Table 2.
Genes showing at least two-fold differential expression (induction/repression) in Arabidopsis AtTIL knock-out plants.
| Differential expression (absolute values) |
||||||||
| KO | KO 4°C | WT 4°C | KO 4°C | |||||
| vs | vs | vs | vs | Regulation | ||||
| Putative Function and Reference | Locus ID | ProbesetIDs | WT | KO | WT | WT 4°C | ||
| Upregulated Genes | ||||||||
| Transcription Factors: | ||||||||
| pseudo-response regulator 5 (APRR5) | At5g24470 | 249741_at | 5,3 | 6,3 | 33,8 | -1,0 | † | |
| zinc-binding family protein (DUF597) | At1g76590 | 259977_at | 2,9 | 2,1 | 5,7 | 1,1 | # | |
| WRKY family transcription factor (WRKY54) | At2g40750 | 257382_at | 2,8 | 2,2 | 4,8 | 1,3 | # | |
| DRE-binding protein (DREB1A)/CRT/DRE-binding factor 3 (CBF3) | At4g25480 | 254066_at | 2,3 | 4,0 | 12,9 | -1,4 | ||
| ABA-responsive element-binding protein (ABRE) | At1g49720 | 261613_at | 2,2 | 2,4 | 4,9 | 1,1 | ||
| sigA-binding protein | At3g56710 | 246293_at | 2,2 | 1,8 | 3,6 | 1,1 | # | |
| heat shock factor protein, putative (HSF5) (HSTF5) | At1g67970 | 259992_at | 2,1 | 2,2 | 4,0 | 1,2 | # | |
| gigantea protein (GI) | At1g22770 | 264211_at | 2,0 | 3,6 | 6,9 | 1,1 | † | |
| zinc finger (MYND type) family protein | At5g50450 | 248502_at | 2,1 | 2,2 | 4,4 | 1,1 | ||
| zinc finger (C3HC4-type RING finger) family protein | At1g49230 | 260753_at | 2,1 | 1,4 | 2,9 | 1,0 | # | |
| CONSTANS-LIKE 13 zinc finger (B-box type) family protein | At2g47890 | 266514_at | 2,1 | 3,5 | 6,5 | 1,1 | ||
| ABI3-interacting protein 1 (AIP1) (TOC1) | At5g61380 | 247525_at | 2,1 | 3,1 | 5,4 | 1,2 | † | |
| Signal Transduction: | ||||||||
| invertase/pectin methylesterase inhibitor family protein | At5g62360 | 247478_at | 5,2 | 1,3 | 5,8 | 1,1 | # | |
| cold circadian rhythm-RNA binding 2; CCR2 | At2g21660 | 263548_at | 4,4 | 3,2 | 13,4 | 1,1 | ||
| acid phosphatase class B family protein | At2g39920 | 267361_at | 4,0 | -1,1 | 3,4 | 1,0 | # | |
| auxin-regulated protein kinase, putative | At2g33830 | 267461_at | 3,2 | -1,6 | 1,7 | 1,1 | * | |
| peptidyl-prolyl cis-trans isomerase/cyclophilin (CYP2)/rotamase | At2g21130 | 264019_at | 2,3 | 2,9 | 6,4 | 1,1 | ||
| ankyrin repeat family protein (ACD6) | At4g14400 | 245265_at | 2,2 | 2,0 | 4,5 | -1,0 | ||
| protein kinase, putative BIK kinase | At3g55450 | 251789_at | 2,2 | 2,1 | 4,2 | 1,1 | # | |
| phosphorylase family protein | At4g24340 | 254163_s_at | 2,1 | -3,3 | -1,3 | -1,2 | * | |
| Stress Reponse, Cell Rescue and Defense: | ||||||||
| DNAJ heat shock N-terminal domain-containing protein | At5g23240 | 249850_at | 6,5 | 2,1 | 11,6 | 1,2 | # | |
| DNAJ heat shock N-terminal domain-containing protein | At1g56300 | 256221_at | 4,4 | -1,2 | 3,1 | 1,2 | # | |
| hydrophobic protein, low temperature and salt responsive protein | At4g30650 | 253627_at | 2,3 | 7,8 | 17,5 | 1,0 | ||
| senescence-associated protein-related (SAG102) | At1g53885 | 262226_at | 2,3 | -4,7 | -2,1 | 1,0 | ||
| hydrophobic protein, low temperature and salt responsive protein | At4g30660 | 253581_at | 2,1 | -2,7 | -1,1 | -1,2 | * | |
| universal stress protein (USP) family protein | At3g62550 | 251221_at | 2,0 | -2,4 | -1,3 | 1,1 | * | |
| heavy-metal-associated domain-containing protein | At1g51090 | 245749_at | 2,0 | 5,7 | 11,1 | 1,0 | ||
| pathogenesis-related thaumatin family protein (calcium storage) | At1g20030 | 261248_at | 2,0 | -1,7 | 1,0 | 1,0 | * | |
| cold-regulated protein (cor15b) | At2g42530 | 263495_at | 2,0 | 24,0 | 47,7 | 1,0 | ||
| pathogen and circadian controlled 1 (PCC1) | At3g22231 | 256766_at | 2,0 | 1,6 | 2,9 | 1,0 | # | |
| Metabolism: | ||||||||
| riboflavin biosynthesis protein, putative | At2g22450 | 264045_at | 2,8 | 1,2 | 3,2 | -1,0 | # | |
| pyruvate decarboxylase, putative | At5g54960 | 248138_at | 2,6 | 1,6 | 3,7 | 1,1 | # | |
| preprotein and amino acid transporter | At4g26670 | 253981_at | 2,4 | 1,8 | 4,0 | 1,1 | # | |
| succinate-semialdehyde dehydrogenase (SSADH1) | At1g79440 | 262892_at | 2,2 | 2,6 | 5,6 | 1,0 | ||
| aldose 1-epimerase family protein | At3g47800 | 252387_at | 2,2 | 1,6 | 3,7 | -1,1 | # | |
| nucellin protein, putative | At4g33490 | 253331_at | 2,1 | -1,1 | 1,7 | 1,1 | * | |
| auxin-responsive family protein | At5g35735 | 249719_at | 2,1 | 1,2 | 2,4 | 1,0 | # | |
| acyl CoA:diacylglycerol acyltransferase (DGAT) | At2g19450 | 267280_at | 2,1 | 3,0 | 5,9 | 1,1 | ||
| isoamylase, putative/starch debranching enzyme, putative | At4g09020 | 255070_at | 2,1 | 3,0 | 6,0 | 1,0 | ||
| 2-oxoacid-dependent oxidase, putative (DIN11) | At3g49620 | 252265_at | 2,1 | -2,8 | -1,2 | -1,1 | * | |
| OEP16-like protein | At2g28900 | 266225_at | 2,1 | 2,7 | 5,8 | -1,0 | ||
| starch phosphorylase, putative | At3g46970 | 252468_at | 2,1 | 1,6 | 2,9 | 1,1 | # | |
| glycoside hydrolase starch-binding domain-containing protein | At5g26570 | 246829_at | 2,0 | 2,5 | 4,9 | 1,0 | ||
| amino acid permease family protein or GABA permease | At2g01170 | 265790_at | 2,0 | 1,1 | 2,1 | 1,0 | # | |
| Expressed Protein | ||||||||
| expressed protein | At4g16146 | 245319_at | 4,0 | 4,2 | 14,7 | 1,2 | ||
| expressed protein | At1g53035 | 261318_at | 2,6 | 5,1 | 12,0 | 1,1 | ||
| expressed protein | At4g04330 | 255331_at | 2,6 | -1,6 | 1,5 | 1,1 | * | |
| expressed protein | At2g14560 | 265837_at | 2,5 | 2,9 | 6,1 | 1,2 | ||
| expressed protein | At2g15890 | 265478_at | 2,4 | -3,0 | -1,4 | 1,1 | * | |
| expressed protein | At1g70420 | 264314_at | 2,1 | -1,8 | 1,6 | -1,3 | * | |
| expressed protein | At1g14870 | 262832_at | 2,1 | 4,0 | 5,9 | 1,4 | ||
| Downregulated Genes | ||||||||
| Transcription Factors: | ||||||||
| late elongated hypocotyl (LHY) | At1g01060 | 261569_at | -3,2 | 6,2 | 2,1 | -1,1 | † | |
| CONSTANS-LIKE 2 (COL2) | At3g02380 | 258497_at | -2,4 | -2,0 | -3,2 | -1,5 | # | † |
| Signal Transduction: | ||||||||
| cysteine proteinase, putative | At2g27420 | 265665_at | -2,3 | 2,3 | 1,0 | -1,0 | * | |
| calcium-binding RD20 protein (RD20) | At2g33380 | 255795_at | -2,1 | -2,1 | -3,7 | -1,2 | # | |
| Stress response, Cell Rescue and Defense: | ||||||||
| At TIL, lipocalin | At5g58070 | 247851_at | -3,6 | -1,7 | 1,5 | -8,8 | * | |
| putative membrane related protein CP5 | At1g55960 | 260603_at | -2,2 | -2,0 | -4,3 | -1,0 | # | |
| phosphate-responsive protein, putative (EXO) | At4g08950 | 255064_at | -2,0 | -2,0 | -5,3 | 1,3 | ||
| Metabolism: | ||||||||
| dehydrodolichyl diphosphate synthase, putative | At5g58770 | 247780_at | -3,1 | -2,8 | -7,6 | -1,1 | ||
| trehalose-6-phosphate phosphatase (TPPA) | At5g51460 | 248404_at | -2,8 | -2,6 | -6,7 | -1,1 | ||
| starch synthase, putative | At1g32900 | 261191_at | -2,5 | 6,4 | 2,7 | -1,1 | ||
| carbonic anhydrase family protein | At3g52720 | 252011_at | -2,2 | -3,3 | -6,9 | -1,1 | ||
| glutathione S-transferase, putative (ERD9) | At1g10370 | 264436_at | -2,2 | 4,5 | 2,1 | -1,0 | ||
| adenosylmethionine decarboxylase family protein | At5g15950 | 246490_at | -2,0 | 6,6 | 3,5 | -1,1 | ||
| Expressed Protein | ||||||||
| expressed protein | At3g28270 | 256603_at | -2,3 | -1,9 | -4,0 | -1,1 | # | |
| expressed protein | At1g68440 | 259856_at | -2,1 | -2,5 | -4,6 | -1,1 | ||
* 12 genes regulated (induced or repressed) only in the KO line (not regulated by exposure of the WT to LT)
# 22 genes for which the regulation in KO is at least 50% of the regulation seen in WT exposed at 4°C
† key regulators of the circadian clock