Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G‐protein action
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...
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| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Springer Nature
2010-06-01
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| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/msb.2010.28 |
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| _version_ | 1849225807374843904 |
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| author | Sona Pandey Rui‐Sheng Wang Liza Wilson Song Li Zhixin Zhao Timothy E Gookin Sarah M Assmann Réka Albert |
| author_facet | Sona Pandey Rui‐Sheng Wang Liza Wilson Song Li Zhixin Zhao Timothy E Gookin Sarah M Assmann Réka Albert |
| author_sort | Sona Pandey |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-efe1fcb2a49b45ccbd206f31fe3648d3 |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2010-06-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-efe1fcb2a49b45ccbd206f31fe3648d32025-08-24T12:00:23ZengSpringer NatureMolecular Systems Biology1744-42922010-06-016111710.1038/msb.2010.28Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G‐protein actionSona Pandey0Rui‐Sheng Wang1Liza Wilson2Song Li3Zhixin Zhao4Timothy E Gookin5Sarah M Assmann6Réka Albert7Department of Biology, Pennsylvania State UniversityDepartment of Physics, Pennsylvania State UniversityDepartment of Biology, Pennsylvania State UniversityDepartment of Biology, Pennsylvania State UniversityDepartment of Biology, Pennsylvania State UniversityDepartment of Biology, Pennsylvania State UniversityDepartment of Biology, Pennsylvania State UniversityDepartment of Physics, Pennsylvania State UniversityAbstract 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.https://doi.org/10.1038/msb.2010.28abscisic acidArabidopsis thalianaBoolean modelingheterotrimeric G‐proteintranscriptome |
| spellingShingle | Sona Pandey Rui‐Sheng Wang Liza Wilson Song Li Zhixin Zhao Timothy E Gookin Sarah M Assmann Réka Albert Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G‐protein action Molecular Systems Biology abscisic acid Arabidopsis thaliana Boolean modeling heterotrimeric G‐protein transcriptome |
| title | Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G‐protein action |
| title_full | Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G‐protein action |
| title_fullStr | Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G‐protein action |
| title_full_unstemmed | Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G‐protein action |
| title_short | Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G‐protein action |
| title_sort | boolean modeling of transcriptome data reveals novel modes of heterotrimeric g protein action |
| topic | abscisic acid Arabidopsis thaliana Boolean modeling heterotrimeric G‐protein transcriptome |
| url | https://doi.org/10.1038/msb.2010.28 |
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