Co-expression and hormonal regulation of genes in response to gravity and mechanical stimulation in the Arabidopsis root apex.

Plant roots direct their growth in response to gravity, light, and mechanical stimuli. Spatial changes in the rates of cell elongation and division are responsible for the directional growth. Local changes in hormone concentration and/or sensitivity have been shown to be part of the signal transduction and response mechanisms that result in those tropic growth resonses. Part of most hormone regulated mechanisms are regulation of transcription and transcript stability. We have focussed our analysis of whole genome microarrays on the differential regulation of transcript abundance changes during the first hour after gravity and mechanical stimulation with respect to the involvement of hormones – especially auxins and brassinosteroids. Root apices from 7-day-old etiolated Arabidopsis seedlings were harvested and analyzed for relative changes in transcript levels in response to gravistimulation and mechanical stimulation using the Arabidopsis ATH1 GeneChip (Affymetrix). In a time course experiment, approximately 150 root tips were harvested before (0 time point) and 2, 5, 15, 30, 60 min after 135◦ reorientation by pouring RNAlater (Ambion) onto the plates and cutting off the root apex (~7.5 mm). Mechanical stress control seedlings (0, 2, 5, 15, 30, 60 min) were moved horizontally for 5 sec without changing their orientation towards the vector of gravity and were processed in an identical manner. Total RNA was extracted and purified (RNeasy column, Qiagen), amplified and hybridized to microarrays using standard protocols (Kimbrough et al. 2004). From 24,000 transcripts analyzed, we found 1730 with significant changes in abundance at two consecutive time points after reorientation (gravity) and 1691 transcripts regulated after mechanical stimulation (mechanical). While both stresses had 1641 regulated transcripts in common (Figure 1), 65 genes were gravity-specific up regulated and 26 were specifically regulated by the mechanical stimulus. Of those regulated by mechanical stimulus, 16 showed an increase in abundance and 10 transcripts showed a decrease compared to the vertical control. Of the transcripts regulated by both stimuli, 897 showed an increase in abundance and 744 a decrease (Kimbrough et al. 2004). Many of the stimuli specific genes exhibited co-regulation throughout the time course (Figure 2). Figure 1: Genes regulated (up or down) by both stimuli were classified into functional groups. The number represents the percentage of genes in each functional group from all genes regulated under both stimuli.