title: Genome-Wide Analysis of the TORC1 and Osmotic Stress Signaling Network in Saccharomyces cerevisiae.
abstract: The Target of Rapamycin kinase Complex I (TORC1) is a master regulator of cell growth and metabolism in eukaryotes. Studies in yeast and human cells have shown that nitrogen/amino acid starvation signals act through Npr2/Npr3 and the small GTPases Gtr1/Gtr2 (Rags in humans) to inhibit TORC1. However, it is unclear how other stress and starvation stimuli inhibit TORC1, and/or act in parallel with the TORC1 pathway, to control cell growth. To help answer these questions, we developed a novel automated pipeline and used it to measure the expression of a TORC1-dependent ribosome biogenesis gene (NSR1) during osmotic stress in 4700 Saccharomyces cerevisiae strains from the yeast knock-out collection. This led to the identification of 440 strains with significant and reproducible defects in NSR1 repression. The cell growth control and stress response proteins deleted in these strains form a highly connected network, including 56 proteins involved in vesicle trafficking and vacuolar function; 53 proteins that act downstream of TORC1 according to a rapamycin assay--including components of the HDAC Rpd3L, Elongator, and the INO80, CAF-1 and SWI/SNF chromatin remodeling complexes; over 100 proteins involved in signaling and metabolism; and 17 proteins that directly interact with TORC1. These data provide an important resource for labs studying cell growth control and stress signaling, and demonstrate the utility of our new, and easily adaptable, method for mapping gene regulatory networks.
authors.affiliation: Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, 85721-0206.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Worley
authors.affiliation: Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, 85721-0206.
authors.forename: Arron
authors.initials: A
authors.lastname: Sullivan
authors.affiliation: Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, 85721-0206.
authors.forename: Xiangxia
authors.initials: X
authors.lastname: Luo
authors.affiliation: Functional Genomics Core Facility, University of Arizona, Tucson, Arizona, 85721-0206.
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Kaplan
authors.affiliation: Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, 85721-0206 Functional Genomics Core Facility, University of Arizona, Tucson, Arizona, 85721-0206 capaldi@email.arizona.edu.
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Capaldi
mesh_terms: D016000:Cluster Analysis; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D055786:Gene Knockout Techniques; D053263:Gene Regulatory Networks; D016681:Genome, Fungal; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D000076222:Mechanistic Target of Rapamycin Complex 1; D046912:Multiprotein Complexes / Q000235:genetics / Q000378:metabolism*; D009154:Mutation; D009997:Osmotic Pressure; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism*; D015398:Signal Transduction; D013312:Stress, Physiological / Q000235:genetics; D058570:TOR Serine-Threonine Kinases / Q000235:genetics / Q000378:metabolism*
chemical_list: D046912:Multiprotein Complexes; D000076222:Mechanistic Target of Rapamycin Complex 1; D058570:TOR Serine-Threonine Kinases
keywords: TORC1; high-throughput screen; osmotic stress; yeast knock-out collection