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Surveying regulatory feedback among yeast transcription factors
Author(s) -
Brem Rachel B
Publication year - 2008
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.22.1_supplement.400.1
Subject(s) - transcription factor , negative feedback , positive feedback , biology , signal transduction , computational biology , systems biology , regulator , saccharomyces cerevisiae , gene regulatory network , yeast , transcription (linguistics) , microbiology and biotechnology , genetics , gene expression , gene , physics , linguistics , philosophy , quantum mechanics , voltage , electrical engineering , engineering
Complex quantitative cellular behaviors—such as binary switching, signal amplification, and adaptation—are at the heart of systems biology. To date, most such behaviors have been characterized by tour de force experiments on a handful of model pathways. The full spectrum of pathways in which nature has quantitatively tuned the signaling machinery is almost unknown. Many signaling behaviors are thought to require regulatory feedback, in which a protein influences its own expression or abundance. With the goal of using feedback as a signpost for signaling behaviors of interest, we have surveyed the prevalence of this motif across transcription factors in S. cerevisiae. We find evidence that direct feedback, in which a transcription factor protein binds upstream of its own gene, and indirect feedback, mediated by multiple signaling intermediates, are both common. We also find that positive and negative feedback, respectively the up‐ or down‐regulation of abundance of a transcription factor by its own action, are both prevalent. And we observe cases of an unusual feedback model in which a transcription factor regulates its own subcellular localization. Our results shed light on the functional genomics of feedback, and they identify particular yeast circuits as novel, testable candidates for binary switches and other systems properties.