Computational identification of root hair-specific genes in Arabidopsis

Abstract

Activated cortical domains (AC Ds) are regions of the plant cell cortex performing localized membrane turnover, delimited by concerted action of the cortical cytoskeleton and endomembrane compartments. Arabidopsis thaliana rhizodermis consists of two cell types differing by a single AC D (trichoblasts, carrying tip-growing root hairs, and hairless atrichoblasts), providing a model for the study of AC D determination. We compiled a set of genes specifically upregulated in root hairs from published transcriptome data and compared it with a "virtual Arabidopsis root hair proteome", i.e., a list of computationally identified homologs of proteins from the published soybean root hair proteome. Both data sets were enriched in genes and proteins associated with root hairs in functional studies, but there was little overlap between the transcriptome and the proteome: The former captured gene products specific to root hairs, while the latter selected those abundant in root hairs but not necessarily specific to them. Decisive steps in AC D specification may be performed by signaling proteins of high expression specifity and low abundance. Nevertheless, 73 genes specifically transcribed in Arabidopsis trichoblasts or root hairs encode homologs of abundant root hair proteins from soybean. Most of them encode "housekeeping" proteins required for rapid tip growth. However, among the "candidates" is also a generative actin isoform, ACT11. Preliminary characterization of an act11 mutant allele indeed suggests a hitherto unexpected role for this gene in root and root hair development. © 2010 Landes Bioscience.