Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G-protein action.
Heterotrimeric G-proteins mediate crucial and diverse signaling pathways in eukaryotes. Here, we generate and analyze microarray data from guard cells and leaves of G-protein subunit mutants of the model plant Arabidopsis thaliana, with or without treatment with the stress hormone, abscisic acid. Although G-protein control of the transcriptome has received little attention to date in any system, transcriptome analysis allows us to search for potentially uncommon yet significant signaling mechanisms. We describe the theoretical Boolean mechanisms of G-protein x hormone regulation, and then apply a pattern matching approach to associate gene expression profiles with Boolean models. We find that (1) classical mechanisms of G-protein signaling are well represented. Conversely, some theoretical regulatory modes of the G-protein are not supported; (2) a new mechanism of G-protein signaling is revealed, in which Gbeta regulates gene expression identically in the presence or absence of Galpha; (3) guard cells and leaves favor different G-protein modes in transcriptome regulation, supporting system specificity of G-protein signaling. Our method holds significant promise for analyzing analogous 'switch-like' signal transduction events in any organism.
Pandey
Sona
S
Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
Wang
Rui-Sheng
RS
Wilson
Liza
L
Li
Song
S
Zhao
Zhixin
Z
Gookin
Timothy E
TE
Assmann
Sarah M
SM
Albert
Réka
R
D000040:Abscisic Acid / Q000494:pharmacology; D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D017343:Genes, Plant / Q000235:genetics; D020962:Heterotrimeric GTP-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D008957:Models, Genetic; D009154:Mutation / Q000235:genetics; D015398:Signal Transduction / Q000187:drug effects / Q000235:genetics
D029681:Arabidopsis Proteins; D000040:Abscisic Acid; D020962:Heterotrimeric GTP-Binding Proteins