Abstract
Phytochrome-interacting factors (PIFs), as the basic helix–loop–helix (bHLH) transcription factors, are the primary signaling partners for phytochromes (PHY) that play a key role in PHY-mediated light signal transduction. At present, there are few studies on PIFs in fruit trees. In order to clarify the status of PIFs in grapevines, we identified members of the grape PIFs family and conducted phylogenetic and expression analysis. We identified PIF1, PIF3, PIF4, and PIF7 in PIFs families of the grapevine (Vitis vinifera L.), which were distributed on four different chromosomes with similar gene structures. Except for the closer relationship with PIF1 of citrus, PIFs of grape were distant from the other fruit species such as apple, pear, peach, and strawberry. The VvPIFs (except VvPIF4) were located in the syntenic block with those from Arabidopsis thaliana, Solanum lycopersicum, or Citrus sinensis. In addition to PIF1, all PIFs in grapevines have conserved active PHYB binding (APB) sequences. VvPIF1 has a conserved PIF1-specific active PHYA binding (APA) sequence, while amino acid mutations occurred in the specific APA sequence in VvPIF3. Interestingly, two specific motifs were found in the PIF4 amino acid sequence. The photoreceptor-related elements in the VvPIFs promoter region were the most abundant. PIF1, LONG HYPOCOTYL 5 (HY5) and PIF3, PIF4, GIBBERELLIC ACID INSENSITIVE 1 (GAI1) may interact with each other and participate together in light signal transduction. The relative expression levels of the VvPIFs showed diverse patterns in the various organs at different developmental stages, of which PIF4 was most highly expressed. Prior to maturation, the expression of PIF4 and PIF7 in the skin of the different cultivars increased, while the expression of all PIFs in the flesh decreased. The transcription level of PIFs in grape leaves was sensitive to changes in lighting and shading. Shading treatment was beneficial for enhancing the transcription level of VvPIFs, but the effect on VvPIF3 and VvPIF4 was time-controlled. We concluded that PIFs in grapevines are both conservative and species-specific. The identification and analysis of grape PIFs could provide a theoretical foundation for the further construction of grape light regulation networks.
Highlights
Plants undergo the developmental program of photomorphogenesis in the presence of light [1].Phytochromes, acting as red/far red-light sensors, are one of the most important photoreceptors in plants, and have been investigated extensively in terms of photochemistry, protein structures, andGenes 2018, 9, 451; doi:10.3390/genes9090451 www.mdpi.com/journal/genesGenes 2018, 9, 451 transduction of light signal [2,3]
The four members were named as PIF1, PIF3, PIF4, and PIF7, respectively and their corresponding serial numbers are LOC100264869, LOC100247781, LOC100262490, and LOC100262138 in NCBI, VIT_07s0005g05100, VIT_14s0060g00260, VIT_12s0028g01110, and VIT_17s0000g06930 in CRIBI, and
Similar to the expression changes of PIF3, PIF4 showed a significant peak at 10 h. These results indicated that shading was beneficial to increase the expression of PIF3 and PIF4 in leaves, but the effect of shading was limited by circadian or the length of shading time
Summary
Plants undergo the developmental program of photomorphogenesis in the presence of light [1].Phytochromes, acting as red/far red-light sensors, are one of the most important photoreceptors in plants, and have been investigated extensively in terms of photochemistry, protein structures, andGenes 2018, 9, 451; doi:10.3390/genes9090451 www.mdpi.com/journal/genesGenes 2018, 9, 451 transduction of light signal [2,3]. Plants undergo the developmental program of photomorphogenesis in the presence of light [1]. Phytochromes, acting as red/far red-light sensors, are one of the most important photoreceptors in plants, and have been investigated extensively in terms of photochemistry, protein structures, and. Genes 2018, 9, 451 transduction of light signal [2,3]. There are various types of phytochromes in plants. PHYA, PHYB, PHYC, PHYD, and PHYE were reported in Arabidopsis thaliana, PHYA, PHYB, PHYC in Oryza sativa, PHYA1, PHYB1, PHYC1 and their homologous genes PHYA2, PHYB2, PHYC2 in Zea mays [1]. PHYs exist in both Pr and Pfr forms. Red-light activates PHYs by converting the Pr form to the Pfr form, whereas far red-light inactivates Pfr by converting it back to the Pr form
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