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Table 2 Up or down regulated transcripts upon different temperature and light treatments

From: Light has a specific role in modulating Arabidopsis gene expression at low temperature

AGI-code and Description Cold and Dehydration Responsive Genes Control Cold/Light Cold/Dark Dark
At1g09350 galactinol synthase, AtGolS3 0.9 ± 0.1 42.0 ± 3.0* 17.1 ± 1.5 1.0 ± 0.4
At3g50970 dehydrin (XERO2) (Low-temperature-induced protein, LTI30) 1.0 ± 0.1 17.8 ± 3.0 11.7 ± 5.3 0.4 ± 0.1
At5g52310 low-temperature-induced protein 78, (RD29A) (UP) 1.3 ± 0.2 11.6 ± 3.5* (a) 3.6 ± 1.7 0.1 ± 0.1
At1g20450 dehydrin (ERD10, Low-temperature-induced protein, LTI45) 1.3 ± 0.2 10.4 ± 1.4* 3.8 ± 0.6 0.6 ± 0.1
At4g19120 ERD3 protein 1.3 ± 0.2 3.5 ± 0.6* 1.6 ± 0.4 0.4 ± 0.1
At5g15960 stress-induced protein KIN1 (UP) 1.3 ± 0.1 2.6 ± 0.9 1.7 ± 0.2 0.1 ± 0.1
At1g56600 galactinol synthase, AtGolS2 (Down) 1.2 ± 0.2 2.1 ± 0.2* 1.2 ± 0.3 0.7 ± 0.2
At5g55400 dehydrin RAB18 1.2 ± 0.1 2.0 ± 0.3 0.9 ± 1.0 0.5 ± 0.3
LHCB genes     
At3g27690 light harvesting chlorophyll A/B binding protein, LHCB 2.4 (Down) 1.2 ± 0.2 15.8 ± 4.1* 1.7 ± 0.2 0.5 ± 0.3
At2g05070 light-harvesting chlorophyll A/B binding protein, LHCB 2.2 (Down) 1.2 ± 0.1 8.1 ± 2.3* 1.3 ± 0.2 0.6 ± 0.3
At3g08940 chlorophyll a/b-binding protein, LHCB 4.2 (Down) 1.2 ± 0.1 2.7 ± 0.8* 0.7 ± 0.2 1.7 ± 0.2
At3g22840 early light-induced protein, ELIP1 (Up) 1.0 ± 0.1 2.4 ± 0.3* 1.1 ± 0.1 0.8 ± 0.2
At1g29930 light harvesting chlorophyll A/B binding protein (Down) 1.1 ± 0.1 2.1 ± 0.3* 0.9 ± 0.1 1.2 ± 0.2
Photosystem I related genes     
At5g64040 photosystem I reaction center subunit, PSI-N (Down) 1.2 ± 0.2 2.5 ± 0.3* 1.3 ± 0.2 0.8 ± 0.1
At1g08570 thioredoxin 1.1 ± 0.1 2.0 ± 0.2 1.7 ± 0.2 1.7 ± 0.2
Genes encoding chloroplast targeted proteases     
At1g49630 Zn metalloprotease 1.2 ± 0.1 5.5 ± 0.9* 1.9 ± 0.2 0.6 ± 0.1
At5g42270 FTSH protease (H5) (Up) 1.1 ± 0.1 2.9 ± 0.4* 1.0 ± 0.2 0.6 ± 0.1
At1g50250 FTSH protease (H1) (Up) 1.2 ± 0.1 2.3 ± 0.3* 1.2 ± 0.2 0.6 ± 0.1
At1g06430 FTSH protease (H8) 1.1 ± 0.1 2.1 ± 0.3* 0.9 ± 0.2 0.7 ± 0.1
At1g09130 ATP-dependent CLP protease (CLPR3)(-) 1.1 ± 0.1 2.1 ± 0.5 1.7 ± 0.7 1.3 ± 0.1
At5g51070 ATP-dependent CLP protease (CLPD), ERD1 protein (-) 1.1 ± 0.1 0.4 ± 0.1 0.5 ± 0.1 1.5 ± 0.1
Genes Encoding Chloroplast Targeted ROS Scavenging Enzymes     
At4g11600 glutathione peroxidise (Up) 1.3 ± 0.1 5.7 ± 1.1* 1.4 ± 0.2 0.7 ± 0.1
At4g25100 iron superoxide dismutase (FeSOD) (Up) 1.2 ± 0.3 3.2 ± 0.4* 1.7 ± 0.2 1.8 ± 0.3
At2g25080 glutathione peroxidise (Down) 1.3 ± 0.2 2.8 ± 0.3* 1.4 ± 0.3 1.4 ± 0.2
At3g54660 gluthatione reductase (-) 1.2 ± 0.1 2.1 ± 0.2* 1.4 ± 0.1 0.6 ± 0.1
Expression of Catalase and Ascorbate Reductase Genes     
At4g35090 catalase 2 (Up) 1.3 ± 0.1 6.4 ± 1.4 3.8 ± 1.2 2.5 ± 0.4
At3g09940 monodehydroascorbate reductase 0.9 ± 0.1 0.9 ± 0.1 1.2 ± 0.2 0.8 ± 0.1
At3g52880 monodehydroascorbate reductase 1.3 ± 0.1 0.9 ± 0.2 0.7 ± 0.1 0.7 ± 0.1
At1g20630 catalase 1 (Down) 1.1 ± 0.1 0.8 ± 0.1 0.9 ± 0.2 1.2 ± 0.2
At1g75270 dehydroascorbate reductase 0.9 ± 0.1 0.6 ± 0.1 0.6 ± 0.1 0.5 ± 0.2
At5g03630 monodehydroascorbate reductase 1.3 ± 0.1 0.5 ± 0.1 0.6 ± 0.1 0.9 ± 0.2
At1g19570 dehydroascorbate reductase 0.9 ± 0.2 0.4 ± 0.2 0.4 ± 0.1 0.3 ± 0.1
At1g20620 catalase 3 (Down) 1.5 ± 0.3 0.4 ± 0.1 0.5 ± 0.1 2.4 ± 0.2
Carotenoid Biosynthesis Genes     
At5g67030 zeaxanthin epoxidase precursor, (LOS6/ABA1)(ZEP) 1.3 ± 0.2 3.8 ± 0.6* 1.7 ± 0.5 0.7 ± 0.1
At1g74470 geranylgeranyl reductase 1.4 ± 0.1 3.0 ± 0.4* 1.1 ± 0.1 1.3 ± 0.2
At4g32770 tocopherol cyclase (SXD1) 1.0 ± 0.1 2.1 ± 0.2* 1.0 ± 0.1 0.8 ± 0.2
At1g08550 violaxanthin de-epoxidase precursor, (NPQ1) 1.2 ± 0.1 0.9 ± 0.1 0.7 ± 0.1 0.6 ± 0.1
Chlorophyll Biosynthesis Genes     
At1g58290 glutamyl-tRNA reductase 1 (GluTR) (HEMA1) 1.0 ± 0.1 6.5 ± 0.7* 2.6 ± 0.9 1.2 ± 0.2
At3g56940 dicarboxylate diiron protein, (CHL27, CRD1) 1.2 ± 0.1 4.5 ± 0.6* 1.4 ± 0.1 1.1 ± 0.2
At5g13630 Mg-chelatase H-subunit (CHLH) 1.2 ± 0.1 2.2 ± 0.2* 1.2 ± 0.2 0.9 ± 0.1
Phenylpropanoid Pathway Genes     
At5g17050 UDP glucose:flavonoid 3-o-glucosyl-transferase 1.0 ± 0.1 12.6 ± 3.7* 1.9 ± 0.8 0.8 ± 0.1
At3g53260 phenylalanine ammonia-lyase (PAL2)(-) 1.2 ± 0.2 3.7 ± 0.6 1.9 ± 0.7 1.2 ± 0.1
At5g13930 chalcone synthase (naringenin-chalcone synthase) (Up) 1.0 ± 0.1 2.9 ± 1.0 1.0 ± 0.2 0.6 ± 0.4
At4g30210 NADPH-cytochrome p450 reductase, (ATR2) 1.2 ± 0.1 2.5 ± 0.2 2.1 ± 0.3 1.3 ± 0.5
At1g15950 cinnamoyl-CoA reductase 1.0 ± 0.1 2.5 ± 0.2* 1.4 ± 0.3 0.9 ± 0.2
At4g34050 caffeoyl-CoA 3-O-methyltransferase 1.1 ± 0.1 2.2 ± 0.5 1.1 ± 0.2 0.6 ± 0.1
Carbon metabolism genes     
At1g32900 starch synthase 1.3 ± 0.4 6.1 ± 2.1 4.0 ± 3.2 1.1 ± 0.2
At4g17090 glycosyl hydrolase family 14 (beta-amylase) 1.2 ± 0.1 6.1 ± 0.7 3.2 ± 1.4 0.5 ± 0.2
At1g08920 sugar transporter, putative similar to ERD6 protein 1.0 ± 0.1 3.4 ± 0.8 2.2 ± 0.3 0.8 ± 0.1
At3g01550 triose/phosphate translocator 1.1 ± 0.1 2.4 ± 0.2* 1.3 ± 0.2 1.0 ± 0.1
At4g38970 plastidic fructose-bisphosphate aldolase (UP) 1.3 ± 0.2 2.0 ± 0.2 2.4 ± 0.4 0.3 ± 0.2
At1g69830 alpha-amylase (1,4-alpha-D-glucan glucanohydrolase) 1.3 ± 0.2 1.0 ± 0.2 0.5 ± 0.1 0.3 ± 0.1
At4g36670 sugar transporter 1.0 ± 0.1 0.9 ± 0.2 2.0 ± 0.5 1.8 ± 0.2
At3g46970 starch phosphorylase, alpha-glucan phosphorylase, H isozyme 0.9 ± 0.1 0.9 ± 0.1 0.5 ± 0.1 0.6 ± 0.2
At1g71880 sucrose transporter SUC1 (sucrose-proton symporter) 1.0 ± 0.1 0.8 ± 0.1 2.9 ± 0.7* 0.5 ± 0.2
Anaerobic Carbon Metabolism Related Genes     
At4g33070 pyruvate decarboxylase-1, (PDC1) 1.1 ± 0.1 6.3 ± 1.3 3.3 ± 0.6 0.9 ± 0.2
At1g77120 alcohol dehydrogenase, (ADH)(-) 0.9 ± 0.1 2.0 ± 0.3 1.5 ± 0.1 1.0 ± 0.2
At4g17260 L-lactate dehydrogenase, (LDH) 1.0 ± 0.1 1.7 ± 0.1 1.8 ± 0.1 1.0 ± 0.2
  1. Control represents internal variation (technical and/or biological) of different leaf samples from growth condition. Value ± s.e. indicates expression ratio of Treatment/Control after normalization ± standard error of the mean (n = 3–4). Genes in the table are listed in decreasing expression ratios according to Cold/Light treatment in each group of genes. (a)Genes that differ significantly (Students t test p-value less than 0.05) in their expression between the Cold/Light and Cold/Dark condition are marked with an asterisk (*). Values in bold indicate the quality control of gene expression (a statistical test of differential expression for a specific condition, Students t test p-value less than 0.05). A comparison between Cold/Light and moderate high light responsive gene expression [4] is indicated after description of the gene: (UP); a gene up regulated under moderate high light, (Down); a gene down regulated under moderate high light and (-); no change in the gene expression under moderate high light.