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

Sona Pandey, Rui Sheng Wang, Liza Wilson, Song Li, Zhixin Zhao, Timothy E. Gookin, Sarah M. Assmann, Réka Albert

Research output: Contribution to journalArticle

69 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Article number372
JournalMolecular Systems Biology
Volume6
DOIs
StatePublished - Jun 14 2010

Fingerprint

G Protein
Heterotrimeric GTP-Binding Proteins
G-proteins
Transcriptome
GTP-Binding Proteins
transcriptome
Proteins
Modeling
Guard Cell
Hormones
guard cells
Gene expression
Leaves
hormones
Signal transduction
Abscisic Acid
Boolean Model
Pattern matching
Arabidopsis Thaliana
gene expression

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Agricultural and Biological Sciences(all)
  • Applied Mathematics

Cite this

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Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G-protein action. / Pandey, Sona; Wang, Rui Sheng; Wilson, Liza; Li, Song; Zhao, Zhixin; Gookin, Timothy E.; Assmann, Sarah M.; Albert, Réka.

In: Molecular Systems Biology, Vol. 6, 372, 14.06.2010.

Research output: Contribution to journalArticle

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