TOP TEN perturbations for Q93WY4 (Arabidopsis thaliana)

Organism: Arabidopsis thaliana
Gene: Q93WY4
Selected probe(set): 266886_at
Platform: Affymetrix Arabidopsis ATH1 Genome Array

Expression of Q93WY4 (266886_at) across 3243 perturbations tested by GENEVESTIGATOR:

oxt6:AtCPSF30 / Col-0

Relative Expression (log2-ratio):-2.2804947
Number of Samples:4 / 3
Experimental oxt6:AtCPSF30
Oxt6 (polyadenylation factor subunit) transformant that carries a gene encoding just the smaller of the two At1g30460-encoded proteins.
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).

ant-1 seu-3 / ant-1

Relative Expression (log2-ratio):2.0645857
Number of Samples:4 / 4
Experimental ant-1 seu-3
Double mutant carrying a 22bp deletion in the second exon of ANT (AINTEGUMENTA, At4g37750) (the deletion results in a frameshift and premature termination of translation) and nonsense mutation (Gln 127 → stop) in SEU (SEUSS, At1g43850). ANT is an APETALA2-type sequence-specific DNA binding transcription factor needed for the proper formation of ovules from the carpel margin meristem (CMM). SEU is a transcriptional adaptor which does not bind specific DNA sequences itself but rather makes complexes with sequence-specific DNA binding proteins thus regulating transcription of the target genes. The ant-1 seu-3 double mutant is semidwarf and shows abnormalities in all whorls of the flower: ant-1 seu-3 contains narrow sepals (in average 2.6 per flower instead of 4); small radialized filamentous structures (in average 2.9 per flower) instead of 4 petals; sterile stamens (in average 3.7 per flower instead of 6); short pistil with split stigma and style and completely lacking ovules. In ant-1 seu-3, ovule primordia do not initiate. The adaxial leaf epidermal cells of ant-1 seu-3 are slightly more lobed, more variable in size than those of Col-0 wild type (Klucher et al., 1996, Plant Cell 8: 137-153; Azhakanandam et al., 2008, Plant Physiol. 146: 1165-1181; Pfluger and Zambryski, 2004, Development 131: 4697-4707).
Control ant-1
Mutant originally isolated from Feldmann collection (Feldmann, 1991, Plant J. 1: 71-82) and then backcrossed to Col-0 wild type. ant-1 carries a 22bp deletion in the second exon of ANT (AINTEGUMENTA, At4g37750); the deletion results in a frameshift and premature termination of translation. ANT is an APETALA2-type sequence-specific DNA binding transcription factor needed for the proper formation of ovules from the carpel margin meristem (CMM). ant-1 is female sterile and shows abnormal ovule development. In both ant-1 and Col-0 wild type carpels, ovule primordia initiate from the carpel margin meristems (flower stage 8) and enlarge (flower stage 9) but the inner and outer integuments initiate (flower stage 10) and grow (flower stages 11-12) only in the wild type, not in ant-1. The megasporocyte forms within the nucellus of both ant-1 and the wild type (flower stage 9) but then the wild type megasporocyte undergoes megasporogenesis and megagametogenesis (flower stages 10-12) resulting in the seven-celled, eight-nucleate female gametophyte whereas ant-1 megasporocyte does not develop into the gametophyte. Aberrant development of the central septum has also been observed in some ant-1 pistils. ant-1 shows abnormalities not only in the pistil but also in other whorls of the flower: ant-1 flowers contain 3, 4 or 5 sepals (the wild type flower has 4 sepals); 2, 4 or no petals, which are, when present, shorter and narrower than those of the wild type (the wild type flower has 4 petals); 4 stamens, some of which are fused (the wild type flower has 6 separate stamens) (Klucher et al., 1996, Plant Cell 8: 137-153; Azhakanandam et al., 2008, Plant Physiol. 146: 1165-1181).

ant-1 seu-3 / Col-0

Relative Expression (log2-ratio):1.9460678
Number of Samples:4 / 3
Experimental ant-1 seu-3
Double mutant carrying a 22bp deletion in the second exon of ANT (AINTEGUMENTA, At4g37750) (the deletion results in a frameshift and premature termination of translation) and nonsense mutation (Gln 127 → stop) in SEU (SEUSS, At1g43850). ANT is an APETALA2-type sequence-specific DNA binding transcription factor needed for the proper formation of ovules from the carpel margin meristem (CMM). SEU is a transcriptional adaptor which does not bind specific DNA sequences itself but rather makes complexes with sequence-specific DNA binding proteins thus regulating transcription of the target genes. The ant-1 seu-3 double mutant is semidwarf and shows abnormalities in all whorls of the flower: ant-1 seu-3 contains narrow sepals (in average 2.6 per flower instead of 4); small radialized filamentous structures (in average 2.9 per flower) instead of 4 petals; sterile stamens (in average 3.7 per flower instead of 6); short pistil with split stigma and style and completely lacking ovules. In ant-1 seu-3, ovule primordia do not initiate. The adaxial leaf epidermal cells of ant-1 seu-3 are slightly more lobed, more variable in size than those of Col-0 wild type (Klucher et al., 1996, Plant Cell 8: 137-153; Azhakanandam et al., 2008, Plant Physiol. 146: 1165-1181; Pfluger and Zambryski, 2004, Development 131: 4697-4707).
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).

shoot regeneration study 2 (Ws) / callus formation study 5 (Ws)

Relative Expression (log2-ratio):1.8690481
Number of Samples:3 / 3
Experimental shoot regeneration study 2 (Ws)
Pistils were excised from Ws plants and incubated for 20 days on solid callus inducing medium (Murashige and Skoog (MS) salts, 0.5mg/l 2,4-D (2,4-dichlorophenoxyacetic acid), 1mg/l 6-benzylaminopurine (6-BAP)). The formed calli were then placed on solid shoot inducing medium (MS salts, 0.01mg/l indole-3-acetic acid (IAA), 2mg/l zeatin) and incubated for 6 days under continuous light. Plant growth conditions prior the pistil excision: solid MS medium; 16h light / 8h dark cycles; 22°C.
Control callus formation study 5 (Ws)
Pistils were excised from Ws plants and incubated for 20 days on solid callus inducing medium (Murashige and Skoog salts, 0.5mg/l 2,4-D (2,4-dichlorophenoxyacetic acid), 1mg/l 6-benzylaminopurine (6-BAP)). The formed calli were harvested. Plant growth conditions prior the pistil excision: solid Murashige and Skoog medium; 16h light / 8h dark cycles; 22°C.

NAA study 2 (5d) / untreated inflorescence stem internode cell samples

Relative Expression (log2-ratio):-1.5227718
Number of Samples:3 / 2
Experimental NAA study 2 (5d)
A piece of the first internode (2.5cm to 4cm above the stem base) was cut out from the inflorescence stem of Col-0 and placed on „split-plate“ containing solid 1/2 strength Murashige and Skoog (MS) medium with 1µg/ml NAA (1-naphthalene acetic acid, synthetic auxin) on one side, 6mm wide gap with no medium, and solid 1/2 MS medium on the other side. The stem piece was placed such that the originally apical end of it layed on the NAA containing medium, the basal end layed on MS medium without NAA, and the middle part had no direct contact with any of the media (bridge over the gap). After 5 days of incubation, internode cells except starch sheath and vascular bundle cells were isolated using LCM (laser capture microdissection) from the middle part of the stem piece. Plant growth conditions prior cutting: 3 weeks under 8h light (10 000 LUX) / 16h dark cycles, 21°C, then 16h light (10 000 LUX) at 21°C / 8h darkness at 16°C till the primary inflorescence stem reached 15-20cm height.
Control untreated inflorescence stem internode cell samples
A piece of the first internode (2.5cm to 4cm above the stem base) was cut out from the inflorescence stem of Col-0. Internode cells except starch sheath and vascular bundle cells were isolated using LCM (laser capture microdissection) from the middle part of the stem piece. Plant growth conditions prior cutting: 3 weeks under 8h light (10 000 LUX) / 16h dark cycles, 21°C, then 16h light (10 000 LUX) at 21°C / 8h darkness at 16°C till the primary inflorescence stem reached 15-20cm height.

fd-3 / Col-0

Relative Expression (log2-ratio):1.4288254
Number of Samples:2 / 2
Experimental fd-3
Mutant carrying T-DNA insertion (SALK_054421) in the 5`-UTR (35bp upstream of the translation initiation codon) of FD (AtbZIP14, At4g35900). FD is a bZIP transcription factor that physically interacts with FT (FLOWERING LOCUS T, At1g65480). FD and FT are required for induction of SOC1 expression at the shoot apical meristem during the transition to flowering. FD promotes flowering both under long (16h light (approx.60µmol photons m-2 s-1) / 8h dark) and short (8h light (approx.100µmol photons m-2 s-1) / 16h dark) day conditions. Under the long day conditions (as indicated above), fd-3 flowers having 20-29 rosette leaves whereas Col-0 wild type flowers having 10-17 rosette leaves (i.e. fd-3 is a late flowering mutant) (Abe et al., 2005, Science 309: 1052-1056; Searle et al., 2006, Genes & Dev. 20: 898-912).
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).

shoot regeneration (Ws) / callus formation study 5 (Ws)

Relative Expression (log2-ratio):1.4244423
Number of Samples:3 / 3
Experimental shoot regeneration (Ws)
Pistils were excised from Ws plants and incubated for 20 days on solid callus inducing medium (Murashige and Skoog (MS) salts, 0.5mg/l 2,4-D (2,4-dichlorophenoxyacetic acid), 1mg/l 6-benzylaminopurine (6-BAP)). The formed calli were then placed on solid shoot inducing medium (MS salts, 0.01mg/l indole-3-acetic acid (IAA), 2mg/l zeatin) and incubated for 4 days under continuous light. Plant growth conditions prior the pistil excision: solid MS medium; 16h light / 8h dark cycles; 22°C.
Control callus formation study 5 (Ws)
Pistils were excised from Ws plants and incubated for 20 days on solid callus inducing medium (Murashige and Skoog salts, 0.5mg/l 2,4-D (2,4-dichlorophenoxyacetic acid), 1mg/l 6-benzylaminopurine (6-BAP)). The formed calli were harvested. Plant growth conditions prior the pistil excision: solid Murashige and Skoog medium; 16h light / 8h dark cycles; 22°C.

ant-1 seu-3 / seu-3

Relative Expression (log2-ratio):1.408225
Number of Samples:4 / 4
Experimental ant-1 seu-3
Double mutant carrying a 22bp deletion in the second exon of ANT (AINTEGUMENTA, At4g37750) (the deletion results in a frameshift and premature termination of translation) and nonsense mutation (Gln 127 → stop) in SEU (SEUSS, At1g43850). ANT is an APETALA2-type sequence-specific DNA binding transcription factor needed for the proper formation of ovules from the carpel margin meristem (CMM). SEU is a transcriptional adaptor which does not bind specific DNA sequences itself but rather makes complexes with sequence-specific DNA binding proteins thus regulating transcription of the target genes. The ant-1 seu-3 double mutant is semidwarf and shows abnormalities in all whorls of the flower: ant-1 seu-3 contains narrow sepals (in average 2.6 per flower instead of 4); small radialized filamentous structures (in average 2.9 per flower) instead of 4 petals; sterile stamens (in average 3.7 per flower instead of 6); short pistil with split stigma and style and completely lacking ovules. In ant-1 seu-3, ovule primordia do not initiate. The adaxial leaf epidermal cells of ant-1 seu-3 are slightly more lobed, more variable in size than those of Col-0 wild type (Klucher et al., 1996, Plant Cell 8: 137-153; Azhakanandam et al., 2008, Plant Physiol. 146: 1165-1181; Pfluger and Zambryski, 2004, Development 131: 4697-4707).
Control seu-3
EMS-generated mutant carrying nonsense mutation (Gln 127 → stop) in SEU (SEUSS, At1g43850). SEU is a transcriptional adaptor which does not bind specific DNA sequences itself but rather makes complexes with sequence-specific DNA binding proteins thus regulating transcription of the target genes. Compared to Col-0 wild type, seu-3 has smaller petals and stamens. The stigma and style of seu-3 pistil are split. seu-3 flowers are semi-fertile (produce few seeds when selfed) due to both male and female fertility defects. Compared to the wild type, seu-3 is less responsive to auxin: apical dominance is decreased in seu-3 (mutant plants produce more lateral inflorescences than the wild type); seu-3 develops fewer lateral roots and is less sensitive to exogenously added auxin (naphthaleneacetic acid); gravitropic response is impaired in seu-3 roots (Pfluger and Zambryski, 2004, Development 131: 4697-4707).

myb50 / Col-0

Relative Expression (log2-ratio):-1.2898226
Number of Samples:3 / 3
Experimental myb50
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).

5-AC / solvent treated seedling samples (Ws)

Relative Expression (log2-ratio):1.2729282
Number of Samples:3 / 3
Experimental 5-AC
Ws wild type was germinated in liquid 0.5xMS medium containing 1% sucrose for 4 days, 5-AC (5-aza-2′ deoxycytidine, inhibitor of DNA methylation; 20mg/l) was then added and seedlings were incubated for 10 days (5 days into the treatment, medium and inhibitor were replaced with fresh aliquots); whole seedlings were harvested. Other conditions: continuous white light, 21°C.
Control solvent treated seedling samples (Ws)
Ws wild type was germinated in liquid 0.5xMS medium containing 1% sucrose for 4 days, DMSO was then added and seedlings were incubated for 10 days (5 days into the treatment, medium and DMSO were replaced with fresh aliquots); whole seedlings were harvested. Other conditions: continuous white light, 21°C.