Plant Tropisms

tained short, conserved sequences in their promoters, suggesting a potential role for these
DNA motifs as cis-elements in the regulation of gene expression by gravistimulation
(Moseyko et al. 2002).
Although this initial study provided exciting new information on transcriptional re-
sponses to gravistimulation in Arabidopsisseedlings, it suffered from the fact that entire
seedlings were analyzed, including organs that respond in opposite ways to gravistimula-
tion (hypocotyls and roots), and from probing only a fraction of the Arabidopsisgenome.
A second study used similar strategies to monitor transient changes in gene expression in
primary root tips of Arabidopsis thalianaseedlings in a time course during the first hour
of gravity- and/or mechano-stimulation. The whole-genome Affymetrix ATH1 microar-
ray was used in this analysis (Kimbrough et al. 2004).
This study helped uncover clusters of genes that show similar kinetics of expression
change in the root tip upon gravistimulation. A vast majority of the differentially ex-
pressed genes (1,665 genes, or 96% of the regulated genes) were regulated by both
gravity- and mechano-stimulation. Only 65 differentially expressed genes showed spe-
cific up-regulation in response to gravistimulation. Five were up-regulated by a factor of
three or more within 2 min of gravistimulation, and remained high during the first 30 min
of the response (Kimbrough et al. 2004). These fast graviresponding genes did not
change their expression in response to gravistimulation in arg1-2 andarl2-3mutant back-
grounds, confirming the key role played by ARG1 and ARL2 in early phases of gravity
signal transduction in Arabidopsisroot tips, upstream of the transcriptional responses
(Yester et al. 2006).
Most of the genes found to be regulated by gravity- or mechano-stimulation again fell
into only a few functional classes: Transcription (258 genes); Metabolism (144 genes);
Protein fate (114 genes); and Signal transduction (97 genes). Only a minority of the dif-
ferentially expressed genes fell in the Defense (31) and Stress (14) functional categories,
which were the most highly represented classes in Moseyko et al. (2002). Furthermore,
only three genes were found to be regulated by gravity and/or touch in both studies
(Moseyko et al. 2002; Kimbrough et al. 2004). The difference in results between these
two studies probably reflects differences in experimental procedures, as discussed in
Kimbrough et al. (2004).
Now that multiple genes have been identified whose expression varies in response to
gravistimulation, they can be tested for a contribution to gravity signal transduction by
reverse genetics (Kimbrough et al. 2004).
Although global expression profiling is useful for identifying clusters of genes with
similar expression profiles under defined conditions, it cannot uncover post-transcriptional
regulatory processes. Hence, attempts have been made at identifying proteins whose
abundance, localization, and/or post-translational modifications are altered by gravistim-
ulation.
That gravistimulation promotes changes in protein abundance or post-translational
modification was first demonstrated in pioneering studies comparing protein profiles be-
tween vertical and gravistimulated Arabidopsisseedlings grown in the presence of^35 S-
labeled methionine. Gravistimulation was provided by rotating the dishes in which
seedlings were growing 90 degrees and allowing the organs to reorient over a period of
24 hours. Subsequently, proteins were extracted from vertical control and gravistimulated

CHAPTER 2 SIGNAL TRANSDUCTION IN GRAVITROPISM 33