Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G‐protein action

Abstract

Classical mechanisms of heterotrimeric G-protein signaling are observed to function in regulation of the transcriptome. Conversely, many theoretical regulatory modes of the G-protein are not manifested in the transcriptomes we investigate.A new mechanism of G-protein signaling is revealed, in which the β subunit regulates gene expression identically in the presence or absence of the α subunit.We find evidence of cross-talk between G-protein-mediated and hormone-mediated transcriptional regulation.We find evidence of system specificity in G-protein signaling.

Ethylene-Induced Flavonol Accumulation in Guard Cells Suppresses Reactive Oxygen Species and Moderates Stomatal Aperture

“…CHS promoter-driven GUS product accumulated specifically in guard cells and not in surrounding epidermal pavement cells, which suggests that production of CHS, a key flavonol biosynthesis enzyme, is localized to Arabidopsis guard cells. This result is consistent with previous research that shows the presence of transcripts encoding enzymes of flavonol biosynthesis in guard cell protoplasts, including chalcone isomerase, flavanone 3-hydroxylase, flavonol synthase1, and flavonoid 39hydroxylase (Pandey et al, 2010). This result extends previous study in two ways.…”

“…First, it minimized the damage to cells that is the result of creating protoplasts, which may increase the expression of flavonoid biosynthesis genes in cells where they are not normally produced (Dixon and Paiva, 1995;WinkelShirley, 2002). Second, the available microarray data do not have a pavement cell transcriptome for comparison (Pandey et al, 2010). Using very different experimental methods in Vicia faba, flavonols were previously reported to accumulate in guard cells and surrounding epidermal cells (Schnabl et al, 1986;Takahama, 1988).…”

Gene-Sharing Networks Reveal Organizing Principles of Transcriptomes in Arabidopsis and Other Multicellular Organisms

“…For the Arabidopsis data set, we compiled and appropriately normalized gene expression data from 80 samples from three data sets: an Arabidopsis tissue expression atlas (Schmid et al, 2005), a cell type-specific expression atlas of Arabidopsis roots (Birnbaum et al, 2003;Brady et al, 2007), and a cell type-specific expression data set of Arabidopsis guard cells (Pandey et al, 2010). All three data sets were generated by ATH1 microarray with Columbia (Col) wild-type Arabidopsis without designated environmental stimuli or hormonal perturbation (see Methods; see Supplemental Figure 1, Supplemental Methods 1, and Supplemental References 1 online).…”

“…The root data set (ROOT data set) was obtained from GSE5749 and GSE8934 data sets in the Gene Expression Omnibus database (Birnbaum et al, 2003;Brady et al, 2007). Guard cell and whole leaf microarray data sets were generated in our laboratory (GC data set) (Pandey et al, 2010). A total of 237 raw CEL files from 80 tissues were analyzed for Arabidopsis.…”

“…For stomatal aperture measurements, plants were grown under identical conditions as for guard cell isolation for microarray analysis (Pandey et al, 2010). For each sample, two fully expanded leaves from 5-week-old plants were harvested just before the beginning of the light period.…”