Investigating tissue- and organ-specific phytochrome responses using FACS-assisted cell-type specific expression profiling in Arabidopsis thaliana

Spatiotemporal Phytochrome Signaling during Photomorphogenesis: From Physiology to Molecular Mechanisms and Back

Light exposure results in distinct responses in specific seedling tissues during photomorphogenesis. Light promotes growth of cotyledons and leaves, as well as development and elongation of roots, whereas light inhibits elongation of hypocotyls. For distinct plant responses such as shade avoidance, far-red light or shifts in spectral light quality similarly have disparate impacts on distinct plant tissues, resulting in elongation of stems or petioles and a reduction in growth of leaf blades for many species. The physiological bases of such tissue- and organ-specific light responses were initially studied using localized irradiation of specific tissues and organs, or irradiation of dissected plant parts. These historical approaches were used to identify spatial-specific pools of photoreceptors responsible for regulating local, i.e., tissue- or organ-specific, or distal, i.e., interorgan, plant responses. The red/far-red responsive phytochromes have been the most widely studied among photoreceptors in this regard. Whereas, the spatial localization of photoreceptors regulating many tissue- or organ-specific light responses were identified, the underlying signaling networks responsible for mediating the observed responses have not been well defined. Recent approaches used to investigate the molecular bases of spatiotemporal light responses include selective irradiation of plants harboring mutations in specific photoreceptors, tissue-specific expression of photoreceptors, primarily in photoreceptor mutant backgrounds, or tissue-specific biochemical ablation of photoreceptor accumulation. Progressive integration of such approaches for regulating the availability of localized pools of phytochromes with the use of transcriptomic or proteomic analyses for assessing the genes or proteins which these spatially discrete pools of phytochrome regulate is yielding emergent insight into the molecular bases of spatiotemporal phytochrome signaling pathways responsible for regulating spatiotemporal light responses of which we have been aware of at the physiological level for decades. Here, I discuss historical and emerging approaches to elucidating spatiotemporal signaling mediated by phytochromes during photomorphogenesis.

Cell specific analysis of Arabidopsis leaves using fluorescence activated cell sorting

After initiation of the leaf primordium, biomass accumulation is controlled mainly by cell proliferation and expansion in the leaves¹. However, the Arabidopsis leaf is a complex organ made up of many different cell types and several structures. At the same time, the growing leaf contains cells at different stages of development, with the cells furthest from the petiole being the first to stop expanding and undergo senescence¹. Different cells within the leaf are therefore dividing, elongating or differentiating; active, stressed or dead; and/or responding to stimuli in sub-sets of their cellular type at any one time. This makes genomic study of the leaf challenging: for example when analyzing expression data from whole leaves, signals from genetic networks operating in distinct cellular response zones or cell types will be confounded, resulting in an inaccurate profile being generated.

To address this, several methods have been described which enable studies of cell specific gene expression. These include laser-capture microdissection (LCM)² or GFP expressing plants used for protoplast generation and subsequent fluorescence activated cell sorting (FACS)^3,4, the recently described INTACT system for nuclear precipitation⁵ and immunoprecipitation of polysomes⁶.

FACS has been successfully used for a number of studies, including showing that the cell identity and distance from the root tip had a significant effect on the expression profiles of a large number of genes^3,7. FACS of GFP lines have also been used to demonstrate cell-specific transcriptional regulation during root nitrogen responses and lateral root development⁸, salt stress⁹ auxin distribution in the root¹⁰ and to create a gene expression map of the Arabidopsis shoot apical meristem¹¹. Although FACS has previously been used to sort Arabidopsis leaf derived protoplasts based on autofluorescence^12,13, so far the use of FACS on Arabidopsis lines expressing GFP in the leaves has been very limited⁴. In the following protocol we describe a method for obtaining Arabidopsis leaf protoplasts that are compatible with FACS while minimizing the impact of the protoplast generation regime. We demonstrate the method using the KC464 Arabidopsis line, which express GFP in the adaxial epidermis¹⁴, the KC274 line, which express GFP in the vascular tissue¹⁴ and the TP382 Arabidopsis line, which express a double GFP construct linked to a nuclear localization signal in the guard cells (data not shown; Figure 2). We are currently using this method to study both cell-type specific expression during development and stress, as well as heterogeneous cell populations at various stages of senescence.