TOP TEN perturbations for O80438 (Arabidopsis thaliana)

Organism: Arabidopsis thaliana
Gene: O80438
Selected probe(set): 267145_at
Platform: Affymetrix Arabidopsis ATH1 Genome Array

Expression of O80438 (267145_at) across 3240 perturbations tested by GENEVESTIGATOR:

shift 28°C to 19°C study 3 (35S:RPS4-HS) / 28°C (35S:RPS4-HS)

Relative Expression (log2-ratio):1.790595
Number of Samples:3 / 3
Experimental shift 28°C to 19°C study 3 (35S:RPS4-HS)
Leaf samples of 35S:RPS4-HS plants grown for 3.5 weeks on soil at 28°C and then shifted to 19°C for 24h. Other conditions: growth chamber, 10h light (150-200µmol photons m-2 s-1) / 14h dark cycles, 65% relative humidity.
Control 28°C (35S:RPS4-HS)
Leaf samples of 35S:RPS4-HS plants grown for 3.5 weeks on soil at 28°C under 10h light (150-200µmol photons m-2 s-1) / 14h dark cycles, 65% relative humidity.

germination (48h) / seed desiccation

Relative Expression (log2-ratio):-1.7722759
Number of Samples:3 / 3
Experimental germination (48h)
Col-0 seeds were harvested, allowed to dessicate for 15 days in darkness, sterilized, plated on Murashige and Skoog medium (containing 3% sucrose), stratified at 4°C in darkness for 48h, and then transferred to continuous light (100µmol photons m-2 s-1) at 22°C for 48h.
Control seed desiccation
Col-0 seeds were harvested and allowed to dessicate for 15 days in darkness.

35S:RPS4-HS eds1-2 / 35S:RPS4-HS

Relative Expression (log2-ratio):-1.6495991
Number of Samples:3 / 3
Experimental 35S:RPS4-HS eds1-2
Transgenic mutant line over-expressing Col-0 RPS4 (tagged with HA-StrepII) from the constitutive CaMV35S promoter and carrying fast neutron generated 939bp deletion in the coding region of the EDS1 (ENHANCED DISEASE SUSCEPTIBILITY1, At3g48090) gene (the deletion includes part of the exon 2, exon 3, part of the exon 4, and introns 2 and 3). RPS4 (At5g45250) is a TNL (Toll/Interleukin-1 (TIR) type nucleotide-binding domain leucine-rich repeat (NB-LRR)) receptor that recognizes bacterial Type III secreted effector AvrRps4. RPS4 is localized both at the membranes of endoplasmic reticulum and in the nucleus. EDS1 is a nucleus-cytoplasmic immune-regulator required for basal resistance against virulent pathogens and for TNL receptor-mediated effector-triggered immunity. Function of RPS4 depends on EDS1. 35S:RPS4-HS eds1-2 plants are similar to Col-0 wild type in terms of rosette diameter when grown at 19°C-22°C or 28°C for 3.5 weeks. At 19-22°C, 35S:RPS4-HS eds1-2 plants are slightly more sensitive to virulent Pseudomonas syringae pv. tomato strain DC3000 than the wild type and equally sensitive as the eds1-2 mutant without the 35S:RPS4-HS transgene (i.e. basal resistance of 35S:RPS4-HS eds1-2 is compromised). At 19-22°C, 35S:RPS4-HS eds1-2 is as sensitive to P. syringae pv. tomato strain DC3000 expressing AvrRps4 as eds1-2 whereas Col-0 wild type and 35S:RPS4-HS (plants with the transgene and wild type EDS1) are resistant. When grown at 28°C for 3.5 weeks and then shifted to 19°C, 35S:RPS4-HS eds1-2 plants, like the wild type, show neither leaf chlorosis nor cell death (Wirthmueller et al., 2007, Curr Biol. 17: 2023-2029; Heidrich et al., 2013, Front Plant Sci. 4: 403; Falk et al., 1999, PNAS 96: 3292-3297).
Control 35S:RPS4-HS
Transgenic line over-expressing Col-0 RPS4 (tagged with HA-StrepII) from the constitutive CaMV35S promoter. RPS4 (At5g45250) is a TNL (Toll/Interleukin-1 (TIR) type nucleotide-binding domain leucine-rich repeat (NB-LRR)) receptor that recognizes bacterial Type III secreted effector AvrRps4. RPS4 is localized both at the membranes of endoplasmic reticulum and in the nucleus. Presence of RPS4 in the nucleus is necessary for triggering the immune response but recognition of AvrRps4 does not change the distribution of RPS4. When grown at 19-22°C for 3.5 weeks, 35S:RPS4-HS plants are severely stunted (rosette diameter of 35S:RPS4-HS is reduced by approx. 62% compared to that of Col-0 wild type). At 19-22°C, 35S:RPS4-HS plants are more resistant to virulent Pseudomonas syringae pv. tomato strain DC3000 than the wild type (i.e. basal resistance is enhanced in 35S:RPS4-HS). At 19-22°C, 35S:RPS4-HS is slightly more resistant to P. syringae pv. tomato strain DC3000 expressing AvrRps4 than Col-0 wild type (although the wild type is also quite resistant as its endogenous RPS4 recognizes AvrRps4). When plants are grown at 28°C for 3.5 weeks, diameter of 35S:RPS4-HS rosettes is similar to that of wild type rosettes. When grown at 28°C for 3.5 weeks and then shifted to 19°C, 35S:RPS4-HS plants show leaf chlorosis and cell death (i.e. overexpression of RPS4-HS triggers temperature-dependent auto-immune response) (Wirthmueller et al., 2007, Curr Biol. 17: 2023-2029; Heidrich et al., 2013, Front Plant Sci. 4: 403).

cycloheximide study 4 (pBeaconRFP_GR-ABI3) / mock treated root protoplast samples (pBeaconRFP_GR-ABI3)

Relative Expression (log2-ratio):-1.5794096
Number of Samples:3 / 3
Experimental cycloheximide study 4 (pBeaconRFP_GR-ABI3)
Col-0 root protoplasts were transfected with the pBeaconRFP_GR-ABI3 vector (50μg plasmid DNA / 10^6 protoplasts; polyethylene glycol method), incubated for 16h at room temperature, then treated with 35μM cycloheximide (an inhibitor of protein synthesis) for 16h. Prior RNA isolation, the successfully transfected protoplasts were harvested using FACS (Fluorescence Activated Cell Sorting), possible due to the expression of mRFP (monomeric red fluorescent protein) from the pBeaconRFP_GR-ABI3 vector.
Control mock treated root protoplast samples (pBeaconRFP_GR-ABI3)
Col-0 root protoplasts were transfected with the pBeaconRFP_GR-ABI3 vector (50μg plasmid DNA / 10^6 protoplasts; polyethylene glycol method), incubated for 16h at room temperature, then mock-treated with solvents, ethanol and DMSO, for 16h. Prior RNA isolation, the successfully transfected protoplasts were harvested using FACS (Fluorescence Activated Cell Sorting), possible due to the expression of mRFP (monomeric red fluorescent protein) from the pBeaconRFP_GR-ABI3 vector.

P. syringae pv. maculicola (Col-0) / mock treated leaf samples (Col-0)

Relative Expression (log2-ratio):1.5669079
Number of Samples:3 / 3
Experimental P. syringae pv. maculicola (Col-0)
Leaves of 4 weeks old Col-0 plants were injected with Pseudomonas syringae pv. maculicola ES4326 (10e5 cfu cm-2; bacteria suspended in 5mM MgSO4) and harvested 24h after the treatment. Plant growth conditions:12h light / 12h dark cycles; 22°C; 75% relative humidity.
Control mock treated leaf samples (Col-0)
Leaves of 4 weeks old Col-0 plants were injected with 5mM MgSO4 and harvested 24h after the mock treatment. Plant growth conditions: 12h light / 12h dark cycles; 22°C; 75% humidity.

shift 28°C to 19°C study 3 (35S:RPS4-HS rrs1-11) / 28°C (35S:RPS4-HS rrs1-11)

Relative Expression (log2-ratio):1.5130615
Number of Samples:3 / 3
Experimental shift 28°C to 19°C study 3 (35S:RPS4-HS rrs1-11)
Leaf samples of 35S:RPS4-HS rrs1-11 plants grown for 3.5 weeks on soil at 28°C and then shifted to 19°C for 24h. Other conditions: growth chamber, 10h light (150-200µmol photons m-2 s-1) / 14h dark cycles, 65% relative humidity.
Control 28°C (35S:RPS4-HS rrs1-11)
Leaf samples of 35S:RPS4-HS rrs1-11 plants grown for 3.5 weeks on soil at 28°C under 10h light (150-200µmol photons m-2 s-1) / 14h dark cycles, 65% relative humidity.

cycloheximide / dexamethasone study 2 (pBeaconRFP_GR-ABI3) / mock treated root protoplast samples (pBeaconRFP_GR-ABI3)

Relative Expression (log2-ratio):-1.4635935
Number of Samples:3 / 3
Experimental cycloheximide / dexamethasone study 2 (pBeaconRFP_GR-ABI3)
Col-0 root protoplasts were transfected with the pBeaconRFP_GR-ABI3 vector (50μg plasmid DNA / 10^6 protoplasts; polyethylene glycol method), incubated for 16h at room temperature, then treated with 35μM cycloheximide (an inhibitor of protein synthesis) and 10μM dexamethasone for 16h (cycloheximide was added to the protoplasts 30min prior adding dexamethasone). Prior RNA isolation, the successfully transfected protoplasts were harvested using FACS (Fluorescence Activated Cell Sorting), possible due to the expression of mRFP (monomeric red fluorescent protein) from the pBeaconRFP_GR-ABI3 vector.
Control mock treated root protoplast samples (pBeaconRFP_GR-ABI3)
Col-0 root protoplasts were transfected with the pBeaconRFP_GR-ABI3 vector (50μg plasmid DNA / 10^6 protoplasts; polyethylene glycol method), incubated for 16h at room temperature, then mock-treated with solvents, ethanol and DMSO, for 16h. Prior RNA isolation, the successfully transfected protoplasts were harvested using FACS (Fluorescence Activated Cell Sorting), possible due to the expression of mRFP (monomeric red fluorescent protein) from the pBeaconRFP_GR-ABI3 vector.

shift low to high light study 4 (Col-0) / low light study 5 (Col-0)

Relative Expression (log2-ratio):-1.3930683
Number of Samples:3 / 3
Experimental shift low to high light study 4 (Col-0)
Rosette samples of Col-0 plants grown on soil for 21 day under short day standard intensity light conditions (10h light (100µmol m-2 s-1) at 23°C / 14h dark at 18°C cycles), then shifted to low light (10h (8µmol m-2 s-1) at 23°C / 14h dark at 18°C) for 10 days, and then shifted to high light (800µmol m-2 s-1) for 6h. Other conditions: 55% relative humidity; soil mixture: Fruhsdorfer Erde Klocke P, perlite, and vermiculite (1:1:1).
Control low light study 5 (Col-0)
Rosette samples of Col-0 plants grown on soil for 21 day under short day standard intensity light conditions (10h light (100µmol m-2 s-1) at 23°C / 14h dark at 18°C cycles), then shifted to low light (10h (8µmol m-2 s-1) at 23°C / 14h dark at 18°C) for 10 days and 6h. For the last 6h the plants were kept in light. Other conditions: 55% relative humidity; soil mixture: Fruhsdorfer Erde Klocke P, perlite, and vermiculite (1:1:1).

germination (24h) / seed desiccation

Relative Expression (log2-ratio):-1.2984352
Number of Samples:3 / 3
Experimental germination (24h)
Col-0 seeds were harvested, allowed to dessicate for 15 days in darkness, sterilized, plated on Murashige and Skoog medium (containing 3% sucrose), stratified at 4°C in darkness for 48h, and then transferred to continuous light (100µmol photons m-2 s-1) at 22°C for 24h.
Control seed desiccation
Col-0 seeds were harvested and allowed to dessicate for 15 days in darkness.

non-polysomal mRNA (rpl24b) / total RNA study 2 (rpl24b)

Relative Expression (log2-ratio):1.2938385
Number of Samples:3 / 3
Experimental non-polysomal mRNA (rpl24b)
Non-polysomal (monosomal and free) mRNA was isolated from shoots of 10-12 days old rpl24b seedlings grown on solid medium (1x Murashige and Skoog salts, 1% (w/v) sucrose; pH 5.7) under 16h light (80µmol photons m-2 s-1) / 8h dark cycles at 22°C. Samples were harvested 6h after the beginning of the light period.
Control total RNA study 2 (rpl24b)
Total RNA was isolated from shoots of 10-12 days old rpl24b seedlings grown on solid medium (1x Murashige and Skoog salts, 1% (w/v) sucrose; pH 5.7) under 16h light (80µmol photons m-2 s-1) / 8h dark cycles at 22°C. Samples were harvested 6h after the beginning of the light period.