TOP TEN perturbations for At4g36430 (Arabidopsis thaliana)

Organism: Arabidopsis thaliana
Gene: At4g36430
Selected probe(set): 246228_at
Platform: Affymetrix Arabidopsis ATH1 Genome Array

Expression of At4g36430 (246228_at) across 3240 perturbations tested by GENEVESTIGATOR:

SCL3-OE / Col-0

Relative Expression (log2-ratio):-5.048478
Number of Samples:3 / 2
Experimental SCL3-OE
Transgenic line ectopically expressing SCL3 (SCARECROW-LIKE 3, At1g50420) from the constitutive CaMV35S promoter. SCL3 is a nuclear GRAS transcription regulator involved in gibberellin (GA) signalling in the root endodermis. The SCL3 protein has been found to be present in root quiescent center, cortex/endodermis initial, and endodermis. When seedlings are grown in the presence of paclobutrazol (1µM), GA biosynthesis inhibitor, SCL3-OE has slightly longer roots and longer root elongation/differentiation zone than Col-0 wild type. Frequency of the formative periclinal division, which gives rise to root endodermis and middle cortex, is lower in 7, 8, 10, and 12-days-old SCL3-OE than in the wild type (in the absence of paclobutrazol and exogenous bioactive GA). In the presence of paclobutrazol, frequency of the formative periclinal division is also lower in SCL3-OE seedlings than in wild type seedlings (Heo et al., 2011, PNAS 108: 2166-2171).
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).

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

Relative Expression (log2-ratio):4.970473
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.

shift to pH 4.6 (LZ4) / mock treated root samples (LZ4)

Relative Expression (log2-ratio):-4.91523
Number of Samples:2 / 2
Experimental shift to pH 4.6 (LZ4)
Root maturation zone (longitudinal zone 4) samples of Col-0 grown for 5 days at pH 5.7 on 1x Murashige and Skoog medium supplemented with 0.5g/L MES, 1% sucrose, and 1% agar, then transferred to pH 4.6 on 1x Murashige and Skoog medium supplemented with 3mM DMG, 1% sucrose, 1% agar for 24h.
Control mock treated root samples (LZ4)
Root maturation zone (longitudinal zone 4) samples of Col-0 grown for 5 days at pH 5.7 on 1x Murashige and Skoog medium supplemented with 0.5g/L MES, 1% sucrose, and 1% agar, then transferred to pH 5.7 on 1x Murashige and Skoog medium supplemented with 3mM DMG, 1% sucrose, 1% agar for 24h.

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

Relative Expression (log2-ratio):-4.911483
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 + estradiol (35S:VND7-HER) / cycloheximide study 3 (35S:VND7-HER)

Relative Expression (log2-ratio):4.8740406
Number of Samples:2 / 2
Experimental cycloheximide + estradiol (35S:VND7-HER)
Samples of Arabidopsis leaf protoplasts transfected with the CaMV35S:VND7-HER-RR:NOS (35S:VND7-HER; in the pBI221 vector) construct and then treated with 2μM cycloheximide (an inhibitor of protein synthesis) and 2μM β-estradiol for 6h.
Control cycloheximide study 3 (35S:VND7-HER)
Samples of Arabidopsis leaf protoplasts transfected with the CaMV35S:VND7-HER-RR:NOS (35S:VND7-HER; in the pBI221 vector) construct and then treated with 2μM cycloheximide (an inhibitor of protein synthesis) for 6h.

callus formation study 2 (96h) / untreated shoot samples

Relative Expression (log2-ratio):4.786022
Number of Samples:3 / 3
Experimental callus formation study 2 (96h)
Shoot segments were cut out from 10-days-old Col-0 plantlets and incubated on callus inducing medium for 96h. Plant growth conditions prior the treatment: solid Murashige and Skoog medium, 22°C, 16h light / 8h dark.
Control untreated shoot samples
Shoot segments were cut out from 10-days-old Col-0 plantlets grown on solid Murashige and Skoog medium, 22°C, 16h light / 8h dark.

EF-Tu (elf18) study 4 (Col-0) / mock treated seedling samples (Col-0)

Relative Expression (log2-ratio):4.6906166
Number of Samples:3 / 3
Experimental EF-Tu (elf18) study 4 (Col-0)
Seedling samples of Col-0 grown for 5-6 days on solid medium (1/2 strength Murashige and Skoog salts, 25mM sucrose), then transferred to liquid medium (1/2 strength Murashige and Skoog salts, 25mM sucrose) for 5-6 days, and then treated with 1µM elf18 for 10h. Other growth conditions: 12h light / 12h dark cycles. Elf18 is an N-acetylated peptide comprising the first 18 amino acids of the bacterial elongation factor EF-Tu. Elf18 is fully active as an inducer of defense responses in Arabidopsis.
Control mock treated seedling samples (Col-0)
Seedling samples of Col-0 grown for 5-6 days on solid medium (1/2 strength Murashige and Skoog salts, 25mM sucrose), then transferred to liquid medium (1/2 strength Murashige and Skoog salts, 25mM sucrose) for 5-6 days. Other growth conditions: 12h light / 12h dark cycles.

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

Relative Expression (log2-ratio):4.601663
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.

salt / FACS study 4 (8h) / root stele protoplast samples of mock treated pWOL::GFP (1h)

Relative Expression (log2-ratio):4.55252
Number of Samples:3 / 3
Experimental salt / FACS study 4 (8h)
Root stele protoplast samples were obtained by FACS-sorting of protoplasts isolated from whole roots of pWOL::GFP seedlings that had been grown for 5 days on a mesh placed on top of standard medium, then transferred (together with the mesh) on standard medium supplemented with 140mM NaCl for 8h. Standard medium: 1x Murashige and Skoog salts, 0.5g/L MES, 1% sucrose, 1% agar; pH 5.7; prior protoplasting the seedlings were kept under 16h light / 8h dark cycles. FACS, Fluorescence Activated Cell Sorting.
Control root stele protoplast samples of mock treated pWOL::GFP (1h)
Root stele protoplast samples were obtained by FACS-sorting of protoplasts isolated from whole roots of pWOL::GFP seedlings that had been grown for 5 days on a mesh placed on top of standard medium, then transferred (together with the mesh) on fresh standard medium for 1h. Standard medium: 1x Murashige and Skoog salts, 0.5g/L MES, 1% sucrose, 1% agar; pH 5.7; prior protoplasting the seedlings were kept under 16h light / 8h dark cycles. FACS, Fluorescence Activated Cell Sorting.

ABA + DMTU (20h) / solvent treated cell suspension samples (20h)

Relative Expression (log2-ratio):-4.5343447
Number of Samples:3 / 3
Experimental ABA + DMTU (20h)
Cell suspension (cell line T87) was cultured in Gamborg B5 medium containing 3% sucrose and 0.5µM 1-naphthaleneacetic acid at 20°C under 16h light (24 μmol photons s−1 m−2) / 8h dark cycles, with shaking at 120rpm and subculturing every 7 days (10ml of the cell suspension were transferred to 90 ml of fresh medium). At the exponential phase of growth (approx. 120h after subculturing) ABA (abscisic acid) and DMTU (dimethylthiourea) were added to the final concentrations of 50μM (ABA) and 5mM (DMTU) and the cell suspension was cultured for another 20h prior harvesting the cells. DMTU is an H2O2 scavenger.
Control solvent treated cell suspension samples (20h)
Cell suspension (cell line T87) was cultured in Gamborg B5 medium containing 3% sucrose and 0.5µM 1-naphthaleneacetic acid at 20°C under 16h light (24 μmol photons s−1 m−2) / 8h dark cycles, with shaking at 120rpm and subculturing every 7 days (10ml of the cell suspension were transferred to 90 ml of fresh medium). At the exponential phase of growth (approx. 120h after subculturing) the cell suspension was treated with ethanol for 20h.