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Inferring causal metabolic signals that regulate the dynamic TORC1-dependent transcriptome

Oliveira, A. P. and Dimopoulos, S. and Busetto, A. G. and Christen, S. and Dechant, R. and Falter, L. and Haghir, C. M. and Jozefczuk, S. and Ludwig, C. and Rudroff, F. and Schulz, J. C. and González, A. and Soulard, A. and Stracka, D. and Aebersold, R. and Buhmann, J. M. and Hall, M. N. and Peter, M. and Sauer, U. and Stelling, J.. (2015) Inferring causal metabolic signals that regulate the dynamic TORC1-dependent transcriptome. Molecular systems biology, Vol. 11, H. 4. p. 802.

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Official URL: http://edoc.unibas.ch/dok/A6381785

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Abstract

Cells react to nutritional cues in changing environments via the integrated action of signaling, transcriptional, and metabolic networks. Mechanistic insight into signaling processes is often complicated because ubiquitous feedback loops obscure causal relationships. Consequently, the endogenous inputs of many nutrient signaling pathways remain unknown. Recent advances for system-wide experimental data generation have facilitated the quantification of signaling systems, but the integration of multi-level dynamic data remains challenging. Here, we co-designed dynamic experiments and a probabilistic, model-based method to infer causal relationships between metabolism, signaling, and gene regulation. We analyzed the dynamic regulation of nitrogen metabolism by the target of rapamycin complex 1 (TORC1) pathway in budding yeast. Dynamic transcriptomic, proteomic, and metabolomic measurements along shifts in nitrogen quality yielded a consistent dataset that demonstrated extensive re-wiring of cellular networks during adaptation. Our inference method identified putative downstream targets of TORC1 and putative metabolic inputs of TORC1, including the hypothesized glutamine signal. The work provides a basis for further mechanistic studies of nitrogen metabolism and a general computational framework to study cellular processes.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Growth & Development > Biochemistry (Hall)
UniBasel Contributors:Hall, Michael N.
Item Type:Article, refereed
Article Subtype:Research Article
Bibsysno:Link to catalogue
Publisher:EMBO
ISSN:1744-4292
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:05 Jun 2015 08:53
Deposited On:05 Jun 2015 08:53

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