Gene profiling of the red light signalling pathways in roots

Red light, acting through the phytochromes, controls numerousaspects of plant development. Many of the signal transductionelements downstream of the phytochromes have been identifiedin the aerial portions of the plant; however, very few elementsin red-light signalling have been identified specifically forroots. Gene profiling studies using microarrays and quantitativeReal-Time PCR were performed to characterize gene expressionchanges in roots of Arabidopsis seedlings exposed to 1 h ofred light. Several factors acting downstream of phytochromesin red-light signalling in roots were identified. Some of thegenes found to be differentially expressed in this study havealready been characterized in the red-light-signalling pathwayfor whole plants. For example, PHYTOCHROME KINASE 1 (PKS1),LONG HYPOCOTYL 5 (HY5), EARLY FLOWERING 4 (ELF4), and GIGANTEA(GI) were all significantly up-regulated in roots of seedlingsexposed to 1 h of red light. The up-regulation of SUPPRESSOROF PHYTOCHROME A RESPONSES 1 (SPA1) and CONSTITUTIVE PHOTOMORPHOGENIC1-like (COP1-like) genes suggests that the PHYA-mediated pathwaywas attenuated by red light. In addition, genes involved inlateral root and root hair formation, root plastid development,phenylpropanoid metabolism, and hormone signalling were alsoregulated by exposure to red light. Interestingly, members ofthe RPT2/NPH3 (ROOT PHOTOTROPIC 2/NON PHOTOTROPIC HYPOCOTYL3) family, which have been shown to mediate blue-light-inducedphototropism, were also differentially regulated in roots inred light. Therefore, these results suggest that red and bluelight pathways interact in roots of seedlings and that manyelements involved in red-light-signalling found in the aerialportions of the plant are differentially expressed in rootswithin 1 h of red light exposure. Key words: Arabidopsis, gene profiling, microarray, photomorphogenesis, red light, roots