Protein identification and mRNA analysis of phytochrome-regulated genes in Arabidopsis under red light

Phytochromes are a family of plant photoreceptors that mediate physiological and developmental responses to red and far-red light. According to the affymetrix ATH1 microarray, phytochrome A (phyA) and phytochrome B (phyB) together play a key role in transducing the Rc signals to light-responsive genes. In order to select those red light-responsive genes associated with phyA or phyB, a proteomic approach based on two-dimensional gel electrophoresis (2-DE) was used to compare the protein expression patterns of the phyAphyB double mutant and the wild type of Arabidopsis thaliana (col-4) which grew under constant red light conditions for 7 d. Thirty-two protein spots which exhibited differences in protein abundance were identified by matrix-assisted laser desorption/ionization-time of flight/time of flight mass spectrometry. The expression of ten genes corresponding to ten protein spots was analyzed by a semiquantitative reverse transcription-polymerase chain reaction. Two of the ten genes were confirmed by quantitative PCR (Q-PCR). The results showed that phytochromes may exert their function by regulating mRNA or protein expressions. Proteomic analysis may provide a novel pathway for identifying phytochrome-dependent genes.