Experiment: Rbz gene knockout
 
Please note that TAIR stopped accepting new microarray data submissions in June 2005. Newer and more comprehensive microarray data sets are available at GEO, ArrayExpress and NASCArrays.
 
Experiment Summary
Submission Number 38
TAIR Accession ExpressionSet:1005823530
Author(s) John Mundy
Experimental Variables Rbz knockout
Variable Type
Plant Material
Experiment Category non-wildtype comparison
Experiment Goals chloroplast localization
Description We identified the Rbz gene by Ds tagging (Sundaresan et al. 1995 Genes Develop. 9, 1797-810) and by rbz complementation with a full cDNA (unpublished). The recessive rbz knockout is slow to green (wt. vs. rbz), similar to cue (Li et al. 1995 Plant Cell 7, 1599-1610) or yellow heart (Redei 1965 Arab. Info. Serv.) mutants, although crosses show it is not allelic to those on the same chromosome 5. rbz epithelium is normal but the leaves collapse due to retarded chloroplast and palisade cell development. The 80kD RBZ protein has Cys4 zinc fingers with a consensus specific to cytoplasmic nucleoporins which bind Ran (Nakielny et al. 1999 EMBO J. 18, 1982-1995; Haizel et al. 1997 Plant J. 11, 93-103). RBZ also contains three novel repeats, and proline-rich regions similar to SH3 interaction domains (Nguyen et al., 1998 Science 282, 2088-2092). We identified three proteins by yeast 2-hybrid screening and in vitro binding assays which specifically interact with RBZ: 1) IFAP, a coiled-coil, intermediate filament protein which may be nuclear membrane associated (AF004556; McNulty & Saunders 1992 J. Cell Sci. 103, 407-414); 2) another coiled-coil protein (MXM12.P4) similar to a yeast intermediate filament protein involved in intracellular protein transport (P25386); and 3) neoxanthin cleavage enzyme (Z93765), a chloroplast-targeted enzyme. Such RBZ and partner features, as well as the rbz phenotype, suggest that RBZ is involved in nuclear to chloroplast trafficking or signaling via novel cytoskeletal components (Jarvis et al. 1998 Science 282, 100-03). Initial northerns indicate that chalcone synthase and RBCS are over-expressed 5 fold in rbz vs. Ler wt., suggestive of an aberration in light signalling (Mayer et al. 1996 Plant Cell 8, 1951-59). Microarray analysis of rbz vs. wt. would provide a profile of global gene expression in the mutant and lead to a better understanding of RBZ function. We have already prepared 5ug mRNA from whole three week old plantlets of Ler wt. and rbz using TRIzol/Qiagen Oligotex, a protocol we have used for other mutant microarray analyses at Monsanto.
Data Counts
Number of Slides     Number of Replicate Sets     Number of BioSamples
2   2   2
Sample Information
Sample: 10653_Cy5.10654_Cy3
Sample Description:   rbz knockout in Ler background
Organism:   Arabidopsis thaliana
Tissue Origin :   seed
Germplasm:   RBZ KNOCKOUT
Sample Type :   test
Labeling Protocol:   cDNA Synthesis and Labeling
 
Environmental Conditions & Treatments
condition type name variable
germplasm  Rbz gene knockout  yes 
 

Sample: 10653_Cy3.10654_Cy5
Sample Description:   wildtype Ler
Organism:   Arabidopsis thaliana
Tissue Origin :   seed
Sample Type :   reference
Labeling Protocol:   cDNA Synthesis and Labeling
 
Environmental Conditions & Treatments
condition type name variable
germplasm  Ler wildtype  yes 
 
Slide Information
Slide Details
Slide
(name :
description)
External
ID
Replicate
(id :name)
Replicate
type
Reverse
replicate
Sample Experimental
variables
Label Get Data
Mundy slide 1 (10-12-00) :
Rbz gene knockout and protein interactions slide 1(10-12-00)
AFGC:
10653
111:
Rbz gene knockout and protein interactions
technical    10653_Cy3.10654_Cy5 Ler wildtype   Cy3
10653_Cy5.10654_Cy3 Rbz gene knockout   Cy5
Mundy slide 2 (10-12-00) :
Rbz gene knockout and protein interactions slide 2 (10-12-00)
AFGC:
10654
112:
Rbz gene knockout and protein interactions
technical  111   10653_Cy5.10654_Cy3 Rbz gene knockout   Cy3
10653_Cy3.10654_Cy5 Ler wildtype   Cy5
 
Analysis Info
Slide : Mundy slide 1 (10-12-00)
Normalization Info :
User Normalization Description: computed
Normalization Factor: 0.94
Submitted ANOVA sector: 0.076
Submitted ANOVA plate: 0.097
TAIR ANOVA sector: 0.0
Analysis Info:
Scanning software GenePix
Scanning hardware ScanArray 5000
Scanning parameters 19 TIME

Slide : Mundy slide 2 (10-12-00)
Normalization Info :
User Normalization Description: computed
Normalization Factor: 1.23
Submitted ANOVA sector: 0.077
Submitted ANOVA plate: 0.046
TAIR ANOVA sector: 0.0
Analysis Info:
Scanning software GenePix
Scanning hardware ScanArray 5000
Scanning parameters 20 TIME
Array Information
Array Info :
Name: CIW-2_05-00
Manufacturer: AFGC
Platform type : spotted
Surface type : glass
Number of elements : 11904
Slides: all slides had this array design

Hybridization Info:
Hybridization protocol : DNA Microarray Hybridization