TOP TEN perturbations for At3g50990 (Arabidopsis thaliana)

Organism: Arabidopsis thaliana
Gene: At3g50990
Selected probe(set): 252138_at
Platform: Affymetrix Arabidopsis ATH1 Genome Array

Expression of At3g50990 (252138_at) across 3240 perturbations tested by GENEVESTIGATOR:

dcl1-15 / DCL1 sib

Relative Expression (log2-ratio):1.9973621
Number of Samples:3 / 3
Experimental dcl1-15
EMS-generated mutant with leaky recessive missense mutation (Gly →Glu at amino acid position 1692) in DCL1 (At1g01040). DCL1 (RNase III DICER-LIKE1) is a part of a complex that cleaves precursor miRNA thus generating miRNAs. dcl1-15 embryos develop normally till the early globular stage, then the patterns of cell division become abnormal. dcl1-15 embryos mature faster than the wild type: dcl1-15 embryos start to accumulate chlorophyll already at the early globular stage and are visibly green at the heart stage whereas embryos of the wild type siblings are white at the heart stage (although they start accumulating chlorophyll in the protodermis at this stage); at the heart stage, chloroplasts of dcl1-15 embryos are more developed (more grana stacks per chloroplast, more thylakoids per grana stack) than those of the wild type. dcl1-15 embryos abort late in embryogenesis and this abortion is not due to desiccation intolerance (Willmann et al., 2011, Plant Physiol. 155: 1871-84).
Control DCL1 sib
Wild type sibling of dcl1-15 mutant. DCL1 sib was obtained by backcrossing heterozygous (dcl1-15 DCL1) plants (initially in the Ws genetic background) to Ler wild type at least four times (Willmann et al., 2011, Plant Physiol. 155: 1871-84).

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

Relative Expression (log2-ratio):1.9169941
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.

cycloheximide / dexamethasone study 2 (pBeaconRFP_GR-ABI3) / cycloheximide study 4 (pBeaconRFP_GR-ABI3)

Relative Expression (log2-ratio):1.2277374
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 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.

germination (1h) / seed desiccation

Relative Expression (log2-ratio):-1.0578756
Number of Samples:2 / 3
Experimental germination (1h)
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 1h.
Control seed desiccation
Col-0 seeds were harvested and allowed to dessicate for 15 days in darkness.

stratification (48h) / seed desiccation

Relative Expression (log2-ratio):-0.9880066
Number of Samples:3 / 3
Experimental stratification (48h)
Col-0 seeds were harvested, allowed to dessicate for 15 days in darkness, then sterilized, plated on Murashige and Skoog medium (containing 3% sucrose), and stratified at 4°C in darkness for 48h.
Control seed desiccation
Col-0 seeds were harvested and allowed to dessicate for 15 days in darkness.

germination (24h) / seed desiccation

Relative Expression (log2-ratio):-0.9871712
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.

germination (12h) / seed desiccation

Relative Expression (log2-ratio):-0.9021368
Number of Samples:3 / 3
Experimental germination (12h)
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 12h.
Control seed desiccation
Col-0 seeds were harvested and allowed to dessicate for 15 days in darkness.

germination (6h) / seed desiccation

Relative Expression (log2-ratio):-0.83049965
Number of Samples:3 / 3
Experimental germination (6h)
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 6h.
Control seed desiccation
Col-0 seeds were harvested and allowed to dessicate for 15 days in darkness.

stratification (12h) / seed desiccation

Relative Expression (log2-ratio):-0.82286453
Number of Samples:3 / 3
Experimental stratification (12h)
Col-0 seeds were harvested, allowed to dessicate for 15 days in darkness, then sterilized, plated on Murashige and Skoog medium (containing 3% sucrose), and stratified at 4°C in darkness for 12h.
Control seed desiccation
Col-0 seeds were harvested and allowed to dessicate for 15 days in darkness.

LeB4::AtHb1 / Col-0

Relative Expression (log2-ratio):0.78880215
Number of Samples:3 / 3
Experimental LeB4::AtHb1
Transgenic line (T3 generation of an independent transformant L1-1) carrying the coding region of AtHb1 (At2g16060) under the control of the seed-specific LeB4 promoter and OCS terminator. The line also contains the selectable marker gene BAR conferring resistance to phosphinothrycin. AtHb1 is a non-symbiotic hemoglobin of class-1 with superior affinity for oxygen. LeB4::AtHb1 plants express AtHb1 mainly in seeds and to a certain extent in roots. Under standard growth conditions, transgenic plants are overtly similar to Col-0 wild type, except that their mature seeds are approx. 30% heavier. Under moderate hypoxia (10.5% O2), LeB4::AtHb1 embryos had lower nitric oxide (NO) levels than wild type embryos. Under moderate hypoxia, developing LeB4::AtHb1 seeds had approx. 40% higher respiration rate, higher total ATP level, higher adenylate energy status and showed less changes in metabolite (e.g. T6P, sucrose) levels than wild type seeds. Compared to the wild type, LeB4::AtHb1 seeds had higher H2O2 levels under normal oxygen (21% O2) conditions but under hypoxia H2O2 concentration did not further increase in LeB4::AtHb1 seeds, whereas in wild type it increased (Thiel et al., 2011, BMC Plant Biol. 11: 48).
Control Col-0
Arabidopsis accession Columbia-0. Origin: Poland; latitude of origin: 52°73'N, longitude of origin: 15°15'E. Col-0 is resistant to the isolate AG8 and susceptible to the isolate AG2-1 of soil-borne necrotrophic fungus Rhizoctonia solani. Freezing tolerance of non-acclimated Col-0 leaves: LT50 (temperature of 50% electrolyte leakage) = −5.34°C; freezing tolerance of Col-0 leaves after acclimation at 4°C under 16h photoperiod (90µmol photons m-2 s-1) for 14 days: LT50 = −9.68°C. Acclimated Col-0 leaves accumulate approx. 20µmol g FW-1 glucose, 10µmol g FW-1 fructose, 20µmol g FW-1 sucrose, 4µmol g FW-1 raffinose, 5.5µmol g FW-1 proline (Zuther et al., 2012, Plant Cell Environ. 35: 1860-1878). Col-0 is comparatively tolerant to ozone: ozone treated (400nl L-1 O3 for 6h) Col-0 shows less cell death than ozone treated Te-0 accession (Xu et al., 2015, Plant Cell Environ. 38: 1418-1433). Col-0 is susceptible to bacterial pathogen Pseudomonas syringae pv tomato (Pst) strain DC3000. As Col-0 carries the resistance gene RPS4 (At5g45250), it is resistant to Pst DC3000 expressing the bacterial effector avrRps4 (Howard et al., 2013, PLoS One 8: e74183). When 4-day-old Col-0 seedlings are exposed to mild drought stress (soil water content (SWC) of 1.2g H2O g-1 dry soil) for 6 days, area of their 3rd rosette leaf is reduced by approx. 30% compared to that of control Col-0 seedlings grown for 4+6 days at SWC of 2.2g H2O g-1 dry soil. When 4-day-old Col-0 seedlings are exposed to mild drought stress for 18 days (SWC is kept at 1.2g H2O g-1 dry soil for the first 6 days, then slowly decreases and is kept at 0.7g H2O g-1 dry soil till the end of the treatment), area of their 3rd rosette leaf is reduced by approx. 59% compared to that of control Col-0 plants grown for 4+18 days at SWC of 2.2g H2O g-1 dry soil (Clauw et al., 2015, Plant Physiol. 167: 800-816). In the study by (Nakano et al., 2020, Front Plant Sci. 11: 405), aluminum tolerance of Col-0 was 53.3; calculated as: (root length of 5-day-old seedlings grown in the presence of 5µM AlCl3 at pH 5.0 / root length of 5-day-old seedlings grown without Al at pH 5.0) x 100. Col-0 is moderately tolerant to submergence. For example, when rosette-stage Col-0 plants were completely submerged in water for 2 days under short-day conditions, the photosynthetic rate in their leaves decreased by approx. 36.4% compared to untreated Col-0 (Meng et al., 2020, Plant J. 103: 227-247).