Table 1 Characterization of the selected transcription factors and the TFBSs with unknown transcription factors that were identified in the promoter regions of the Ppd-1 genes
Family | Transcription factors/TFBSs with unknown TF | Description |
|---|---|---|
Phytochrome regulated transcription factors | ||
VOZ | VOZ2 | VOZ2 was identified as one of the highly conserved transcriptional factors in land plant genes that are PhyB-interacting factors [58]. |
bHLH | Phytochrome Interacting Factor3 (PIF3) | The G-box, CACGTG, is a target sequence for PIF3 [59]. PIF3 plays important roles in the Phy-mediated light responses. This factor can regulate the downstream genes either positively or negatively [60]. In Arabidopsis, PIF3 was suggested to play an important role in the control of flowering by the regulation of CO and FT gene expression [61]. |
bHLH | Phytochrome Interacting Factor3-Like5 (PIL1) | PIL5 interacts with the Pfr forms of Phytochrome A (PhyA) and Phytochrome B (PhyB) [62]. |
FAR1 | Far-Red Elongated Hypokotyls3/Far-Red-Impaired Response1 (FHY3/FAR1) | Transcription factor FHY3/FAR1 modulates PhyA-signaling in higher plants [63]. Other investigations demonstrated that FHY3 plays a principal role in the circadian clock, heading date control and regulation of heading time through ELF4 (EARLY FLOWERING4) [64]. |
Myb/SANT; MYB-related | RVE7/EPR1 | RVE7/EPR1 is regulated by both PhyA and PhyB and negatively regulates flowering [65]. |
– | SORLIP2AT and SORLIP1AT | Sequences over-represented in the light-induced promoters SORLIP2AT and SORLIP1AT were identified in the PhyA-induced promoters [66]. |
– | RE1ASPHYA3 | RE1ASPHYA3 (RE1, putative repressor element) is a highly conserved motif in the most monocot PhyA promoters and is responsible for the Pfr-directed repression [67]; this motif was detected in certain other genes [68]. |
Circadian-clock regulated transcription factors | ||
AP2/RAV/B3 | RAV1 | RAV1 is a negative component in the regulation of plant development [69]. |
AP2/RAV/B3 | TEMPRANILLO1 (TEM1) TEMPRANILLO2 (TEM2) | TEM1 and TEM2 genes act as direct repressors of FT [70]. |
MYB-related | REVEILLE1 (RVE1) | RVE1 is a morning-phased transcription factor that integrates the circadian clock and auxin pathways [71]. |
Myb/SANT; MYB-related | REVEILLE 8 (RVE8) | RVE8 promotes the expression of some evening element that contains clock genes and forms a negative feedback loop with PRR5 [72, 73]. |
MYB | Circadian Clock Associated 1 (CCA1); Late Elongated Hypocotyl (LHY) | The MYB transcription factors CCA1 and LHY are some of the key genes in the central oscillator of the plant circadian clock [74]. LHY and CCA1 negatively regulate TOC1 expression. |
TCP | CCA1 HIKING EXPEDITION (CHE) | The TCP transcription factor CHE is a clock component that is partially redundant with LHY in the repression of CCA1 [75]. |
Other light regulated transcription factors | ||
GATA/tify | GATA2 | GATA2 directly regulates genes that respond to light [76]. |
GATA/tify | GATA12 | GATA12 is involved in the regulation of many light-responsive genes [77, 78]. |
MADF; Trihelix | GT-1 | GT-1 may act as a light-responsive transcription factor [79]. |
bHLH | AtMYC2 | AtMYC2 acts as a negative regulator of blue light–mediated photomorphogenic growth and blue and far-red-light–regulated gene expression [80]. |
– | BOXIIPCCHS | BOXIIPCCHS was suggested to be essential for light regulation [29, 81]. |
– | TBOXATGAPB | Mutations in TBOXATGAPB cause a reduction in light-activated transcription [82, 83]. |
– | IBOXCORENT | I-box core motif IBOXCORENT in the conserved DNA modular arrays is associated with the light-responsive promoter regions [84]. |
– | LREBOXIIPCCHS1 | Light responsive element LREBOXIIPCCHS1, which was detected in parsley, is required for light responsiveness [85]. |
– | IBOXCORE | Conserved sequence in the 5′ UTR of light-regulated genes IBOXCORE may be involved in the regulation of transcription by light and the circadian clock. This sequence was detected in both monocots and dicots [86]. |