173279-13174278
AT2G30950 1.0kb downstream 1.0kb downstream 3945   true Chr2: 13174279-13178223
AT2G30950 1.0kb downstream 1.0kb downstream 1000   false Chr2: 13177224-13178223
AT2G30950 3.0kb upstream 3.0kb upstream 5945   true Chr2: 13171279-13177223
AT2G30950 3.0kb upstream 3.0kb upstream 3000   false Chr2: 13171279-13174278
AT2G30950 3.0kb downstream 3.0kb downstream 5945   true Chr2: 13174279-13180223
AT2G30950 3.0kb downstream 3.0kb downstream 3000   false Chr2: 13177224-13180223


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11 Data Sets

Name Description Version
BAR Annotations Lookup Mapping(s) between AGI locus and Affy Probeset identifier 10/08/2013
Genome Annotation Araport11 protein-coding, non-coding and transposable element genes Araport11 (06/2016)
RNA-seq expression Measure of gene expression levels (Transcripts per Million, TPM) quantified by Salmon Araport11 (06/2016)
PubMed to gene mapping Curated associations between publications and NCBI Gene records 8/12/2016
GO Annotation from GOC GO annotations assigned by the GO Consortium 8/01/2016
PO Annotation from TAIR Literature-based annotations of genes to Plant Ontology (PO) terms 06/30/2015
Swiss-Prot data set High-quality, manually annotated, non-redundant protein sequence database 2016_07
Panther data set PANTHER paralogs from Arabidopsis 11.0
GeneRIF Concise phrase describing gene function and publication associated with NCBI Gene records 8/12/2016
IntAct interactions data set Curated binary and complex protein-protein interactions for Arabidopsis thaliana 8/02/2016
BioGRID interaction data set Curated set of genetic and physical interactions for Arabidopsis thaliana 3.4.139