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Table 3 The top 25 ranked non-COS genes based on treatment-frequency fold change values at 26 hours

From: Frequency-based time-series gene expression recomposition using PRIISM

Rank

Annotation

Comments

P Value (Treatment-Frequency Fold Change, 26 Hours)

Cold Upregulation Category*[54]

11

AT1G02820: Late embryogenesis abundant 3 family protein/LEA3 family protein

LEA family proteins are associated with dehydration stress (and therefore cold) and general environmental stress in plants, and desiccation tolerance in other organisms including bacteria [60]. Cold response genes COR15A COR15B and COR47 are classified as LEA genes. Although not to the same degree as the COR genes, expression of this gene was upregulated by cold according to quantitative RT-PCR [60]

3.29E-13

Soil

13

AT2G23910: Cinnamoyl-CoA reductase-related

Implicated in the biosynthesis of phenylpropanoids [61, 62], which contribute to many different plant responses to biotic and abiotic stress/challenge [63]

9.97E-13

Plate

23

AT1G61800: GPT2 (Glucose-6-Phosphate Translocator 2)

A gpt2 mutant shows an impairment in photosynthetic acclimation in response to shifts to high irradiance light, which can be exacerbated under cold conditions [64]

1.37E-09

Plate

29

AT5G06760: Late embryogenesis abundant group 1 (LEA group 1) domain-containing protein

Similar to other LEA above (AT1G02820), expression of this gene is upregulated by cold according to quantitative RT-PCR [60]

1.86E-08

Soil

37

AT3G51240: F3H; TT6 (Flavanone 3-Hydroxylase; Transparent Testa 6)

Implicated in freezing stress response [65]

7.07E-08

Plate

50

AT1G60190: Armadillo/beta-catenin repeat family/U-box domain-containing

 

1.92E-06

Soil

53

AT5G24120: SIGE/SIG5 (RNA polymerase sigma subunit E); DNA binding/DNA-directed RNA polymerase/sigma/transcription factor

Regulated in blue light by cryptochromes and involved in light-dependent regulation of the photosynthetic apparatus [66]. In a separate study shown to be essential for Arabidopsis[67]

3.24E-06

Soil

55

AT1G10370: ATGSTU17/ERD9/(Early-Responsive to Dehydration 9)

Dehydration responsive [68]

4.43E-06

Plate

57

AT1G32900: Starch synthase, putative

Identified in a study on light/cold interactions [69]. Upregulated by cold generally, but upregulated more under cold/light conditions than cold/dark

6.47E-06

Novel

60

AT4G33905: Peroxisomal membrane protein 22 kDa, putative

Upregulated by stress, including cold treatment [70]

7.71E-06

Novel

61

AT1G01520: Myb family transcription factor

Upregulated in mutant that has improved freezing tolerance (i.e. esk1 mutant) [71].

1.63E-05

Novel

63

AT5G57760: Unknown

 

1.95E-05

Plate

70

AT5G14760: AO (L-aspartate oxidase)

Involved in the synthesis of NAD [72], which is phosphorylated by cold in other plants [73]

4.96E-05

Novel

71

AT1G10585: Transcription factor

Upregulated under conditions associated with oxidative stress/high light [74]

5.66E-05

Soil

72

AT5G07010: Sulfotransferase family

Jasmonate responsive [68]

5.95E-05

Soil

75

AT2G22590: Glycosyltransferase family protein

In the same gene family as UGT91A1, (a target of a TF that regulates flavonol synthesis), and is thus proposed to impact flavonol biosynthesis, which is a product associated with cold response [75, 76]

6.55E-05

Plate

76

AT3G17609: HYH (HY5-Homolog); DNA binding/transcription factor

Involved in phyB signaling [77]; Required for low temperature-induced anthocyanin accumulation [78]

6.78E-05

Novel

81

AT1G17170: ATGSTU24 (Arabidopsis thaliana Glutathione S-Transferase (TAU) 24)

Member of the Glutathione S-transferase family (involved in flavonoid synthesis and general abiotic stress response) [79]

0.000123

Soil

82

AT5G07990: TT7 (Transparent Testa 7); flavonoid 3′-monooxygenase

Flavonoid biosynthesis protein, which is a product associated with cold response [68, 76]

0.000125

Plate

83

AT3G55940: Phosphoinositide-specific phospholipase C, putative

Phospholipase C genes, to which this is related, have been associated with responses to stress in Arabidopsis[80]

0.000142

Plate

84

AT3G21560: UGT84A2; UDP-glycosyltransferase/sinapate 1-glucosyltransferase

Upregulated by cold via the phospholipase D-dependent phosphatidic acid production [81]

0.000145

Plate

85

AT5G49480: ATCP1 (CA2 + −Binding Protein 1)

A “cold regulated signaling gene” that is altered in an ice1 mutant background (ICE1 is a cold/freezing related TF) [51]. Regulation altered under drought conditions [82]. Also (like UGT84A2, above) upregulated by cold via phospholipase D-dependent phosphatidic acid production [81]

0.000168

Soil

86

AT5G44110: POP1

Shown to be upregulated by cold in supplemental table of [83]. Response to Red and Far-Red light via phyA [84]. Also a target of HY5[85], which is a transcription factor in light signaling/responsiveness, but also shown to be important for cold dependent anthocyanin accumulation together with HYH (above) [78]

0.00017

Soil

87

AT5G36910: THI2.2 (Thionin 2.2); toxin receptor binding

Downregulated under high temperature stress [86], associated with jasmonic acid/salicylic acid signalling [87] and target of FAR1 and FHY3, which function in phyA signaling [88]

0.000174

Novel

88

AT2G31380: STH1 (salt tolerance homologue); transcription factor/zinc ion binding, also previously denoted ZF3

Like POP1 above, shown to be upregulated by cold in supplemental table of [83]. Circadian-controlled zinc finger gene with role in light signaling [89]. Additional evidence for role in light signaling and regulation by phytochrome [90, 91], and like THI2 (above), target of FAR1 and FHY3, which function in phyA signaling [88]

0.000176

Soil

  1. *“ Cold Upregulation Category” indicates whether a gene was upregulated in the cold when plants were grown in soil (“Soil”), on agar plates (“Plate”), on both growth mediums (“COS”), or on neither (“Novel”) in Vogel et al’s study [54].