Mapping diverse omics data sets on a given phenotype or cell type provides a way to understand physiological or developmental processes at a systems level. Parallel profiling of transcripts and proteins was conducted on root hair-forming cells (trichoblasts) in protoplasts isolated from plants carrying a GFP reporter coupled to the trichoblast-specific EXP7 protein. GFP-expressing cells were separated from non-active cells by FACS equipped with a cooling device. RNA collected from several runs was pooled and analyzed by RNAseq using the Solexa II Genomic Analyzer platform without amplification. In total, 23 million uniquely mapped 150-bp paired-end reads were generated, matching to 20,890 transcripts. As anticipated, genes coding for cell wall hydrolytic enzymes and enzymes involved in cell extension were highly expressed in root hairs. Expression of genes encoding the negative regulators of the root hair cell fate GL2 and WER was < 1 RKMB, while CPC, a positive regulator showed high transcript abundance. Transcripts of RHD6 and RSL4, encoding bHLH-type transcription factors that control early stages of root hair differentiation, were also highly abundant. A total of 1600 proteins were identified in trichoblasts by LC-MS/MS on a LTQ Orbitrap Velos. The GO categories 'intracellular protein transport', 'glycolysis' and 'amino acid biosynthesis' were strongly enriched at the protein level. The corresponding transcript for a subset of proteins was not detected. Some of these proteins carry secretion signals, indicative of their possible lateral or radial movement into trichoblasts. In summary, through correct confrontation of deep transcriptomic and proteomic data sets, we provide a systems view into the metabolism of a single cell type that undergoes highly dynamic developmental changes.
