TOP TEN perturbations for AT5G50630 (Arabidopsis thaliana)

Organism: Arabidopsis thaliana
Gene: AT5G50630
Selected probe(set): 248521_s_at
Platform: Affymetrix Arabidopsis ATH1 Genome Array

Expression of AT5G50630 (248521_s_at) across 3240 perturbations tested by GENEVESTIGATOR:

shift 28°C to 19°C study 2 (35S:RPS4-HS) / 28°C (35S:RPS4-HS)

Relative Expression (log2-ratio):1.8295593
Number of Samples:3 / 3
Experimental shift 28°C to 19°C study 2 (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 8h. 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 28°C to 19°C study 2 (35S:RPS4-HS rrs1-11) / 28°C (35S:RPS4-HS rrs1-11)

Relative Expression (log2-ratio):1.7999582
Number of Samples:3 / 3
Experimental shift 28°C to 19°C study 2 (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 8h. 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.

ccr1-1 / Col-0

Relative Expression (log2-ratio):-1.5096359
Number of Samples:3 / 3
Experimental ccr1-1
EMS generated mutation resulting in premature stop codon in exon 2 of CCR1 (At1g77300). CCR1 (CAROTENOID CHLOROPLAST REGULATORY1) is the same gene as SDG8 (SET DOMAIN GROUP 8) and encodes a SET2 domain histone methyltransferase that methylates histone H3. ccr1-1 has altered carotenoid composition and increased shoot branching, probably due to altered DNA accessibility to regulatory factors at sites of several genes, i.e CRTISO (CAROTENOID ISOMERASE).
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 rrs1-11) / 28°C (35S:RPS4-HS rrs1-11)

Relative Expression (log2-ratio):1.4882174
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.

met1-1 / Ws

Relative Expression (log2-ratio):1.4695435
Number of Samples:3 / 3
Experimental met1-1
EMS-generated mutant carrying missense mutation (Pro 1300 → Ser) in MET1 (METHYLTRANSFERASE 1, At5g49160). The met1-1 mutant was originally isolated in Col genetic background and later backcrossed to Ws wild type. MET1 is a cytosine-DNA-methyltransferase responsible for maintaining cytosine methylation directly at the CG sites and indirectly at the non-CG sites. In the original met1-1 mutant (Col genetic background), cytosine methylation at the TCGA sites is reduced by approx. 70% compared to Col wild type. When calli, which had been induced on pistil or root explants, are placed on shoot inducing medium, met1-1 and Ws wild type regenerate similar numbers of shoots. However, shoot regeneration in met1-1 takes less time than in the wild type: e.g. at day 4 on shoot inducing medium, wild type calli are white whereas most of met1-1 calli have green regions from which the shoots would regenerate. Cytosine methylation of several genes (WUS, ARF3, ARF4, IAA18, BLH7) is reduced in met1-1 calli compared to wild type calli (Kankel et al., 2003, Genetics 163: 1109-1122; Bartee and Bender, 2001, Nucleic Acids Res. 29: 2127-2134; Li et al.,2011, PLoS Genet. 7: e1002243).
Control Ws
Arabidopsis accession: Wassilewskija. Ws is susceptible to isolate Emwa1 of biotrophic filamentous oomycete pathogen Hyaloperonospora arabidopsidis (Hok et al., 2011, Plant Cell Environ. 34: 1944-1957).

Te-0 / Col-0

Relative Expression (log2-ratio):-1.4024153
Number of Samples:3 / 2
Experimental Te-0
Arabidopsis natural accession: Tenela-0 from Tenela, Finland (latitude of origin: 60°07'N, longitude of origin: 23°18'E). Freezing tolerance of non-acclimated Te-0 leaves: LT50 (temperature of 50% electrolyte leakage) = −7.00°C; freezing tolerance of Te-0 leaves after acclimation at 4°C under 16h photoperiod (90µmol photons m-2 s-1) for 14 days: LT50 = −10.87°C. Acclimated Te-0 leaves accumulate approx. 25µmol g FW-1 glucose, 15µmol g FW-1 fructose, 10µmol g FW-1 sucrose, 4µmol g FW-1 raffinose, 5µmol g FW-1 proline (Zuther et al., 2012, Plant Cell Environ. 35: 1860-1878). Te-0 is sensitive to ozone: ozone treated (400nl L-1 O3 for 6h) Te-0 plants show enhanced cell death compared to ozone treated Col-0 and C24 accessions. When plants are exposed to 400nl L-1 ozone for 4h, both stomatal O3 uptake rate and cumulative O3 dose received by the plants during the treatment are higher in Te-0 than in C24 (Xu et al., 2015, Plant Cell Environ. 38: 1418-1433).
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).

Te-0 / Col-0

Relative Expression (log2-ratio):-1.3974218
Number of Samples:3 / 3
Experimental Te-0
Arabidopsis natural accession: Tenela-0 from Tenela, Finland (latitude of origin: 60°07'N, longitude of origin: 23°18'E). Freezing tolerance of non-acclimated Te-0 leaves: LT50 (temperature of 50% electrolyte leakage) = −7.00°C; freezing tolerance of Te-0 leaves after acclimation at 4°C under 16h photoperiod (90µmol photons m-2 s-1) for 14 days: LT50 = −10.87°C. Acclimated Te-0 leaves accumulate approx. 25µmol g FW-1 glucose, 15µmol g FW-1 fructose, 10µmol g FW-1 sucrose, 4µmol g FW-1 raffinose, 5µmol g FW-1 proline (Zuther et al., 2012, Plant Cell Environ. 35: 1860-1878). Te-0 is sensitive to ozone: ozone treated (400nl L-1 O3 for 6h) Te-0 plants show enhanced cell death compared to ozone treated Col-0 and C24 accessions. When plants are exposed to 400nl L-1 ozone for 4h, both stomatal O3 uptake rate and cumulative O3 dose received by the plants during the treatment are higher in Te-0 than in C24 (Xu et al., 2015, Plant Cell Environ. 38: 1418-1433).
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).

Myb28OX3 / Col-0

Relative Expression (log2-ratio):-1.3843317
Number of Samples:2 / 2
Experimental Myb28OX3
Arabidopsis (ecotype Col-0) Myb28-overexpressing line.
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).

met1-1 / Ws

Relative Expression (log2-ratio):1.3808966
Number of Samples:3 / 3
Experimental met1-1
EMS-generated mutant carrying missense mutation (Pro 1300 → Ser) in MET1 (METHYLTRANSFERASE 1, At5g49160). The met1-1 mutant was originally isolated in Col genetic background and later backcrossed to Ws wild type. MET1 is a cytosine-DNA-methyltransferase responsible for maintaining cytosine methylation directly at the CG sites and indirectly at the non-CG sites. In the original met1-1 mutant (Col genetic background), cytosine methylation at the TCGA sites is reduced by approx. 70% compared to Col wild type. When calli, which had been induced on pistil or root explants, are placed on shoot inducing medium, met1-1 and Ws wild type regenerate similar numbers of shoots. However, shoot regeneration in met1-1 takes less time than in the wild type: e.g. at day 4 on shoot inducing medium, wild type calli are white whereas most of met1-1 calli have green regions from which the shoots would regenerate. Cytosine methylation of several genes (WUS, ARF3, ARF4, IAA18, BLH7) is reduced in met1-1 calli compared to wild type calli (Kankel et al., 2003, Genetics 163: 1109-1122; Bartee and Bender, 2001, Nucleic Acids Res. 29: 2127-2134; Li et al.,2011, PLoS Genet. 7: e1002243).
Control Ws
Arabidopsis accession: Wassilewskija. Ws is susceptible to isolate Emwa1 of biotrophic filamentous oomycete pathogen Hyaloperonospora arabidopsidis (Hok et al., 2011, Plant Cell Environ. 34: 1944-1957).

shift low to high light study 3 (2h) / low light study 4 (6h)

Relative Expression (log2-ratio):-1.3664284
Number of Samples:3 / 3
Experimental shift low to high light study 3 (2h)
Detached rosette leaves of 3.5-week-old Col-0 plants were kept in a growth chamber for 6h under low light (65µmol photons m-2 s-1) at 22°C, then exposed for 2h to high light (1300µmol photons m-2 s-1) at 22°C, and then harvested.
Control low light study 4 (6h)
Detached rosette leaves of 3.5- week-old Col-0 plants were kept in a growth chamber for 6h under low light (65µmol photons m-2 s-1) at 22°C and then harvested.