Open AccessBoolean modeling of transcriptome data reveals novel modes of heterotrimeric G‐protein action
Author(s) -
Pandey Sona,
Wang RuiSheng,
Wilson Liza,
Li Song,
Zhao Zhixin,
Gookin Timothy E,
Assmann Sarah M,
Albert Réka
Publication year - 2010
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.1038/msb.2010.28
Subject(s) - biology , heterotrimeric g protein , transcriptome , signal transduction , computational biology , genetics , microbiology and biotechnology , gene , microarray analysis techniques , g protein , gene expression
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 × 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 Gβ regulates gene expression identically in the presence or absence of Gα; (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.